Pub Date : 2025-04-23DOI: 10.1016/j.ejsobi.2025.103728
Lingxia Feng , Bing Cao
Climate warming can directly or indirectly influence soil phosphorus (P) availability. Soil microorganisms are essential driving forces of P cycling. However, how the soil microbes and P cycling genes respond to variations in soil P availability on climate warming in the P-limited desert steppe is unclear. In this study, we conducted a field experiment using two temperature levels (control, warming) and three P fertilizer addition rates (0, 5, 10 g P m−2·yr−1) in the desert steppe. Microbiological and metagenomic analyses were used to explore the shifts in the relative abundance and compositions of soil microbial and P cycling genes in response to warming and P inputs. The results demonstrated that warming decreased soil labile P (7.04 %) by reducing the percentages of resin-P, NaHCO3-Pi, and HCl-Pi in inorganic P (Pi). P inputs significantly increased soil TP, MBP, Pi, and inorganic P fractions contents, and further enhanced soil labile P (1.27–3.55 times), moderately labile P (7.04–17.59 %), and stable P (4.23-10.47 %). The interaction of warming and P addition increased NaHCO3-Pi, the percentages of NaHCO3-Pi in Pi, and improved soil labile P (1.68–2.05 times) and stable P (5.38–10.38 %). Soil P availability was mainly regulated by TP and MBP, which were positively correlated with the organic P mineralization gene (phnW). Our findings indicated that soil bacteria and fungi did not alter in response to changes in P availability under warming and P input. The phnW gene played an essential role in regulating soil P availability in the desert steppe.
{"title":"Regulation of soil microorganisms and phosphorus cycling genes on soil phosphorus availability in desert steppe under warming and phosphorus input","authors":"Lingxia Feng , Bing Cao","doi":"10.1016/j.ejsobi.2025.103728","DOIUrl":"10.1016/j.ejsobi.2025.103728","url":null,"abstract":"<div><div>Climate warming can directly or indirectly influence soil phosphorus (P) availability. Soil microorganisms are essential driving forces of P cycling. However, how the soil microbes and P cycling genes respond to variations in soil P availability on climate warming in the P-limited desert steppe is unclear. In this study, we conducted a field experiment using two temperature levels (control, warming) and three P fertilizer addition rates (0, 5, 10 g P m<sup>−2</sup>·yr<sup>−1</sup>) in the desert steppe. Microbiological and metagenomic analyses were used to explore the shifts in the relative abundance and compositions of soil microbial and P cycling genes in response to warming and P inputs. The results demonstrated that warming decreased soil labile P (7.04 %) by reducing the percentages of resin-P, NaHCO<sub>3</sub>-Pi, and HCl-Pi in inorganic P (Pi). P inputs significantly increased soil TP, MBP, Pi, and inorganic P fractions contents, and further enhanced soil labile P (1.27–3.55 times), moderately labile P (7.04–17.59 %), and stable P (4.23-10.47 %). The interaction of warming and P addition increased NaHCO<sub>3</sub>-Pi, the percentages of NaHCO<sub>3</sub>-Pi in Pi, and improved soil labile P (1.68–2.05 times) and stable P (5.38–10.38 %). Soil P availability was mainly regulated by TP and MBP, which were positively correlated with the organic P mineralization gene (<em>phnW</em>). Our findings indicated that soil bacteria and fungi did not alter in response to changes in P availability under warming and P input. The <em>phnW</em> gene played an essential role in regulating soil P availability in the desert steppe.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"125 ","pages":"Article 103728"},"PeriodicalIF":3.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143860172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-15DOI: 10.1016/j.ejsobi.2025.103727
Sichen Pan , Caiyun Luo , Xin Chen , Dongdong Chen , Qi Li , Fuquan He , Yukun Zhang , Li Zhang , Liang Zhao
Potentially toxic elements (PTEs) of soil are crucial for sustaining the equilibrium of grassland "vegetation-soil-microorganism" systems and influencing terrestrial biogeochemical cycles. This study investigated how PTEs influence microbial community structure and carbon metabolism by comparing soil microbial differences under fencing enclosure (FE), winter grazing (WG), and artificial unicast oat (AU) management practices. This was done in alpine meadows using metagenomic sequencing techniques. The results indicated that management measures significantly changed the distribution of the Cr, Hg, and As, with Cr and As being the highest in AU and Hg being the highest in FE. In the purine metabolic pathway, Hg had a significant positive effect on soil microbial biomass carbon (SMBC) metabolism, which was catabolized by the prokaryote Chloroflexi and the fungal organism Chytridiomycota during guanosine triphosphate (GTP) catabolism and xanthosine monophosphate (XMP) synthesis to promote soil SMBC cycling. Cr had a significant negative effect on soil organic carbon (SOC) and SMBC metabolism during the synthesis of xanthonsine, urate, 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate and CO2. Additionally, the enrichment and decomposition of Cr by the prokaryotic organisms Proteobacteria and Verrucomicrobia, inhibited SMBC and SOC transformation and affected soil CO2 emissions. Further, by comparing resistance genes, it was found that alpine meadows were more resistant to Hg and Cr and that fungal organisms were more tolerant to Cr than prokaryotes. Overall, Cr and Hg interact with microorganisms to influence SOC and SMBC metabolic processes and have a positive effect on carbon sequestration in alpine meadows.
{"title":"Soil potentially toxic elements promote carbon metabolism in alpine meadows on the Qinghai-Xizang Plateau","authors":"Sichen Pan , Caiyun Luo , Xin Chen , Dongdong Chen , Qi Li , Fuquan He , Yukun Zhang , Li Zhang , Liang Zhao","doi":"10.1016/j.ejsobi.2025.103727","DOIUrl":"10.1016/j.ejsobi.2025.103727","url":null,"abstract":"<div><div>Potentially toxic elements (PTEs) of soil are crucial for sustaining the equilibrium of grassland \"vegetation-soil-microorganism\" systems and influencing terrestrial biogeochemical cycles. This study investigated how PTEs influence microbial community structure and carbon metabolism by comparing soil microbial differences under fencing enclosure (FE), winter grazing (WG), and artificial unicast oat (AU) management practices. This was done in alpine meadows using metagenomic sequencing techniques. The results indicated that management measures significantly changed the distribution of the Cr, Hg, and As, with Cr and As being the highest in AU and Hg being the highest in FE. In the purine metabolic pathway, Hg had a significant positive effect on soil microbial biomass carbon (SMBC) metabolism, which was catabolized by the prokaryote Chloroflexi and the fungal organism Chytridiomycota during guanosine triphosphate (GTP) catabolism and xanthosine monophosphate (XMP) synthesis to promote soil SMBC cycling. Cr had a significant negative effect on soil organic carbon (SOC) and SMBC metabolism during the synthesis of xanthonsine, urate, 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate and CO<sub>2</sub>. Additionally, the enrichment and decomposition of Cr by the prokaryotic organisms Proteobacteria and Verrucomicrobia, inhibited SMBC and SOC transformation and affected soil CO<sub>2</sub> emissions. Further, by comparing resistance genes, it was found that alpine meadows were more resistant to Hg and Cr and that fungal organisms were more tolerant to Cr than prokaryotes. Overall, Cr and Hg interact with microorganisms to influence SOC and SMBC metabolic processes and have a positive effect on carbon sequestration in alpine meadows.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"125 ","pages":"Article 103727"},"PeriodicalIF":3.7,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143833564","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-14DOI: 10.1016/j.ejsobi.2025.103726
Yuan Zhang , Benli Liu , Jianjun Qu
Biological soil crusts (BSCs) cover approximately 12 % of the earth's terrestrial surface and play vital ecological roles in various dry habitats. However, most research on BSCs has focused on deserts in arid and semi-arid regions, with limited studies on BSCs under sensitive, fragile, and cold conditions, such as those found in the Qinghai-Tibet Plateau. Notably, investigations into the complete successional stages of BSCs in these regions are exceedingly rare. In this study, we examined four successional stages of BSCs across five sites at elevations ranging from 2862 to 4274 m in the northeastern Qinghai-Tibet Plateau. High-throughput sequencing was used to analyze the bacterial, fungal, and archaeal communities in the soil, and their diversity, interactions, spatial distribution patterns, and influencing factors were investigated. Our results indicated that in alpine degraded grassland ecosystems, the altitude gradient played a significant role in shaping the distribution patterns of microbial communities during the succession of BSCs. At lower elevations (2862–3405 m), the successional patterns of α-diversity for the three microbial communities were relatively consistent. In contrast, α-diversity patterns at higher altitudes showed greater variability. Differences in bacterial composition between high-altitude areas (3760 m and 4274 m) increased with the development and succession of BSCs, while the differences between low-altitude areas (2862 m and 3405 m) showed opposite trend. The differences in fungal composition across all altitude regions gradually decreased with the succession of BSCs. Additionally, bacterial and fungal composition demonstrated more distinct altitudinal zonation characteristics compared to archaea. Within the bacterial, fungal, or archaeal communities, mutualistic interactions were stronger than competitive interactions, facilitating adaptation to the harsh high-altitude environment. Furthermore, mean annual precipitation, mean annual temperature, pH, and sand content collectively influenced the microbial community distribution patterns in alpine degraded grassland ecosystems. Our research provides scientific references for the distribution and resource protection of BSCs in the Qinghai-Tibet plateau.
{"title":"Changes in microbial communities in biological soil crusts along an altitudinal gradient in the northeastern Qinghai-Tibet plateau","authors":"Yuan Zhang , Benli Liu , Jianjun Qu","doi":"10.1016/j.ejsobi.2025.103726","DOIUrl":"10.1016/j.ejsobi.2025.103726","url":null,"abstract":"<div><div>Biological soil crusts (BSCs) cover approximately 12 % of the earth's terrestrial surface and play vital ecological roles in various dry habitats. However, most research on BSCs has focused on deserts in arid and semi-arid regions, with limited studies on BSCs under sensitive, fragile, and cold conditions, such as those found in the Qinghai-Tibet Plateau. Notably, investigations into the complete successional stages of BSCs in these regions are exceedingly rare. In this study, we examined four successional stages of BSCs across five sites at elevations ranging from 2862 to 4274 m in the northeastern Qinghai-Tibet Plateau. High-throughput sequencing was used to analyze the bacterial, fungal, and archaeal communities in the soil, and their diversity, interactions, spatial distribution patterns, and influencing factors were investigated. Our results indicated that in alpine degraded grassland ecosystems, the altitude gradient played a significant role in shaping the distribution patterns of microbial communities during the succession of BSCs. At lower elevations (2862–3405 m), the successional patterns of α-diversity for the three microbial communities were relatively consistent. In contrast, α-diversity patterns at higher altitudes showed greater variability. Differences in bacterial composition between high-altitude areas (3760 m and 4274 m) increased with the development and succession of BSCs, while the differences between low-altitude areas (2862 m and 3405 m) showed opposite trend. The differences in fungal composition across all altitude regions gradually decreased with the succession of BSCs. Additionally, bacterial and fungal composition demonstrated more distinct altitudinal zonation characteristics compared to archaea. Within the bacterial, fungal, or archaeal communities, mutualistic interactions were stronger than competitive interactions, facilitating adaptation to the harsh high-altitude environment. Furthermore, mean annual precipitation, mean annual temperature, pH, and sand content collectively influenced the microbial community distribution patterns in alpine degraded grassland ecosystems. Our research provides scientific references for the distribution and resource protection of BSCs in the Qinghai-Tibet plateau.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"125 ","pages":"Article 103726"},"PeriodicalIF":3.7,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-04-08DOI: 10.1016/j.ejsobi.2025.103724
Adolfo Perdomo-González , Raquel Pérez-Reverón , Marta Goberna , Heriberto López , Paula Arribas , J. Alfredo Reyes-Betancort , Carmelo Andújar , Francisco J. Díaz-Peña
Reforestation with exotic species has often been used in arid and semiarid areas to restore degraded ecosystems. However, the effects of these plantations on soil biodiversity are still under debate. In the present study, we aimed to evaluate the long-term impacts (>60 years) of exotic plantations with Acacia cyclops and Pinus halepensis on soil biodiversity in an insular arid ecosystem of high ecological value. To do so, we study soil quality and soil arthropod communities in patches of vegetation under uniform edaphoclimatic conditions. Soil quality assessment was carried out by developing an ad-hoc Soil Quality Index (SQI) across seven sites, including two plantations (Pinus or Acacia), two degraded areas with a low cover of native species, and three sites with a high cover of native species. Whole organism community DNA (wocDNA) metabarcoding and barcoding were used to analyse key soil arthropod groups (Coleoptera, Acari and Collembola) recognized as habitat quality and biodiversity indicators. Our findings show that exotic plantations improved soil quality compared to degraded sites, with a considerable increase in the organic carbon pool, macronutrients and microbiological activity (SQI = 0.53 ± 0.12 vs. 0.29 ± 0.06). This improvement did not reach the values recorded in soils with a high cover of preserved native flora (SQI = 0.65 ± 0.12), with some exceptions. Richness of mesofauna and Coleoptera was lower in degraded areas (4.4 ± 1.6 and 0.4 ± 0.7, respectively) followed by exotic plantations (9.5 ± 2.6 and 1.2 ± 0.9) and permanent native vegetation (14.1 ± 5.5 and 2.2 ± 1.8). Soil quality significantly explained up to 52 % and 17 % of the variance in the richness of mesofauna and Coleoptera, respectively. While exotic plantations appear to prevent further land degradation in terms of soil quality, multivariate analysis shows that the structure of soil arthropod communities, particularly in Pinus plantations and to a lesser extent in Acacia plantations, differs significantly from that of soils in ecosystems with remnant native flora. These results highlight the need for a careful balance between biodiversity conservation and soil health management, especially in areas susceptible to desertification.
{"title":"The hidden shift: The role of exotic plantations in modulating soil arthropod communities in an arid island","authors":"Adolfo Perdomo-González , Raquel Pérez-Reverón , Marta Goberna , Heriberto López , Paula Arribas , J. Alfredo Reyes-Betancort , Carmelo Andújar , Francisco J. Díaz-Peña","doi":"10.1016/j.ejsobi.2025.103724","DOIUrl":"10.1016/j.ejsobi.2025.103724","url":null,"abstract":"<div><div>Reforestation with exotic species has often been used in arid and semiarid areas to restore degraded ecosystems. However, the effects of these plantations on soil biodiversity are still under debate. In the present study, we aimed to evaluate the long-term impacts (>60 years) of exotic plantations with <em>Acacia cyclops</em> and <em>Pinus halepensis</em> on soil biodiversity in an insular arid ecosystem of high ecological value. To do so, we study soil quality and soil arthropod communities in patches of vegetation under uniform edaphoclimatic conditions. Soil quality assessment was carried out by developing an ad-hoc Soil Quality Index (SQI) across seven sites, including two plantations (<em>Pinus</em> or <em>Acacia</em>), two degraded areas with a low cover of native species, and three sites with a high cover of native species. Whole organism community DNA (wocDNA) metabarcoding and barcoding were used to analyse key soil arthropod groups (Coleoptera, Acari and Collembola) recognized as habitat quality and biodiversity indicators. Our findings show that exotic plantations improved soil quality compared to degraded sites, with a considerable increase in the organic carbon pool, macronutrients and microbiological activity (SQI = 0.53 ± 0.12 <em>vs.</em> 0.29 ± 0.06). This improvement did not reach the values recorded in soils with a high cover of preserved native flora (SQI = 0.65 ± 0.12), with some exceptions. Richness of mesofauna and Coleoptera was lower in degraded areas (4.4 ± 1.6 and 0.4 ± 0.7, respectively) followed by exotic plantations (9.5 ± 2.6 and 1.2 ± 0.9) and permanent native vegetation (14.1 ± 5.5 and 2.2 ± 1.8). Soil quality significantly explained up to 52 % and 17 % of the variance in the richness of mesofauna and Coleoptera, respectively. While exotic plantations appear to prevent further land degradation in terms of soil quality, multivariate analysis shows that the structure of soil arthropod communities, particularly in <em>Pinus</em> plantations and to a lesser extent in <em>Acacia</em> plantations, differs significantly from that of soils in ecosystems with remnant native flora. These results highlight the need for a careful balance between biodiversity conservation and soil health management, especially in areas susceptible to desertification.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"125 ","pages":"Article 103724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143792634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-03-28DOI: 10.1016/j.ejsobi.2025.103725
XinYue Yan , Yang Li , TianQi Qin , Ying Gan , Na Li
Arid and semi-arid climates are vital components of ecosystem, however, the mechanisms by which microorganisms respond to soil dissolved organic matter (DOM) in these regions under the constraint of ammonium nitrogen remain unknown. In this study, we investigated the differences in microbial diversity, composition, abundance, and DOM composition in soils with varying ammonia-nitrogen (NH4+-N) concentrations in arid and semi-arid regions. We also explored the connectivity between the co-occurrence networks of microorganisms and DOM. In high NH4+-N environments, the phyla of soil microorganisms that showed an increase included Anabaena and Thick-walled Bacteria. Moreover, the abundance of microorganisms such as Reyranella, Actinophyfocala, and Arhrobacter also increased. The main metabolic modes of these microorganisms were lysine biosynthesis and D-amino acid metabolism. Metabolites that exhibited elevated levels along with the increase in NH4+-N content included those related to chlorocyclohexane and chlorobenzene degradation, as well as geraniol degradation. NH4+-N was identified as the most significant environmental factor influencing the relationship between microorganisms and DOM. In high-ammonia environments, the number of links, average clustering coefficient, density, and connectivity of the microorganisms and DOM co-occurrence network were significantly higher. This indicates that the co-occurrence network was more complex and stable. In contrast, low NH4+-N environments restricted microbial metabolic processes and altered the DOM composition, leading to a further limitation of microbial activity. This study elucidated the response mechanism of soil microorganisms to DOM under the limitation of NH4+-N in arid and semi-arid regions and emphasized the crucial role of soil NH4+-N concentration in the soil biological cycle. It offers a reference for monitoring soil quality, preventing soil degradation, and maintaining ecological environment and food security.
{"title":"The light shifts in ammonia nitrogen affected soil microbial communities with their related dissolved organic matter in the arid region","authors":"XinYue Yan , Yang Li , TianQi Qin , Ying Gan , Na Li","doi":"10.1016/j.ejsobi.2025.103725","DOIUrl":"10.1016/j.ejsobi.2025.103725","url":null,"abstract":"<div><div>Arid and semi-arid climates are vital components of ecosystem, however, the mechanisms by which microorganisms respond to soil dissolved organic matter (DOM) in these regions under the constraint of ammonium nitrogen remain unknown. In this study, we investigated the differences in microbial diversity, composition, abundance, and DOM composition in soils with varying ammonia-nitrogen (NH<sub>4</sub><sup>+</sup>-N) concentrations in arid and semi-arid regions. We also explored the connectivity between the co-occurrence networks of microorganisms and DOM. In high NH<sub>4</sub><sup>+</sup>-N environments, the phyla of soil microorganisms that showed an increase included Anabaena and Thick-walled Bacteria. Moreover, the abundance of microorganisms such as <em>Reyranella</em>, <em>Actinophyfocala</em>, and <em>Arhrobacter</em> also increased. The main metabolic modes of these microorganisms were lysine biosynthesis and D-amino acid metabolism. Metabolites that exhibited elevated levels along with the increase in NH<sub>4</sub><sup>+</sup>-N content included those related to chlorocyclohexane and chlorobenzene degradation, as well as geraniol degradation. NH<sub>4</sub><sup>+</sup>-N was identified as the most significant environmental factor influencing the relationship between microorganisms and DOM. In high-ammonia environments, the number of links, average clustering coefficient, density, and connectivity of the microorganisms and DOM co-occurrence network were significantly higher. This indicates that the co-occurrence network was more complex and stable. In contrast, low NH<sub>4</sub><sup>+</sup>-N environments restricted microbial metabolic processes and altered the DOM composition, leading to a further limitation of microbial activity. This study elucidated the response mechanism of soil microorganisms to DOM under the limitation of NH<sub>4</sub><sup>+</sup>-N in arid and semi-arid regions and emphasized the crucial role of soil NH<sub>4</sub><sup>+</sup>-N concentration in the soil biological cycle. It offers a reference for monitoring soil quality, preventing soil degradation, and maintaining ecological environment and food security.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"125 ","pages":"Article 103725"},"PeriodicalIF":3.7,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143715461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-03-01DOI: 10.1016/j.ejsobi.2025.103714
Biyensa Gurmessa , Ranjith P. Udawatta , R. Tharindu Rambadagalla , Timothy Reinbott
Understanding the long-term impacts of cover cropping on soil health indicators is vital for developing sustainable farming practices. The aim of the current study was to investigate the impacts of long-term mixed cover crops practice in a no-till system on soil bacterial community abundance and diversity using 16S rRNA sequencing. We compared three cover crop practices againist a no-cover crop control (NCC): cereal rye only (Rye), a mixture of cereal rye and hairy vetch (RyeHV), and a mixture of cereal rye, hairy vetch, crimson clover, and Australian winter pea (Mixed). These treatments were arranged in a completely randomized block design with four replications. The abundance of soil bacteria was lower in the Rye treatment compared to the Mixed and RyeHV treatments, possibly due to the uniform supply of resources (exudates) and the limited root structure, rather than due to the increased soil bulk density or reduced organic carbon. This reduction was observed in the total operational taxonomic units and the dominant taxa groups, including Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria. Non-metric Multidimensional Scaling analysis, using Bray-Curtis dissimilarity, revealed distinct bacterial community structure between the Rye and the rest of treatments, but with a potential overlap of that of NCC with all the cover crop treatments. In conclusion, our study revealed that unlike mixed species cover crops, a single species cover crops may compete for resources with soil bacterial community, leading to a reduced abundance of soil bacteria. Moreover, possible positive impact of cover cropping on soil physicochemical properties may not always have relationships with soil bacterial alpha diversity. Future research should explore attributes of mixed cover crops that may be crucial in driving microbial community structure.
{"title":"Soil bacterial communities benefit from long-term cover crop mixtures","authors":"Biyensa Gurmessa , Ranjith P. Udawatta , R. Tharindu Rambadagalla , Timothy Reinbott","doi":"10.1016/j.ejsobi.2025.103714","DOIUrl":"10.1016/j.ejsobi.2025.103714","url":null,"abstract":"<div><div>Understanding the long-term impacts of cover cropping on soil health indicators is vital for developing sustainable farming practices. The aim of the current study was to investigate the impacts of long-term mixed cover crops practice in a no-till system on soil bacterial community abundance and diversity using 16S rRNA sequencing. We compared three cover crop practices againist a no-cover crop control (NCC): cereal rye only (Rye), a mixture of cereal rye and hairy vetch (RyeHV), and a mixture of cereal rye, hairy vetch, crimson clover, and Australian winter pea (Mixed). These treatments were arranged in a completely randomized block design with four replications. The abundance of soil bacteria was lower in the Rye treatment compared to the Mixed and RyeHV treatments, possibly due to the uniform supply of resources (exudates) and the limited root structure, rather than due to the increased soil bulk density or reduced organic carbon. This reduction was observed in the total operational taxonomic units and the dominant taxa groups, including Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria. Non-metric Multidimensional Scaling analysis, using Bray-Curtis dissimilarity, revealed distinct bacterial community structure between the Rye and the rest of treatments, but with a potential overlap of that of NCC with all the cover crop treatments. In conclusion, our study revealed that unlike mixed species cover crops, a single species cover crops may compete for resources with soil bacterial community, leading to a reduced abundance of soil bacteria. Moreover, possible positive impact of cover cropping on soil physicochemical properties may not always have relationships with soil bacterial alpha diversity. Future research should explore attributes of mixed cover crops that may be crucial in driving microbial community structure.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"124 ","pages":"Article 103714"},"PeriodicalIF":3.7,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-01-30DOI: 10.1016/j.ejsobi.2025.103713
Milan Varsadiya , Fatemeh Dehghani , Shiyue Yang , Evgenia Blagodatskaya , Thomas Maskow , Dimitri V. Meier , Tillmann Lueders
Microbial carbon use efficiency (CUE), the ratio of carbon retained in biomass vs. total C uptake, is central to our understanding of organic C turnover in soil. A precise quantification of CUE in soils can be challenging, given the considerable analytical uncertainties of organic and inorganic C backgrounds. At the same time, CUE measured for model pure cultures will be distinct from a diverse microbiota in soil. As a proxy between laboratory cultures and complex soil microbiomes, we tested soil-free microbial cell extracts (SFCE) to unravel patterns of C utilization in soil-derived microbiomes of reduced complexity. For this, we have revisited and optimized established protocols to extract microbial cells from agricultural soil via Nycodenz density centrifugation. The total extracted cells were quantified, accounting for up to ∼3.5 × 107 cells g−1 soil and representing ∼12.5 % of the original soil microbiome. The diversity of microbes in SFCE, while consistently reduced compared to soil, still retained a surprisingly high proportion of the original soil microbiome, with ASVs recovered from 21 phyla. We then inferred CUE from calorespirometric measurements (metabolic heat flow and CO2 production) to compare values between SFCE and intact soil. Both were amended with substrates (glucose, glutamine, and glycerol) of different C and N content, and C oxidation state (NOSC). SFCE showed CUE values principally comparable to that of the intact soil, but with substrate-specific distinctions. Amplicon sequencing and qPCR-based quantification showed typical soil taxa like Pseudomonas, Pseudarthrobacter, and Bacteroidota to respond to substrate addition in soil and SFCE. Our results support the use of SFCE as a valuable and complementary approach toward elucidating microbial CUE and growth patterns for complex soil microbiota.
{"title":"Carbon and energy utilization in microbial cell extracts from soil","authors":"Milan Varsadiya , Fatemeh Dehghani , Shiyue Yang , Evgenia Blagodatskaya , Thomas Maskow , Dimitri V. Meier , Tillmann Lueders","doi":"10.1016/j.ejsobi.2025.103713","DOIUrl":"10.1016/j.ejsobi.2025.103713","url":null,"abstract":"<div><div>Microbial carbon use efficiency (CUE), the ratio of carbon retained in biomass vs. total C uptake, is central to our understanding of organic C turnover in soil. A precise quantification of CUE in soils can be challenging, given the considerable analytical uncertainties of organic and inorganic C backgrounds. At the same time, CUE measured for model pure cultures will be distinct from a diverse microbiota in soil. As a proxy between laboratory cultures and complex soil microbiomes, we tested soil-free microbial cell extracts (SFCE) to unravel patterns of C utilization in soil-derived microbiomes of reduced complexity. For this, we have revisited and optimized established protocols to extract microbial cells from agricultural soil via Nycodenz density centrifugation. The total extracted cells were quantified, accounting for up to ∼3.5 × 10<sup>7</sup> cells g<sup>−1</sup> soil and representing ∼12.5 % of the original soil microbiome. The diversity of microbes in SFCE, while consistently reduced compared to soil, still retained a surprisingly high proportion of the original soil microbiome, with ASVs recovered from 21 phyla. We then inferred CUE from calorespirometric measurements (metabolic heat flow and CO<sub>2</sub> production) to compare values between SFCE and intact soil. Both were amended with substrates (glucose, glutamine, and glycerol) of different C and N content, and C oxidation state (NOSC). SFCE showed CUE values principally comparable to that of the intact soil, but with substrate-specific distinctions. Amplicon sequencing and qPCR-based quantification showed typical soil taxa like <em>Pseudomonas</em>, <em>Pseudarthrobacter</em>, and <em>Bacteroidota</em> to respond to substrate addition in soil and SFCE. Our results support the use of SFCE as a valuable and complementary approach toward elucidating microbial CUE and growth patterns for complex soil microbiota.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"124 ","pages":"Article 103713"},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143152991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Extreme climatic events, such as prolonged dry spells, are causing more intense soil droughts, which can be a major threat to soil life. Soil animals in general are rather sensitive to strong fluctuations in soil moisture content but may be able to escape from drought by moving deeper into the soil. Bioturbation, for example by burrowing activity of earthworms, may facilitate such vertical movement and hence moderate the consequences of drought for soil animals. Here, we investigated if earthworm burrows enable soil-dwelling Collembola to move deeper into the soil and escape drought conditions. We also tested if drought affects bioturbation activity of earthworms, and measured evaporation from soil under drought conditions. Using transparent 2D-terraria, we analyzed the effect of four burrow treatments (i.e. burrows from an anecic earthworm species, burrows from an endogeic earthworm species, artificially made burrows, no burrows), each subjected to either drought or normal soil moisture conditions. We added 40 euedaphic springtails (Folsomia candida) per terrarium. After two weeks, we recorded survival of the springtails and their vertical localization in the soil. We used computer vision to estimate the cover and average depth of bioturbated area from photographs of the 2D-terraria. We found that the presence of Aporrectodea caliginosa (endogeic) increased the survival of springtails. Under normal moisture conditions, springtails were found deeper in the soil in the presence of A. longa (anecic). Aporrectodea longa strongly increased evaporation under normal soil moisture conditions. Our experiment showed that earthworms may moderate the impact of drought on euedaphic springtails, which opens up the hypothesis that other soil fauna may benefit as well from earthworm burrowing activity.
{"title":"Earthworm burrows affect vertical distribution of springtails in soil","authors":"A.F. Krediet , B.S. Mönnich , J. Ellers , M.P. Berg","doi":"10.1016/j.ejsobi.2025.103710","DOIUrl":"10.1016/j.ejsobi.2025.103710","url":null,"abstract":"<div><div>Extreme climatic events, such as prolonged dry spells, are causing more intense soil droughts, which can be a major threat to soil life. Soil animals in general are rather sensitive to strong fluctuations in soil moisture content but may be able to escape from drought by moving deeper into the soil. Bioturbation, for example by burrowing activity of earthworms, may facilitate such vertical movement and hence moderate the consequences of drought for soil animals. Here, we investigated if earthworm burrows enable soil-dwelling Collembola to move deeper into the soil and escape drought conditions. We also tested if drought affects bioturbation activity of earthworms, and measured evaporation from soil under drought conditions. Using transparent 2D-terraria, we analyzed the effect of four burrow treatments (i.e. burrows from an anecic earthworm species, burrows from an endogeic earthworm species, artificially made burrows, no burrows), each subjected to either drought or normal soil moisture conditions. We added 40 euedaphic springtails (<em>Folsomia candida</em>) per terrarium. After two weeks, we recorded survival of the springtails and their vertical localization in the soil. We used computer vision to estimate the cover and average depth of bioturbated area from photographs of the 2D-terraria. We found that the presence of <em>Aporrectodea caliginosa</em> (endogeic) increased the survival of springtails. Under normal moisture conditions, springtails were found deeper in the soil in the presence of <em>A. longa</em> (anecic). <em>Aporrectodea longa</em> strongly increased evaporation under normal soil moisture conditions. Our experiment showed that earthworms may moderate the impact of drought on euedaphic springtails, which opens up the hypothesis that other soil fauna may benefit as well from earthworm burrowing activity.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"124 ","pages":"Article 103710"},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143152990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-30DOI: 10.1016/j.ejsobi.2025.103711
Shiqiang Ge , Muhammad Shoaib Rana , Zixuan Li , Yongjian Chen , Zixuan Wang , Chang Shen , Tantan Zhang , Yinghua Shu , Jianwu Wang
Long-term agricultural management practices alter the biochemical properties of soil, leading to the formation of distinct soil legacies. Sugarcane-soybean intercropping is recognized as a sustainable and stable agricultural practice, while the application of nitrogen (N) fertilizer is essential for enhancing crop yields. However, research on the effects of long-term sugarcane-soybean intercropping coupled with varying N levels on soil legacies remains limited. Therefore, we selected four treatments in a long-term field experiment: sugarcane monoculture with reduced N application (MSN1), sugarcane monoculture with conventional N application (MSN2), sugarcane-soybean intercropping with reduced N application (SB2N1), and sugarcane-soybean intercropping with conventional N application (SB2N2). The study aims to investigate the effects of soybean intercropping coupled with varying N application levels on soil abiotic (chemical properties) and biotic (microbial communities) legacies. The results showed that under conventional N application (525 kg ha−1), intercropping, compared to monoculture, significantly increased the contents of total potassium (TK), nitrate nitrogen (NO3−), available zinc (AZn) and the network complexity of the arbuscular mycorrhizal fungi (AMF) community. Under intercropping conditions, reduced N application (300 kg ha⁻1), compared to conventional N application, significantly increased the content of exchangeable calcium (ECa), pH, as well as the alpha diversity and network complexity of the bacterial community. Under monocropping conditions, conventional N application significantly increased the complexity of the bacterial community network. Stochastic processes dominated the assembly of bacterial and AMF communities, but under the same cropping pattern, deterministic processes in fungal communities increased with N application. Soil pH, N nutrients, and trace metal elements are key factors affecting the diversity and composition of soil microbial communities. These findings highlight the significant impact of intercropped soybean on soil legacies, whereas the N level of application plays a key role in regulating the effectiveness of biotic and abiotic soil legacies. This study provides valuable insights into managing soil legacies and provides a theoretical basis for the development of sustainable agriculture.
{"title":"Effects of long-term sugarcane-soybean intercropping coupled with varying levels of nitrogen input on soil legacies: A field experimental study","authors":"Shiqiang Ge , Muhammad Shoaib Rana , Zixuan Li , Yongjian Chen , Zixuan Wang , Chang Shen , Tantan Zhang , Yinghua Shu , Jianwu Wang","doi":"10.1016/j.ejsobi.2025.103711","DOIUrl":"10.1016/j.ejsobi.2025.103711","url":null,"abstract":"<div><div>Long-term agricultural management practices alter the biochemical properties of soil, leading to the formation of distinct soil legacies. Sugarcane-soybean intercropping is recognized as a sustainable and stable agricultural practice, while the application of nitrogen (N) fertilizer is essential for enhancing crop yields. However, research on the effects of long-term sugarcane-soybean intercropping coupled with varying N levels on soil legacies remains limited. Therefore, we selected four treatments in a long-term field experiment: sugarcane monoculture with reduced N application (MSN1), sugarcane monoculture with conventional N application (MSN2), sugarcane-soybean intercropping with reduced N application (SB2N1), and sugarcane-soybean intercropping with conventional N application (SB2N2). The study aims to investigate the effects of soybean intercropping coupled with varying N application levels on soil abiotic (chemical properties) and biotic (microbial communities) legacies. The results showed that under conventional N application (525 kg ha<sup>−1</sup>), intercropping, compared to monoculture, significantly increased the contents of total potassium (TK), nitrate nitrogen (NO<sub>3</sub><sup>−</sup>), available zinc (AZn) and the network complexity of the arbuscular mycorrhizal fungi (AMF) community. Under intercropping conditions, reduced N application (300 kg ha⁻<sup>1</sup>), compared to conventional N application, significantly increased the content of exchangeable calcium (ECa), pH, as well as the alpha diversity and network complexity of the bacterial community. Under monocropping conditions, conventional N application significantly increased the complexity of the bacterial community network. Stochastic processes dominated the assembly of bacterial and AMF communities, but under the same cropping pattern, deterministic processes in fungal communities increased with N application. Soil pH, N nutrients, and trace metal elements are key factors affecting the diversity and composition of soil microbial communities. These findings highlight the significant impact of intercropped soybean on soil legacies, whereas the N level of application plays a key role in regulating the effectiveness of biotic and abiotic soil legacies. This study provides valuable insights into managing soil legacies and provides a theoretical basis for the development of sustainable agriculture.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"124 ","pages":"Article 103711"},"PeriodicalIF":3.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143153809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 : 2025-01-27DOI: 10.1016/j.ejsobi.2025.103712
Lixia Wang , Shiyu Song , Huichao Li , Yang Liu , Lin Xu , Han Li , Chengming You , Sining Liu , Hongwei Xu , Bo Tan , Zhenfeng Xu , Li Zhang , Hans Lambers , Douglas Godbold
Ectomycorrhizal (ECM) fungi or their associated microbes play key roles in mobilizing phosphorus (P) from soil organic matter. Forest conversion often alters soil P availability. However, the correlation between P dynamics caused by forest conversion and changes in ECM fungi is not clear. To dress this issue, we create ECM-reduction (trenched) and ECM-intact (untrenched) conditions in the natural forest and plantation. We then measured soil microbial properties, fungal communities, and P fractions. Our results showed that the natural forest exhibited a higher proportion of inorganic phosphorus (Pi) and a lower proportion of organic phosphorus (Po) compared to the plantation, indicating that forest conversion resulted in a decrease in P mineralization. Under ECM-reduction conditions, resin-Pi contents increased in both forest types. ECM-reduction led to an increase in NaOH-Pi and a decrease in NaOH-Po in both forest types. However, ECM-reduction decreased the 1 M HCl-Pi content in the natural forest while increasing it in the plantation. Structural equation modeling revealed that in the natural forest, trenching directly affected the reads number of ECM fungi, which subsequently influenced 1 M HCl-Pi and resin-Pi contents. In the plantation, trenching impacted NaOH-Po and ECM reads number, which were associated with changes in residual-P and resin-Pi contents. These findings highlight that ECM fungi differ in their utilization of resin-Pi and their ability to mobilize primary mineral Pi (1 M HCl-Pi) and poorly-available P, depending on the soil quality of natural forests and plantations.
{"title":"Soil phosphorus dynamics and its correlation with ectomycorrhizal fungi following forest conversion in subtropical conifer (Picea asperata) forests","authors":"Lixia Wang , Shiyu Song , Huichao Li , Yang Liu , Lin Xu , Han Li , Chengming You , Sining Liu , Hongwei Xu , Bo Tan , Zhenfeng Xu , Li Zhang , Hans Lambers , Douglas Godbold","doi":"10.1016/j.ejsobi.2025.103712","DOIUrl":"10.1016/j.ejsobi.2025.103712","url":null,"abstract":"<div><div>Ectomycorrhizal (ECM) fungi or their associated microbes play key roles in mobilizing phosphorus (P) from soil organic matter. Forest conversion often alters soil P availability. However, the correlation between P dynamics caused by forest conversion and changes in ECM fungi is not clear. To dress this issue, we create ECM-reduction (trenched) and ECM-intact (untrenched) conditions in the natural forest and plantation. We then measured soil microbial properties, fungal communities, and P fractions. Our results showed that the natural forest exhibited a higher proportion of inorganic phosphorus (Pi) and a lower proportion of organic phosphorus (Po) compared to the plantation, indicating that forest conversion resulted in a decrease in P mineralization. Under ECM-reduction conditions, resin-Pi contents increased in both forest types. ECM-reduction led to an increase in NaOH-Pi and a decrease in NaOH-Po in both forest types. However, ECM-reduction decreased the 1 M HCl-Pi content in the natural forest while increasing it in the plantation. Structural equation modeling revealed that in the natural forest, trenching directly affected the reads number of ECM fungi, which subsequently influenced 1 M HCl-Pi and resin-Pi contents. In the plantation, trenching impacted NaOH-Po and ECM reads number, which were associated with changes in residual-P and resin-Pi contents. These findings highlight that ECM fungi differ in their utilization of resin-Pi and their ability to mobilize primary mineral Pi (1 M HCl-Pi) and poorly-available P, depending on the soil quality of natural forests and plantations.</div></div>","PeriodicalId":12057,"journal":{"name":"European Journal of Soil Biology","volume":"124 ","pages":"Article 103712"},"PeriodicalIF":3.7,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143153810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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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