Pub Date : 2025-01-24DOI: 10.1016/j.soilbio.2025.109729
Nikolaos Kaloterakis, Adriana Giongo, Andrea Braun-Kiewnick, Mehdi Rashtbari, Priscilla Zamberlan, Bahar S. Razavi, Kornelia Smalla, Rüdiger Reichel, Nicolas Brüggemann
Plant-soil feedbacks drive productivity in winter wheat (WW; Triticum aestivum L.) rotations. Although this is a frequent observation, the underlying plant-soil-microbe interactions remain unclear. We aimed to investigate the effects of WW rotational positions on soil bacterial and archaeal communities, as well as nitrogen (N) cycling, as potential drivers of WW yield decline in successively-grown WW. WW following oilseed rape (W1; Brassica napus L.) was compared with WW in self-succession (W2) in a rhizotron study using agricultural soil with a sandy loam texture. Samples were collected at tillering and grain ripening. At tillering, we found a higher NO3- content in W1 soil, especially in the 60-100 cm subsoil layer, associated with the N-rich residues of the preceding oilseed rape crop, while this trend was reversed at grain ripening. Analysis of enzyme kinetics revealed an increase in leucine aminopeptidase activity in W1 and an increase in β-glucosidase activity in W2 at tillering, possibly related to the residue quality of the preceding crop. No differences in bacterial and archaeal alpha diversity were observed at both sampling times, but beta diversity showed a significant role of both rotational position and soil depth in shaping the microbial community. The gene copy numbers of amoA genes of ammonia-oxidizing bacteria (AOB), nifH and nirS were significantly higher in W2 compared to W1 at tillering, suggesting a strong effect of rotational position on N cycling of the following WW. The abundances of amoA (AOB) and nirS were also higher in W2 at grain ripening. Our results highlight the persistent soil legacy of the preceding crop on both nutrient cycling and bacterial and archaeal community composition, contributing to yield reduction in successively grown WW. Understanding plant-microbe interactions and keeping them at the center of productive WW rotations is, and will continue to be, critical to future agriculture.
{"title":"Rotational diversity shapes the bacterial and archaeal communities and confers positive plant-soil feedback in winter wheat rotations","authors":"Nikolaos Kaloterakis, Adriana Giongo, Andrea Braun-Kiewnick, Mehdi Rashtbari, Priscilla Zamberlan, Bahar S. Razavi, Kornelia Smalla, Rüdiger Reichel, Nicolas Brüggemann","doi":"10.1016/j.soilbio.2025.109729","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109729","url":null,"abstract":"Plant-soil feedbacks drive productivity in winter wheat (WW; <em>Triticum aestivum</em> L.) rotations. Although this is a frequent observation, the underlying plant-soil-microbe interactions remain unclear. We aimed to investigate the effects of WW rotational positions on soil bacterial and archaeal communities, as well as nitrogen (N) cycling, as potential drivers of WW yield decline in successively-grown WW. WW following oilseed rape (W1; <em>Brassica napus</em> L.) was compared with WW in self-succession (W2) in a rhizotron study using agricultural soil with a sandy loam texture. Samples were collected at tillering and grain ripening. At tillering, we found a higher NO<sub>3</sub><sup>-</sup> content in W1 soil, especially in the 60-100 cm subsoil layer, associated with the N-rich residues of the preceding oilseed rape crop, while this trend was reversed at grain ripening. Analysis of enzyme kinetics revealed an increase in leucine aminopeptidase activity in W1 and an increase in β-glucosidase activity in W2 at tillering, possibly related to the residue quality of the preceding crop. No differences in bacterial and archaeal alpha diversity were observed at both sampling times, but beta diversity showed a significant role of both rotational position and soil depth in shaping the microbial community. The gene copy numbers of <em>amoA</em> genes of ammonia-oxidizing bacteria (AOB), <em>nifH</em> and <em>nirS</em> were significantly higher in W2 compared to W1 at tillering, suggesting a strong effect of rotational position on N cycling of the following WW. The abundances of <em>amoA</em> (AOB) and <em>nirS</em> were also higher in W2 at grain ripening<em>.</em> Our results highlight the persistent soil legacy of the preceding crop on both nutrient cycling and bacterial and archaeal community composition, contributing to yield reduction in successively grown WW. Understanding plant-microbe interactions and keeping them at the center of productive WW rotations is, and will continue to be, critical to future agriculture.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"36 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031094","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 : 2025-01-20DOI: 10.1016/j.soilbio.2025.109713
José Schreckinger, Michael Mutz, Mark O. Gessner, Linda Gerull, Aline Frossard
Knowledge on microbial community shifts during ecosystem succession from bare surfaces resulting from massive landscape stripping is extremely limited. Here we took advantage of an artificially created experimental catchment (6 ha) to assess structural and functional changes of microbial communities in ephemeral stream sediments and adjacent soils between 3 and 13 years after catchment construction. The catchment has since developed in undisturbed conditions, with major transformations in its morphology, hydrology and vegetation reflected by changes in microbial community structure and function. Initially dominated by cyanobacteria (42% of 16S rRNA reads in 2008 and 0.3% in 2018), the bacterial community shifted to an essentially heterotrophic composition within 10 years, when Alphaproteobacteria (12 vs 21%) and Planctomycetes (3 vs 16%), in particular, gained in importance. Similarly, Sordariomycetes (5% of ITS reads in 2008 and 27% in 2018) replaced Dothideomycetes (53 vs 14%) as the prevailing fungal class. Microbial respiration rates increased tenfold, from an average of 0.5 to 4.4 μg CO2 g-1 DM h-1, accompanied by an increase in potential enzyme activities. Seasonal patterns of microbial community functions were accentuated over a decade of catchment development, whereas structural community changes were less pronounced. Spatial variation of community composition also increased, with differences between soils and sediments intensifying over time. However, a striking disconnect between microbial community structure and function in 2008 had vanished by 2018. Thus, a decade of ecosystem succession resulted in fundamental shifts in microbial community structure and function, highlighting the intricate interplay between changing environmental conditions and microbial responses.
在生态系统演替过程中，由于大规模的景观剥离而导致裸露表面的微生物群落变化的知识非常有限。在这里，我们利用人工创建的实验集水区（6公顷）来评估集水区建设后3至13年间短暂的河流沉积物和邻近土壤中微生物群落的结构和功能变化。此后，该流域在未受干扰的条件下发展，其形态、水文和植被发生了重大变化，反映在微生物群落结构和功能的变化上。最初由蓝藻菌（2008年占16S rRNA读取量的42%，2018年占0.3%）主导，细菌群落在10年内转变为本质上的异养组成，特别是Alphaproteobacteria（12对21%）和Planctomycetes（3对16%）变得尤为重要。同样，Sordariomycetes（2008年占ITS读数的5%，2018年占27%）取代Dothideomycetes（53%对14%）成为主要的真菌类别。微生物呼吸速率增加了10倍，从平均0.5到4.4 μg CO2 g-1 DM h-1，伴随着潜在酶活性的增加。随着流域的发展，微生物群落功能的季节变化趋势明显，而群落结构变化不明显。群落组成的空间差异也增加了，土壤和沉积物之间的差异随着时间的推移而加剧。然而，2008年微生物群落结构和功能之间的显著脱节在2018年消失了。因此，十年的生态系统演替导致了微生物群落结构和功能的根本变化，突出了变化的环境条件和微生物响应之间复杂的相互作用。
{"title":"Fundamental shifts in soil and sediment microbial communities and functions during 10 year of early catchment succession","authors":"José Schreckinger, Michael Mutz, Mark O. Gessner, Linda Gerull, Aline Frossard","doi":"10.1016/j.soilbio.2025.109713","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109713","url":null,"abstract":"Knowledge on microbial community shifts during ecosystem succession from bare surfaces resulting from massive landscape stripping is extremely limited. Here we took advantage of an artificially created experimental catchment (6 ha) to assess structural and functional changes of microbial communities in ephemeral stream sediments and adjacent soils between 3 and 13 years after catchment construction. The catchment has since developed in undisturbed conditions, with major transformations in its morphology, hydrology and vegetation reflected by changes in microbial community structure and function. Initially dominated by cyanobacteria (42% of 16S rRNA reads in 2008 and 0.3% in 2018), the bacterial community shifted to an essentially heterotrophic composition within 10 years, when Alphaproteobacteria (12 vs 21%) and Planctomycetes (3 vs 16%), in particular, gained in importance. Similarly, Sordariomycetes (5% of ITS reads in 2008 and 27% in 2018) replaced Dothideomycetes (53 vs 14%) as the prevailing fungal class. Microbial respiration rates increased tenfold, from an average of 0.5 to 4.4 μg CO<sub>2</sub> g<sup>-1</sup> DM h<sup>-1</sup>, accompanied by an increase in potential enzyme activities. Seasonal patterns of microbial community functions were accentuated over a decade of catchment development, whereas structural community changes were less pronounced. Spatial variation of community composition also increased, with differences between soils and sediments intensifying over time. However, a striking disconnect between microbial community structure and function in 2008 had vanished by 2018. Thus, a decade of ecosystem succession resulted in fundamental shifts in microbial community structure and function, highlighting the intricate interplay between changing environmental conditions and microbial responses.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"107 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142990658","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 : 2025-01-19DOI: 10.1016/j.soilbio.2025.109716
Bing Zhang, Xin Li, Haozhen Chen, Mingqin Deng, Haijun Xiao, Shikui Dong, Stefan Scheu, Shaopeng Wang
The elemental composition of organisms is crucial to their survival and growth, as well as their ecological functions. Although variations in carbon (C), nitrogen (N), and phosphorus (P) among species have been well documented, knowledge on whether such variations also exist within species and hold for other elements is limited. Within species, variations in element concentrations may arise from differences in individual traits (e.g., body mass) or heterogeneities under environmental conditions. To explore whether body mass and environment interactively affect intraspecific multi-element composition, we examined the concentrations of 11 elements (C, N, P, S, K, Ca, Na, Mg, Zn, Mn, and Cu) in 114 individuals from three ground beetle species surveyed in four forest types (poplar, oak, larch and oak-larch mixed forest). We investigated among- and within-species variation in each individual element and in the multi-element composition. Our results showed that (i) across all beetle individuals, body mass and species identity explained most of the variation in the concentrations of most elements, whereas forest type only played a minor role; (ii) within all beetle species, the concentration of C increased with body mass, while that of other elements tended to decrease; and (iii) multidimensional stoichiometric analyses also revealed large variations within species, which were again largely explained by variation in body mass and additionally by forest type. By revealing substantial variation in element composition within species and the role of body mass in driving this variation, our study provides empirical evidence for theoretical modeling of stoichiometry and new insights for integrating morphological and stoichiometric traits.
{"title":"Adult body mass influences multi-element stoichiometry in ground beetles","authors":"Bing Zhang, Xin Li, Haozhen Chen, Mingqin Deng, Haijun Xiao, Shikui Dong, Stefan Scheu, Shaopeng Wang","doi":"10.1016/j.soilbio.2025.109716","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109716","url":null,"abstract":"The elemental composition of organisms is crucial to their survival and growth, as well as their ecological functions. Although variations in carbon (C), nitrogen (N), and phosphorus (P) among species have been well documented, knowledge on whether such variations also exist within species and hold for other elements is limited. Within species, variations in element concentrations may arise from differences in individual traits (e.g., body mass) or heterogeneities under environmental conditions. To explore whether body mass and environment interactively affect intraspecific multi-element composition, we examined the concentrations of 11 elements (C, N, P, S, K, Ca, Na, Mg, Zn, Mn, and Cu) in 114 individuals from three ground beetle species surveyed in four forest types (poplar, oak, larch and oak-larch mixed forest). We investigated among- and within-species variation in each individual element and in the multi-element composition. Our results showed that (i) across all beetle individuals, body mass and species identity explained most of the variation in the concentrations of most elements, whereas forest type only played a minor role; (ii) within all beetle species, the concentration of C increased with body mass, while that of other elements tended to decrease; and (iii) multidimensional stoichiometric analyses also revealed large variations within species, which were again largely explained by variation in body mass and additionally by forest type. By revealing substantial variation in element composition within species and the role of body mass in driving this variation, our study provides empirical evidence for theoretical modeling of stoichiometry and new insights for integrating morphological and stoichiometric traits.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"7 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142988982","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 : 2025-01-17DOI: 10.1016/j.soilbio.2025.109714
Partho Das, Claire Barker, Yujin Park, François Perreault, Paul Westerhoff, C Ryan Penton
Graphite nano additive (GNA) has shown potential for enhanced soil N retention and plant productivity. To obtain mechanistic understanding on such beneficial effects, lettuce (Lactuca sativa) was grown in a greenhouse with an exposure of GNA at an application range of 0-500 mg/kg soil for seven weeks. Changes in microbial enzyme activities, N cycling gene abundances, and bacterial community composition were investigated as responses to GNA addition. GNA doses ≤ 100 mg/kg soil resulted in elevated soil microbial biomass carbon at week 3 and contributed to enhanced plant yield during the final harvest at week 7. GNA significantly influenced rhizosphere soil enzyme activities, with notable increases observed across all assayed enzymes at week 5, corresponding to the peak in lettuce growth. GNA addition decreased bacterial amoA abundance, which indicated suppressed soil nitrification potentials in both the bulk and rhizosphere soils. This was coupled with an increase in nifH-harboring bacteria in the bulk, but not rhizosphere, soil. Although the gene that encodes for the terminal step in denitrification (nosZ) was not significantly impacted, nirS and nirK abundances indicated a potential for enhanced denitrification in the bulk soil and suppression of denitrification in the rhizosphere soil. 16S rRNA gene-based abundances indicated no significant decreases in the total bacterial community with GNA amendment in both the bulk and rhizosphere soils which indicates that GNA had limited microbiocidal effect on the broad community. However, GNA imposed selection for certain microbial functional clades and taxonomic lineages and demonstrated a significant impact on the overall composition of the microbial community. GNA demonstrated the potential to augment several beneficial bacterial groups while suppressing others. Overall, these data indicate that GNA significantly impacted the bacterial composition, potential N cycling, and enzyme-based activities of the soil community in a fashion that positively impacted the growth of lettuce in our study, principally within the plant rhizosphere.
{"title":"Impact of Graphite Nano Amendments on Soil Enzyme Activities, Functional Genes and Microbiome Composition in a Soil-Plant System","authors":"Partho Das, Claire Barker, Yujin Park, François Perreault, Paul Westerhoff, C Ryan Penton","doi":"10.1016/j.soilbio.2025.109714","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109714","url":null,"abstract":"Graphite nano additive (GNA) has shown potential for enhanced soil N retention and plant productivity. To obtain mechanistic understanding on such beneficial effects, lettuce (<em>Lactuca sativa</em>) was grown in a greenhouse with an exposure of GNA at an application range of 0-500 mg/kg soil for seven weeks. Changes in microbial enzyme activities, N cycling gene abundances, and bacterial community composition were investigated as responses to GNA addition. GNA doses ≤ 100 mg/kg soil resulted in elevated soil microbial biomass carbon at week 3 and contributed to enhanced plant yield during the final harvest at week 7. GNA significantly influenced rhizosphere soil enzyme activities, with notable increases observed across all assayed enzymes at week 5, corresponding to the peak in lettuce growth. GNA addition decreased bacterial <em>amoA</em> abundance, which indicated suppressed soil nitrification potentials in both the bulk and rhizosphere soils. This was coupled with an increase in <em>nifH</em>-harboring bacteria in the bulk, but not rhizosphere, soil. Although the gene that encodes for the terminal step in denitrification (<em>nosZ</em>) was not significantly impacted, <em>nirS</em> and <em>nirK</em> abundances indicated a potential for enhanced denitrification in the bulk soil and suppression of denitrification in the rhizosphere soil. <em>16S rRNA</em> gene-based abundances indicated no significant decreases in the total bacterial community with GNA amendment in both the bulk and rhizosphere soils which indicates that GNA had limited microbiocidal effect on the broad community. However, GNA imposed selection for certain microbial functional clades and taxonomic lineages and demonstrated a significant impact on the overall composition of the microbial community. GNA demonstrated the potential to augment several beneficial bacterial groups while suppressing others. Overall, these data indicate that GNA significantly impacted the bacterial composition, potential N cycling, and enzyme-based activities of the soil community in a fashion that positively impacted the growth of lettuce in our study, principally within the plant rhizosphere.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"12 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142988983","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}
Tree species effects on soil organic carbon (SOC) stocks became a hot topic in soil science during the past decades. Increasing evidence has shown that tree species have contrasting effects on SOC stocks, yet the underlying mechanism remains incompletely understood. The decomposition control hypothesis states that tree species producing recalcitrant litter with low decomposability could facilitate SOC accumulation. In contrast, the formation control hypothesis argues that tree species producing labile litter, which can be efficiently transformed to soil organic matter by soil microbes, could increase SOC stocks. To unravel this controversy, we leveraged a 40-year-old common garden with replicated monoculture stands of eight tree species and examined relationships between leaf litter and fine root traits, soil bacterial and fungal community composition, four C-degrading enzymes, and SOC stocks. There was more than two-fold variation in SOC, particulate organic C (POC) and mineral-associated organic C (MAOC) concentrations among the eight tree species. Specific peroxidase and phenol oxidase activities explained more variation in POC and MAOC concentrations than leaf litter and fine root traits. Specific peroxidase activity was positively correlated with the relative abundance of fungi with genetic potential to produce peroxidase (Fungi_per) and acidobacteria, and specific phenol oxidase activity was positively correlated with relative abundance of actinobacteria. Tree species producing labile leaf and fine root litter characterized by rich nitrogen and poor lignin concentrations were associated with low relative abundance of Fungi_per and high relative abundance of actinobacteria. Collectively, our results suggest that oxidative enzymes that catalyze the decomposition of chemically recalcitrant compounds, and cause destabilization of mineral-bound organic matter, play critical roles in determining tree species effects on SOC stocks.
{"title":"Oxidative enzymes underlie tree species effects on soil organic carbon stocks: a common garden test with eight tree species","authors":"Kailiang Shi, Yanzhen Sun, De-Hui Zeng, Zimeng Sheng, Yansong Zhang, Guigang Lin","doi":"10.1016/j.soilbio.2025.109715","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109715","url":null,"abstract":"Tree species effects on soil organic carbon (SOC) stocks became a hot topic in soil science during the past decades. Increasing evidence has shown that tree species have contrasting effects on SOC stocks, yet the underlying mechanism remains incompletely understood. The decomposition control hypothesis states that tree species producing recalcitrant litter with low decomposability could facilitate SOC accumulation. In contrast, the formation control hypothesis argues that tree species producing labile litter, which can be efficiently transformed to soil organic matter by soil microbes, could increase SOC stocks. To unravel this controversy, we leveraged a 40-year-old common garden with replicated monoculture stands of eight tree species and examined relationships between leaf litter and fine root traits, soil bacterial and fungal community composition, four C-degrading enzymes, and SOC stocks. There was more than two-fold variation in SOC, particulate organic C (POC) and mineral-associated organic C (MAOC) concentrations among the eight tree species. Specific peroxidase and phenol oxidase activities explained more variation in POC and MAOC concentrations than leaf litter and fine root traits. Specific peroxidase activity was positively correlated with the relative abundance of fungi with genetic potential to produce peroxidase (Fungi_per) and acidobacteria, and specific phenol oxidase activity was positively correlated with relative abundance of actinobacteria. Tree species producing labile leaf and fine root litter characterized by rich nitrogen and poor lignin concentrations were associated with low relative abundance of Fungi_per and high relative abundance of actinobacteria. Collectively, our results suggest that oxidative enzymes that catalyze the decomposition of chemically recalcitrant compounds, and cause destabilization of mineral-bound organic matter, play critical roles in determining tree species effects on SOC stocks.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"20 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142987036","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 : 2025-01-08DOI: 10.1016/j.soilbio.2025.109711
Yuting Fu, Sabine Ravnskov, Marcos Paradelo, Lis W. de Jonge, Emmanuel Arthur
Organic material (OM) decomposition is crucial to soil fertility. We evaluated the hypothesis that long-term manure application induces changes in soil properties which affect the decomposition of OM in the first three months. We buried standardized plant litter with different C/N ratios, i.e., green tea (high-quality OM) and rooibos tea (low-quality OM), in five long-term organic fertilization experiments across different soil types in Europe. Intact 100 cm3 soil cores and bulk soil around the buried OM were analyzed for soil properties, including the physicochemical environment (nutrient contents, pore structure, etc) and microbiological properties (biomass of arbuscular mycorrhizal fungi, fungi, actinobacteria, Gram-positive and Gram-negative bacteria, and fluorescein diacetate [FDA] enzyme activity). Despite the difference in microbial growth and activity and soil pore structure between treatments and crops, the effect of manure on OM decomposition was inconsistent across the fields and varied with soil texture and standing crop species. Decomposition of high-quality OM was reduced by 5–7% in two sandy fields with manure treatment and that of low-quality OM was reduced by 22% in one silty manured field, while in the other fields, the decomposition was not affected by manure. The decomposition of both OM types was higher in the maize field than in the barley and grass fields in one sandy site. Soil texture and electrical conductivity were negatively linked to the mass loss of both OM types. For the high-quality OM, its decomposition was also negatively linked to soil organic carbon and nutrient content, but positively linked to FDA enzyme activity. In contrast, the decomposition of low-quality OM was positively impacted by the bacterial biomass and soil total porosity. In conclusion, the effect of long-term manure application on OM decomposition depends on the soil texture and the standing crop species, and the edaphic drivers for OM decomposition vary with OM quality.
{"title":"Unraveling the Edaphic Factors Driving Organic Material Decay: Insights from Long-Term Manure Application Studies","authors":"Yuting Fu, Sabine Ravnskov, Marcos Paradelo, Lis W. de Jonge, Emmanuel Arthur","doi":"10.1016/j.soilbio.2025.109711","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109711","url":null,"abstract":"Organic material (OM) decomposition is crucial to soil fertility. We evaluated the hypothesis that long-term manure application induces changes in soil properties which affect the decomposition of OM in the first three months. We buried standardized plant litter with different C/N ratios, i.e., green tea (high-quality OM) and rooibos tea (low-quality OM), in five long-term organic fertilization experiments across different soil types in Europe. Intact 100 cm<sup>3</sup> soil cores and bulk soil around the buried OM were analyzed for soil properties, including the physicochemical environment (nutrient contents, pore structure, etc) and microbiological properties (biomass of arbuscular mycorrhizal fungi, fungi, actinobacteria, Gram-positive and Gram-negative bacteria, and fluorescein diacetate [FDA] enzyme activity). Despite the difference in microbial growth and activity and soil pore structure between treatments and crops, the effect of manure on OM decomposition was inconsistent across the fields and varied with soil texture and standing crop species. Decomposition of high-quality OM was reduced by 5–7% in two sandy fields with manure treatment and that of low-quality OM was reduced by 22% in one silty manured field, while in the other fields, the decomposition was not affected by manure. The decomposition of both OM types was higher in the maize field than in the barley and grass fields in one sandy site. Soil texture and electrical conductivity were negatively linked to the mass loss of both OM types. For the high-quality OM, its decomposition was also negatively linked to soil organic carbon and nutrient content, but positively linked to FDA enzyme activity. In contrast, the decomposition of low-quality OM was positively impacted by the bacterial biomass and soil total porosity. In conclusion, the effect of long-term manure application on OM decomposition depends on the soil texture and the standing crop species, and the edaphic drivers for OM decomposition vary with OM quality.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"44 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142936685","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 : 2025-01-08DOI: 10.1016/j.soilbio.2025.109712
Tom Sizmur, Alexey Larionov
Epigenetics is a phenomenon whereby a stable hereditable change in gene expression can occur without changing the DNA sequence. DNA methylation (the addition of a methyl group to specific nucleotides in specific DNA motifs) is the most studied epigenetic mechanism and is widely observed in both eukaryotic and prokaryotic cells. We hypothesise that the soil methylome may play an important role in the manifestation of soil abiotic legacy effects, whereby temporary exposure of soil microbial communities to particular environmental conditions influences future soil microbial function. These abiotic legacy effects are important because they underpin the delivery of key ecosystem services in response to global environmental change. Third generation long-read sequencing technologies, such as Pacific Bioscience Single-Molecule Real-Time sequencing (SMRT-seq) and Oxford Nanopore sequencing provide an opportunity to study methylome heterogeneity in complex microbial communities. The simultaneous measurement of epigenetic, transcriptional, and microbial community composition changes may lead to the development of biomarkers of historic environmental stress and a greater understanding of the role of the soil methylome in the resilience of soil microbial communities to future environmental perturbations. It is therefore timely to add the meta-epigenetic layer to the multi-omics analysis of the soil microbiome to advance our understanding of soil abiotic legacy effects.
{"title":"The soil microbial methylome: a tool to explore the role of epigenetic memory in driving soil abiotic legacy effects","authors":"Tom Sizmur, Alexey Larionov","doi":"10.1016/j.soilbio.2025.109712","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109712","url":null,"abstract":"Epigenetics is a phenomenon whereby a stable hereditable change in gene expression can occur without changing the DNA sequence. DNA methylation (the addition of a methyl group to specific nucleotides in specific DNA motifs) is the most studied epigenetic mechanism and is widely observed in both eukaryotic and prokaryotic cells. We hypothesise that the soil methylome may play an important role in the manifestation of soil abiotic legacy effects, whereby temporary exposure of soil microbial communities to particular environmental conditions influences future soil microbial function. These abiotic legacy effects are important because they underpin the delivery of key ecosystem services in response to global environmental change. Third generation long-read sequencing technologies, such as Pacific Bioscience Single-Molecule Real-Time sequencing (SMRT-seq) and Oxford Nanopore sequencing provide an opportunity to study methylome heterogeneity in complex microbial communities. The simultaneous measurement of epigenetic, transcriptional, and microbial community composition changes may lead to the development of biomarkers of historic environmental stress and a greater understanding of the role of the soil methylome in the resilience of soil microbial communities to future environmental perturbations. It is therefore timely to add the meta-epigenetic layer to the multi-omics analysis of the soil microbiome to advance our understanding of soil abiotic legacy effects.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"16 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142936812","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 : 2025-01-06DOI: 10.1016/j.soilbio.2025.109710
A.D. Mitchell, Helgason B.L
Hillslope erosion in hummocky landscapes can lead to the accumulation of C-rich topsoil in depositional positions that eventually becomes buried if erosion persists. Our objective in this study was to evaluate the persistence of SOC and the thermodynamic efficiency of the microbial community in C-rich buried surface horizons from five sites with varied texture and organic matter contents. Surface Ah (0-10 cm) and buried surface (Ahb) horizons were isolated from intact cores, sieved (<2 mm) and incubated under ideal conditions of temperature and moisture. Ahb soils had an average organic C content (25.6 mg OC g-1 soil) similar to the corresponding Ah soil (30.9 mg OC g-1 soil). Using isothermal calorimetry, we determined that Ah horizons produced significantly more heat and CO2 but had smaller calorespirometric ratios than Ahb soils, under both basal (841 vs 3106 kJ mol-1 CO2-C) and glucose metabolism (627 vs. 697 kJ mol-1 CO2-C).100-day basal respiration was nearly four times greater in Ah vs. Ahb horizons. While MAOM correlated with basal heat production in both horizons, it only correlated with C persistence in the Ah horizons (Rho = 0.67, p < 0.01), suggesting variability in C persistence was not primarily driven by organo-mineral bonds in Ahb horizons, although energy use efficiency is. Microbial community structure in Ahb horizons was distinct from the surface soils, and changed minimally during incubation, suggesting co-development of the community as decomposition proceeded over the decades of burial, leading to persistent C. These relatively large volume buried surface soils may provide unique opportunities to understand microbial hotspot C processes that are typically difficult to isolate at a spatially explicit scale (e.g., an aggregate interior). We propose that the co-development of distinct microbial communities in C-rich buried horizons leads to more thermally stable SOC, but further research is required to test this hypothesis.
{"title":"Thermodynamics of Microbial Decomposition of Persistent Carbon in Erosion-Buried Topsoils","authors":"A.D. Mitchell, Helgason B.L","doi":"10.1016/j.soilbio.2025.109710","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109710","url":null,"abstract":"Hillslope erosion in hummocky landscapes can lead to the accumulation of C-rich topsoil in depositional positions that eventually becomes buried if erosion persists. Our objective in this study was to evaluate the persistence of SOC and the thermodynamic efficiency of the microbial community in C-rich buried surface horizons from five sites with varied texture and organic matter contents. Surface Ah (0-10 cm) and buried surface (Ahb) horizons were isolated from intact cores, sieved (<2 mm) and incubated under ideal conditions of temperature and moisture. Ahb soils had an average organic C content (25.6 mg OC g<sup>-1</sup> soil) similar to the corresponding Ah soil (30.9 mg OC g<sup>-1</sup> soil). Using isothermal calorimetry, we determined that Ah horizons produced significantly more heat and CO<sub>2</sub> but had smaller calorespirometric ratios than Ahb soils, under both basal (841 vs 3106 kJ mol<sup>-1</sup> CO<sub>2</sub>-C) and glucose metabolism (627 vs. 697 kJ mol<sup>-1</sup> CO<sub>2</sub>-C).100-day basal respiration was nearly four times greater in Ah vs. Ahb horizons. While MAOM correlated with basal heat production in both horizons, it only correlated with C persistence in the Ah horizons (Rho = 0.67, p < 0.01), suggesting variability in C persistence was not primarily driven by organo-mineral bonds in Ahb horizons, although energy use efficiency is. Microbial community structure in Ahb horizons was distinct from the surface soils, and changed minimally during incubation, suggesting co-development of the community as decomposition proceeded over the decades of burial, leading to persistent C. These relatively large volume buried surface soils may provide unique opportunities to understand microbial hotspot C processes that are typically difficult to isolate at a spatially explicit scale (e.g., an aggregate interior). We propose that the co-development of distinct microbial communities in C-rich buried horizons leads to more thermally stable SOC, but further research is required to test this hypothesis.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"21 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142929483","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 : 2025-01-04DOI: 10.1016/j.soilbio.2024.109707
Lennel Camuy-Velez, Ditam Chakraborty, Addisyn Young, Sakshi Paudel, Rylie Elvers, Miranda Vanderhyde, Kelly Walter, Chantal Herzog, Samiran Banerjee
Arbuscular Mycorrhizal Fungi (AMF) contribute to host performance under stress conditions; however, the type and intensity of stress can shape this contribution. Importantly, the benefits of mycorrhizal symbiosis may also vary with the functional group of host plants. It also remains unclear whether multi-species inocula confer greater stress alleviation to hosts or if single-species inocula are sufficient for host resilience. To address these knowledge gaps, we conducted a global meta-analysis of 252 studies from 36 countries on six continents. Our analysis revealed that mycorrhizal associations enhance the phosphorus and nitrogen content of host biomass under these global change factors. However, contrary to previous meta-analyses that found consistently strong impacts of AMF, we found variable contributions of AMF under heat, cold, drought, salinity, pesticide, and heavy metal pollution. Each stress type has a unique impact on the contribution of AMF to host performance, but this impact also varies with the intensity of stress. Single-species AMF inocula contribute more significantly to host performance under stress compared to multi-species inocula. We also show that the contribution of AMF to plant growth response significantly varies across different plant functional groups, with grasses and legumes significantly benefiting from mycorrhizal associations under global change factors. Overall, this study highlights that the contribution of AMF to host performance under stress is highly context-dependent and influenced by various factors, including the type and intensity of stress, the type of inocula, and the functional groups of host plants. Thus, our meta-analysis can help develop hypotheses that can be tested with mechanistic experiments to gain a better understanding of the synergistic relationship between AMF and host plants in overcoming stress.
{"title":"Context-dependent contributions of arbuscular mycorrhizal fungi to host performance under global change factors","authors":"Lennel Camuy-Velez, Ditam Chakraborty, Addisyn Young, Sakshi Paudel, Rylie Elvers, Miranda Vanderhyde, Kelly Walter, Chantal Herzog, Samiran Banerjee","doi":"10.1016/j.soilbio.2024.109707","DOIUrl":"https://doi.org/10.1016/j.soilbio.2024.109707","url":null,"abstract":"Arbuscular Mycorrhizal Fungi (AMF) contribute to host performance under stress conditions; however, the type and intensity of stress can shape this contribution. Importantly, the benefits of mycorrhizal symbiosis may also vary with the functional group of host plants. It also remains unclear whether multi-species inocula confer greater stress alleviation to hosts or if single-species inocula are sufficient for host resilience. To address these knowledge gaps, we conducted a global meta-analysis of 252 studies from 36 countries on six continents. Our analysis revealed that mycorrhizal associations enhance the phosphorus and nitrogen content of host biomass under these global change factors. However, contrary to previous meta-analyses that found consistently strong impacts of AMF, we found variable contributions of AMF under heat, cold, drought, salinity, pesticide, and heavy metal pollution. Each stress type has a unique impact on the contribution of AMF to host performance, but this impact also varies with the intensity of stress. Single-species AMF inocula contribute more significantly to host performance under stress compared to multi-species inocula. We also show that the contribution of AMF to plant growth response significantly varies across different plant functional groups, with grasses and legumes significantly benefiting from mycorrhizal associations under global change factors. Overall, this study highlights that the contribution of AMF to host performance under stress is highly context-dependent and influenced by various factors, including the type and intensity of stress, the type of inocula, and the functional groups of host plants. Thus, our meta-analysis can help develop hypotheses that can be tested with mechanistic experiments to gain a better understanding of the synergistic relationship between AMF and host plants in overcoming stress.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"27 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142924658","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}
The trends in 21st century climate change will be largely modulated by the amount of carbon respired via the enzymatic depolymerization of soil organic carbon (SOC). As soil pH serves as a key indicator of global change, understanding how soil respiration responds to pH induced changes in enzyme kinetic properties will provide valuable insights into the feedback of soil carbon to climate change. In a Pinus tabuliformis forest of northern China, a soil pH gradient ranging from 4.91 to 7.89 was constructed by applying ammonium nitrate at rates of 5, 10, 20, and 40 g N m-2 yr-1 (N5, N10, N20, and N40) and lime at rates of 50, 100, 200, and 400 g m-2 yr-1 (L50, L100, L200, and L400) since 2015. In August 2022, soil basal respiration, the β-glucosidase (BG) activity, and soil microbial properties were measured. Results revealed that soil basal respiration increased from 1.46 μmol CO2 m-2 s-1 in N40 treatment to 2.36 CO2 m-2 s-1 in L400 treatment, while the binding affinity of BG rose from 0.018 to 0.032 under the same treatments. The maximum activity of BG decreased from 119.82 nmol MUB·h-1·g-1 SOM in N40 treatment to 66.80 nmol MUB·h-1·g-1 SOM in L400 treatment. The temperature sensitivity of soil respiration showed a bell-shaped response to soil pH, with an optimal pH of about pH 6.7. Our findings demonstrated that it was the binding affinity instead of the activity of BG that positively promoted soil respiration across the established soil pH gradient. The underpinning mechanisms linking soil respiration with enzyme functions were ascribed to the soil acid-base microenvironment, which affected the bioavailability of key nutrient and the content of soil inorganic nitrogen. Additionally, these results will improve the understanding of enzymatic mechanisms in driving the biogeochemical cycle of SOC.
21世纪气候变化的趋势将在很大程度上受到土壤有机碳酶解聚合所呼吸的碳量的调节。由于土壤pH值是全球变化的关键指标，了解土壤呼吸如何响应pH值引起的酶动力学性质的变化将为土壤碳对气候变化的反馈提供有价值的见解。2015年以来，通过施用5、10、20和40 g N - m-2年-1 （N5、N10、N20和N40）的硝酸铵和施用50、100、200和400 g N - m-2年-1 （L50、L100、L200和L400）的石灰，在中国北方油松森林中构建了4.91 ~ 7.89的土壤pH梯度。2022年8月，测定了土壤基础呼吸、β-葡萄糖苷酶（BG）活性和土壤微生物特性。结果表明，N40处理的土壤基础呼吸从1.46 μmol CO2 m-2 s-1增加到L400处理的2.36 μmol CO2 m-2 s-1，而BG的结合亲和力从0.018增加到0.032。BG的最大活性由N40处理的119.82 nmol MUB·h-1·g-1 SOM降至L400处理的66.80 nmol MUB·h-1·g-1 SOM。土壤呼吸的温度敏感性对土壤pH呈钟形响应，最佳pH值约为pH 6.7。我们的研究结果表明，在既定的土壤pH梯度中，是结合亲和力而不是BG的活性积极促进了土壤呼吸。土壤酸碱微环境影响土壤关键养分的生物有效性和土壤无机氮含量，是土壤呼吸与酶功能联系的基础机制。此外，这些结果将提高对酶驱动有机碳生物地球化学循环机制的理解。
{"title":"Soil pH promoted respiration is stimulated by exoenzyme kinetic properties for a Pinus tabuliformis forest of northern China","authors":"Mengyao Xu, Zhiyong Zhou, Yinhua Guo, Ying Shen, Huan Zhang, Qiang Yu","doi":"10.1016/j.soilbio.2025.109709","DOIUrl":"https://doi.org/10.1016/j.soilbio.2025.109709","url":null,"abstract":"The trends in 21<sup>st</sup> century climate change will be largely modulated by the amount of carbon respired via the enzymatic depolymerization of soil organic carbon (SOC). As soil pH serves as a key indicator of global change, understanding how soil respiration responds to pH induced changes in enzyme kinetic properties will provide valuable insights into the feedback of soil carbon to climate change. In a <em>Pinus tabuliformis</em> forest of northern China, a soil pH gradient ranging from 4.91 to 7.89 was constructed by applying ammonium nitrate at rates of 5, 10, 20, and 40 g N m<sup>-2</sup> yr<sup>-1</sup> (N5, N10, N20, and N40) and lime at rates of 50, 100, 200, and 400 g m<sup>-2</sup> yr<sup>-1</sup> (L50, L100, L200, and L400) since 2015. In August 2022, soil basal respiration, the β-glucosidase (BG) activity, and soil microbial properties were measured. Results revealed that soil basal respiration increased from 1.46 μmol CO<sub>2</sub> m<sup>-2</sup> s<sup>-1</sup> in N40 treatment to 2.36 CO<sub>2</sub> m<sup>-2</sup> s<sup>-1</sup> in L400 treatment, while the binding affinity of BG rose from 0.018 to 0.032 under the same treatments. The maximum activity of BG decreased from 119.82 nmol MUB·h<sup>-1</sup>·g<sup>-1</sup> SOM in N40 treatment to 66.80 nmol MUB·h<sup>-1</sup>·g<sup>-1</sup> SOM in L400 treatment. The temperature sensitivity of soil respiration showed a bell-shaped response to soil pH, with an optimal pH of about pH 6.7. Our findings demonstrated that it was the binding affinity instead of the activity of BG that positively promoted soil respiration across the established soil pH gradient. The underpinning mechanisms linking soil respiration with enzyme functions were ascribed to the soil acid-base microenvironment, which affected the bioavailability of key nutrient and the content of soil inorganic nitrogen. Additionally, these results will improve the understanding of enzymatic mechanisms in driving the biogeochemical cycle of SOC.","PeriodicalId":21888,"journal":{"name":"Soil Biology & Biochemistry","volume":"15 1","pages":""},"PeriodicalIF":9.7,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142917756","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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