Pedobiologia最新文献

Bacterial assemblies in acidic dryland vs. paddy soils across depth profiles in southern China's red soil region

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-27 DOI: 10.1016/j.pedobi.2025.151034

Xin Li , Yun Ge , Fangjing Hu , Yongxiu Qi , Lingzhi Li , Xu Chen , Xi-En Long

Red soils in China are essential for food security, ecological balance, and rural development. Red soil's varied microbial populations help maintain soil health, cycle nutrients, and sustain ecosystems. The variation in bacterial community assembly and distribution with soil depth in acidic dryland and paddy soils is unknown. We sampled dryland and paddy soil profiles from nearby farms in southern China's red soil region. Five soil layers (0–20 cm, 20–40 cm, 40–60 cm, 60–80 cm, 80–100 cm) were taken from a 1-meter soil profile at Yichun, Jiangxi, China. In paddy soils, ammonium nitrogen, available iron, and soil organic matter (SOM) were greater than in dryland soils. While both soil types showed considerable variation in diversity indices (Chao1, Sobs, PD) over the soil profile, paddy soils showed a more wave-like pattern in microbial diversity indicators. Dryland soils had higher relative abundances of Actinobacteriota (3.6–7.3 %) and GAL15 (1.3–8.6 %), while paddy soils had Bacteroidota (3.9–9.2 %), Desulfobacterota (4.2–7.7 %), and Nitrospirota (2.1–12.7 %). Acidobacteriota (29.5–59.1 %), Chloroflexi (6.3–30.9 %), and Proteobacteria (7.5–21.5 %) predominated at both soil types. Taxonomic alterations in Acidobacteriota, Chloroflexi, and Proteobacteria highlighted how microbial communities adapted to dryland vs paddy soils. The assembly of bacterial communities was mostly stochastic, with varied dispersion and assembly dynamics across soil types and depths. Network analysis showed that paddy soils had more complicated interspecies relationships than dryland soils, with a greater average clustering coefficient and lower modularity. Drylands had higher biosynthetic and metabolic activity, especially amino acid metabolism and secondary metabolite production, whereas paddy soils had higher energy metabolism. This research emphasizes how land use affects soil physicochemical properties and microbiological populations. Microbial profiles and functional adaptations of dryland and paddy soils provide soil management techniques to optimize soil health and production in diverse agricultural systems.

{"title":"Bacterial assemblies in acidic dryland vs. paddy soils across depth profiles in southern China's red soil region","authors":"Xin Li , Yun Ge , Fangjing Hu , Yongxiu Qi , Lingzhi Li , Xu Chen , Xi-En Long","doi":"10.1016/j.pedobi.2025.151034","DOIUrl":"10.1016/j.pedobi.2025.151034","url":null,"abstract":"<div><div>Red soils in China are essential for food security, ecological balance, and rural development. Red soil's varied microbial populations help maintain soil health, cycle nutrients, and sustain ecosystems. The variation in bacterial community assembly and distribution with soil depth in acidic dryland and paddy soils is unknown. We sampled dryland and paddy soil profiles from nearby farms in southern China's red soil region. Five soil layers (0–20 cm, 20–40 cm, 40–60 cm, 60–80 cm, 80–100 cm) were taken from a 1-meter soil profile at Yichun, Jiangxi, China. In paddy soils, ammonium nitrogen, available iron, and soil organic matter (SOM) were greater than in dryland soils. While both soil types showed considerable variation in diversity indices (Chao1, Sobs, PD) over the soil profile, paddy soils showed a more wave-like pattern in microbial diversity indicators. Dryland soils had higher relative abundances of <em>Actinobacteriota</em> (3.6–7.3 %) and GAL15 (1.3–8.6 %), while paddy soils had <em>Bacteroidota</em> (3.9–9.2 %), <em>Desulfobacterota</em> (4.2–7.7 %), and <em>Nitrospirota</em> (2.1–12.7 %). <em>Acidobacteriota</em> (29.5–59.1 %), Chloroflexi (6.3–30.9 %), and <em>Proteobacteria</em> (7.5–21.5 %) predominated at both soil types. Taxonomic alterations in <em>Acidobacteriota</em>, <em>Chloroflexi</em>, and <em>Proteobacteria</em> highlighted how microbial communities adapted to dryland vs paddy soils. The assembly of bacterial communities was mostly stochastic, with varied dispersion and assembly dynamics across soil types and depths. Network analysis showed that paddy soils had more complicated interspecies relationships than dryland soils, with a greater average clustering coefficient and lower modularity. Drylands had higher biosynthetic and metabolic activity, especially amino acid metabolism and secondary metabolite production, whereas paddy soils had higher energy metabolism. This research emphasizes how land use affects soil physicochemical properties and microbiological populations. Microbial profiles and functional adaptations of dryland and paddy soils provide soil management techniques to optimize soil health and production in diverse agricultural systems.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"109 ","pages":"Article 151034"},"PeriodicalIF":2.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Millipede (Spirobolus walker) prefers feeding on a high-quality litter from a companion species when combined with Masson pine litter

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-26 DOI: 10.1016/j.pedobi.2025.151033

Cong Li , Lige Liu , Zhangming Wu , Wengong Wang , Shenghan Wang , Xinhua He , Xinglei Cui , Jiujin Xiao , Yang Liu

Monoculture plantations, particularly the coniferous species (Pinus massoniana), often impede nutrient cycling, leading to declines in biodiversity and soil fertility. Selection of suitable companion tree species, especially a native broadleaf species is thus essential for improving forest ecosystem functions. Millipedes (Spirobolus walker), a widely distributed large arthropod to primarily consume litter, play a pivotal role in organic matter decomposition and nutrient cycling in terrestrial ecosystems. Addressing the feeding preferences of millipedes in relation to litter quality could provide insights into selection of appropriate mixed tree species, thereby facilitating the sustainable management of Masson pine plantations. Millipede feeding experiments on leaf litter from three typical subtropical broadleaf species – Camptotheca acuminata (high-quality litter), Quercus variabilis (intermediate-quality), and Michelia wilsonii (low-quality), were conducted in combination with Masson litter. We found that millipedes responded more to litter morphology rather than chemical characteristics. Acid insoluble components, consisting mainly of condensed tannins and lignin in litter had almost no effects on millipede feeding preferences. Despite C. acuminata containing high levels of tannins and phenols, millipedes exhibited the highest consumption rate (44 mg·g⁻¹·d⁻¹) on it, due to its higher tubularity and nitrogen concentration. Additionally, when multiple litter sources were available, millipedes showed greater preference for consuming high-quality litter, an indication of the better suitability of C. acuminata for mixture with Masson pine. A transformation of mono-species into a multiple-species based plantation forest would therefore enhance circulation of materials, particularly carbon and nitrogen, through millipedes’ preferential feeding activity.

{"title":"Millipede (Spirobolus walker) prefers feeding on a high-quality litter from a companion species when combined with Masson pine litter","authors":"Cong Li , Lige Liu , Zhangming Wu , Wengong Wang , Shenghan Wang , Xinhua He , Xinglei Cui , Jiujin Xiao , Yang Liu","doi":"10.1016/j.pedobi.2025.151033","DOIUrl":"10.1016/j.pedobi.2025.151033","url":null,"abstract":"<div><div>Monoculture plantations, particularly the coniferous species (<em>Pinus massoniana</em>), often impede nutrient cycling, leading to declines in biodiversity and soil fertility. Selection of suitable companion tree species, especially a native broadleaf species is thus essential for improving forest ecosystem functions. Millipedes (<em>Spirobolus walker</em>), a widely distributed large arthropod to primarily consume litter, play a pivotal role in organic matter decomposition and nutrient cycling in terrestrial ecosystems. Addressing the feeding preferences of millipedes in relation to litter quality could provide insights into selection of appropriate mixed tree species, thereby facilitating the sustainable management of Masson pine plantations. Millipede feeding experiments on leaf litter from three typical subtropical broadleaf species – <em>Camptotheca acuminata</em> (high-quality litter), <em>Quercus variabilis</em> (intermediate-quality), and <em>Michelia wilsonii</em> (low-quality), were conducted in combination with Masson litter. We found that millipedes responded more to litter morphology rather than chemical characteristics. Acid insoluble components, consisting mainly of condensed tannins and lignin in litter had almost no effects on millipede feeding preferences. Despite <em>C. acumina</em>ta containing high levels of tannins and phenols, millipedes exhibited the highest consumption rate (44 mg·g<sup>−1</sup>·d<sup>−1</sup>) on it, due to its higher tubularity and nitrogen concentration. Additionally, when multiple litter sources were available, millipedes showed greater preference for consuming high-quality litter, an indication of the better suitability of <em>C. acuminata</em> for mixture with Masson pine. A transformation of mono-species into a multiple-species based plantation forest would therefore enhance circulation of materials, particularly carbon and nitrogen, through millipedes’ preferential feeding activity.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"109 ","pages":"Article 151033"},"PeriodicalIF":2.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143561814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The effect of forest edges on soil nematode community structures between broadleaf secondary forest and coniferous plantation

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-26 DOI: 10.1016/j.pedobi.2025.151032

Yudai Kitagami , Yota Imao , Yosuke Matsuda

Habitat edges between two forest types significantly affect the community structure and dynamics of soil organisms Nematodes are a major group of soil microfauna and the most abundant animals on Earth. This study aimed to determine the edge effects of two forest types on soil nematode community composition. We hypothesized that nematode diversity and abundance would be greater in forest edges due to increased heterogeneity of aboveground litter and belowground root traits at the boundary between two forest types, as well as microclimatic variation, enhanced resource inputs, higher plant diversity, and unique soil moisture dynamics characteristic of edge environments. The soil was collected from two adjacent forests, a broadleaf Quercus serrata forest and a coniferous Cryptomeria japonica plantation, with the zone where the two forests transition into one another being referred to as the "forest edge”. Soil nematodes were morphologically identified at the genus/family level and examined for both community structure and trophic composition. Our results showed that there was a significant positive correlation between the relative abundance of herbivorous nematodes and the physical distance from the broadleaf forest to the C. japonica plantation. The diameter of coniferous C. japonica fine roots were greater than those of broadleaf Q. serrata, suggesting that herbivorous nematodes had easily access to edible resources leading to an increase their populations. Moreover, the nematode community structures had a spatial autocorrelation within a 32 m range, their community structures changed significantly from broadleaf forests to C. japonica plantations and that soil pH and C/N significantly influenced the structuring of nematode communities. This study showed that nematode taxonomic and trophic compositions can be influenced by tree root traits within a range of several tens of meters around forest edges facing different forest types. Our results highlighted that forest edges enhance soil nematode taxonomic turnover.

{"title":"The effect of forest edges on soil nematode community structures between broadleaf secondary forest and coniferous plantation","authors":"Yudai Kitagami , Yota Imao , Yosuke Matsuda","doi":"10.1016/j.pedobi.2025.151032","DOIUrl":"10.1016/j.pedobi.2025.151032","url":null,"abstract":"<div><div>Habitat edges between two forest types significantly affect the community structure and dynamics of soil organisms Nematodes are a major group of soil microfauna and the most abundant animals on Earth. This study aimed to determine the edge effects of two forest types on soil nematode community composition. We hypothesized that nematode diversity and abundance would be greater in forest edges due to increased heterogeneity of aboveground litter and belowground root traits at the boundary between two forest types, as well as microclimatic variation, enhanced resource inputs, higher plant diversity, and unique soil moisture dynamics characteristic of edge environments. The soil was collected from two adjacent forests, a broadleaf <em>Quercus serrata</em> forest and a coniferous <em>Cryptomeria japonica</em> plantation, with the zone where the two forests transition into one another being referred to as the \"forest edge”. Soil nematodes were morphologically identified at the genus/family level and examined for both community structure and trophic composition. Our results showed that there was a significant positive correlation between the relative abundance of herbivorous nematodes and the physical distance from the broadleaf forest to the <em>C. japonica</em> plantation. The diameter of coniferous <em>C. japonica</em> fine roots were greater than those of broadleaf <em>Q. serrata</em>, suggesting that herbivorous nematodes had easily access to edible resources leading to an increase their populations. Moreover, the nematode community structures had a spatial autocorrelation within a 32 m range, their community structures changed significantly from broadleaf forests to <em>C. japonica</em> plantations and that soil pH and C/N significantly influenced the structuring of nematode communities. This study showed that nematode taxonomic and trophic compositions can be influenced by tree root traits within a range of several tens of meters around forest edges facing different forest types. Our results highlighted that forest edges enhance soil nematode taxonomic turnover.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"109 ","pages":"Article 151032"},"PeriodicalIF":2.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of litter quality on soil nematode communities with the intensifies of grassland degradation: Shifting from resource input to environmental stress

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2025.151021

Pingting Guan , Mengya Chen , Jianan Li , Junqi Zuo , Shitong Wei , Donghui Wu

Litter quality determines the resource input from aboveground processes in regulating soil biota function in degraded grassland. However, the knowledge of litter quality along with the degradation on the contribution to the soil biota remains sparse, particularly across different trophic groups, given their varying demands for food resources. A 240-day decomposition experiment was conducted to investigate the effect of the litter quality (high-quality and low-quality litters) on soil nematode communities at different intensities of grassland degradation (light, moderate and heavy). The results showed that, even though degradation induced the abundance of microbivorous nematode, the high trophic group nematode reduction was the primary factor that caused the decrease of top-down control from omnivore-predator (OP). Moreover, the metabolic footprint of omnivore-predator was more sensitive than its abundance with OP footprint taking over 40 % of the total footprint while its abundance taking 15 % of total abundance at the light degradation. At the light degraded level, high-quality litter promoted abundance and metabolic footprint of OP nematodes by 69.37 % and 88.27 %, respectively, compared to low-quality litter. These changes in the nematode communities and functions were primarily determined by the N resource change resulting from litter quality. On the contrary, at the moderate and heavy degraded levels, the execrable soil conditions, characterized by high soil pH, simplified the nematode food web. Therefore, the environmental stress screening on soil nematode communities from degradation exceeded the bottom-up effect from litter input. These results suggested that the community structure determined by long-term harsh soil conditions required more attention on the fundamental approach to soil quality rather than litter quality alone. It is critical to adapt appropriate management practices for rehabilitation in the maintenance of belowground communities in grassland restoration.

{"title":"Impact of litter quality on soil nematode communities with the intensifies of grassland degradation: Shifting from resource input to environmental stress","authors":"Pingting Guan , Mengya Chen , Jianan Li , Junqi Zuo , Shitong Wei , Donghui Wu","doi":"10.1016/j.pedobi.2025.151021","DOIUrl":"10.1016/j.pedobi.2025.151021","url":null,"abstract":"<div><div>Litter quality determines the resource input from aboveground processes in regulating soil biota function in degraded grassland. However, the knowledge of litter quality along with the degradation on the contribution to the soil biota remains sparse, particularly across different trophic groups, given their varying demands for food resources. A 240-day decomposition experiment was conducted to investigate the effect of the litter quality (high-quality and low-quality litters) on soil nematode communities at different intensities of grassland degradation (light, moderate and heavy). The results showed that, even though degradation induced the abundance of microbivorous nematode, the high trophic group nematode reduction was the primary factor that caused the decrease of top-down control from omnivore-predator (OP). Moreover, the metabolic footprint of omnivore-predator was more sensitive than its abundance with OP footprint taking over 40 % of the total footprint while its abundance taking 15 % of total abundance at the light degradation. At the light degraded level, high-quality litter promoted abundance and metabolic footprint of OP nematodes by 69.37 % and 88.27 %, respectively, compared to low-quality litter. These changes in the nematode communities and functions were primarily determined by the N resource change resulting from litter quality. On the contrary, at the moderate and heavy degraded levels, the execrable soil conditions, characterized by high soil pH, simplified the nematode food web. Therefore, the environmental stress screening on soil nematode communities from degradation exceeded the bottom-up effect from litter input. These results suggested that the community structure determined by long-term harsh soil conditions required more attention on the fundamental approach to soil quality rather than litter quality alone. It is critical to adapt appropriate management practices for rehabilitation in the maintenance of belowground communities in grassland restoration.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151021"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Food choice and pharyngeal pumping activity of bacterial-feeding nematodes are driven by different functional traits

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2024.151018

Christin Ortlieb , Ben Katzer , Robin Liess , Martha Gartz , Michael Steinert , Liliane Ruess

The feeding behavior of free-living nematodes is shaped by several factors, including food choice and food consumption. The latter is commonly investigated by determining the pumping rate of the pharynx. However, whether the pharyngeal pumping activity also reflects food selection, i.e. whether the pumping rate for preferred food is increased, is largely unknown. The aim of this study was to investigate the relation between pumping rate and food choice. For this, the preference of the nematodes Diploscapter coronatus, Diploscapter pachys, Plectus similis and Plectus sp. were examined in binary choice assays. The bacteria Bacillus subtilis, Kitasatospora sp., Sphingomonas trueperi, Pseudomonas fluorescens and two Legionella pneumophila strains were tested against Escherichia coli OP50. The nematode pumping rates were determined for each bacterial diet. Additionally, the effects of bacterial species and size, and of nematode species and genus, size of buccal cavity and pharynx morphology, were investigated.

The nematodes showed a preference for P. fluorescens (except D. pachys) and avoidance of B. subtilis, Kitasatospora sp. and L. pneumophila. The determinants of food choice were nematode species, bacterial species and size, while the pumping rates varied with genus and pharynx proportion. The food preference determined by the choice assay was not necessarily associated with an upregulation of pharyngeal pumping, e.g. Plectus preferred P. fluorescens over E. coli OP50 when having a choice but pumped significantly faster when feeding on the latter. Although the pumping rate changed with bacterial species, there was no clear pattern that allowed a correlation with food choice across the tested nematode taxa, suggesting that pumping frequency is no indicator for food preference. Relating these results to nematode foraging strategy, food choice was determined by bacterial traits associated with diet quality and search, while food consumption was linked to nematode traits affecting diet handling.

{"title":"Food choice and pharyngeal pumping activity of bacterial-feeding nematodes are driven by different functional traits","authors":"Christin Ortlieb , Ben Katzer , Robin Liess , Martha Gartz , Michael Steinert , Liliane Ruess","doi":"10.1016/j.pedobi.2024.151018","DOIUrl":"10.1016/j.pedobi.2024.151018","url":null,"abstract":"<div><div>The feeding behavior of free-living nematodes is shaped by several factors, including food choice and food consumption. The latter is commonly investigated by determining the pumping rate of the pharynx. However, whether the pharyngeal pumping activity also reflects food selection, i.e. whether the pumping rate for preferred food is increased, is largely unknown. The aim of this study was to investigate the relation between pumping rate and food choice. For this, the preference of the nematodes <em>Diploscapter coronatus</em>, <em>Diploscapter pachys</em>, <em>Plectus similis</em> and <em>Plectus</em> sp. were examined in binary choice assays. The bacteria <em>Bacillus subtilis</em>, <em>Kitasatospora</em> sp., <em>Sphingomonas trueperi</em>, <em>Pseudomonas fluorescens</em> and two <em>Legionella pneumophila</em> strains were tested against <em>Escherichia coli</em> OP50. The nematode pumping rates were determined for each bacterial diet. Additionally, the effects of bacterial species and size, and of nematode species and genus, size of buccal cavity and pharynx morphology, were investigated.</div><div>The nematodes showed a preference for <em>P. fluorescens</em> (except <em>D. pachys</em>) and avoidance of <em>B. subtilis</em>, <em>Kitasatospora</em> sp. and <em>L. pneumophila</em>. The determinants of food choice were nematode species, bacterial species and size, while the pumping rates varied with genus and pharynx proportion. The food preference determined by the choice assay was not necessarily associated with an upregulation of pharyngeal pumping, e.g. <em>Plectus</em> preferred <em>P. fluorescens</em> over <em>E. coli</em> OP50 when having a choice but pumped significantly faster when feeding on the latter. Although the pumping rate changed with bacterial species, there was no clear pattern that allowed a correlation with food choice across the tested nematode taxa, suggesting that pumping frequency is no indicator for food preference. Relating these results to nematode foraging strategy, food choice was determined by bacterial traits associated with diet quality and search, while food consumption was linked to nematode traits affecting diet handling.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151018"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling the hidden world beneath: A showcase of soil microorganisms at MikroMondo

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2024.151015

Heribert Insam , Julia Ecker , Theo Hug , Suzanne Kapelari , Edoardo Mandolini , Thorsten Schwerte , Julia Zöhrer , Judith Ascher-Jenull

MikroMondo, a forthcoming science center in Austria, will be dedicated to the fascinating world of microorganisms, with a special focus on soil and its intricate biodiversity. Designed to promote soil literacy among the public, MikroMondo will feature cutting-edge exhibits, among them Europe's tallest Winogradsky column, live demonstrations of plant-microbe interactions (e.g., mycorrhization of pine seedlings in transparent soil columns), and engaging sound-producing slime molds. These exhibits aim to captivate visitors and highlight the vital role of microorganisms in soil ecosystems. The center will also offer interactive, hands-on activities tailored for school pupils, students, and educators, designed to deepen understanding of microbiological processes such as carbon and nutrient cycling, plant-microbe symbiosis, and soil microbial diversity. Activities will include guided microscopy sessions, microbial cultivation, the creation of Winogradsky columns, and decomposition and gas production experiments. MikroMondo’s innovative approach will inspire curiosity and enhance public appreciation of the hidden world beneath our feet, fostering a new generation of soil stewards and microbial enthusiasts.

{"title":"Unveiling the hidden world beneath: A showcase of soil microorganisms at MikroMondo","authors":"Heribert Insam , Julia Ecker , Theo Hug , Suzanne Kapelari , Edoardo Mandolini , Thorsten Schwerte , Julia Zöhrer , Judith Ascher-Jenull","doi":"10.1016/j.pedobi.2024.151015","DOIUrl":"10.1016/j.pedobi.2024.151015","url":null,"abstract":"<div><div>MikroMondo, a forthcoming science center in Austria, will be dedicated to the fascinating world of microorganisms, with a special focus on soil and its intricate biodiversity. Designed to promote soil literacy among the public, MikroMondo will feature cutting-edge exhibits, among them Europe's tallest Winogradsky column, live demonstrations of plant-microbe interactions (e.g., mycorrhization of pine seedlings in transparent soil columns), and engaging sound-producing slime molds. These exhibits aim to captivate visitors and highlight the vital role of microorganisms in soil ecosystems. The center will also offer interactive, hands-on activities tailored for school pupils, students, and educators, designed to deepen understanding of microbiological processes such as carbon and nutrient cycling, plant-microbe symbiosis, and soil microbial diversity. Activities will include guided microscopy sessions, microbial cultivation, the creation of Winogradsky columns, and decomposition and gas production experiments. MikroMondo’s innovative approach will inspire curiosity and enhance public appreciation of the hidden world beneath our feet, fostering a new generation of soil stewards and microbial enthusiasts.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151015"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Organic matter content rather than farming practices modulates microbial activities in vineyard soils

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2024.151017

Pierre Blondel , Nicolas Fanin , Benjamin Joubard , Sylvie Milin , Adrien Rusch , Brice Giffard

Soil functioning is a growing concern in intensively-managed agricultural landscapes such as vineyards. Mechanical disturbance of the soil and pesticide use have deleterious impact on microbial activity, which is a key parameter for organic matter decomposition and nutrient cycling. This study aims to assess the response of soil microbial activities under different farming systems (organic and conventional systems) and inter-rows management (grassy or tilled inter-rows). We selected 18 fields in the southwest of France, supporting tilled and grassy inter-rows (alternating treatment) - 9 fields were managed organically and 9 were managed conventionally. We assessed extracellular enzymatic activities relative to C, N, P acquisition and Microresp™, which allows to measure catabolic capacities of soil microbial communities. Our results showed that organic systems had a higher soil organic matter (SOM) content than conventional ones. At the inter-row scale, grassy inter-rows of organic vineyards differed from tilled inter-rows in catabolic capacities of microbial communities; with overall a higher complexity of C-substrates respired by microbial communities. Furthermore, N- and P-related enzymes were positively correlated to SOM and soil pH across sites and managements, suggesting that increasing SOM may positively impact nutrient recycling and notably NO₃^-. Altogether, our results pointed out the importance of soil organic matter content on soil microbial functioning in vineyards as well as the possible benefit of organic matter inputs on nutrient recycling and nitrogen directly available in the vineyard.

{"title":"Organic matter content rather than farming practices modulates microbial activities in vineyard soils","authors":"Pierre Blondel , Nicolas Fanin , Benjamin Joubard , Sylvie Milin , Adrien Rusch , Brice Giffard","doi":"10.1016/j.pedobi.2024.151017","DOIUrl":"10.1016/j.pedobi.2024.151017","url":null,"abstract":"<div><div>Soil functioning is a growing concern in intensively-managed agricultural landscapes such as vineyards. Mechanical disturbance of the soil and pesticide use have deleterious impact on microbial activity, which is a key parameter for organic matter decomposition and nutrient cycling. This study aims to assess the response of soil microbial activities under different farming systems (organic and conventional systems) and inter-rows management (grassy or tilled inter-rows). We selected 18 fields in the southwest of France, supporting tilled and grassy inter-rows (alternating treatment) - 9 fields were managed organically and 9 were managed conventionally. We assessed extracellular enzymatic activities relative to C, N, P acquisition and Microresp™, which allows to measure catabolic capacities of soil microbial communities. Our results showed that organic systems had a higher soil organic matter (SOM) content than conventional ones. At the inter-row scale, grassy inter-rows of organic vineyards differed from tilled inter-rows in catabolic capacities of microbial communities; with overall a higher complexity of C-substrates respired by microbial communities. Furthermore, N- and P-related enzymes were positively correlated to SOM and soil pH across sites and managements, suggesting that increasing SOM may positively impact nutrient recycling and notably NO<sub>3</sub><sup>-</sup>. Altogether, our results pointed out the importance of soil organic matter content on soil microbial functioning in vineyards as well as the possible benefit of organic matter inputs on nutrient recycling and nitrogen directly available in the vineyard.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151017"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Responses of N2O production and associated functional genes to increasing temperature and moisture in surface and subsurface soils of a temperate forest

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2025.151020

Lifei Sun, Yanci Qiao, Liquan Song, Yujiao Peng, Baoqing Hu

The effects of increasing temperature and moisture on soil nitrous oxide (N₂O) emissions across different soil horizons remain poorly understood. Here, we investigated how increased temperature (15 °C and 25 °C) and moisture (30 %, 45 %, and 60 % water-filled pore space (WFPS)) influence N₂O emissions from surface (0–5 cm) and subsurface (5–20 cm) soils in a temperate forest. We found that increasing temperature and moisture promoted N₂O production from subsurface soil due to the stimulation of both nitrification- and denitrification-derived N₂O production. However, in surface soil, the effect of increasing temperature on N₂O production is soil moisture dependent, increasing it at 30 % WFPS but decreasing it at 60 % WFPS. This reduction was caused by decreased denitrification-derived N₂O production. Nitrification was identified as the dominant source of N₂O production in both soils, rather than denitrification. Denitrification-derived N₂O production was positively related to nirK gene abundance but not nirS gene abundance, suggesting that nirK-type denitrifiers may be more active than nirS-type denitrifiers. Furthermore, the proportion of nitrified N emitted as N₂O decreased with rising temperature in both soils. Our results underscore the importance of incorporating variable proportions of nitrified N emitted as N₂O in Earth system model to more accurately predict soil N₂O emission in the context of global climate changes.

{"title":"Responses of N2O production and associated functional genes to increasing temperature and moisture in surface and subsurface soils of a temperate forest","authors":"Lifei Sun, Yanci Qiao, Liquan Song, Yujiao Peng, Baoqing Hu","doi":"10.1016/j.pedobi.2025.151020","DOIUrl":"10.1016/j.pedobi.2025.151020","url":null,"abstract":"<div><div>The effects of increasing temperature and moisture on soil nitrous oxide (N<sub>2</sub>O) emissions across different soil horizons remain poorly understood. Here, we investigated how increased temperature (15 °C and 25 °C) and moisture (30 %, 45 %, and 60 % water-filled pore space (WFPS)) influence N<sub>2</sub>O emissions from surface (0–5 cm) and subsurface (5–20 cm) soils in a temperate forest. We found that increasing temperature and moisture promoted N<sub>2</sub>O production from subsurface soil due to the stimulation of both nitrification- and denitrification-derived N<sub>2</sub>O production. However, in surface soil, the effect of increasing temperature on N<sub>2</sub>O production is soil moisture dependent, increasing it at 30 % WFPS but decreasing it at 60 % WFPS. This reduction was caused by decreased denitrification-derived N<sub>2</sub>O production. Nitrification was identified as the dominant source of N<sub>2</sub>O production in both soils, rather than denitrification. Denitrification-derived N<sub>2</sub>O production was positively related to <em>nirK</em> gene abundance but not <em>nirS</em> gene abundance, suggesting that <em>nirK</em>-type denitrifiers may be more active than <em>nirS</em>-type denitrifiers. Furthermore, the proportion of nitrified N emitted as N<sub>2</sub>O decreased with rising temperature in both soils. Our results underscore the importance of incorporating variable proportions of nitrified N emitted as N<sub>2</sub>O in Earth system model to more accurately predict soil N<sub>2</sub>O emission in the context of global climate changes.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151020"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A field mesocosm method for manipulation of soil mesofauna communities and repeated measurement of their ecological functions over months to years

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-02-01 DOI: 10.1016/j.pedobi.2024.151019

Kara S. Gibson , Nancy C. Johnson , Deborah A. Neher , Anita J. Antoninka

In situ manipulation of mesofauna communities is necessary to understand their functional importance in complex natural systems. Field mesocosms that control the recolonization of defaunated soil and litter by mesofauna are well suited to this purpose, but are infrequently used and can produce undesirable side effects on microclimate. Here, we present an inexpensive and easy to construct field mesocosm design that is intended to address some limitations of existing mesocosm methods. Our mesocosms were engineered to manipulate mesofauna communities over one or two years via mesh treatments (21 µm, 41 µm, and 1000 µm mesh opening sizes) while minimizing mesh treatment side effects and allowing repeated access to mesocosm interiors for measurement of microclimate differences and mesofauna functions through time. They are also compatible with LI-COR survey chambers, enabling measurement of gas flux from mesocosms. We tested these mesocosms in untreated and thinned/burned ponderosa pine (Pinus ponderosa) forests in Valles Caldera National Preserve, New Mexico, USA to compare their performance in differing abiotic and biotic contexts. The mesocosm treatments successfully manipulated microarthropods > 150 µm for fifteen months but were only partially effective at manipulating microarthropods < 150 µm. This mesocosm technique advances our ability to disentangle the functional contributions of mesofauna in complex natural systems because it enables manipulation experiments with repeated sampling in time and space.

{"title":"A field mesocosm method for manipulation of soil mesofauna communities and repeated measurement of their ecological functions over months to years","authors":"Kara S. Gibson , Nancy C. Johnson , Deborah A. Neher , Anita J. Antoninka","doi":"10.1016/j.pedobi.2024.151019","DOIUrl":"10.1016/j.pedobi.2024.151019","url":null,"abstract":"<div><div><em>In situ</em> manipulation of mesofauna communities is necessary to understand their functional importance in complex natural systems. Field mesocosms that control the recolonization of defaunated soil and litter by mesofauna are well suited to this purpose, but are infrequently used and can produce undesirable side effects on microclimate. Here, we present an inexpensive and easy to construct field mesocosm design that is intended to address some limitations of existing mesocosm methods. Our mesocosms were engineered to manipulate mesofauna communities over one or two years via mesh treatments (21 µm, 41 µm, and 1000 µm mesh opening sizes) while minimizing mesh treatment side effects and allowing repeated access to mesocosm interiors for measurement of microclimate differences and mesofauna functions through time. They are also compatible with LI-COR survey chambers, enabling measurement of gas flux from mesocosms. We tested these mesocosms in untreated and thinned/burned ponderosa pine (<em>Pinus ponderosa</em>) forests in Valles Caldera National Preserve, New Mexico, USA to compare their performance in differing abiotic and biotic contexts. The mesocosm treatments successfully manipulated microarthropods > 150 µm for fifteen months but were only partially effective at manipulating microarthropods < 150 µm. This mesocosm technique advances our ability to disentangle the functional contributions of mesofauna in complex natural systems because it enables manipulation experiments with repeated sampling in time and space.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"108 ","pages":"Article 151019"},"PeriodicalIF":2.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabarcoding of a mock community of soil invertebrates: DNA extraction, false positives, and data filtration

IF 2 3区农林科学 Q3 ECOLOGY

Pedobiologia

Pub Date : 2025-01-22 DOI: 10.1016/j.pedobi.2025.151022

Ivan V. Sotnikov , Maxim V. Vecherskii , Vladimir S. Cheptsov , Alexei V. Tiunov

Metabarcoding is a powerful tool widely used to analyze soil communities but methodological difficulties can introduce biases, resulting in inaccurate estimation of species diversity. We evaluated five DNA extraction methods, two PCR programs, and three post-bioinformatic processing techniques (multiple databases, filtering based on the level of similarity and on the number of reads obtained) using a mock community of soil invertebrates containing 24 species, 23 genera, and 15 families of arthropods and annelids. The choice of DNA extraction kit significantly influenced the accuracy of the metabarcoding results. Kits developed for the isolation of DNA from soil and alkaline lysis without purification showed worse results compared to those designed for isolating DNA from tissues. In the best variant of sample processing, metabarcoding yielded correct identification of 67 % species and 94 % families. Post-bioinformatic filtering dramatically increased the proportion of true positives achieving 100 % at the family, over 73 % at the genus, and more than 60 % at the species level. Thus, an acceptable level of accuracy may be achieved in field surveys with relatively little time and effort.

{"title":"Metabarcoding of a mock community of soil invertebrates: DNA extraction, false positives, and data filtration","authors":"Ivan V. Sotnikov , Maxim V. Vecherskii , Vladimir S. Cheptsov , Alexei V. Tiunov","doi":"10.1016/j.pedobi.2025.151022","DOIUrl":"10.1016/j.pedobi.2025.151022","url":null,"abstract":"<div><div>Metabarcoding is a powerful tool widely used to analyze soil communities but methodological difficulties can introduce biases, resulting in inaccurate estimation of species diversity. We evaluated five DNA extraction methods, two PCR programs, and three post-bioinformatic processing techniques (multiple databases, filtering based on the level of similarity and on the number of reads obtained) using a mock community of soil invertebrates containing 24 species, 23 genera, and 15 families of arthropods and annelids. The choice of DNA extraction kit significantly influenced the accuracy of the metabarcoding results. Kits developed for the isolation of DNA from soil and alkaline lysis without purification showed worse results compared to those designed for isolating DNA from tissues. In the best variant of sample processing, metabarcoding yielded correct identification of 67 % species and 94 % families. Post-bioinformatic filtering dramatically increased the proportion of true positives achieving 100 % at the family, over 73 % at the genus, and more than 60 % at the species level. Thus, an acceptable level of accuracy may be achieved in field surveys with relatively little time and effort.</div></div>","PeriodicalId":49711,"journal":{"name":"Pedobiologia","volume":"109 ","pages":"Article 151022"},"PeriodicalIF":2.0,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143130098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0