Article
Soil Science
Karen Baumann, Kai-Uwe Eckhardt, Ingo Schoening, Marion Schrumpf, Peter Leinweber
Summary: The study found that grassland management plays a significant role in influencing the composition and stability of soil organic matter (SOM), impacting the dynamics of SOM in grasslands. However, the proportion and composition of the soil clay fraction, particularly when the soil clay/OC ratio is low, can override the effects of grassland management on SOM composition and stability.
SOIL USE AND MANAGEMENT
(2022)
Article
Multidisciplinary Sciences
Rachelle Davenport, Benjamin P. Bowen, Laurel M. Lynch, Suzanne M. Kosina, Itamar Shabtai, Trent R. Northen, Johannes Lehmann
Summary: Soil organic matter (SOM) is composed of reactive carbon molecules that impact SOM formation and persistence. Microbial decomposition drives variability in the molecular diversity of SOM across ecosystems, with ecosystem type and soil horizon being significant factors. Microbial degradation in the soil profile has a greater influence on the molecular diversity of SOM than environmental factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Engineering, Environmental
Victor Moinard, Florent Levavasseur, Sabine Houot
Summary: The study examines the potential of recycling urban organic waste in agriculture in peri-urban areas, finding that while local EOM recycling varies, it contributes significantly to C storage and partial nutrient substitution.
RESOURCES CONSERVATION AND RECYCLING
(2021)
Article
Agriculture, Multidisciplinary
Fengshi Li, Hugjiltu Minggagud, Scott Jarvie, Yonghui Wang, Yongzhi Yan, Xiaoqian Gong, Peng Han, Qing Zhang
Summary: This study investigates the effects of fertilization and mowing on plant, soil bacterial, and soil fungal diversity. The results show that fertilization reduces plant diversity, while fertilization + mowing increases plant diversity. Fertilization and fertilization + mowing have no significant effect on soil bacterial and fungal diversity, but can alter their community structure through changing soil pH.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Soil Science
Matthias Waibel, Kevin McDonnell, Maria Tuohy, Sally Shirran, Sylvia Synowsky, Barry Thornton, Eric Paterson, Fiona Brennan, Florence Abram
Summary: Soil organic matter (SOM) is complex and important for providing nutrients to plants. Understanding SOM utilisation processes can improve fertiliser management for plant growth and reduce environmental losses. Metaproteomics can characterise protein profiles and provide insights into SOM microbial decomposition mechanisms. This study applied different extraction methods to recover SOM with different characteristics in two soil types and analysed peptide identification using liquid chromatography and tandem mass spectrometry. The results showed contrasting protein and humic substance content in different extracts, and diverse peptide hits associated with Proteobacteria and derived taxa. This work suggests areas for optimisation in chromatography and mass spectrometry to characterise SOM-associated metaproteomes.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2023)
Article
Multidisciplinary Sciences
Julia E. Macray, David R. Montgomery
Summary: Regenerative agricultural methods aim to repair soil degradation by building topsoil and soil organic matter. The University of Washington student farm has observed over a 20-year period that these methods can increase topsoil thickness and organic matter content, demonstrating the potential of soil-health-focused practices for sustainable urban agriculture.
Article
Environmental Sciences
Daniel A. Kane, Mark A. Bradford, Emma Fuller, Emily E. Oldfield, Stephen A. Wood
Summary: Higher levels of soil organic matter are associated with greater yields, lower yield losses, and lower rates of crop insurance payouts under drought in the United States. The positive effects of soil organic matter on yield resilience are partially explained by its impact on available water capacity and cation exchange capacity, with potential additional mechanisms not fully captured by those metrics. Overall, soil organic matter predicts yield resilience at regional scales and should be considered in agricultural policy and financial planning.
ENVIRONMENTAL RESEARCH LETTERS
(2021)
Article
Soil Science
Daniel P. Bebber, Victoria R. Richards
Summary: Organic agriculture, employing manures or composts, has been proposed as a way of mitigating undesirable impacts of mineral fertilizer use. However, the effects of fertilizers on soil microbial diversity remain poorly understood and require further research.
APPLIED SOIL ECOLOGY
(2022)
Article
Soil Science
YunFei Zhao, Xia Wang, Fei Chen, Jia Li, JinHong Wu, YuXin Sun, YuanYe Zhang, Tao Deng, SiLong Jiang, XiaoHe Zhou, HuiYing Liu
Summary: In this study, the link between aboveground biomass (AGB) and soil organic matter (SOM) across 209 alpine grassland sites on the Tibetan Plateau was evaluated. It was found that AGB decreased with increasing aridity severity above a threshold of 0.37. Additionally, a stronger positive relationship between AGB and SOM was observed in more arid conditions beyond an aridity threshold of 0.64. The results highlight the importance of soil carbon sequestration strategies for biomass production and climate change mitigation in arid areas.
Article
Agronomy
Johannes Wilhelmus Maria Pullens, Peter Sorensen, Bo Melander, Jorgen Eivind Olesen
Summary: Organic farming typically results in lower crop yields compared to conventional farming, with the success depending on local climate and crop and soil management. A long-term study in Denmark showed that the legacy effects of soil fertility management on crop yield, particularly through nitrogen inputs from cover crops and manure, are significant. Organic cropping systems should focus on weed suppression, soil fertility improvement, and targeted manure inputs to enhance nitrogen uptake for optimal yields.
EUROPEAN JOURNAL OF AGRONOMY
(2021)
Article
Geosciences, Multidisciplinary
Hugo Mariano Rodrigues de Oliveira, Antonio Clementino dos Santos, Rubson da Costa Leite, Leonardo Bernardes Taverny de Oliveira, Ivo Ribeiro da Silva, Teogenes Senna de Oliveira
Summary: Research on the impact of pasture use systems on soil C and N stocks revealed that silvopastoral systems with 60% shading had the highest carbon stock, while systems with lower shading performed poorly in terms of C and N stocks. Isotopic enrichments were observed in all systems studied.
Article
Agronomy
Caio Fernandes Zani, Mohamed Abdalla, Geoffrey Denis Abbott, James Arnold Taylor, Marcelo Valadares Galdos, Julia Mary Cooper, Elisa Lopez-Capel
Summary: Recently, many countries have implemented policies promoting sustainable agricultural practices, but the lack of long-term data has created uncertainties regarding the effectiveness of these practices. This study used the DayCent model to assess the long-term effects of different agricultural systems, grazing regimes, fertility sources, and crop rotations on soil carbon stocks. The simulations showed that grazing and higher ley time proportions can increase soil carbon stocks for at least 30 years, as well as compost fertiliser. However, further research is needed to balance sustainability and productivity aspects.
Article
Biodiversity Conservation
Jinwei Zhang, Xuefeng Wu, Yujie Shi, Chengji Jin, Yuheng Yang, Xiaowei Wei, Chunsheng Mu, Junfeng Wang
Summary: The study found that there is a unimodal relationship between species diversity and soil pH, and that biomass production did not reach its maximum in patch types with the greatest plant diversity, but live vegetation N storage reached its maximum. Additionally, the largest SOC and SNC storage values were found in the highly diverse patches.
ECOLOGICAL INDICATORS
(2021)
Article
Green & Sustainable Science & Technology
Joao Serrano, Shakib Shahidian, Jose Marques da Silva, Luis Paixao, Mario de Carvalho, Francisco Moral, Julio Nogales-Bueno, Ricardo F. M. Teixeira, Marjan Jongen, Tiago Domingos, Ana Elisa Rato
Summary: The Montado, a unique agro-silvo-pastoral ecosystem in the Mediterranean region, relies on soil fertility indicators such as Soil Organic Matter and Phosphorus for assessing soil health. This study demonstrated the potential of NIRS combined with multivariate data analysis in accurately estimating SOM and P2O5, providing a useful tool for farm managers to make informed decisions for dynamic management practices.
Article
Soil Science
Heppy Suci Wulanningtyas, Yingting Gong, Peiran Li, Nobuo Sakagami, Junko Nishiwaki, Masakazu Komatsuzaki
Summary: This study found that no-tillage systems and cover crop management can improve soil organic carbon, total nitrogen, available phosphorus, exchangeable potassium-magnesium, bulk density, soil penetration resistance, and substrate-induced respiration which serve as indicators of soil health. The combination of no-till and rye cover crops appears to be a promising technique for enhancing SOC and soil health in Andisols. The melanic index values suggest that the soil is fulvic Andisols with low degree of humification, indicating that the no-till with rye system can enhance SOC and soil health.
SOIL & TILLAGE RESEARCH
(2021)
Article
Plant Sciences
Eline A. Ampt, Jasper van Ruijven, Mark P. Zwart, Jos M. Raaijmakers, Aad J. Termorshuizen, Liesje Mommer
Summary: Research shows that neighboring plants can either reduce or increase the transmission of pathogens. These effects are determined by the age of the neighbors, and cannot be simply explained by a dichotomy between hosts and non-host neighbors.
Article
Microbiology
Rosa Ana Sueiro, Jose Manuel Leiro, Veronica Blanco-Abad, Jos Raaijmakers, Irene de Bruijn, Ron P. H. Dirks, Jesus Lamas
Summary: This study evaluated the toxicity of several natural compounds to Philasterides dicentrarchi, a scuticociliate that causes high mortalities in farmed fish. Tomatine, plumbagin, and 2',4'-dihydroxychalcone showed the highest anticiliate activity, with a dose-dependent response. Additionally, 2',4'-dihydroxychalcone exhibited lower toxicity to fish cells compared to other compounds. Furthermore, the surfactant Pseudomonas H6 (PS) showed toxicity to the ciliate but lower toxicity to fish cells. The findings suggest that 2',4'-dihydroxychalcone and PS can be used to reduce parasite levels in seawater and decrease the risk of scuticociliatosis infection in cultured fish.
Article
Microbiology
Shanshan Yang, Lourens Poorter, Eiko E. Kuramae, Ute Sass-Klaassen, Marcio F. A. Leite, Ohana Y. A. Costa, George A. Kowalchuk, Johannes H. C. Cornelissen, Jurgen van Hal, Leo Goudzwaard, Mariet M. Hefting, Richard S. P. van Logtestijn, Frank J. Sterck
Summary: Dead wood quantity and quality play a crucial role in forest biodiversity by influencing wood-inhabiting fungal communities. The diversity of fungal communities varies across tree species and stem compartments, with bark exhibiting higher fungal diversity than wood. Different fungal communities are associated with gymnosperms and angiosperms, and distinctive fungi are found in the inner wood compared to other compartments. Stem traits, including accessibility, stem chemistry, and physical defense, have significant effects on fungal community structure in decaying stems.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ana Shein Lee Diaz, Muhammad Syamsu Rizaludin, Hans Zweers, Jos M. Raaijmakers, Paolina Garbeva
Summary: Root volatile compounds emitted by tomato plants under insect herbivore attack were found to be influenced by species, stress, and material. The domesticated and wild tomato species showed different root volatile profiles, with the wild species presenting the largest change in root volatile compounds. Both sorbent materials were required to comprehensively characterize the root volatilome.
Article
Agronomy
Getahun Mitiku, Dominika Rybka, Paulien Klein-Gunnewiek, Taye Tessema, Jos M. Raaijmakers, Desalegn W. Etalo
Summary: The soil seedbank of the devastating parasitic weed, Striga hermonthica, is a major factor contributing to its prevalence and persistence in Sub-Saharan Africa. However, there is limited information on the seedbank density in agricultural fields in this region. A high-throughput method combining density- and size-based separation techniques with qPCR-based detection of Striga seeds was developed to accurately map the seedbank and assess the impact of management strategies.
Article
Agronomy
Gisell Garcia-Giraldo, Luisa F. Posada, Juan E. Perez-Jaramillo, Victor J. Carrion, Jos M. Raaijmakers, Valeska Villegas-Escobar
Summary: The inoculation of banana plants with B. subtilis EA-CB0575 reduces the severity of black Sigatoka disease and alters the composition of the root bacterial community. Additionally, there are differences in the bacterial communities between in vitro banana roots and greenhouse plants.
Article
Plant Sciences
Je-Seung Jeon, Dominika Rybka, Natalia Carreno-Quintero, Ric De Vos, Jos M. Raaijmakers, Desalegn W. Etalo
Summary: Research finds that rhizobacteria can promote plant growth and induce systemic resistance against leaf pathogens and herbivores. The phenylpropanoid pathway plays an important role in rhizobacteria-induced plant phenotypes. Inhibition of flavonoid biosynthesis is associated with growth promotion, while growth reduction is associated with increased levels of flavonoids. Additionally, rhizobacterial treatment significantly increases the levels of pharmaceutically and nutritionally relevant metabolites in plant shoot.
PLANT CELL AND ENVIRONMENT
(2022)
Review
Plant Sciences
Linda Gouka, Jos M. Raaijmakers, Viviane Cordovez
Summary: The phyllosphere, which refers to the aerial parts of plants, is home to various microorganisms, including bacteria, fungi, viruses, and yeasts. Most research on yeasts has focused on Saccharomyces cerevisiae and Candida albicans, with little known about the ecology and functions of other yeasts found in the phyllosphere. This study explores the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves, and suggests using tools and approaches developed for model yeasts to unravel the ecology and natural functions of phyllosphere yeasts. Initial genomic survey reveals the untapped functional potential of phyllosphere yeasts.
TRENDS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Ben O. Oyserman, Stalin Sarango Flores, Thom Griffioen, Xinya Pan, Elmar van der Wijk, Lotte Pronk, Wouter Lokhorst, Azkia Nurfikari, Joseph N. Paulson, Mercedeh Movassagh, Nejc Stopnisek, Anne Kupczok, Viviane Cordovez, Victor J. Carrion, Wilco Ligterink, Basten L. Snoek, Marnix H. Medema, Jos M. Raaijmakers
Summary: In this study, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
NATURE COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Xinya Pan, Jos M. Raaijmakers, Victor J. Carrion
Summary: Bacteroidetes are widely found in soil ecosystems, and they interact with various eukaryotic hosts such as plants, animals, and humans. Their adaptability and genomic plasticity highlight their versatility in different environments. While much research has focused on clinically relevant Bacteroidetes, the study of plant-associated Bacteroidetes has been relatively understudied. To enhance our understanding of the functional roles of Bacteroidetes in plants and other hosts, this review explores their taxonomy, ecology, and their roles in nutrient cycling and host fitness. The review emphasizes their distribution, stress tolerance, genomic diversity, and importance in diverse ecosystems, including plant-associated microbiomes.
TRENDS IN MICROBIOLOGY
(2023)
Article
Soil Science
Lucas P. P. Braga, Andrew J. Tanentzap, Benjamin Lee, Siu Mui Tsai, Jos M. Raaijmakers, Rodrigo Mendes, Lucas W. Mendes
Summary: This study tested the influence of resistance breeding on the composition of rhizosphere viruses and viroids. By analyzing metatranscriptomes from common bean (Phaseolus vulgaris) cultivars with varying resistance to the soil-borne pathogen Fusarium oxysporum, it was found that the resistant cultivar harbored more viroids and a different composition of viroids and viruses than less resistant plants. This study suggests that changes in the rhizosphere infectome are an important consideration in breeding for resistance against soil-borne pathogens.
APPLIED SOIL ECOLOGY
(2023)
Article
Ecology
Peter Erdmann Dougherty, Tue Kjaergaard Nielsen, Leise Riber, Helen Helga Lading, Laura Milena Forero-Junco, Witold Kot, Jos M. Raaijmakers, Lars Hestbjerg Hansen
Summary: This study reveals the widespread and diverse prophages in phyllosphere bacteria and their roles in bacterial interactions. The researchers use a novel sequencing method to identify and quantify spontaneously induced prophages, discovering high levels of prophage activity in both culture and plant environments. They also find that E. aphidicola prophages contribute to intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in microbial warfare.
Article
Genetics & Heredity
Lucas William Mendes, Jos M. Raaijmakers, Mattias de Hollander, Edis Sepo, RuthGomez Exposito, Alisson Fernando Chiorato, Rodrigo Mendes, Siu Mui Tsai, Victor J. Carrion
Summary: This study found that Fusarium oxysporum infection had different effects on the composition and gene expression of the root microbiome in fox-susceptible and fox-resistant common bean cultivars. The infection increased microbial diversity, network complexity, and the abundance of certain bacterial genera in the rhizosphere and endosphere of the fox-resistant cultivar. Metagenome and metatranscriptome analysis also revealed the enrichment of terpene biosynthesis genes with potential disease-suppressive functions in the fox-resistant cultivar upon fungal pathogen invasion.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Microbiology
Sewunet Abera, Mahdere Shimels, Taye Tessema, Jos M. Raaijmakers, Francisco Dini-Andreote
Summary: The study analyzed the taxonomic diversity and biogeographical distribution of bacterial taxa in sorghum fields in Ethiopia. It identified a core rhizosphere microbiome and its association with sorghum genotypic traits.
FEMS MICROBIOLOGY ECOLOGY
(2022)
Article
Ecology
E. A. Mcdaniel, J. J. M. van Steenbrugge, D. R. Noguera, K. D. Mcmahon, J. M. Raaijmakers, M. H. Medema, B. O. Oyserman
Summary: This article presents an approach for assessing the trait landscape of microbial communities using genome-resolved time-series metatranscriptomics. The study found that most traits have niche-differentiating expression attributes among multiple genomes.
ISME COMMUNICATIONS
(2022)
Article
Soil Science
C. Beraud, F. Piola, J. Gervaix, G. Meiffren, C. Creuze des Chatelliers, A. Delort, C. Boisselet, S. Poussineau, E. Lacroix, A. A. M. Cantarel
Summary: This study investigated the soil factors influencing the development of biological denitrification inhibition (BDI) and found that initial soil moisture, ammonium concentration, and the initial abundance of certain microbial genes play significant roles in BDI development. Additionally, the research highlighted the relevance of biotic factors in explaining BDI and proposed the use of procyanidin concentration from plant belowground system as a new proxy for measuring BDI intensity.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Yizhu Qiao, Tingting Wang, Qiwei Huang, Hanyue Guo, He Zhang, Qicheng Xu, Qirong Shen, Ning Ling
Summary: Soil microbial community coalescence, the mixing and interaction of microbial communities, has been found to enhance the stability and complexity of rhizobacterial networks, leading to improved plant health and biomass. This study investigated the effects of different degrees of bacterial community coalescence on plant disease resistance by mixing soils from healthy and diseased habitats for watermelon planting. The results showed that mixing in more healthy soil reduced the plant disease index and increased biomass by improving the stability and complexity of the rhizobacterial network. Core taxa Nitrospirillum and Singulisphaera were enriched in the rhizosphere from healthy soils and played important roles in disease suppression and regulating the positive cohesion and modularity of the networks. Overall, these findings provide insights into the potential mechanism of microbial community coalescence for improving plant microbial community function and suggest new tools for enhancing plant fitness via soil microbiota mixing.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Mengqiu He, Shending Chen, Lei Meng, Xiaoqian Dan, Wenjie Wang, Qinying Zhu, Zucong Cai, Jinbo Zhang, Pierfrancesco Nardi, Christoph Mueller
Summary: Maize genotypes directly affect gene expression and nitrogen uptake capacity. The feedback between maize genotypes and soil nitrogen transformations, as well as their regulations on nitrogen uptake capacity, have been studied. The findings suggest that maize genotypes play a central role in regulating these feedbacks, which are important for maize breeding and enhancing maize production.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Ke Shi, Jiahui Liao, Xiaoming Zou, Han Y. H. Chen, Manuel Delgado-Baquerizo, Zhengming Yan, Tingting Ren, Honghua Ruan
Summary: Through rewilding, microbial extracellular and cellular residues can continuously accumulate in soils and significantly contribute to soil organic carbon sequestration. Extracellular residues are mainly driven by fine root biomass, while cellular residues are mainly driven by soil nitrogen and organic carbon content.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Sensen Chen, Ying Teng, Yongming Luo, Eiko Kuramae, Wenjie Ren
Summary: This study comprehensively assesses the effects of NMs on the soil microbiome through a global meta-analysis. The results reveal significant negative impacts of NMs on soil microbial diversity, biomass, activity, and function. Metal NMs, especially Ag NMs, have the most pronounced negative effects on various soil microbial community metrics.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Shareen K. D. Sanders, Gerard Martinez-De Leon, Ludovico Formenti, Madhav P. Thakur
Summary: Collembolans, the diverse group of soil invertebrates, are affected by anthropogenic climate warming, which alters their diversity and density. In addition to abiotic stressors, changes in food availability, specifically the abundance of saprotrophic and mycorrhizal fungi, influence Collembola responses to climate warming. Collembolans prefer saprotrophic fungi but rely on mycorrhizal fungi when food sources are scarce. Understanding the mechanisms behind these dietary shifts in warm-dry and warm-wet soil conditions is crucial for predicting the impact of climate change on Collembola-fungal interactions.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Wimonsiri Pingthaisong, Sergey Blagodatsky, Patma Vityakon, Georg Cadisch
Summary: A study found that mixing high-C/N ratio rice straw with low-C/N ratio groundnut stover can improve the chemical composition of the input, stimulate microbial growth, decrease the loss of residue-derived carbon in the soil, and reduce native soil carbon and nitrogen consumption.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)
Article
Soil Science
Jiachen Wang, Jie Zhao, Rong Yang, Xin Liu, Xuyuan Zhang, Wei Zhang, Xiaoyong Chen, Wende Yan, Kelin Wang
Summary: Nitrogen is vital for ecosystem productivity, restoration, and succession processes. This study found that legume intercropping was more effective than chemical nitrogen fertilizers in promoting the complexity and stability of the soil micro-food web, as it increased microbial and nematode communities and enhanced energy flow patterns.
SOIL BIOLOGY & BIOCHEMISTRY
(2024)