Article
Soil Science
Qian Huang, Yimei Huang, Baorong Wang, Michaela A. Dippold, Haohao Li, Na Li, Penghui Jia, Haixing Zhang, Shaoshan An, Yakov Kuzyakov
Summary: CO2-fixing microorganisms play a crucial role in carbon sequestration in vegetation restricted areas. This study identified the genes responsible for eight CO2 fixation pathways in semiarid soil microorganisms and found that CO2 fixation rates increased along the precipitation gradient. The study also revealed that different pathways had varying effects on soil organic matter under different precipitation conditions.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Bin Li, Jue Liang, Hamid R. Baniasadi, Margaret A. Phillips, Anthony J. Michael
Summary: Viruses manipulate host cells' metabolic and replication systems to produce more viruses. They acquire metabolic genes from ancestral hosts and use the encoded enzymes to subvert host metabolism. This study identified and characterized various phage and virus-encoded polyamine metabolic enzymes and pathways, supporting the important role of spermidine in virus biology on a global scale.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Virology
Chengcheng Li, Zengmeng Wang, Jiulong Zhao, Long Wang, Guosi Xie, Jie Huang, Yongyu Zhang
Summary: To prevent animal diseases in aquaculture and avoid the negative effects of antibiotics, using phage as a method has shown promise. A lytic phage named vB_VcaS_HC was isolated, infecting the pathogen Vibrio campbellii. This phage has a high bactericidal activity and could be a potential treatment for V. campbellii infections.
Article
Environmental Sciences
Hetian Zhang, Jingyi Huang, Weiai Zeng, Qinzhi Xiao, Yi Zhu, Wuyuan Kong, Junliang Zou, Tianbo Liu, Huaqun Yin
Summary: Research on the soil viral community and its influencing factors is limited. In this study, viral genes involved in detoxifying heavy metals were found in soil metagenomic samples contaminated with metals. Viral proteins related to nutrient uptake and metabolism, cellular function, polysaccharides production, and biomineralization were also detected. The study suggests that viruses facilitate the acquisition of metal-resistance abilities in their hosts through horizontal gene transfer.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Biodiversity Conservation
Qi Qi, Jianshu Zhao, Renmao Tian, Yufei Zeng, Changyi Xie, Qun Gao, Tianjiao Dai, Hao Wang, Jin-Sheng He, Konstantinos T. Konstantinidis, Yunfeng Yang, Jizhong Zhou, Xue Guo
Summary: The alpine grasslands of the Tibetan Plateau store a significant amount of soil organic carbon, and climate warming has a strong impact on the microbial community and functional genes in the soil, leading to increased methane and carbon dioxide uptake and emissions. Microbially enhanced methane uptake in alpine grasslands may play a crucial role in mitigating climate warming.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Microbiology
Kailun Zhang, Kiara Pankratz, Hau Duong, Matthew Theodore, Jingwen Guan, Anxiao Andrew Jiang, Yiruo Lin, Lanying Zeng
Summary: Phage P1 is a temperate phage that can make lytic or lysogenic decisions when infecting bacteria. The behavior of P1 in lysogenization is independent of the number of phages infecting a cell (MOI), with the activity of the major repressor C1 being a key factor. Increasing the distance between phages that infect a single cell can lead to a lambda-like, MOI-dependent lysogenization upon P1 infection.
Article
Microbiology
Jiulong Zhao, Hongmei Jing, Zengmeng Wang, Long Wang, Huahua Jian, Rui Zhang, Xiang Xiao, Feng Chen, Nianzhi Jiao, Yongyu Zhang
Summary: This study uncovered novel viral communities in the Mariana Trench sediments using metagenomic analysis. These viruses have high diversity and novelty, with a significant number of them representing novel genera. The viruses carry various auxiliary metabolic genes, suggesting their potential adaptive characteristics in the extreme environment and their involvement in biogeochemical cycles.
Article
Food Science & Technology
Lijun You, Chengcong Yang, Hao Jin, Lai-Yu Kwok, Zhihong Sun, Heping Zhang
Summary: This study utilized deep metagenomic sequencing to analyze the microbiomes of various fermented milk products, revealing microbial diversity and unique characteristics. New species belonging to Lactobacillus, Streptococcus, Acetobacter, and Rothia genera were identified, indicating potential influences on food flavor and quality. The common presence of bacteriocins and bacteriophage sequences in these products was also highlighted, showcasing their importance in controlling undesirable microorganisms and uncovering complex interactions within microbial communities.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Microbiology
Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew D. Millard, Willem van Schaik
Summary: In this study, ten state-of-the-art phage identification tools were compared and evaluated for their usage in microbiome research. VIBRANT and VirSorter2 achieved the highest F1 scores in the RefSeq artificial contigs dataset, while Kraken2 performed the best in the mock community benchmark. This study provides important metrics for assessing the performance of phage detection tools and discusses optimal strategies for their usage.
Article
Biotechnology & Applied Microbiology
Amel Chaib, Olivier Claisse, Elodie Delbarre, Jade Bosviel, Claire Le Marrec
Summary: Malolactic fermentation (MLF) is crucial in winemaking, driven by the lactic acid bacterium Oenococcus oeni, with prophages play a significant role in affecting the quality and stability of wines. Survey in three wineries in Bordeaux revealed the presence of lysogens in the LAB population driving spontaneous MLF, with varying rates across wineries.
Article
Microbiology
Philip Lauman, Jonathan J. Dennis
Summary: The spread of antimicrobial resistance is a global threat to public health, especially for bacteria such as Burkholderia cepacia complex (Bcc) that cause respiratory infections and are highly resistant to antibiotics. Phage therapy, the use of phages to treat bacterial infections, is a promising alternative, but its current paradigm of using only lytic phages limits its effectiveness. This study challenges the prevailing paradigm by showing that lysogenization-capable phages can be therapeutically effective.
MICROBIOLOGY SPECTRUM
(2023)
Article
Plant Sciences
Dangjun Wang, Huakun Zhou, Juan Zuo, Peng Chen, Yandi She, Buqing Yao, Shikui Dong, Jianshuang Wu, Fan Li, Denis Mburu Njoroge, Guoxi Shi, Xufeng Mao, Li Ma, Zhonghua Zhang, Zhun Mao
Summary: The study investigates the impact of degradation and restoration processes on the dynamics of microbial community and soil quality in alpine grasslands on the Tibetan Plateau. It finds that heavy degradation significantly deteriorates soil quality, and fungal communities are more sensitive to grassland succession than bacterial communities. The findings suggest that artificial grasslands can be effective in restoring degraded grasslands, but the soil functions may not fully recover even after 10 years of restoration.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Siyuan Shen, Dongxue Huo, Chenchen Ma, Shuaiming Jiang, Jiachao Zhang
Summary: This study identified five potential intestinal bacteriophages as CRC biomarkers, demonstrating their high diagnostic value across different populations. The results from the validation cohort and cross-disease cohorts support the potential of these biomarkers in CRC diagnosis and gut phagotherapy.
MICROBIOLOGY SPECTRUM
(2021)
Article
Environmental Sciences
Ya Cao, Xing-Zhuo Yang, Li-Jun Zhang, Min Li, Ming-Long Yuan
Summary: This study characterized the gut bacterial communities of two Gynaephora species inhabiting different altitudes of the Tibetan Plateau. The research found evident compositional and functional differences in gut bacteria between the two species, likely associated with ecological adaptation. Investigating the composition and function of Gynaephora species provides valuable information about probiotics and pest control.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Anders Kokkenborg Varming, Kim Krighaar Rasmussen, Zhiyou Zong, Peter Waaben Thulstrup, Mogens Kilstrup, Leila Lo Leggio
Summary: The genetic switch of the lactococcal temperate bacteriophage TP901-1 is controlled by two regulatory proteins, CI repressor and MOR antirepressor, with the length of their interdomain linker playing a crucial role in DNA binding and subsequent genetic switch function. Shortening or lengthening the linker can significantly affect the affinity to the operator site responsible for lytic gene transcription repression.
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
Geosciences, Multidisciplinary
Jesse Alan Roebuck, Kevin D. Bladon, David Donahue, Emily B. Graham, Samantha Grieger, Karl Morgenstern, Matthew J. Norwood, Katie A. Wampler, Lisa Erkert, Lupita Renteria, Robert Danczak, Susan Fricke, Allison N. Myers-Pigg
Summary: The warmer and drier climate has led to an increase in large, high severity wildfires in the Pacific Northwest, raising concerns about water quality and ecosystem recovery. This study quantified the spatiotemporal patterns of dissolved organic matter (DOM) chemistry in streams burned by wildfires in Oregon, USA in 2020. The results showed that the composition of DOM was temporally variable and linked with burn severity, suggesting distinct gradients of burn severity impact DOM dynamics immediately following fire activity.
GEOPHYSICAL RESEARCH LETTERS
(2022)
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
Microbiology
Ryan McClure, Yuliya Farris, Robert Danczak, William Nelson, Hyun-Seob Song, Aimee Kessell, Joon-Yong Lee, Sneha Couvillion, Christopher Henry, Janet K. Jansson, Kirsten S. Hofmockel
Summary: This study investigates microbial interactions during chitin decomposition in a model soil consortium. The findings reveal emergent properties of species and the community, highlighting the importance of community context in species phenotypes. These conclusions provide critical insights into soil microbial interaction networks and central soil microbiome functions.
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
Ecology
Emily B. Graham, Joseph E. Knelman
Summary: Understanding the processes of microbial community assembly is crucial for comprehending the role of microorganisms in ecosystem restoration and for optimizing management strategies. Important factors to consider when evaluating microbial community structure in the context of ecosystem recovery include: variations in community assembly processes, linkages to ecosystem function, and measurable microbial community attributes.
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.
Review
Microbiology
Janet K. Jansson, Ruonan Wu
Summary: Soil viruses play important roles in soil ecology and are influenced by climate change, which affects their diversity and ecology.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Anna B. Turetcaia, Vanessa A. Garayburu-Caruso, Matthew H. Kaufman, Robert E. Danczak, James C. Stegen, Rosalie K. Chu, Jason G. Toyoda, M. Bayani Cardenas, Emily B. Graham
Summary: This study investigates the impact mechanisms of carbon and nitrogen limitations on dissolved organic matter (DOM) metabolism in hyporheic zones (HZs). The results show that the thermodynamics of DOM and organic nitrogen are relevant at different depths in the HZ, suggesting that aerobic respiration (AR) is limited by multiple competing processes in the HZ.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
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.
Editorial Material
Immunology
Tingtao Chen, Ruonan Wu, Lei Cheng, Qinping Liao, Zhangran Chen
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
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)
Article
Ecology
Emily B. Graham, Hyun-Seob Song, Samantha Grieger, Vanessa A. Garayburu-Caruso, James C. Stegen, Kevin D. Bladon, Allison N. Myers-Pigg
Summary: Pyrogenic organic matter (PyOM) from wildfires is resistant to biological degradation, but recent studies suggest that it may be more bioavailable than previously thought. This study used a substrate-explicit model to assess the potential bioavailability of representative PyOM compounds compared to dissolved organic matter (DOM). The results showed that PyOM has a greater range of potential bioavailability than natural DOM, but the predicted thermodynamics and metabolic rates were similar between the two. The study also found that different chemistries within PyOM have varying carbon use efficiencies, which could impact process-based model representations.