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
Zijie Yu, Xinhua He, Zhitong Li, Shuang Zhou, Dalu Guo, Hao Pu, Hongyan Luo
Summary: This study investigated the existence, abundance, and diversity of anaerobic ammonium oxidation (anammox) bacteria in purple paddy soils at different temperatures. By using C-13-DNA stable-isotope probe and Illumina MiSeq high-throughput sequencing, the researchers found differences in the abundance and diversity of anammox bacteria in purple paddy soils at different temperatures. These findings contribute to a better understanding of the regulation of soil nitrogen cycling.
FRONTIERS IN MICROBIOLOGY
(2023)
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
Soil Science
Hui Tong, Jiahui Li, Manjia Chen, Yujuan Fang, Xiu Yi, Leheng Dong, Qi Jiang, Chengshuai Liu
Summary: This study investigated the acetate-assimilating microbial community and the key microorganisms involved in nitrate-dependent Fe(II) oxidation in flooded soil. The results showed that NO3- was required for Fe(II) oxidation, and the presence of acetate stimulated the reduction of NO3-, Fe(III), and SO42-. The addition of NO3- and Fe(II) influenced the microbial community, with different genera enriched in different treatments. Zoogloea and Pseudogulbenkiania were identified as key microorganisms associated with NO3- reduction and nitrate-dependent Fe(II) oxidation, respectively. These findings highlight the importance of Fe and N cycling in soil biogeochemistry processes.
SOIL BIOLOGY & BIOCHEMISTRY
(2023)
Article
Engineering, Environmental
Jiang Liu, Lei Zhao, Kun Kong, Mahmoud A. Abdelhafiz, Shanyi Tian, Tao Jiang, Bo Meng, Xinbin Feng
Summary: This study investigated the geochemical fractionation of newly deposited mercury (Hg) in paddy soils during the rice-growing period using a stable Hg isotope tracing technique. The results showed that the coupling of autochthonous dissolved organic matter and poorly crystalline Fe (oxyhydr)oxides played a predominant role in controlling the redistribution of the newly deposited Hg among geochemical fractions. This study is important for evaluating the environmental risks of Hg from atmospheric depositions.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Environmental Sciences
Kaikuo Wu, Ping Gong, Wei Bai, Zhe Zhang, Zhanbo Wei, Chunxiao Yu, Yuchao Song, Yan Xue, Lili Zhang
Summary: This study found that ammonia oxidation pathway is an important pathway for N2O production in flooded paddy soils, and mixed inhibitors can reduce N2O production from NN, ND, NCD, and HD pathways. The development of mixed inhibitor application strategies suitable for paddy fields is of great significance for mitigating the global greenhouse effect.
JOURNAL OF SOILS AND SEDIMENTS
(2022)
Article
Environmental Sciences
Xiaodi Zheng, Guilin Han, Bin Liang, Guangyou Zhu
Summary: Understanding Zn biogeochemical cycling is crucial for sustainable development and monitoring Zn supply during land use conversion. Little is known about the impact of paddy soil conversion to abandoned land on Zn isotope signature. A field observation in Thailand showed that Zn retention was slightly higher in paddy soils compared to abandoned paddy soils, and more Zn isotopes entered the river during rice cultivation cessation in abandoned paddy soils. Rice harvest and root decay contributed to heavy 66Zn isotopes accumulation, and the release of assimilated Zn and high Zn adsorption in the Fe-SOM-metal(loid)s ternary system influenced Zn concentration in paddy soils. These findings provide valuable insights into the terrestrial Zn geochemical cycle.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
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
Engineering, Environmental
Muhammad Aamir, Zili Guo, Jiawei Yu, Lu Zhao, Dongmei Xu, Xiaohui Sun, Chao Xu, Lili Niu, Weiping Liu
Summary: This study investigates the behavior and fate of organic pollutants in paddy fields in China using soil samples and analytical techniques. The results show that various factors such as altitude, soil temperature, and pH significantly influence the transformation of these pollutants.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Environmental Sciences
Guilin Han, Anton Eisenhauer
Summary: Nutrient depletion in the ecosystem primarily occurs through the leaching of base cations. Isotope technology offers new insights into nutrient behavior in ecosystems. Strontium (Sr) isotopes, both stable and radiogenic, were analyzed in various environmental samples from a karst forest in Southwest China, revealing the sources and cycling of Sr in the ecosystem. The Sr-87/Sr-86 ratios provide information on sources, while the delta Sr-88/86 values reflect the biogeochemical cycling within the ecosystem.
ENVIRONMENTAL EARTH SCIENCES
(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
Soil Science
Nasrin Sultana, Jun Zhao, Yuanfeng Cai, G. K. M. Mustafizur Rahman, Mohammad Saiful Alam, Mohammad Faheem, Adrian Ho, Zhongjun Jia
Summary: Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions. This study found that soil organic carbon accumulation is associated with microbial methane oxidation, with 23.6%-60.0% of methane being converted to soil organic carbon. The results suggest that methanotrophs play an important role in soil organic matter 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
Environmental Sciences
Longda Gong, Jingwen Wang, Touqeer Abbas, Qichun Zhang, Mei Cai, Muhammad Tahir, Dan Wu, Hongjie Di
Summary: This study investigates the effects of a mixed chemical amendment on soil Cd content, plant Cd accumulation, and soil microbial community. The results show that the mixed amendment significantly reduces soil Cd content and plant Cd accumulation, while also improving soil microbial diversity and species richness, accelerating nutrient turnover by microbes.
Article
Environmental Sciences
Yu Liu, Kunkun Wang, Shipeng Liao, Tao Ren, Xiaokun Li, Rihuan Cong, Jianwei Lu
Summary: The study found that paddy-upland rotation and/or straw return can improve soil structure and nutrient availability, but also affect ammonia, nitrous oxide, and methane emissions. Returning straw can increase soil organic carbon and total nitrogen content, but may lead to increased methane emissions in summer and ammonia, nitrous oxide, and methane emissions in winter.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Plant Sciences
Mengli Zhao, Jun Zhao, Jun Yuan, Lauren Hale, Tao Wen, Qiwei Huang, Jorge M. Vivanco, Jizhong Zhou, George A. Kowalchuk, Qirong Shen
Summary: This study investigated the effects of root exudates from different growth stages of Arabidopsis thaliana plants on soil bacterial communities, soil nutrients, and plant growth. The results showed that fast-growing stage root exudates had a significant impact on soil bacterial community structure, induced higher nutrient mineralization, and enhanced plant growth. Plants may adjust their exudation patterns during different growth phases to meet increased nutrient demands for faster growth.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Ecology
Qiao-Dong Chi, Jing Wang, Yu-Qing Liu, Jun Zhao, Yi Cheng, Zu-Cong Cai, Xiao-Juan Feng, Jin-Bo Zhang
Summary: The study found that climate, soil properties, and gross nitrogen dynamics have different interactive effects on biomass production in natural grasslands, and climate influences biomass production by directly and indirectly regulating soil gross nitrogen mineralization.
EUROPEAN JOURNAL OF SOIL BIOLOGY
(2021)
Article
Soil Science
Xiaoxiang He, Qiaodong Chi, Chang Zhao, Yi Cheng, Xinqi Huang, Jun Zhao, Zucong Cai, Jinbo Zhang, Christoph Mueller
Summary: Plants have significant interactions with gross rates of soil nitrogen transformations, with NH4+-preferring plants outcompeting microbial NH4+ acquisition. Heterotrophic nitrification stimulated by the presence of plants is a major contributor to total NO3 production, providing additional nitrogen for plant and microbial N requirements. This study highlights the importance of understanding the feedbacks between plant N acquisition and soil N transformations.
SOIL BIOLOGY & BIOCHEMISTRY
(2021)
Correction
Biotechnology & Applied Microbiology
Liangliang Liu, Yuanyuan Yan, Huanxin Ding, Jun Zhao, Zucong Cai, Chuanchao Dai, Xinqi Huang
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Liangliang Liu, Yuanyuan Yan, Huanxin Ding, Jun Zhao, Zucong Cai, Chuanchao Dai, Xinqi Huang
Summary: The study reveals a direct relationship between soil properties and plant health status, with the fungal community composition being most important for predicting plant health. Microbiome disease-suppressive activity in soils with low disease incidences (LDS) could be transferred to soils with high disease incidences (HDS). Certain fungal genera like Acremonium, Mycothermus, and Chryseolinea are identified as potential disease-suppressive agents.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Soil Science
Xiaoxiang He, Qiaodong Chi, Lei Meng, Chang Zhao, Mengqiu He, Xiaoqian Dan, Xinqi Huang, Jun Zhao, Zucong Cai, Jinbo Zhang, Christoph Mueller
Summary: In this study, it was found that plants with a preference for NO3- can stimulate nitrification to meet their demand for NO3-.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Plant Sciences
Yuqing Liu, Qiaodong Chi, Hui Cheng, Huanxin Ding, Teng Wen, Jun Zhao, Xiaojuan Feng, Jinbo Zhang, Zucong Cai, Guohua Liu
Summary: This study investigated the abundance and distribution of nitrogen functional genes (NFGs) in different soil layers in grassland habitats in northern China. The results showed that the distribution of NFGs was influenced by soil depth and grassland habitats, with vertical differences having a greater impact. Furthermore, redundancy analysis indicated that soil resource supply may control the vertical distribution of these microorganisms.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Soil Science
Liangliang Liu, Yuanyuan Yan, Ahmad Ali, Jun Zhao, Zucong Cai, Chuanchao Dai, Xinqi Huang, Kaisheng Zhou
Summary: Regulating microbial communities in soil is essential for controlling soil-borne diseases. Treatments such as reductive soil disinfestation and ammonia fumigation can effectively reduce the abundance of harmful pathogens like Fusarium oxysporum, leading to improved plant health and increased crop yield. Soil pH plays a crucial role in shaping the microbial community dynamics during plant cultivation, highlighting the importance of soil management strategies for disease control.
APPLIED SOIL ECOLOGY
(2022)
Article
Microbiology
Ahmad Ali, Ahmed S. Elrys, Liangliang Liu, Muhammad Iqbal, Jun Zhao, Xinqi Huang, Zucong Cai
Summary: This study found that cover crops such as spinach, non-heading Chinese cabbage, and coriander can enhance rhizosphere immunity and protect cucumber plants from diseases by altering fungal community composition. These cover crops suppress fusarium wilt and root-knot nematode, increase cucumber biomass, and improve fruit quality.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Ahmad Ali, Ahmed S. Elrys, Liangliang Liu, Qing Xia, Baoying Wang, Yunlong Li, Xiaoqian Dan, Muhammad Iqbal, Jun Zhao, Xinqi Huang, Zucong Cai
Summary: Application of reductive soil disinfestation, biochar, and antagonistic microbes has shown to be effective in controlling soil-borne diseases. This study investigated the combined effect of these methods on cucumber Fusarium wilt suppression and found that they can alter soil chemical properties and microbial communities.
Article
Environmental Sciences
Chang Zhao, Xiaoxiang He, Xiaoqian Dan, Mengqiu He, Jun Zhao, Han Meng, Zucong Cai, Jinbo Zhang
Summary: This study evaluated the effects of root exudates on soil dissolved organic matter (DOM), bacterial communities, and nitrogen transformation rates. The results showed that the presence of wheat significantly increased the composition of DOM in soil, particularly in nitrogen metabolism pathways. Wheat planting also led to changes in bacterial abundance and diversity, with soil DOM having a stronger influence on bacterial communities compared to soil available nutrients. It was found that N-transformation related bacteria were positively correlated with soil gross nitrification rate, indicating enhanced nitrogen transformation in both acidic and alkaline soils.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Soil Science
Jingjing Li, Yongbo Xu, Jun Zhao, Xinhua Yin, Zhuoying Xu
Summary: This study investigated the changes in bacterial and fungal community composition in red soil under different continuous cropping years, and their relationship with environmental factors. The results showed that continuous cropping led to a decrease in soil pH, affecting the structure and stability of the soil microbial community. The diversity of bacterial communities increased, while the diversity of fungal communities decreased after continuous cropping. Soil pH was identified as a key factor in predicting the structure of soil microbial communities. Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were identified as the dominant bacterial phyla.
EURASIAN SOIL SCIENCE
(2022)
Article
Plant Sciences
Xing Zhou, Liangliang Liu, Jun Zhao, Jinbo Zhang, Zucong Cai, Xinqi Huang
Summary: The host-associated microbiome plays a crucial role in determining plant health. The diversity of organic resources can shape microbial community structure and enhance their ability to control pathogens. Additionally, high carbohydrate diversity can upregulate microbial functions related to plant immune system regulation.
Article
Agriculture, Multidisciplinary
Yang Zhang, Bao-Ying Wang, Jun Zhang, Ying-Han Liu, Jun Zhao, Chuan-Chao Dai
Summary: This study investigates the application of Effective Microorganisms (EM) as a biological amendment in the rice-crayfish cocropping (RC) model. The findings demonstrate that EM significantly improves the chemical properties of the model and reconstructs a more stable microbial cooccurrence network. The community induced by EM shows positive effects on ecosystem multifunctionality. This study provides strong evidence for understanding the microbiological mechanisms of exogenous biological agents in agricultural ecosystems.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2023)
Article
Microbiology
Baoying Wang, Yulan Lin, Wenhao Yu, Qing Xia, Ahmad Ali, Fugang Wei, Chuanchao Dai, Jinbo Zhang, Zucong Cai, Jun Zhao
Summary: Continuous cultivation of Sanqi ginseng can lead to changes in the beneficial microbial community and their functions. This study found that with successive plantings of Sanqi ginseng, the beneficial bacterial community changed, carbon source utilization capacity increased, and autotoxin degradation functions decreased.
MICROBIOLOGY SPECTRUM
(2023)