Article
Geosciences, Multidisciplinary
Renshan Li, Xingyi Guo, Jianming Han, Qingpeng Yang, Weidong Zhang, Xin Yu, Xinkuan Han, Longchi Chen, Xin Guan, Zhangquan Zeng, Huixia Yang, Silong Wang
Summary: Stable residue size in leaf litter decomposition is influenced by initial nitrogen, lignin, and manganese concentrations, as well as the type of litter and environmental factors such as temperature, latitude, and precipitation. The initial traits of litter have a stronger explanatory ability for the variance in stable residue size compared to climatic factors. These findings contribute to a better understanding and prediction of global-scale soil organic layer accumulation.
Article
Environmental Sciences
Yuncai Miao, Yongxin Lin, Zengming Chen, Huijie Zheng, Yuhui Niu, Yakov Kuzyakov, Deyan Liu, Weixin Ding
Summary: This study investigated fungal succession and co-occurrence trends during cellulose decomposition using C-13 stable isotope probing. The findings suggest that compost amendment can increase the decomposition capacity of dominant fungal taxa and facilitate fungal colonization in smaller aggregates. The study also highlights differences in fungal interactions between microaggregates and macroaggregates.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Soil Science
Yong Zheng, Zhengkun Hu, Xu Pan, Xiaoyun Chen, Delphine Derrien, Feng Hu, Manqiang Liu, Stephan Hattenschwiler
Summary: The study reveals that a significant amount of carbon and nitrogen can be input into the soil from decomposing litters, with slowly decomposing litter favoring carbon and nitrogen storage in the soil.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Tristan A. Caro, Jamie McFarlin, Sierra Jech, Noah Fierer, Sebastian Kopf
Summary: In this study, the growth rates of soil microorganisms were measured using hydrogen-stable isotope probing of lipids with 2H-enriched water. The results showed that microbial growth rates in soil are slow, with average generation times of 14 to 45 days. Furthermore, there is a decoupling of microbial abundance and growth in soil microbiomes. This study highlights the importance of measuring growth rates to complement standard analyses of soil microbial communities.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Microbiology
Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone, Jennifer Pett-Ridge
Summary: The study introduced a semi-automated, high-throughput SIP pipeline to support well-replicated experiments in soil microhabitats, showcasing how this approach can improve operational efficiency and reproducibility in studying actively growing microbes within AMF hyphosphere. This method generated a series of metagenome-assembled genomes (MAGs) from C-13-labeled AMF hyphosphere DNA, revealing insights into key processes involved in nutrient cycling within the hyphosphere.
Article
Microbiology
Alex Greenlon, Ella Sieradzki, Olivier Zablocki, Benjamin J. Koch, Megan M. Foley, Jeffrey A. Kimbrel, Bruce A. Hungate, Steven J. Blazewicz, Erin E. Nuccio, Christine L. Sun, Aaron Chew, Cynthia-Jeanette Mancilla, Matthew B. Sullivan, Mary Firestone, Jennifer Pett-Ridge, Jillian F. Banfield
Summary: The growth and physiology of soil microorganisms are influenced by both current and historical soil environmental conditions. By using genome-resolved metagenomics, we found that precipitation levels have a significant impact on the activity and growth rates of soil microorganisms. In addition, the activity of bacteriophages in the soil is correlated with the activity of their hosts. Contrary to expectations, the ability to decompose organic matter and oxidize carbon compounds is broadly distributed among active and inactive bacteria.
Article
Soil Science
Tengfei Guo, Qian Zhang, Chao Ai, Ping He, Wei Zhou
Summary: This study used a DNA-SIP approach to investigate the diversity of soil bacterial communities assimilating C derived from C-13-labelled rice root residues, finding Actinobacteria, Proteobacteria, and Bacteroidetes as dominant decomposers of root residues, with Streptomyces and Pseudomonas consistently playing key roles during decomposition.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2021)
Article
Soil Science
Gbadamassi G. O. Dossa, Yun-Qiang Yang, Weiming Hu, Ekananda Paudel, Douglas Schaefer, Yong-Ping Yang, Kun-Fang Cao, Jian-Chu Xu, Kathryn E. Bushley, Rhett D. Harrison
Summary: Fungi play a crucial role in decomposing woody debris in forests. Changes in fungal diversity and composition were found to influence wood decomposition rates, with wood species and termite presence being key factors impacting fungal diversity. Although fungal diversity was not a significant predictor of wood specific gravity loss, functional replacement was identified as a potential mechanism explaining similar decomposition rates across disturbance gradient.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Article
Microbiology
Samuel E. Barnett, Rob Egan, Brian Foster, Emiley A. Eloe-Fadrosh, Daniel H. Buckley
Summary: Soil microbes play a crucial role in the global carbon cycle, but our understanding of how the carbon cycle operates in soil communities is limited. This is mainly due to the lack of functional genes that define carbon transformations. Through metagenomic stable isotope probing, we linked genomic features of bacteria to their carbon acquisition and growth dynamics in soil. We identified genomic traits that can predict bacterial ecological strategies, providing insights into bacterial interactions with soil carbon.
Article
Engineering, Environmental
Haonan Fan, Shanghua Wu, Wenxu Dong, Xianglong Li, Yuzhu Dong, Shijie Wang, Yong-Guan Zhu, Xuliang Zhuang
Summary: This study identified antibiotic-resistant bacteria in soil-plant systems using stable isotope probing and highlighted the rhizosphere as a hotspot for antibiotic resistance gene transfer.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Ecology
Camille S. Delavaux, Janika K. Angst, Hilario Espinosa, Makenna Brown, Daniel F. Petticord, John W. Schroeder, Kirk Broders, Edward A. Herre, James D. Bever, Thomas W. Crowther
Summary: In this study, the researchers used a reciprocal transplant experiment and amplicon sequencing to investigate the impact of soil microbes on plant community structure and diversity. They found that plant species identity can alter the microbial community, which in turn affects the growth and survival of conspecific plants. The study also revealed that greater dissimilarity between species in their arbuscular mycorrhizal and nonpathogenic fungi predicts increased positive feedback. Additionally, specific microbial taxa that differentially accumulate under conspecific settings were identified.
Article
Microbiology
Jialing Teng, Jing Tian, Romain Barnard, Guirui Yu, Yakov Kuzyakov, Jizhong Zhou
Summary: Soil fungi dominate forest topsoil microbial biomass and play key roles in biogeochemical cycling. This study found that soil fungal richness and composition are strongly influenced by both aboveground and belowground plant traits in forest ecosystems across eastern China.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Ecology
Zheng Zhou, Jing-Zhong Lu, Jooris Preiser, Rahayu Widyastuti, Stefan Scheu, Anton Potapov
Summary: Belowground life in tropical soils relies on both plant litter and living roots, but the importance of root-litter linkage has been understudied. We analyzed the response of 30 soil animal groups to root trenching and litter removal in rainforest and plantations in Sumatra, and found that roots are equally important to soil fauna as litter. Trenching had a stronger effect on soil fauna compared to litter, leading to a decrease in animal abundance in both rainforest and plantations. Litter removal mainly affected animal abundance in rainforest and rubber plantations but not in oil palm plantations. The effects of litter and roots on animal abundances can be explained by body size or vertical distribution.
Article
Microbiology
Anahi Cantoran, Francois Maillard, Petr Baldrian, Peter G. Kennedy
Summary: This study synthesizes information on the composition of bacterial and fungal communities on decomposing fungal necromass and identifies a diverse but common core necrobiome. The composition of the core necrobiome is dynamic over time.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Microbiology
Dariia Vyshenska, Pranav Sampara, Kanwar Singh, Andy Tomatsu, W. Berkeley Kauffman, Erin E. Nuccio, Steven J. Blazewicz, Jennifer Pett-Ridge, Katherine B. Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe-Fadrosh, Ryan M. Ziels, Rex R. Malmstrom
Summary: Answering the questions, who is eating what? and who is active? within complex microbial communities is essential for modeling, predicting, and modifying microbiomes for improved human and planetary health. Stable isotope probing can be used to track the incorporation of labeled compounds into cellular DNA during microbial growth to address these questions. However, traditional stable isotope methods face challenges in establishing links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. This study presents an experimental and analytical workflow that improves the detection of metabolically active microorganisms and provides better quantitative estimates of genome-resolved isotope incorporation, thus refining ecosystem-scale models for carbon and nutrient fluxes within microbiomes.
Article
Soil Science
A. Barreiro, A. Fox, M. Jongen, J. Melo, M. Musyoki, A. Vieira, J. Zimmermann, G. Carlsson, C. Cruz, A. Luscher, F. Rasche, L. Silva, F. Widmer, L. M. Dimitrova Martensson
Summary: This study, which investigates grassland soil microbial communities along a pan-European agro-ecological gradient, shows that environmental properties have the most significant impact on soil bacterial community structure, while soil fungal groups are more responsive to grassland management intensity.
APPLIED SOIL ECOLOGY
(2022)
Review
Plant Sciences
Paul D. Hallett, Maria Marin, Gary D. Bending, Timothy S. George, Chris D. Collins, Wilfred Otten
Summary: There is great potential to utilize plant traits at the root-soil interface, such as rhizodeposition and root hairs, to improve soil structure, enhance carbon storage and resource utilization, enhance resistance to climate stresses, and promote a healthy microbiome. These traits are present in modern crop varieties, but there is room for further improvement as they vary significantly across genotypes and respond to environmental conditions. Future research should focus on studying the impacts of selecting these traits on both plants and soils, from model plants to commercial genotypes, and determining if the effects observed in greenhouse studies can be replicated in the field.
TRENDS IN PLANT SCIENCE
(2022)
Article
Microbiology
Eleanor R. Kirkman, Sally Hilton, Gomathy Sethuraman, Dafydd M. O. Elias, Andrew Taylor, John Clarkson, Aik Chin Soh, David Bass, Gin Teng Ooi, Niall P. McNamara, Gary D. Bending
Summary: The rhizosphere microbiome of oil palm plays a crucial role in plant health and productivity. This study investigated the diversity and composition of the fungal microbiome in oil palm plantations of different ages. The results showed significant variations in the fungal community among the plantations, and the presence of potential plant pathogens in the roots. The mycorrhizal status and dependency of oil palm were also explored, revealing variations in the Glomeromycotinian community composition. Additionally, Mucoromycotinian fungi were detected in low abundance and diversity in the roots. These findings highlight the importance of novel diversity in the oil palm microbiome.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Soil Science
Lion Schoepfer, Uwe Schnepf, Sven Marhan, Franz Bruemmer, Ellen Kandeler, Holger Pagel
Summary: Microplastics (MP) do not significantly impact the abundance and activity of soil microorganisms. Only large particles of hydrolyzable polymer (PLA/PBAT) are mineralized by microorganisms in dry soil. PLA/PBAT plastisphere serves as a specific habitat for lipase-producing soil microorganisms.
BIOLOGY AND FERTILITY OF SOILS
(2022)
Article
Mycology
Evans Were, Jochen Schone, Altus Viljoen, Frank Rasche
Summary: This study reveals the potential mechanism of manipulating iron bioavailability in the banana rhizosphere to suppress Fusarium wilt. The results suggest that iron starvation induces the production of iron-scavenging secondary metabolites, called siderophores, by Foc TR4 as a counteractive mechanism to evade iron starvation.
Article
Agronomy
Moritz Hallama, Carola Pekrun, Paula Mayer-Gruner, Marie Uksa, Yulduz Abdullaeva, Stefan Pilz, Michael Schloter, Hans Lambers, Ellen Kandeler
Summary: This study provides new insights into plant-microbe interactions and phosphorus availability by investigating the phosphorus cycling in cover crops and the enzyme availability of organic phosphorus pools in the rhizosheath soil.
Article
Agronomy
Evans Were, Jochen Schone, Altus Viljoen, Frank Rasche
Summary: This study found that phenolic acids excreted by the roots of Desmodium uncinatum and Mucuna pruriens can inhibit the development and toxin synthesis of the banana wilt pathogen Foc TR4, thereby suppressing the disease.
Article
Agronomy
Sophia Hendricks, Sophie Zechmeister-Boltenstern, Ellen Kandeler, Taru Sanden, Eugenio Diaz-Pines, Joerg Schnecker, Oliver Alber, Julia Miloczki, Heide Spiegel
Summary: This study aimed to investigate the sensitivity of parameters such as active carbon and nitrogen mineralisation potential to different agricultural management practices compared to total organic carbon and total nitrogen. The research found that active carbon and nitrogen mineralisation potential are valuable soil biochemical parameters providing detailed information on carbon and nitrogen dynamics, especially in terms of depth distribution and seasonal dynamics, making them more sensitive indicators for agricultural management practices.
JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE
(2022)
Article
Soil Science
Antonios Apostolakis, Ingo Schoening, Beate Michalzik, Valentin H. Klaus, Runa S. Boeddinghaus, Ellen Kandeler, Sven Marhan, Ralph Bolliger, Markus Fischer, Daniel Prati, Falk Haensel, Thomas Nauss, Norbert Hoelzel, Till Kleinebecker, Marion Schrumpf
Summary: Soil respiration is an important pathway of soil organic carbon losses in temperate grasslands. Fertilization intensity has a positive effect on soil CO2 efflux, while grazing intensity, plant biomass, and plant C:N ratio have no relationship with soil CO2 efflux.
NUTRIENT CYCLING IN AGROECOSYSTEMS
(2022)
Article
Biology
Amy Newman, Emma Picot, Sian Davies, Sally Hilton, Isabelle A. Carre, Gary D. Bending
Summary: Aberrant function of plant circadian clock can lead to altered rhythmicity of rhizosphere bacteria and fungi, resulting in changes in the composition of rhizosphere microbiome with potential consequences for plant health.
Review
Agronomy
Sara L. Bauke, Wulf Amelung, Roland Bol, Luise Brandt, Nicolas Brueggemann, Ellen Kandeler, Nele Meyer, Dani Or, Andrea Schnepf, Michael Schloter, Stefanie Schulz, Nina Siebers, Christian von Sperber, Harry Vereecken
Summary: This article investigates the relationship between soil water status and the cycling of nitrogen, phosphorus, and sulfur in agroecosystems. It discusses the impact of soil water on nutrient imbalance and availability at different scales. Water plays a crucial role in nutrient cycling in agroecosystems, affecting the balance and availability of nutrients across different levels.
JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE
(2022)
Article
Chemistry, Analytical
Sammy Hassan, Ryan M. Mushinski, Tilahun Amede, Gary D. Bending, James A. Covington
Summary: This article describes the design and implementation of an internet-of-things (IoT) platform for monitoring soil carbon dioxide (CO2) concentrations. IoT-connected CO2 sensor probes were developed to measure soil CO2 concentration and capture its spatial distribution across a site using LoRa. The data was communicated to a central gateway and logged locally for analysis. These low-cost systems have the potential to improve accounting of soil CO2 sources.
Article
Environmental Sciences
Ben Stride, Soroush Abolfathi, M. G. N. Odara, Gary D. Bending, Jonathan Pearson
Summary: This study investigates the physical interactions of microplastics within vegetation and turbulent flows of freshwater systems. It develops a hydrodynamic model to quantify the mixing of microplastics in submerged canopies and demonstrates the capability of robust predictions for microplastic transport and fate. The study highlights the correlation between dispersion coefficients of microplastics and solutes within submerged model vegetation.
WATER RESOURCES RESEARCH
(2023)
Article
Environmental Studies
Rudi Hessel, Guido Wyseure, Ioanna S. Panagea, Abdallah Alaoui, Mark S. Reed, Hedwig van Delden, Melanie Muro, Jane Mills, Oene Oenema, Francisco Areal, Erik van den Elsen, Simone Verzandvoort, Falentijn Assinck, Annemie Elsen, Jerzy Lipiec, Aristeidis Koutroulis, Lilian O'Sullivan, Martin A. Bolinder, Luuk Fleskens, Ellen Kandeler, Luca Montanarella, Marius Heinen, Zoltan Toth, Moritz Hallama, Julian Cuevas, Jantiene E. M. Baartman, Ilaria Piccoli, Tommy Dalgaard, Jannes Stolte, Jasmine E. Black, Charlotte-Anne Chivers
Summary: Soils are essential for agriculture and ecosystem services, and their management should focus on improving quality and resilience. The SoilCare project developed the concept of soil-improving cropping systems (SICS) as a holistic approach to promote sustainable and profitable soil management. The adoption of SICS by stakeholders was monitored and evaluated for environmental, sociocultural, and economic effects. The project emphasized the importance of understanding local dynamics in Europe-wide assessments and highlighted the role of economic considerations and social factors such as trust in the uptake of SICS. The results pointed to the need for coherent policies to support a transition to more sustainable agricultural practices.
Article
Environmental Studies
Abdallah Alaoui, Moritz Hallama, Roger Baer, Ioanna Panagea, Felicitas Bachmann, Carola Pekrun, Luuk Fleskens, Ellen Kandeler, Rudi Hessel
Summary: Assessing agricultural sustainability is a challenging task that requires considering multidisciplinary factors and cultural values. This study developed a methodology to assess the sustainability of soil improving cropping systems and tested it in a case study.
Article
Ecology
Edith C. Hammer, Carlos Arellano-Caicedo, Paola Micaela Mafla-Endara, E. Toby Kiers, Tom Shimizu, Pelle Ohlsson, Kristin Aleklett
Summary: This study used microfluidic chips to investigate foraging strategies and habitat modification of Rhizophagus irregularis symbiotically associated with carrot roots. The researchers found that AMF hyphae can forage over long distances, prefer straight passages, and show branching induction when encountering obstacles. They also observed bi-directional transport of cellular content inside the hyphae and strategic allocation of biomass within the mycelium. Additionally, the AMF hyphae modified the pore-spaces in the chips by clogging them with irregularly shaped spores. These findings have important implications for understanding the impact of AMF on water retention in soils.
