Pub Date : 2025-12-05DOI: 10.1016/j.soilbio.2025.110047
Siddharth Uppal, Jamie Woolet, Muthusubramanian Venkateshwaran, Christopher Baxer, Yari Johnson, Ashley Tung, Charlie Siwei Yu, Thea Whitman, Jason C. Kwan
Prescribed fires are a critical tool for ecosystem restoration and for reducing the risk of wildfires, which have grown in frequency and severity in many regions of the globe. Fires typically cause transient reduction of soil bacterial diversity, and we are beginning to identify certain taxa that seem to be common fire-responders. However, a genetic basis for understanding the mechanisms behind post-fire bacterial community recovery is not well-established. Prescribed burns in particular offer an opportunity to study this process through the use of unburned control plots at the same location and the ease of sampling at early timepoints after the fire. Here, we conducted prescribed burns with paired unburned controls at two prairie locations. We analyzed 16S rRNA data at four timepoints over 5 months, then used these data to select a subset of samples to target for deeply sequenced shotgun metagenomics. Although the bacterial community remained distinct during the study timescale, the functional composition appears to return to the baseline levels at five months post-burn. On a species level, however, we determined that post-fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. For example, we found that spore-related genes are associated with burning only in some spore-forming taxa, and our results suggest that predicted doubling time was not a critical determinant of success post-fire in this system. Our study therefore advances the understanding of how both function and composition contribute to soil bacterial community dynamics, post-disturbance.
{"title":"Complex effects of a prescribed burn on a prairie soil bacterial community","authors":"Siddharth Uppal, Jamie Woolet, Muthusubramanian Venkateshwaran, Christopher Baxer, Yari Johnson, Ashley Tung, Charlie Siwei Yu, Thea Whitman, Jason C. Kwan","doi":"10.1016/j.soilbio.2025.110047","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.110047","url":null,"abstract":"Prescribed fires are a critical tool for ecosystem restoration and for reducing the risk of wildfires, which have grown in frequency and severity in many regions of the globe. Fires typically cause transient reduction of soil bacterial diversity, and we are beginning to identify certain taxa that seem to be common fire-responders. However, a genetic basis for understanding the mechanisms behind post-fire bacterial community recovery is not well-established. Prescribed burns in particular offer an opportunity to study this process through the use of unburned control plots at the same location and the ease of sampling at early timepoints after the fire. Here, we conducted prescribed burns with paired unburned controls at two prairie locations. We analyzed 16S rRNA data at four timepoints over 5 months, then used these data to select a subset of samples to target for deeply sequenced shotgun metagenomics. Although the bacterial community remained distinct during the study timescale, the functional composition appears to return to the baseline levels at five months post-burn. On a species level, however, we determined that post-fire survival is more nuanced than possession of previously hypothesized pyrophilous traits. For example, we found that spore-related genes are associated with burning only in some spore-forming taxa, and our results suggest that predicted doubling time was not a critical determinant of success post-fire in this system. Our study therefore advances the understanding of how both function and composition contribute to soil bacterial community dynamics, post-disturbance.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"155 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145673703","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 : 2025-12-04DOI: 10.1016/j.soilbio.2025.110051
Ruiqiao Wu , Ze Zhang , Guanjun Li , Xiangxiang Wang , Yunying Fang , Yakov Kuyakov , Xuebin Xu , Jianping Chen , Tida Ge , Zhenke Zhu
The frequency and nutrient composition of organic inputs jointly regulate soil organic carbon (SOC) dynamics, but their interactive effects on microbial carbon use efficiency (CUE), priming effects (PE), and net soil C balance remain poorly understood in flooded paddy systems. We performed a 40-day incubation experiment using a 13C-labeled simulated root-exudate mixture (glucose:oxalic acid:alanine, 65:30:5) under two input modes (single substrate input vs. continuous substrate input) and four C:N:P stoichiometries. Single substrate inputs generated an early pulse in labile-C mineralization that was 39–64 % greater than under continuous addition, and mineralization rates declined with increasing nutrient supply. Single-pulse addition triggered an early peak in the metabolic quotient (qCO2) and lower tracer-based CUE, whereas continuous addition maintained steadier microbial activity and higher CUE. The C:N:P stoichiometry of the added substrate strongly controlled C partitioning: stoichiometrically balanced inputs reduced CO2–C losses and increased 13C incorporation into microbial biomass and SOC pool. Pulse inputs typically induced negative PEs, whereas continuous inputs tended to cause positive PEs. Therefore, the net C balance was consistently greater following single substrate inputs than following continuous inputs; across nutrient treatments, single pulses produced substantially larger short-term C retention. Combining 13C tracing, enzyme assays and kinetic modelling, we demonstrate that under balanced nutrient inputs, microbes respire less of the added C and allocate more into biomass and necromass, which subsequently contributes to more stable SOC pool. This study provides mechanistic guidance for using C:N:P-balanced amendments to increase SOC retention in flooded cropping systems.
{"title":"Frequency and C:N:P stoichiometry of organic inputs determines intensity of net C balance in paddy soils","authors":"Ruiqiao Wu , Ze Zhang , Guanjun Li , Xiangxiang Wang , Yunying Fang , Yakov Kuyakov , Xuebin Xu , Jianping Chen , Tida Ge , Zhenke Zhu","doi":"10.1016/j.soilbio.2025.110051","DOIUrl":"10.1016/j.soilbio.2025.110051","url":null,"abstract":"<div><div>The frequency and nutrient composition of organic inputs jointly regulate soil organic carbon (SOC) dynamics, but their interactive effects on microbial carbon use efficiency (CUE), priming effects (PE), and net soil C balance remain poorly understood in flooded paddy systems. We performed a 40-day incubation experiment using a <sup>13</sup>C-labeled simulated root-exudate mixture (glucose:oxalic acid:alanine, 65:30:5) under two input modes (single substrate input <em>vs.</em> continuous substrate input) and four C:N:P stoichiometries. Single substrate inputs generated an early pulse in labile-C mineralization that was 39–64 % greater than under continuous addition, and mineralization rates declined with increasing nutrient supply. Single-pulse addition triggered an early peak in the metabolic quotient (qCO<sub>2</sub>) and lower tracer-based CUE, whereas continuous addition maintained steadier microbial activity and higher CUE. The C:N:P stoichiometry of the added substrate strongly controlled C partitioning: stoichiometrically balanced inputs reduced CO<sub>2</sub>–C losses and increased <sup>13</sup>C incorporation into microbial biomass and SOC pool. Pulse inputs typically induced negative PEs, whereas continuous inputs tended to cause positive PEs. Therefore, the net C balance was consistently greater following single substrate inputs than following continuous inputs; across nutrient treatments, single pulses produced substantially larger short-term C retention. Combining <sup>13</sup>C tracing, enzyme assays and kinetic modelling, we demonstrate that under balanced nutrient inputs, microbes respire less of the added C and allocate more into biomass and necromass, which subsequently contributes to more stable SOC pool. This study provides mechanistic guidance for using C:N:P-balanced amendments to increase SOC retention in flooded cropping systems.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110051"},"PeriodicalIF":10.3,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689063","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 : 2025-12-04DOI: 10.1016/j.soilbio.2025.110056
Paige M. Hansen , Yao Zhang , Ksenia Guseva , Christina Kaiser , M. Francesca Cotrufo
Dissolved low molecular weight (LMW) compounds in soil can either be assimilated by microbes or sorb onto mineral surfaces, forming mineral-associated organic matter (MAOM). This creates possible ‘competition’ between microbes and mineral surfaces for LMW compounds, potentially influencing whether particulate organic matter (POM) is retained or depolymerized by microbes to produce LMW substrates. Therefore, microscale interactions between unoccupied mineral surfaces and microbial enzymes may mediate patterns of POM and MAOM storage, particularly in soils varying in MAOM saturation. To explore this, we adapted an individual-based microscale model to simulate POM retention and new MAOM formation under different initial POM qualities (carbon:nitrogen ratio; C:N) and MAOM saturation levels, while also considering microbial social-like dynamics, which emerge from interactions between microbes with different capacities to produce and share public goods (in this case, extracellular enzymes). Consistent with prior findings, the presence of these dynamics slowed decomposition of initial POM pools, particularly at high C:N ratios. Additionally, MAOM saturation affected microbial community properties, MAOM formation, and POM decomposition in ways that depended on POM C:N, but only when social dynamics were included. The patterns of POM decomposition and MAOM formation identified in our work align with observations of simultaneous POM and MAOM formation in undersaturated soils from prior field studies, suggesting that regulation of enzyme production via microbial interactions may be an additional driver of POM and MAOM storage in such soils. Overall, this highlights the importance of explicitly incorporating microbial ecology into our conceptual understanding of C and N cycling, particularly to improve the predictive capacity of ecosystem models and inform soil management strategies that enhance global change mitigation, especially in degraded soils likely to be undersaturated.
{"title":"Microbial community regulation of extracellular enzyme production can mediate patterns of particulate and mineral-associated organic matter accumulation in undersaturated soils","authors":"Paige M. Hansen , Yao Zhang , Ksenia Guseva , Christina Kaiser , M. Francesca Cotrufo","doi":"10.1016/j.soilbio.2025.110056","DOIUrl":"10.1016/j.soilbio.2025.110056","url":null,"abstract":"<div><div>Dissolved low molecular weight (LMW) compounds in soil can either be assimilated by microbes or sorb onto mineral surfaces, forming mineral-associated organic matter (MAOM). This creates possible ‘competition’ between microbes and mineral surfaces for LMW compounds, potentially influencing whether particulate organic matter (POM) is retained or depolymerized by microbes to produce LMW substrates. Therefore, microscale interactions between unoccupied mineral surfaces and microbial enzymes may mediate patterns of POM and MAOM storage, particularly in soils varying in MAOM saturation. To explore this, we adapted an individual-based microscale model to simulate POM retention and new MAOM formation under different initial POM qualities (carbon:nitrogen ratio; C:N) and MAOM saturation levels, while also considering microbial social-like dynamics, which emerge from interactions between microbes with different capacities to produce and share public goods (in this case, extracellular enzymes). Consistent with prior findings, the presence of these dynamics slowed decomposition of initial POM pools, particularly at high C:N ratios. Additionally, MAOM saturation affected microbial community properties, MAOM formation, and POM decomposition in ways that depended on POM C:N, but only when social dynamics were included. The patterns of POM decomposition and MAOM formation identified in our work align with observations of simultaneous POM and MAOM formation in undersaturated soils from prior field studies, suggesting that regulation of enzyme production via microbial interactions may be an additional driver of POM and MAOM storage in such soils. Overall, this highlights the importance of explicitly incorporating microbial ecology into our conceptual understanding of C and N cycling, particularly to improve the predictive capacity of ecosystem models and inform soil management strategies that enhance global change mitigation, especially in degraded soils likely to be undersaturated.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110056"},"PeriodicalIF":10.3,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689059","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 : 2025-12-02DOI: 10.1016/j.soilbio.2025.110050
Jana Šerá , Václav Pecina , Vendula Mašláňová , Martin Brtnický , Adéla Baťová , Jiří Holátko , Tereza Hammerschmiedt , Veronika Kučabová , Ondrej Malíček , Markéta Kadlečková , Jiří Kučerík , Marek Koutný
Biodegradable plastics (BPs) are increasingly presented as sustainable alternatives to conventional plastics; however, their ecological effects on soils are poorly understood. BPs can alter soil microbiomes and nutrient cycling; yet, the extent, dynamics, and effects of the plastisphere on soil organic matter (SOM) after biodegradation remain underexplored. This study characterized the microbial plastisphere of three BPs, poly-3-hydroxybutyrate (PHB), poly(butylene succinate-co-adipate) (PBSA), and polybutylene adipate terephthalate (PBAT), and measured polymer biodegradation to link microbial dynamics with material breakdown. Metagenomics, scanning electron microscopy, and thermogravimetric analysis showed that these polymers formed structured plastispheres that significantly altered microbial communities and SOM. Each polymer hosted a distinct plastisphere; bacterial communities diverged more strongly between polymers than fungal ones. Functional profiling revealed shifts in nitrogen metabolism and ecological strategies at BP surfaces, including a decrease in nitrifiers and an increase in parasitic/pathogenic fungi. The plastisphere extended up to 1.25 mm for bacteria and 2.75 mm for fungi. PHB plastispheres were enriched in Comamonadaceae, Oxalobacteriaceae, and Rhodocyclaceae; PBAT favored Xanthobacteraceae and Burkholderiaceae; Xanthomonadaceae colonized all BPs. Fungal communities were dominated by Nectriaceae, Herpotrichiellaceae, and Aspergillaceae, and their composition changed over time. BP exposure reduced SOM, most strongly for PHB and PBSA, and to a lesser extent for PBAT, suggesting a positive priming effect. Overall, BP degradation promoted nitrogen-limited conditions and host-dependent microbial strategies. Although plastisphere communities showed signs of stabilization after 350 days, full recovery of microbial composition and SOM may require longer, indicating potential long-term impacts of BPs on soil ecosystems. These results underscore that BPs can alter soil microbial ecology and organic matter turnover, highlighting the need for further long-term studies.
{"title":"Unveiling the spatial architecture of biodegradable polyester plastisphere in soil and its implications for organic matter composition","authors":"Jana Šerá , Václav Pecina , Vendula Mašláňová , Martin Brtnický , Adéla Baťová , Jiří Holátko , Tereza Hammerschmiedt , Veronika Kučabová , Ondrej Malíček , Markéta Kadlečková , Jiří Kučerík , Marek Koutný","doi":"10.1016/j.soilbio.2025.110050","DOIUrl":"10.1016/j.soilbio.2025.110050","url":null,"abstract":"<div><div>Biodegradable plastics (BPs) are increasingly presented as sustainable alternatives to conventional plastics; however, their ecological effects on soils are poorly understood. BPs can alter soil microbiomes and nutrient cycling; yet, the extent, dynamics, and effects of the plastisphere on soil organic matter (SOM) after biodegradation remain underexplored. This study characterized the microbial plastisphere of three BPs, poly-3-hydroxybutyrate (PHB), poly(butylene succinate-co-adipate) (PBSA), and polybutylene adipate terephthalate (PBAT), and measured polymer biodegradation to link microbial dynamics with material breakdown. Metagenomics, scanning electron microscopy, and thermogravimetric analysis showed that these polymers formed structured plastispheres that significantly altered microbial communities and SOM. Each polymer hosted a distinct plastisphere; bacterial communities diverged more strongly between polymers than fungal ones. Functional profiling revealed shifts in nitrogen metabolism and ecological strategies at BP surfaces, including a decrease in nitrifiers and an increase in parasitic/pathogenic fungi. The plastisphere extended up to 1.25 mm for bacteria and 2.75 mm for fungi. PHB plastispheres were enriched in <em>Comamonadaceae</em>, <em>Oxalobacteriaceae</em>, and <em>Rhodocyclaceae</em>; PBAT favored <em>Xanthobacteraceae</em> and <em>Burkholderiaceae</em>; <em>Xanthomonadaceae</em> colonized all BPs. Fungal communities were dominated by <em>Nectriaceae</em>, <em>Herpotrichiellaceae</em>, and <em>Aspergillaceae</em>, and their composition changed over time. BP exposure reduced SOM, most strongly for PHB and PBSA, and to a lesser extent for PBAT, suggesting a positive priming effect. Overall, BP degradation promoted nitrogen-limited conditions and host-dependent microbial strategies. Although plastisphere communities showed signs of stabilization after 350 days, full recovery of microbial composition and SOM may require longer, indicating potential long-term impacts of BPs on soil ecosystems. These results underscore that BPs can alter soil microbial ecology and organic matter turnover, highlighting the need for further long-term studies.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110050"},"PeriodicalIF":10.3,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145657199","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 : 2025-11-29DOI: 10.1016/j.soilbio.2025.110049
Daniel F. Petticord , Ran Zhi , Elizabeth H. Boughton , Yuxi Guo , Hui-Ling Liao , Alma L. Reyes , Jiangxiao Qiu , Jed P. Sparks
Sustaining agricultural productivity in phosphorus-poor soils requires innovation to reduce reliance on synthetic fertilizers. One underexplored solution is the role of fungi in enhancing plant phosphorus (P) acquisition. We examined fungal diversity in the rhizosphere and roots of Paspalum notatum, a globally important forage grass, across a soil P gradient in a subtropical pasture. Rhizosphere fungal communities were more diverse than those associated with roots, though root communities were more compositionally distinct among plants. Variation in foliar P concentrations was partially explained by plant-available P, percent carbon, and soil moisture (R2 = 0.58). DESeq2 analysis identified two taxa whose relative abundance shifted with foliar P: a putative Fusarium variasi ASV that increased with P, and an unidentified Clavariaceae ASV that declined. Incorporating these taxa into regression models improved predictions of foliar P, with Total P and the Fusarium ASV together explaining 67.8 % of variation. Although this Fusarium ASV is labeled as a pathogen in the FungalTraits database, not all Fusarium strains negatively affect plants. Many are weakly pathogenic or beneficial, often promoting growth by suppressing more virulent pathogens through competition in the rhizosphere. A key mechanism underlying this competition is iron acquisition. We speculate that this same strategy may have an underrecognized side effect: mobilizing phosphorus from iron-bound pools. In highly weathered tropical soils, where calcium and magnesium are depleted and phosphorus is commonly occluded by iron oxides, such iron competition could indirectly enhance plant P availability. Our findings generate two non-exclusive hypotheses: (a) this Fusarium strain may provide genuine benefits by mobilizing P, or (b) its increased abundance may reflect low-virulence pathogenicity that suppresses biomass more than P uptake, effectively concentrating foliar P. These results highlight the need to reassess the ecological roles of rhizosphere Fusarium and related taxa—not only as potential pathogens but also as contributors to nutrient cycling in P-limited ecosystems.
{"title":"Foliar phosphorus concentrations in Bahiagrass are well-predicted by the abundance of a Fusarium taxa","authors":"Daniel F. Petticord , Ran Zhi , Elizabeth H. Boughton , Yuxi Guo , Hui-Ling Liao , Alma L. Reyes , Jiangxiao Qiu , Jed P. Sparks","doi":"10.1016/j.soilbio.2025.110049","DOIUrl":"10.1016/j.soilbio.2025.110049","url":null,"abstract":"<div><div>Sustaining agricultural productivity in phosphorus-poor soils requires innovation to reduce reliance on synthetic fertilizers. One underexplored solution is the role of fungi in enhancing plant phosphorus (P) acquisition. We examined fungal diversity in the rhizosphere and roots of <em>Paspalum notatum</em>, a globally important forage grass, across a soil P gradient in a subtropical pasture. Rhizosphere fungal communities were more diverse than those associated with roots, though root communities were more compositionally distinct among plants. Variation in foliar P concentrations was partially explained by plant-available P, percent carbon, and soil moisture (R<sup>2</sup> = 0.58). DESeq2 analysis identified two taxa whose relative abundance shifted with foliar P: a putative <em>Fusarium variasi</em> ASV that increased with P, and an unidentified <em>Clavariaceae</em> ASV that declined. Incorporating these taxa into regression models improved predictions of foliar P, with Total P and the <em>Fusarium</em> ASV together explaining 67.8 % of variation. Although this <em>Fusarium</em> ASV is labeled as a pathogen in the FungalTraits database, not all <em>Fusarium</em> strains negatively affect plants. Many are weakly pathogenic or beneficial, often promoting growth by suppressing more virulent pathogens through competition in the rhizosphere. A key mechanism underlying this competition is iron acquisition. We speculate that this same strategy may have an underrecognized side effect: mobilizing phosphorus from iron-bound pools. In highly weathered tropical soils, where calcium and magnesium are depleted and phosphorus is commonly occluded by iron oxides, such iron competition could indirectly enhance plant P availability. Our findings generate two non-exclusive hypotheses: (a) this <em>Fusarium</em> strain may provide genuine benefits by mobilizing P, or (b) its increased abundance may reflect low-virulence pathogenicity that suppresses biomass more than P uptake, effectively concentrating foliar P. These results highlight the need to reassess the ecological roles of rhizosphere <em>Fusarium</em> and related taxa—not only as potential pathogens but also as contributors to nutrient cycling in P-limited ecosystems.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"214 ","pages":"Article 110049"},"PeriodicalIF":10.3,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145613436","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 : 2025-11-27DOI: 10.1016/j.soilbio.2025.110048
Kinsey Reed Close , Damon LeMaster , Ronald Schartiger , Kayla Guthrie , Jennifer Kane , James Kotcon , Ember Morrissey
Soil macroaggregate stability is an essential component of soil health. Microbes can enhance macroaggregate stability; however, which microorganisms are responsible remains poorly understood. Arbuscular mycorrhizal fungi (AMF) have long been credited as the primary biological stabilizers despite conflicting information. Soil bacteria, particularly Actinobacteria, can also possess mycelial-like, filamentous growth and many bacteria produce substantial extracellular polymeric substances that may enhance soil macroaggregate stability. Using a novel combination of phospholipid fatty acid (PLFA) profiling and the SLAKES application, we evaluated microbial PLFA biomarker composition and macroaggregate stability in pasture soils across Appalachia. Here, we show the best predictors of macroaggregate stability to be Actinobacteria, gram-negative bacteria, and gram-positive bacteria. These findings challenge prevailing scientific narrative and highlight the need to further investigate bacteria as a source of macroaggregate stability in soil.
{"title":"Actinobacteria, mycorrhizae, and the biology of soil aggregate stability","authors":"Kinsey Reed Close , Damon LeMaster , Ronald Schartiger , Kayla Guthrie , Jennifer Kane , James Kotcon , Ember Morrissey","doi":"10.1016/j.soilbio.2025.110048","DOIUrl":"10.1016/j.soilbio.2025.110048","url":null,"abstract":"<div><div>Soil macroaggregate stability is an essential component of soil health. Microbes can enhance macroaggregate stability; however, which microorganisms are responsible remains poorly understood. Arbuscular mycorrhizal fungi (AMF) have long been credited as the primary biological stabilizers despite conflicting information. Soil bacteria, particularly Actinobacteria, can also possess mycelial-like, filamentous growth and many bacteria produce substantial extracellular polymeric substances that may enhance soil macroaggregate stability. Using a novel combination of phospholipid fatty acid (PLFA) profiling and the SLAKES application, we evaluated microbial PLFA biomarker composition and macroaggregate stability in pasture soils across Appalachia. Here, we show the best predictors of macroaggregate stability to be Actinobacteria, gram-negative bacteria, and gram-positive bacteria. These findings challenge prevailing scientific narrative and highlight the need to further investigate bacteria as a source of macroaggregate stability in soil.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110048"},"PeriodicalIF":10.3,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609744","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 : 2025-11-26DOI: 10.1016/j.soilbio.2025.110044
Huijun Li , Baorong Wang , Haoning Chen , Na Li , Yue Zhou , Zhaolong Zhu , Jinshi Jian , Gurpal S. Toor , Shaoshan An
Beyond the recognized role of microbial cell wall residues in soil organic carbon (SOC), microbes under drought stress appear to strategically divert C toward the production of extracellular polymers (EPS), positioning them as a dynamic C pool. Their contrasting environmental behavior and turnover create a fundamental uncertainty in predicting SOC dynamics in drying ecosystems. Despite their importance, the dynamics of EPS and microbial necromass (indicated by amino sugars) under prolonged drought, their relative contributions to SOC accumulation, and the factors regulating them remain poorly constrained. We hypothesized that intensified drought would preferentially stimulate EPS accumulation over microbial necromass, as microbes divert more C toward EPS synthesis to mitigate water stress. To test this, a 9-year drought experiment was conducted with four treatments (control and 20 %, 40 %, and 60 % reductions). We found that under prolonged drought, the contents of both EPS and microbial necromass declined, with the former decreasing by 30.2 % and the latter more sharply by 76.0 % under extreme conditions, indicating their asynchronous formation and accumulation. However, increasing drought intensity enhanced the EPS accumulation coefficient rather than that of microbial necromass, indicating a greater microbial C investment in EPS production and higher formation efficiency under water stress. Long-term drought also restructured the microbial community, shifting C allocation from biomass growth and necromass formation (associated with taxa like Proteobacteria and Ascomycota) toward EPS production (e.g., Bacteroidota, Basidiomycota and Glomeromycota). In parallel, abiotic variables such as Olsen phosphorus, nitrate, and ammonium were tightly coupled to EPS accumulation, underscoring EPS role in sustaining bioavailable nutrient pools as soil moisture declines. Collectively, these findings provide direct evidence that EPS contributes more actively to SOC than microbial necromass. The strategic shift in microbial carbon from necromass to EPS buffers SOC pools, with important implications for ecosystem C cycling and climate feedbacks under drought.
{"title":"Increased drought intensity stimulates the extracellular polymeric substance accumulation and their contribution to soil organic carbon rather than microbial necromass","authors":"Huijun Li , Baorong Wang , Haoning Chen , Na Li , Yue Zhou , Zhaolong Zhu , Jinshi Jian , Gurpal S. Toor , Shaoshan An","doi":"10.1016/j.soilbio.2025.110044","DOIUrl":"10.1016/j.soilbio.2025.110044","url":null,"abstract":"<div><div>Beyond the recognized role of microbial cell wall residues in soil organic carbon (SOC), microbes under drought stress appear to strategically divert C toward the production of extracellular polymers (EPS), positioning them as a dynamic C pool. Their contrasting environmental behavior and turnover create a fundamental uncertainty in predicting SOC dynamics in drying ecosystems. Despite their importance, the dynamics of EPS and microbial necromass (indicated by amino sugars) under prolonged drought, their relative contributions to SOC accumulation, and the factors regulating them remain poorly constrained. We hypothesized that intensified drought would preferentially stimulate EPS accumulation over microbial necromass, as microbes divert more C toward EPS synthesis to mitigate water stress. To test this, a 9-year drought experiment was conducted with four treatments (control and 20 %, 40 %, and 60 % reductions). We found that under prolonged drought, the contents of both EPS and microbial necromass declined, with the former decreasing by 30.2 % and the latter more sharply by 76.0 % under extreme conditions, indicating their asynchronous formation and accumulation. However, increasing drought intensity enhanced the EPS accumulation coefficient rather than that of microbial necromass, indicating a greater microbial C investment in EPS production and higher formation efficiency under water stress. Long-term drought also restructured the microbial community, shifting C allocation from biomass growth and necromass formation (associated with taxa like Proteobacteria and Ascomycota) toward EPS production (e.g., Bacteroidota<em>,</em> Basidiomycota and Glomeromycota). In parallel, abiotic variables such as Olsen phosphorus, nitrate, and ammonium were tightly coupled to EPS accumulation, underscoring EPS role in sustaining bioavailable nutrient pools as soil moisture declines. Collectively, these findings provide direct evidence that EPS contributes more actively to SOC than microbial necromass. The strategic shift in microbial carbon from necromass to EPS buffers SOC pools, with important implications for ecosystem C cycling and climate feedbacks under drought.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110044"},"PeriodicalIF":10.3,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145609489","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 : 2025-11-24DOI: 10.1016/j.soilbio.2025.110045
Suzanne Schmidt , Kasun H. Bodawatta , Bertil Jensen Bille , Felix Krogh Vissing , Kolotchèlèma Simon Silué , N'golo A. Koné , Erin L. Cole , Søren Rosendahl , Jonathan Z. Shik , Michael Poulsen
All organisms require a balanced supply of over 20 chemical elements, and even small imbalances can limit performance and fitness. Organisms thus employ diverse adaptations for acquiring and regulating balanced combinations of these elemental resources. In farming mutualisms, adaptations of domesticated crops can guide the accumulation of critical elements from soil or mulched detritus for partner use. It is therefore reasonable to predict systematic shifts in elemental abundance and variance across farming stages – from substrate provisioning and crop assimilation to the final production of edible yield. We tested this hypothesis with fungus-farming termites that cultivate fungi in combs built from a mix of termite-provisioned organic matter and soil, in exchange for edible nutrient-rich fungal nodule structures. Using Inductively Coupled Plasma Mass Spectrometry (ICP-MS), we quantified 24 elements across fungus-farming stages – from soils, through termite guts and fresh and mature fungal combs, to final nodules. Our findings suggest 1) that termite foraging represents an initial nutritional filtering stage that enriches biogenic elemental building blocks for macronutrients (K, S, Na, and Ca) while reducing several non-biogenic and potentially toxic elements (As and Pb) and 2) fungal nodules constitute a final nutritional filtering stage that concentrates a suite of biogenic elements (P, K, S, Cu, and Zn) alongside accumulation of certain non-biogenic elements (Cd and Tl). Within fungus gardens, elemental compositions are homogenised in freshly-build combs relative to the mulch deposited from termite guts. These patterns suggest elemental filtering as reciprocal provisioning between farmers and crops, offering a framework to understand how complex mutualistic nutritional systems regulate and ultimately affect element cycling in soil ecosystems.
{"title":"From soil to symbiosis: elemental filtering in a termite-fungus mutualism","authors":"Suzanne Schmidt , Kasun H. Bodawatta , Bertil Jensen Bille , Felix Krogh Vissing , Kolotchèlèma Simon Silué , N'golo A. Koné , Erin L. Cole , Søren Rosendahl , Jonathan Z. Shik , Michael Poulsen","doi":"10.1016/j.soilbio.2025.110045","DOIUrl":"10.1016/j.soilbio.2025.110045","url":null,"abstract":"<div><div>All organisms require a balanced supply of over 20 chemical elements, and even small imbalances can limit performance and fitness. Organisms thus employ diverse adaptations for acquiring and regulating balanced combinations of these elemental resources. In farming mutualisms, adaptations of domesticated crops can guide the accumulation of critical elements from soil or mulched detritus for partner use. It is therefore reasonable to predict systematic shifts in elemental abundance and variance across farming stages – from substrate provisioning and crop assimilation to the final production of edible yield. We tested this hypothesis with fungus-farming termites that cultivate fungi in combs built from a mix of termite-provisioned organic matter and soil, in exchange for edible nutrient-rich fungal nodule structures. Using Inductively Coupled Plasma Mass Spectrometry (ICP-MS), we quantified 24 elements across fungus-farming stages – from soils, through termite guts and fresh and mature fungal combs, to final nodules. Our findings suggest 1) that termite foraging represents an initial nutritional filtering stage that enriches biogenic elemental building blocks for macronutrients (K, S, Na, and Ca) while reducing several non-biogenic and potentially toxic elements (As and Pb) and 2) fungal nodules constitute a final nutritional filtering stage that concentrates a suite of biogenic elements (P, K, S, Cu, and Zn) alongside accumulation of certain non-biogenic elements (Cd and Tl). Within fungus gardens, elemental compositions are homogenised in freshly-build combs relative to the mulch deposited from termite guts. These patterns suggest elemental filtering as reciprocal provisioning between farmers and crops, offering a framework to understand how complex mutualistic nutritional systems regulate and ultimately affect element cycling in soil ecosystems.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110045"},"PeriodicalIF":10.3,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583720","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 : 2025-11-24DOI: 10.1016/j.soilbio.2025.110046
Yali Zhang , Jiayao Han , Joann K. Whalen , Mingsen Qin , Chenyu Li , Yongjun Liu
High-throughput sequencing (HTS) has become the most widely applied molecular approach for analyzing soil nematode communities, but its consistency with traditional morphology-based methods remains insufficiently validated. Here, we compared molecular (HTS-based) and morphological approaches in characterizing nematode communities, using data from a controlled field experiment with tillage and fertilization treatments (n = 36) and 146 additional datapoints from a systematic meta-analysis. Most community-level metrics, including trophic groups, diversity indices, ecological indicators, overall community structure, and their responses to tillage and fertilization, were consistent between the two approaches, indicating that molecular data can yield reliable ecological insights comparable to those derived from morphological analysis. Nonetheless, the molecular approach detected higher genus richness but lower Shannon and evenness indices, and it tended to over-estimate omnivores-predators while under-estimating herbivores, thereby causing discrepancies in maturity and structure indices. These inconsistencies highlight methodological biases that must be carefully considered when interpreting molecular data. By integrating empirical and meta-analytical evidence, our study provides one of the most comprehensive evaluations to date of the alignment between molecular and morphological assessments of soil nematode communities. Future efforts should focus on refining molecular approaches, including improving primer coverage, expanding reference databases, and linking DNA sequences with functional traits, to further enhance the accuracy and ecological utility of HTS in nematode diversity monitoring and soil ecosystem assessment.
{"title":"Morphological traits comparable to molecular approaches for soil nematode community analysis: a meta-analysis and field experiment","authors":"Yali Zhang , Jiayao Han , Joann K. Whalen , Mingsen Qin , Chenyu Li , Yongjun Liu","doi":"10.1016/j.soilbio.2025.110046","DOIUrl":"10.1016/j.soilbio.2025.110046","url":null,"abstract":"<div><div>High-throughput sequencing (HTS) has become the most widely applied molecular approach for analyzing soil nematode communities, but its consistency with traditional morphology-based methods remains insufficiently validated. Here, we compared molecular (HTS-based) and morphological approaches in characterizing nematode communities, using data from a controlled field experiment with tillage and fertilization treatments (n = 36) and 146 additional datapoints from a systematic meta-analysis. Most community-level metrics, including trophic groups, diversity indices, ecological indicators, overall community structure, and their responses to tillage and fertilization, were consistent between the two approaches, indicating that molecular data can yield reliable ecological insights comparable to those derived from morphological analysis. Nonetheless, the molecular approach detected higher genus richness but lower Shannon and evenness indices, and it tended to over-estimate omnivores-predators while under-estimating herbivores, thereby causing discrepancies in maturity and structure indices. These inconsistencies highlight methodological biases that must be carefully considered when interpreting molecular data. By integrating empirical and meta-analytical evidence, our study provides one of the most comprehensive evaluations to date of the alignment between molecular and morphological assessments of soil nematode communities. Future efforts should focus on refining molecular approaches, including improving primer coverage, expanding reference databases, and linking DNA sequences with functional traits, to further enhance the accuracy and ecological utility of HTS in nematode diversity monitoring and soil ecosystem assessment.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110046"},"PeriodicalIF":10.3,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145583719","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 : 2025-11-21DOI: 10.1016/j.soilbio.2025.110040
Jiao Yuan , Dan Yuan , Tim J. Clough , Xinhui Liu , Lin Ma , Chunsheng Hu , Shuping Qin
Biochar facilitates the reduction of N2O to N2 by promoting denitrification through its electron shuttle function, a mechanism widely recognized as key to its role in mitigating soil N2O accumulation. This electron shuttle capacity is primarily attributed to surface redox-active functional groups, such as quinones and phenolic hydroxyls. Among these, quinone/hydroquinone (Q/QH2) groups serve as reversible redox pairs, enhancing electron transport efficiency through cyclic electron acceptance and donation. However, the mechanisms by which quinone functional groups regulate the electron-shuttling capacity of biochar, and thereby amplify its ability to promote complete denitrification and N2O mitigation, remain unclear. In this study, biochar with enhanced electron-shuttling capacity was prepared by incorporating redox-active quinone groups. The biochar's effectiveness in reducing soil N2O accumulation was evaluated by incorporating it into soil. Quinone-enhanced biochar (QBC) markedly enhanced the biochar's electron-shuttling function and reduced soil N2O accumulation by 82.3 % relative to a control biochar. Furthermore, quinone-loaded biochar increased the relative expression of Acidobacteria and upregulated the abundance of nosZ-II genes, resulting in lower N2O/(N2O + N2) ratios, lower residual NO3−, and higher N2 accumulation that are consistent with more complete denitrification. Our results therefore indicate that the improved electron-shuttling function of biochar is consistent with more complete denitrification and enhanced N2O reduction. These findings indicate that incorporating quinone groups into biochar is a viable strategy to mitigate N2O accumulation by enhancing its electron-shuttling function.
{"title":"Quinone-loaded biochar amplifies soil N2O mitigation by enhancing electron transfer for N2O reduction","authors":"Jiao Yuan , Dan Yuan , Tim J. Clough , Xinhui Liu , Lin Ma , Chunsheng Hu , Shuping Qin","doi":"10.1016/j.soilbio.2025.110040","DOIUrl":"10.1016/j.soilbio.2025.110040","url":null,"abstract":"<div><div>Biochar facilitates the reduction of N<sub>2</sub>O to N<sub>2</sub> by promoting denitrification through its electron shuttle function, a mechanism widely recognized as key to its role in mitigating soil N<sub>2</sub>O accumulation. This electron shuttle capacity is primarily attributed to surface redox-active functional groups, such as quinones and phenolic hydroxyls. Among these, quinone/hydroquinone (Q/QH<sub>2</sub>) groups serve as reversible redox pairs, enhancing electron transport efficiency through cyclic electron acceptance and donation. However, the mechanisms by which quinone functional groups regulate the electron-shuttling capacity of biochar, and thereby amplify its ability to promote complete denitrification and N<sub>2</sub>O mitigation, remain unclear. In this study, biochar with enhanced electron-shuttling capacity was prepared by incorporating redox-active quinone groups. The biochar's effectiveness in reducing soil N<sub>2</sub>O accumulation was evaluated by incorporating it into soil. Quinone-enhanced biochar (QBC) markedly enhanced the biochar's electron-shuttling function and reduced soil N<sub>2</sub>O accumulation by 82.3 % relative to a control biochar. Furthermore, quinone-loaded biochar increased the relative expression of <em>Acidobacteria</em> and upregulated the abundance of <em>nosZ-II</em> genes, resulting in lower N<sub>2</sub>O/(N<sub>2</sub>O + N<sub>2</sub>) ratios, lower residual NO<sub>3</sub><sup>−</sup>, and higher N<sub>2</sub> accumulation that are consistent with more complete denitrification. Our results therefore indicate that the improved electron-shuttling function of biochar is consistent with more complete denitrification and enhanced N<sub>2</sub>O reduction. These findings indicate that incorporating quinone groups into biochar is a viable strategy to mitigate N<sub>2</sub>O accumulation by enhancing its electron-shuttling function.</div></div>","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"213 ","pages":"Article 110040"},"PeriodicalIF":10.3,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145567425","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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