Article
Soil Science
Sydney I. Glassman, James W. J. Randolph, Sameer S. Saroa, Joia K. Capocchi, Kendra E. Walters, M. Fabiola Pulido-Chavez, Loralee Larios
Summary: Wildfires have a stronger impact on microbial communities compared to prescribed burns, but both fires have similar impacts on plant cover. Bacterial and fungal abundance decreased after fire exposure, and their composition also changed. Plant diversity is related to soil microbial diversity, while soil chemistry is more closely related to other aspects of the soil microbial community.
APPLIED SOIL ECOLOGY
(2023)
Article
Ecology
Jessica Graca, Karen Daly, Giulia Bondi, Israel Ikoyi, Fiona Crispie, Raul Cabrera-Rubio, Paul D. Cotter, Achim Schmalenberger
Summary: The study found that soil drainage and phosphorus levels have significant impacts on grassland microbial communities, with drainage status having a more profound influence on bacterial communities and phosphorus availability affecting fungal communities.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2021)
Article
Ecology
Nana Liu, Huifeng Hu, Wenhong Ma, Ye Deng, Dimitar Dimitrov, Qinggang Wang, Nawal Shrestha, Xiangyan Su, Kai Feng, Yuqing Liu, Baihui Hao, Xinying Zhang, Xiaojuan Feng, Zhiheng Wang
Summary: This study assessed the relationships between the diversity and abundance of bacteria, fungi, and archaea in arid regions and found positive correlations among microbial functional groups. Studying microbial diversity patterns from the perspective of functional groups and co-occurrence networks can provide additional insights.
Article
Soil Science
Eve Hellequin, Francoise Binet, Olivier Klarzynski, Sara Hallin, Jaanis Juhanson, Virginie Daburon, Cecile Monard
Summary: This study found that different plant species can influence soil organic carbon dynamics through their effects on soil microbial communities, but these effects do not directly translate to changes in carbon mineralization. Additionally, plant legacy effects impact microbial successions in soil, but do not have specific effects on soil respiration activity.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Review
Agronomy
Justyna Mencel, Agnieszka Mocek-Plociniak, Anna Kryszak
Summary: The usage of grassland significantly affects the microbial and biochemical parameters of soil epipedons. The dominance of bacteria and fungal populations in soil is affected by different grassland management practices, particularly manual mowing. Microbial abundance is highest during spring and summer, likely due to the growth of grass root systems. Grazing increases the activity of urease and slightly decreases the activity of dehydrogenases and acid and alkaline phosphatase. Microbial abundance and enzymatic activity are important indicators of soil fertility and ecosystem biodiversity.
Article
Agronomy
Tomohiro Yokobe, Fujio Hyodo, Ryunosuke Tateno, Naoko Tokuchi
Summary: The topographic positions in natural forests can significantly impact litter traits, soil microbial characteristics, and nitrogen mineralization, leading to plant-soil feedbacks. In a temperate forest dominated by Fagus crenata, it was found that upper slope positions have higher coarse litter abundance and litter C-to-N ratio but lower soil microbial biomass, bacterial abundance, and N mineralization potential. This suggests that fine litter traits and coarse litter abundance are closely related to soil microbial characteristics and N mineralization in forests with varied topography.
Review
Environmental Sciences
Lu-Yao Liu, Guo-Jun Xie, Jie Ding, Bing-Feng Liu, De-Feng Xing, Nan-Qi Ren, Qilin Wang
Summary: This study summarizes the microorganisms involved in the non-methanogenesis process and the possible mechanisms of methane production, including cyanobacteria, algae, fungi, and purple non-sulfur bacteria. These microbes produce methane by utilizing different carbon precursors, which is of significant importance to global methane emissions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Biodiversity Conservation
Jarishma K. Gokul, Gwynneth Matcher, Joanna Dames, Kuhle Nkangala, Paul J. Gordijn, Nigel P. Barker
Summary: This study investigates the impact of fire disturbance on bacterial and fungal communities in South African montane grasslands. The results show that fire significantly affects the composition and structure of these communities. The changes are mediated by seasonal burn patterns, chemical drivers, and mutualistic interactions between bacteria and fungi.
Article
Soil Science
Mohammad Rahmat Ullah, Yolima Carrillo, Feike A. Dijkstra
Summary: Biocides can temporarily increase carbon and nitrogen supply to surviving microbes, leading to higher respiration and nitrogen mineralization, with soil-derived CO2 remaining higher.
APPLIED SOIL ECOLOGY
(2021)
Article
Multidisciplinary Sciences
Puchang Wang, Leilei Ding, Fuxiang Li, Jiafa Liao, Mengya Wang
Summary: This study reveals that camping has significant effects on soil microbial communities, including changes in relative abundance and genes related to various functions. However, camping does not impact taxonomic and functional diversity. Additionally, camping influences the stability of bacterial and fungal networks differently. The findings provide new insights into the effects of animal camping on soil microbial communities in grassland.
Article
Microbiology
Leilei Ding, Lili Tian, Jingyi Li, Yujun Zhang, Mengya Wang, Puchang Wang
Summary: Long-term grazing affects various aspects of grassland ecosystems. This study found that grazing increased soil hardness, available calcium and magnesium content, acid phosphatase activity, bulk density, and pH, while decreasing soil water content, available phosphorus content, and multifunctionality. Grazing also influenced the complexity, stability, and diversity of soil microbial networks.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Nana Liu, Huifeng Hu, Wenhong Ma, Ye Deng, Qinggang Wang, Ao Luo, Jiahui Meng, Xiaojuan Feng, Zhiheng Wang
Summary: This study investigates the deterministic and stochastic processes shaping the taxonomic and phylogenetic beta-diversity of soil microbes in temperate grasslands in northern China. The results indicate that soil microbial beta-diversity is influenced by various factors such as soil depth, species abundance, and phylogenetic turnover.
Article
Biochemistry & Molecular Biology
Sophie Q. van Rijssel, G. F. (Ciska) Veen, Guusje J. Koorneef, J. M. T. (Tanja) Bakx-Schotman, Freddy C. ten Hooven, Stefan Geisen, Wim H. van Der Putten
Summary: The study found that there are differences in microbial community composition between organic and conventional managed fields. Fungal diversity in organic fields increased over time, but this effect disappeared when conventional paired fields were included in the analysis. The study also showed a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi.
Article
Microbiology
Lei Zhong, Jinwu Qing, Min Liu, Xiaoxian Cai, Gaoyuan Li, Frank Yonghong Li, Guanyi Chen, Xingliang Xu, Kai Xue, Yanfen Wang
Summary: This study investigated the contribution of fungi, archaea, and bacteria to N2O production in Chinese grasslands. It found that fungi were dominant in the N2O production processes, followed by archaea. The microbial functional genes were identified as powerful predictors of N2O production potential, particularly when distinguishing between bacterial, fungal, and archaeal processes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Yangquanwei Zhong, Jin Liu, Xiaoyu Jia, Zhuangsheng Tang, Zhouping Shangguan, Ruiwu Wang, Weiming Yan
Summary: This study investigates the responses of soil microbial communities in drylands to environmental stress factors. The results show that bacterial and fungal diversity and community similarity have different sensitivities to environmental stress, with mean annual precipitation being the most important factor. Dominant subcommunities of bacteria and fungi are more sensitive to stress than non-dominant subcommunities. Additionally, certain bacterial and fungal taxa are found to be sensitive to environmental stress and are correlated with carbon and nitrogen cycling-related genes.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Qian Zhao, Allison M. Thompson, Stephen J. Callister, Malak M. Tfaily, Sheryl L. Bell, Sarah E. Hobbie, Kirsten S. Hofmockel
Summary: This study conducted an 8-month aerobic incubation experiment using grassland soils, revealing that the persistence of labile compounds varied under different soil mineralogy conditions, while the richness of more complex organic molecules increased in most cases. The study also demonstrated that N addition decreased soil respiration and inhibited the convergence of SOM chemistry across diverse grassland ecosystems.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Environmental Sciences
Emily B. Graham, Kirsten S. Hofmockel
Summary: Coupled biogeochemical cycles play a crucial role in ecosystem ecology, influencing behaviors at individual and community scales. Developing process-based models that accurately capture these dynamics, especially in SOM decomposition, remains a challenge. Ecological stoichiometry offers a framework for merging biogeochemical and microbiological models and advancing omics-enabled biogeochemical models. Collaboration and exchange of information between high-resolution investigations and large-scale models is essential for refining objectives and specifying dynamics in the field of SOM decomposition modeling.
Article
Biodiversity Conservation
Adrienne B. Keller, Elizabeth T. Borer, Scott L. Collins, Lang C. DeLancey, Philip A. Fay, Kirsten S. Hofmockel, Andrew D. B. Leakey, Melanie A. Mayes, Eric W. Seabloom, Christopher A. Walter, Yong Wang, Qian Zhao, Sarah E. Hobbie
Summary: Nutrient addition experiments have shown that changes in soil carbon and nitrogen pools are influenced by nutrient amendments, with varying effects. Differences in soil carbon and nitrogen pool sizes among sites varied greatly, with moisture index, plant productivity, soil texture, and mineralogy as key predictors of cross-site soil carbon. Protecting highly productive temperate grasslands is crucial for reducing future greenhouse gas emissions from land use change.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Microbiology
Sarah Leichty, Christopher P. Kasanke, Sheryl L. Bell, Kirsten S. Hofmockel
Summary: Soil microorganisms respond primarily to site characteristics, with a secondary impact from cropping systems, highlighting the importance of soil texture and fertility in shaping bacterial and fungal communities. Specific highly abundant prokaryotic and fungal taxa within live communities provide insight into treatment-specific, agriculturally relevant microbial taxa. The associations between live communities and relic DNA reflect the relationship between the ephemeral responses of the live community and the accumulation of DNA within necromass that contributes to soil organic matter.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Guillaume Bay, Conard Lee, Chiliang Chen, Navreet K. Mahal, Michael J. Castellano, Kirsten S. Hofmockel, Larry J. Halverson
Summary: The diversity of cropping systems affects the composition of soil microbial communities, particularly in the rhizosphere and endosphere. Diversified cropping systems recruit a more diverse bacterial community in the rhizosphere, while fungal species richness varies between different cropping systems.
Article
Biotechnology & Applied Microbiology
Darian N. Smercina, Young-Mo Kim, Mary S. Lipton, Dusan Velickovic, Kirsten S. Hofmockel
Summary: Free-living nitrogen-fixing bacteria significantly contribute to terrestrial nitrogen availability, but the forms of nitrogen they contribute are not well understood. Studying soil microorganisms in situ poses challenges due to differences in scale and complexities of the soil system. Our study focused on microorganisms and microbial-scale processes to better understand the nitrogen sources and process rates of nitrogen fixation. We characterized the production of nitrogen-containing metabolites by two common soil bacteria under different growth conditions and found that nitrogen contributions from nitrogen fixation occur in multiple forms. Our findings also highlight the influence of environmental structure and sampling scale on microbial activity. Quantifying microbial-scale processes is crucial for upscaling ecosystem function.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Allison L. Gill, Peter B. Adler, Elizabeth T. Borer, Christopher R. Buyarski, Elsa E. Cleland, Carla M. D'Antonio, Kendi F. Davies, Daniel S. Gruner, W. Stanley Harpole, Kirsten S. Hofmockel, Andrew S. MacDougall, Rebecca L. McCulley, Brett A. Melbourne, Joslin L. Moore, John W. Morgan, Anita C. Risch, Martin Schutz, Eric W. Seabloom, Justin P. Wright, Louie H. Yang, Sarah E. Hobbie
Summary: This study found that nitrogen can accelerate early-stage decomposition of above-ground plant litter in temperate grasslands, but slow down late-stage decomposition. These findings have important implications for the effects of nitrogen on soil organic matter formation.
JOURNAL OF ECOLOGY
(2022)
Article
Microbiology
Darian Smercina, Neerja Zambare, Kirsten Hofmockel, Natalie Sadler, Erin L. Bredeweg, Carrie Nicora, Lye Meng Markillie, Jayde Aufrecht
Summary: Researchers have developed Synthetic Soil Aggregates (SSAs) to simulate natural soil characteristics and provide a transparent cultivation method for studying microbial processes. SSAs can assist researchers in quantifying microbial scale processes and obtaining high-resolution data.
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Ecology
Adrienne B. B. Keller, Christopher A. A. Walter, Dana M. M. Blumenthal, Elizabeth T. T. Borer, Scott L. L. Collins, Lang C. C. DeLancey, Philip A. A. Fay, Kirsten S. S. Hofmockel, Johannes M. H. Knops, Andrew D. B. Leakey, Melanie A. A. Mayes, Eric W. W. Seabloom, Sarah E. E. Hobbie
Summary: Increased nutrient inputs from anthropogenic activities are expected to enhance primary productivity in terrestrial ecosystems. However, changes in allocation between aboveground and belowground areas in response to nutrient additions have different effects on soil carbon storage. Roots play a major role in soil carbon storage, therefore understanding belowground net primary productivity (BNPP) and biomass responses to changes in nutrient availability is crucial for predicting carbon-climate feedbacks.
Article
Multidisciplinary Sciences
Ruonan Wu, Clyde A. Smith, Garry W. Buchko, Ian K. Blaby, David Paez-Espino, Nikos C. Kyrpides, Yasuo Yoshikuni, Jason E. McDermott, Kirsten S. Hofmockel, John R. Cort, Janet K. Jansson
Summary: Metagenomics has revealed the presence of auxiliary metabolic genes (AMGs) in soil viral genomes, and this study provides evidence that these AMGs actually produce functional proteins that can metabolize chitin. The crystal structure of a soil viral AMG product, which exhibits chitosanase activity, has been determined, providing insights into substrate specificity and enzyme mechanism. These findings support the idea that soil viruses contribute auxiliary functions to their hosts.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Bram W. G. Stone, Paul Dijkstra, Brianna K. K. Finley, Raina Fitzpatrick, Megan M. M. Foley, Michaela Hayer, Kirsten S. S. Hofmockel, Benjamin J. J. Koch, Junhui Li, Xiao Jun A. Liu, Ayla Martinez, Rebecca L. L. Mau, Jane Marks, Victoria Monsaint-Queeney, Ember M. M. Morrissey, Jeffrey Propster, Jennifer Pett-Ridge, Alicia M. M. Purcell, Egbert Schwartz, Bruce A. A. Hungate
Summary: The study explores the usage of life history strategies to predict the performance of microorganisms in nature. By applying the copiotroph-oligotroph framework, the study examines if it can forecast the population growth rate of bacterial taxa in different ecosystems. The results show that it is difficult to generalize bacterial life history strategies to broad lineages, and there is a need for direct measurement of microbial communities in soil to advance ecologically realistic frameworks.
Article
Biochemistry & Molecular Biology
Christopher P. Kasanke, Qian Zhao, Trinidad Alfaro, Christopher A. Walter, Sarah E. Hobbie, Tanya E. Cheeke, Kirsten S. Hofmockel
Summary: Nutrient exchange between land plants and AM fungi is based on symbiosis, and environmental factors and nutrient addition have important impacts on the distribution patterns of AM fungi. Our study found that ecosystem type, rather than nutrient treatment, is the main driver of AM fungal colonization, diversity, and community composition. This research provides evidence for the importance of long-term, large scale studies in understanding nutrient addition effects and ecological context.
Article
Microbiology
Katherine I. Naasko, Daniel Naylor, Emily B. Graham, Sneha P. Couvillion, Robert Danczak, Nikola Tolic, Carrie Nicora, Steven Fransen, Haiying Tao, Kirsten S. Hofmockel, Janet K. Jansson
Summary: Climate change leads to increased drought and loss of soil organic carbon. Calcareous soils can help mitigate these losses. This study examined the impact of irrigation and perennial plants on deep soil carbon chemistry in an unfertilized calcareous soil. The results showed that soil microbial community composition was more affected by irrigation and plant cover, while metabolomes, lipidomes, and proteomes varied with soil depth.
Article
Ecology
Jeth Walkup, Chansotheary Dang, Rebecca L. Mau, Michaela Hayer, Egbert Schwartz, Bram W. Stone, Kirsten S. Hofmockel, Benjamin J. Koch, Alicia M. Purcell, Jennifer Pett-Ridge, Chao Wang, Bruce A. Hungate, Ember M. Morrissey
Summary: By studying the growth rates of soil bacteria, we found that the order-genus of bacterial strains could predict their growth rates and explain an average of 31% and up to 58% of the variation in growth rates within ecosystems. Despite limited overlap in community composition across ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
ISME COMMUNICATIONS
(2023)
