Article
Soil Science
Matias Fernandez-Huarte, John G. Elphinstone, Ian P. Adams, Joana G. Vicente, Anne Bhogal, Christine A. Watson, Francois Dussart, Elizabeth A. Stockdale, John Walshaw, Sam McGreig, Robert W. Simmons, Lucie Maskova, Lynda K. Deeks, Matthew R. Goddard
Summary: There is still a significant gap in our understanding of sustainable management of agricultural soils to preserve soil biodiversity. In this study, we evaluated the effects of agricultural management and location on soil microbiology using nine field trials in the United Kingdom. Our analysis revealed that the impact of different management interventions varied greatly across sites, and that location had an equal or greater effect on soil bacterial and fungal diversity compared to most management interventions. These findings suggest that the effect of management on soil biodiversity may depend on location, making it unreliable to generalize findings from trials conducted at only one location.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Ecology
Rodney T. Richardson
Summary: The study found that mistagging rates were consistent across taxa within the datasets analyzed, and modeling mistagging as a binomial process with uniform distribution across dual-index combinations helped control mistag-associated false discoveries.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Sofia Michailidou, Eleftherios Pavlou, Konstantinos Pasentsis, Jonathan Rhoades, Eleni Likotrafiti, Anagnostis Argiriou
Summary: This study analyzed the microbial communities of six popular Greek cheese PDO products, revealing varying bacterial species richness and fungal diversity among different cheeses. Lactic acid bacteria (LAB) were predominant in all samples, while certain fungal families dominated the fungal populations. The identified microbial species contribute to the unique characteristics of Greek PDO cheeses but are influenced by starter cultures and production materials.
Article
Ecology
Florian Caillon, Katharina Besemer, Peter Peduzzi, Jakob Schelker
Summary: Flood events are recognized as important occasions for the transfer of soil microbes to stream ecosystems, affecting bacterial community composition and diversity. Soil inoculation during high flow events in pre-alpine streams and the Oberer Seebach alters stream bacterial community composition, with higher bacterial diversity observed during high flow in headwater streams.
Review
Genetics & Heredity
Hiral G. Chaudhari, Shobha Prajapati, Zuhour Hussein Wardah, Gopal Raol, Vimalkumar Prajapati, Rajesh Patel, Ali A. Shati, Mohammad Y. Alfaifi, Serag Eldin I. Elbehairi, R. Z. Sayyed
Summary: A large part of the Earth's biological systems consists of microorganisms, most of which have not been cultured. Traditional methods of culturing microbes have limitations, prompting the development of culture-independent molecular methods. Metagenomics has revolutionized research by revealing the diversity and novelty of microbial communities and genomes. This review focuses on the development of this field, sequencing techniques and data analysis, as well as interpretation and representation.
FRONTIERS IN GENETICS
(2023)
Article
Biodiversity Conservation
Anais Chanson, Corrie S. Moreau, Christophe Duplais
Summary: This study examines the impact of host ecology and evolutionary history on the microbial communities of Amazonian ants. The research shows that habitat does not play a role in structuring ant microbial communities, but ant diet and nesting mode do influence bacterial communities. Additionally, nesting mode is the determining factor for microbial eukaryote communities, while microbial diversity is not correlated with host phylogeny.
Review
Environmental Sciences
Christopher J. Sweeney, Rishabh Kaushik, Melanie Bottoms
Summary: There is increasing interest in including soil microbial community composition assessment in the plant protection product (PPP) environmental risk assessment using metabarcoding approaches. However, there is currently a lack of standardization and understanding of the bioinformatics and data analysis procedures required for regulatory decision-making. Through a critical review, it is concluded that further research is needed to determine if metabarcoding-based assessments can be used in a statistically and ecologically relevant manner within the PPP risk assessment.
INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT
(2023)
Article
Chemistry, Multidisciplinary
Sydney K. Wheatley, Christopher Cartmell, Elias Madadian, Sara Badr, Bradley A. Haltli, Russell G. Kerr, Ali Ahmadi
Summary: In this study, a mu Microbial-Domestication Pod (mu MD Pod) was developed through the integration of microfabrication, microfluidics, and microbiology. This in situ cultivation device facilitates cell signaling and interactions with environmental stimuli, overcoming the limitations of standard laboratory cultivation methods.
Article
Microbiology
Fabio Fernando Araujo, Gabriela Lozano Oliverio Salvador, Gelci Carlos Lupatini, Arthur Prudencio de Araujo Pereira, Romario Martins Costa, Rhaiana Oliveira de Aviz, Franscisco de Alcantara Neto, Lucas William Mendes, Ademir Sergio Ferreira Araujo
Summary: This study aimed to investigate the effects of different soybean-maize management practices on soil microbial community diversity and composition. The results showed that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems led to distinct responses within the soil microbial community. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness and diversity index.
MICROBIOLOGICAL RESEARCH
(2023)
Article
Microbiology
Julia Moll, Friederike Roy, Claus Baessler, Jacob Heilmann-Clausen, Martin Hofrichter, Harald Kellner, Doris Krabel, Jan Henrik Schmidt, Francois Buscot, Bjorn Hoppe
Summary: Nematodes are a diverse and widespread group of organisms in terrestrial environments, with communities in decaying wood influenced by tree species and wood properties, while their diversity is significantly related to the presence of fungi and bacteria.
Article
Environmental Sciences
Emine Gozde Ozbayram, Reyhan Akcaalan, Melek Isinibilir, Meric Albay
Summary: This study explored the bacterial diversity of marine mucilage in the Marmara Sea and the North Aegean Sea using the metabarcoding approach. The results showed a diverse bacterial community dominated by Proteobacteria and Bacteroidetes species. The study also identified correlations between pH levels and the abundances of certain bacterial orders, as well as a positive correlation between total phosphorus and one bacterial order.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Chandra N. Jack, Renee H. Petipas, Tanya E. Cheeke, Jennifer L. Rowland, Maren L. Friesen
Summary: Microbial inoculants have gained popularity for regulating plant traits and productivity in the past decade as a sustainable and gentle alternative to fertilizers, pesticides, and genetic modification. However, the potential for microbial invasions poses a risk, leading to the need for measures outlined in the TREE approach to prevent such invasions and stimulate proactive discussions on best practices.
TRENDS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Laura Maretto, Saptarathi Deb, Samathmika Ravi, Claudia Chiodi, Paolo Manfredi, Andrea Squartini, Giuseppe Concheri, Giancarlo Renella, Piergiorgio Stevanato
Summary: Microbial diversity is crucial for soil fertility and nutrient cycles, and a novel technology for restoring degraded soils can potentially enhance the active microbial community with distinct diversity and functionality towards genes involved in nutrient biogeochemical cycles, although the restoration effectiveness may vary across different taxonomic ranks.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Agronomy
Ko-Hsuan Chen, Reid Longley, Gregory Bonito, Hui-Ling Liao
Summary: The improved two-step PCR approach significantly enhances sequence quantity and recovery rate, while maintaining high read quality. By incorporating synthetic barcodes independently, this method can be broadly adapted to different genomic regions and organisms of scientific interest.
Article
Soil Science
Jacob Weverka, Gabriel C. Runte, Elizabeth L. Porzig, Chelsea J. Carey
Summary: Soil organic carbon (SOC) is important for soil health and climate change mitigation. Plant and soil microbial communities can serve as indicators of SOC concentrations and future changes. Combining these ecological indicators can improve the prediction of SOC concentration and changes.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Agronomy
Paula A. Buil, Jan Jansa, Alena Blazkova, Ondrej Holubik, Renata Duffkova, Martin Rozmos, David Puschel, Michala Kotianova, Martina Janouskova
Summary: This study examined the effects of native arbuscular mycorrhizal (AM) fungal communities from conventionally managed arable soils on plant growth and nutrient uptake. The results showed that arbuscular mycorrhiza had a negative correlation with P availability, and the positive effects of mycorrhiza were more pronounced in a small subset of soils.
Review
Soil Science
Maede Faghihinia, Jan Jansa, Larry J. Halverson, Philip L. Staddon
Summary: The hyphosphere microbiome associated with arbuscular mycorrhizal fungi (AMF) plays a crucial role in soil carbon and nutrient cycling, soil food web dynamics, and plant nutrition and health. However, there is still incomplete understanding of the identities, roles, and mechanisms of interaction in the AMF hyphosphere. Innovative approaches and tools are needed to address the knowledge gaps and unresolved questions in this field.
BIOLOGY AND FERTILITY OF SOILS
(2023)
Article
Environmental Sciences
Joerg Schnecker, Felix Spiegel, Yue Li, Andreas Richter, Taru Sanden, Heide Spiegel, Sophie Zechmeister-Boltenstern, Lucia Fuchslueger
Summary: In temperate, boreal and arctic soil systems, microbial biomass increases during winter and decreases in spring, potentially stabilizing soil carbon during winter. The causes of this increase, whether it is due to changes in microbial physiology or community composition, remain unclear. In a laboratory study, soil microbial communities responded strongly to cooling, with reduced growth and cell division but unchanged glucose uptake and respiration. Microbes invested glucose-derived carbon in unsaturated fatty acids at colder temperatures, potentially as a precaution to reduced temperatures. This immediate response of soil microorganisms to soil cooling could help explain the high microbial biomass carbon observed in temperate soils in winter.
Article
Ecology
Florian U. U. Moeller, Craig W. W. Herbold, Arno Schintlmeister, Maria Mooshammer, Cherie Motti, Bettina Glasl, Katharina Kitzinger, Faris Behnam, Margarete Watzka, Thomas Schweder, Mads Albertsen, Andreas Richter, Nicole S. S. Webster, Michael Wagner
Summary: Marine sponges play a critical role in marine ecosystems as filter-feeders and reef-builders, and they harbor dense communities of microbes. These microbes contribute to the processing of dissolved organic matter (DOM). A study using metaproteogenomics and laboratory incubations found that a dominant gammaproteobacterial symbiont in a marine sponge expressed a pathway for the import and dissimilation of taurine, a common metabolite in marine sponges. The symbiont also imported and used DMSP as a carbon and sulfur source. These findings highlight the importance of biogenic sulfur compounds in the interaction between marine sponges and their microbial symbionts.
Article
Agronomy
Warren Daniel, Clement Stahl, Benoit Burban, Jean-Yves Goret, Jocelyn Cazal, Andreas A. Richter, Ivan Janssens, Laetitia M. Brechet
Summary: The purpose of this study was to investigate the variation of stem and soil greenhouse gas fluxes along a topographic gradient in a tropical forest. The results showed that both wetland and slope soils and tree stems were sources of CO2, while fluxes of CH4 and N2O were more variable and influenced by temperature and soil water content.
Article
Microbiology
Hiroaki Fujita, Masayuki Ushio, Kenta Suzuki, Masato S. Abe, Masato Yamamichi, Yusuke Okazaki, Alberto Canarini, Ibuki Hayashi, Keitaro Fukushima, Shinji Fukuda, E. Toby Kiers, Hirokazu Toju
Summary: By analyzing the shotgun metagenomic sequencing data of an experimental microbial community, we discovered that the network structure of facilitative interactions in microbial ecosystems can change over time. By using metabolic modeling, we inferred the potential facilitative interaction networks at 13 time points during the 110-day monitoring of the microbiomes. We found that positive feedback loops, which can lead to ecological cascade breakdown, existed in the metabolic interaction networks before the drastic community compositional shift.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Hiroaki Fujita, Masayuki Ushio, Kenta Suzuki, Masato S. Abe, Masato Yamamichi, Koji Iwayama, Alberto Canarini, Ibuki Hayashi, Keitaro Fukushima, Shinji Fukuda, E. Toby Kiers, Hirokazu Toju
Summary: Researchers combined theoretical frameworks and empirical analyses to predict microbiome dynamics. They found that abrupt changes in microbial communities could be forecasted by analyzing time-series data based on statistical physics and non-linear mechanics.
Review
Plant Sciences
Mohanned Abdalla, Michael Bitterlich, Jan Jansa, David Pueschel, Mutez A. Ahmed
Summary: This article reviews the role of arbuscular mycorrhizal fungi (AMF) in improving crop drought tolerance, highlighting their effects on water supply and the biophysical mechanisms involved. Using a soil-plant hydraulic model, the authors demonstrate how AMF can enhance water transport in the soil and extend root length to mitigate the impact of soil drying on plant water potential. The synthesis of evidence and simulations suggest that AMF symbiosis postpones the onset of stress by regulating transpiration rates and leaf water potentials during drought, thus promoting crop survival under limited water availability. The article also calls for future research to integrate soil and root hydraulic dynamics in order to better understand the role of AMF in plant-water relations under changing climate conditions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Tomas Rezanka, Hana Hrselova, Lucie Kyselova, Jan Jansa
Summary: This study focused on the use of complex polar lipids as biomarkers to detect and quantify arbuscular mycorrhizal (AM) fungi in plant and soil samples. The analysis revealed specific molecular species in mycorrhizal roots, suggesting the possibility of using these biomarkers for quantification of AM fungi.
Article
Food Science & Technology
Andras Gregor, Sandra Auernigg-Haselmaier, Manuel Malleier, Stefan Bruckberger, Joana Seneca, Petra Pjevac, Marc Pignitter, Kalina Duszka
Summary: Previously, we found that caloric restriction (CR) led to increased levels of taurine and taurine-conjugated bile acids (BA) in the gut. In this study, we discovered that restrictive diets, such as intermittent fasting and fasting-mimicking diet, had a similar effect as CR. The type of cage bedding affected the levels of BAs and taurine, and removal of cage bedding reversed the CR phenotype. Microbiota transplant from CR mice increased BAs deconjugation. Inhibition of bile salt hydrolase (BSH) prevented the increase in free taurine while increasing taurine-conjugated BA levels. Consuming high fiber diets increased taurine conjugates without elevating BAs levels.
JOURNAL OF FUNCTIONAL FOODS
(2023)
Article
Microbiology
Inga Hiiesalu, Johannes Schweichhart, Roey Angel, John Davison, Jiri Dolezal, Martin Kopecky, Martin Macek, Klara Rehakova
Summary: This study investigated the ecology of AM fungi in alpine environments using DNA metabarcoding. The results showed that the alpha diversity of AM fungal communities declined linearly with elevation, while the within-site taxon turnover was unimodally related to elevation. The composition of AM fungal communities was influenced by vegetation types, elevation, temperature, and precipitation.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Soil Science
Talia Gabay, Eva Petrova, Osnat Gillor, Yaron Ziv, Roey Angel
Summary: Biological soil crusts (biocrusts) are crucial for desert ecosystem functions. In the Negev Desert, phosphate mining has destroyed soil habitats and fragmented the landscape. This study used DNA stable isotope probing to examine bacterial growth in post-mining and adjacent natural biocrusts. The results showed minimal bacterial growth in hyperarid biocrusts after wetting, likely due to harsh climatic conditions. These findings emphasize the importance of active restoration practices following mining.
Article
Soil Science
David Pueschel, Michael Bitterlich, Jana Rydlova, Petra Bukovsk, Radka Sudova, Jan Jansa
Summary: Drought under global change poses a threat to plant growth and nutrition. This study investigated the role of arbuscular mycorrhizal fungus in plant uptake of nitrogen from different sources along a soil moisture gradient. The results showed that mycorrhizal plants had a higher uptake of nitrogen compared to nonmycorrhizal plants, and this advantage was observed across different moisture levels.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Environmental Sciences
Erika Salas, Markus Gorfer, Dragana Bandian, Stephanie A. Eichorst, Hannes Schmidt, Julia Horak, Simon K. -M. R. Rittmann, Christa Schleper, Barbara Reischl, Thomas Pribasnig, Jan Jansa, Christina Kaiser, Wolfgang Wanek
Summary: This study analyzed the AS and NS compounds in the biomass of different taxa and found GlcN to be the most common AS and glucose to be the most common NS. A potential biomarker specific to Euryarchaeota was identified. Multivariate statistical methods were used to compare the variability of these compounds between taxonomic groups and evaluate their potential as necromass residue biomarkers. Conversion factors were proposed to estimate the fungal and bacterial carbon content, as well as the archaeal or all-microbial necromass residue carbon content.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
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)
