Article
Plant Sciences
Mukesh Kumar Malviya, Chang-Ning Li, Prakash Lakshmanan, Manoj Kumar Solanki, Zhen Wang, Anjali Chandrol Solanki, Qian Nong, Krishan K. Verma, Rajesh Kumar Singh, Pratiksha Singh, Anjney Sharma, Dao-Jun Guo, Eldessoky S. Dessoky, Xiu-Peng Song, Yang-Rui Li
Summary: This study investigated the rhizosphere and diazotroph bacterial diversity in wild progenitors of sugarcane, highlighting the importance of genetic background in plant-microbe interactions. The results showed significant microbial diversity and the influence of soil physiochemical properties on the rhizosphere microbiome.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Ecology
Huanhuan Wang, Xu Li, Xinyu Li, Fuli Li, Zhencheng Su, Huiwen Zhang
Summary: The research found that diazotrophs in paddy soils mainly belong to the phylum Proteobacteria, with the highest diversity in the 10-20 cm layer and decreasing with soil depth. The community structure of diazotrophs is significantly influenced by region and soil depth, with soil total C and N content and pH being the main factors affecting vertical variation.
Article
Biodiversity Conservation
Jian Kang, Zebang Deng, Zhongrui Zhang, Shuilian Chen, Jianguo Huang, Xiaogang Ding
Summary: Surface soil nitrogen (SN) is crucial for plant nutrient uptake and is affected by soil properties and diversity indicators. This study examined the spatial patterns and influencing factors of SN in the Xijiang River Basin. The results showed that total nitrogen content in broad-leaved forests was higher than that in coniferous forests. Soil properties were the main explanatory factor for SN, with sub-surface soil nitrogen being the largest explanatory quantity factor. Forest management should avoid damaging sub-surface soils to prevent nitrogen loss, and the effects of nitrogen deposition on SN deserve further investigation.
ECOLOGICAL INDICATORS
(2023)
Article
Soil Science
Natalia Pin Viso, Jimena Ortiz, Mariana Maury, Juan Pablo Frene, Gaston A. Iocoli, Claudio Lorenzon, Maximo Rivarola, Fernando O. Garcia, Vicente Gudelj, Valeria S. Faggioli
Summary: Among agronomical practices, fertilisation greatly influences soil microbial diversity and functionality and severely disturbs the global nitrogen (N) cycle. In this study, the effect of 16 years of mineral fertilisation on soil bacterial-archaeal communities was assessed. Results showed that fertilisation increased the abundance of Proteobacteria and reduced the abundance of Verrucomicrobiota. Indicator species analyses revealed different indicator species at different soil depths and fertilisation rates. The abundance of N-cycling genes showed inconsistent responses depending on the soil depth.
APPLIED SOIL ECOLOGY
(2024)
Article
Multidisciplinary Sciences
Haiming Tang, Chao Li, Lihong Shi, Xiaoping Xiao, Kaikai Cheng, Li Wen, Weiyan Li
Summary: Long-term application of organic manure and crop residue management increase the abundance of soil N-fixing bacteria community in double-cropping rice paddy field, while there is an obvious difference in features of soil N-fixing bacteria community between application of inorganic fertilizer and organic manure treatments.
Article
Environmental Sciences
Bingchen Yuan, Daogeng Yu, An Hu, Yanru Wang, Yuting Sun, Chengzhen Li
Summary: Interplanting different green manure crops in litchi orchards in tropical regions of China effectively increases soil nutrients and reduces weed population. However, the choice of green manure crop should be based on soil conditions, as different crops have different effects on soil nutrient content. Intercropping with green manure crops enhances soil ammonium nitrogen and available phosphorus content, and promotes the abundance of beneficial microbial genera. Therefore, intercropping is an effective management measure in litchi orchards, but the selection of green manure crop should be considered based on soil conditions.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Article
Microbiology
Xin Sui, Beat Frey, Libin Yang, Yingnan Liu, Rongtao Zhang, Hongwei Ni, Mai-He Li
Summary: Acidobacteria are an important component of soil bacteria, and their structure and diversity are influenced by climate changes and human activities. This study investigated the Acidobacterial community and diversity in a typical wetland degradation series in northeastern China. The results showed that the soil physicochemical properties changed significantly along the degradation stages and the composition of Acidobacteria was influenced by different soil environmental factors in wetland and forest stages. These findings highlight the importance of understanding the role of Acidobacteria in wetland ecosystems.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Huihui Wang, Shaoping Kuang, Qiaolin Lang, Lei Wang
Summary: The study investigated the screening of dominant or core oil resistant bacteria in Aged Oil Sludge (AOS) contaminated soil in Daqing and Shengli oilfields in China using High-Throughput Sequencing method. It found that certain microbial genera were significantly enriched after oil treatment, indicating their possible role in the attenuation of petroleum hydrocarbons. The toxicological effect of AOS on the diversity and community structure of bacteria was notable, with Firmicutes showing reduction at phylum level after treatment.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2021)
Article
Forestry
Yubiao Lin, Jiejun Kong, Ling Yang, Qian He, Yan Su, Jiyue Li, Guangyu Wang, Quan Qiu
Summary: The effect of 50% throughfall reduction (TR) on soil microbial communities in a subtropical Eucalyptus plantation was investigated. It was found that TR significantly altered the composition and function of bacterial communities, while showing fewer changes in fungal communities. Soil water content and available phosphorus decreased during TR, resulting in greater changes in the structure of bacterial communities.
Article
Plant Sciences
Liuting Zhou, Jianjuan Li, Ganga Raj Pokhrel, Jun Chen, Yanlin Zhao, Ying Bai, Chen Zhang, Wenxiong Lin, Zeyan Wu, Chengzhen Wu
Summary: The growth and productivity of Casuarina equisetifolia is negatively impacted by planting sickness under long-term monoculture regimes, as the structure of rhizospheric soil diazotrophic community can change, leading to an imbalance in diazotrophic bacteria population.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Qing Qu, Minggang Wang, Hongwei Xu, Ziran Yan, Guobin Liu, Sha Xue
Summary: This study investigated the effects of nitrogen addition on plant community biomass, evenness, and composition in a grassland community. The results showed that nitrogen addition significantly increased plant biomass, but decreased community evenness. The abundance of bacteria and fungi were also affected by nitrogen addition, but their composition remained unchanged.
LAND DEGRADATION & DEVELOPMENT
(2022)
Article
Biodiversity Conservation
Yan Zhang, Li Ji, Lixue Yang
Summary: This study investigated the soil nematode community in the cold-temperate zone of China's Oakley Mountain, revealing a decrease in soil nematode diversity with increasing altitude in high latitudes, with plant-parasites as the dominant trophic group. Altitude, soil bulk density, temperature, pH, soluble organic carbon, and nitrogen were significant factors affecting the altitude distribution of soil nematodes, with pH and soluble organic nitrogen identified as key factors explaining changes in nematode community composition.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Biochemistry & Molecular Biology
Rajesh Kumar Singh, Pratiksha Singh, Anjney Sharma, Dao-Jun Guo, Sudhir K. Upadhyay, Qi-Qi Song, Krishan K. Verma, Dong-Ping Li, Mukesh Kumar Malviya, Xiu-Peng Song, Li-Tao Yang, Yang-Rui Li
Summary: In this study, the existence of novel endophytic diazotrophs in sugarcane plants was investigated, and their contribution to nitrogen fixation was evaluated. The bacterial communities in different tissues showed variations in diversity and abundance, with 16 genera exhibiting potent nitrogen-fixing ability. These findings are important for understanding the biological nitrogen fixation mechanism in sugarcane and for sustainable agriculture production.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Kendra A. A. Turk-Kubo, Britt A. A. Henke, Mary R. R. Gradoville, Jonathan D. D. Magasin, Matthew J. J. Church, Jonathan P. P. Zehr
Summary: In the North Pacific Subtropical Gyre (NPSG), various types of microbes, including previously understudied groups, play a significant role in nitrogen fixation.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biodiversity Conservation
Jing Guo, Yaqiong Wu, Xiaohong Wu, Zhong Ren, Guibin Wang
Summary: This study compared the impacts of four afforestation and agroforestry practices on soil properties and bacterial communities with legacy cropping systems in China. The results showed that afforestation and agroforestry practices significantly increased soil organic carbon and total nitrogen levels while also enhancing bacterial diversity, with a greater effect on bacterial community beta diversity in the topsoil. Land conversion was found to be a key factor influencing taxonomic shifts and functional variations in bacterial communities, particularly in the topsoil.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Microbiology
Jun Feng, Yili Qian, Zhichao Zhou, Sarah Ertmer, Eugenio Vivas, Freeman Lan, Joshua J. Hamilton, Federico E. Rey, Karthik Anantharaman, Ophelia S. Venturelli
Summary: This study investigates the role of polysaccharide utilization loci (PULs) in Bacteroides uniformis (BU), showing that PULs enable glycan digestion and shape ecological dynamics. Using CRISPR-based genome editing, specific PULs are deleted to enhance BU fitness and colonization in the murine gut, modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers, affecting community dynamics and butyrate production.
CELL HOST & MICROBE
(2022)
Article
Biotechnology & Applied Microbiology
Yong-Hui Li, Ji-Dong Gu
Summary: Water plays a crucial role in the initiation of microbial colonization and subsequent biodeterioration processes in cultural heritage materials. The different types of water in materials, along with characteristics like porosity and pore connectivity, affect microbial growth and biodeterioration. Managing water is a fundamental strategy to prevent long-term damage to cultural heritage.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
Microbiology
Jie Pan, Wei Xu, Zhichao Zhou, Zongze Shao, Chunming Dong, Lirui Liu, Zhuhua Luo, Meng Li
Summary: This study revealed the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14 degrees S based on assembled genomes. It showed that a large proportion of microbes could benefit from using both heterotrophic and autotrophic strategies simultaneously in situ. The research also highlighted novel diazotroph members and emphasized the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems.
Article
Microbiology
Zhichao Zhou, Patricia Q. Tran, Adam M. Breister, Yang Liu, Kristopher Kieft, Elise S. Cowley, Ulas Karaoz, Karthik Anantharaman
Summary: Advances in microbiome science have been driven by the ability to study and infer microbial ecology from genomes. METABOLIC is a scalable software that allows for the study of microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. It provides annotation of microbial genomes, metabolic pathway analyses, and determination of microbial contributions to biogeochemical transformations and cycles. METABOLIC is a versatile tool that can be used with various metagenomic datasets, from diverse environments such as marine subsurface, terrestrial subsurface, and human gut.
Editorial Material
Ecology
Xiaobo Liu, Jin-Long Yang, Daniel Rittschof, James S. Maki, Ji-Dong Gu
Summary: Biofouling has significant impacts on the environment, economy, and society. Effective strategies for addressing biofouling should incorporate sustainability concepts and focus on disrupting attachment of organisms or developing innovative surfaces to remove fouling organisms. Other viable options, including eco-friendly antifouling chemicals, should also be considered.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Engineering, Environmental
Ling-Dong Shi, Xiyang Dong, Zongbao Liu, Yuchun Yang, Jih-Gaw Lin, Meng Li, Ji-Dong Gu, Li-Zhong Zhu, He-Ping Zhao
Summary: The diversity of both microorganisms and viruses in activated sludge of wastewater treatment plants plays a crucial role in controlling microbial dynamics and metabolisms. This study reveals the presence of unknown viral genera in activated sludge, indicating an unexplored reservoir for new viruses and viral diversity. The study also shows that viruses can enhance the performance of activated sludge by encoding auxiliary metabolic genes (AMGs) involved in biodegradation, but can also facilitate the spread of antibiotic resistance genes (ARGs) among microorganisms. Overall, this study highlights the mixed blessing of viruses in wastewater treatment plants and their impact on biochemical processes.
Article
Environmental Sciences
Ling Luo, Dahang Deng, Xin Zhao, Hairong Hu, Xinyi Li, Jidong Gu, Yan He, Gang Yang, Ouping Deng, Yinlong Xiao
Summary: This study found that nanoparticles nZVI and nZnO can promote the abundance of tetracycline resistance genes in sediment, but nZVI and bacterial communities can also reduce tetracycline resistance gene abundance when tetracycline is present. The findings are important for understanding the role of nanoparticles in promoting and reducing antibiotic resistance genes in the environment.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Jing Chen, Zhichao Zhou, Ji-Dong Gu
Summary: This study investigated the diversity and abundance of n-damo bacteria in vegetated and non-vegetated sediments of a subtropical mangrove wetland. The results showed that the seasonal changes and vegetation had significant impacts on the n-damo bacterial community. The study further revealed that NH4+ and NH4+/NO2- were important factors influencing the diversity of n-damo bacteria in mangrove wetland sediments.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
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
Biochemistry & Molecular Biology
Yu-Yu Cheng, Zhichao Zhou, James M. Papadopoulos, Jason D. Zuke, Tanya G. Falbel, Karthik Anantharaman, Briana M. Burton, Ophelia S. Venturelli
Summary: The factors influencing HGT via natural transformation in microbial communities, including extracellular DNA release, plasmid properties, donor stress responses and lysis rates, as well as interspecies interactions, have been investigated in a microbial co-culture. It has been found that plasmid release and HGT efficiency are enhanced in the co-culture compared to monocultures, with the key determining factor being the donor's ability to induce SOS response and release plasmids in high concentrations. Notably, HGT efficiency is independent of the viability state of the donor cells.
MOLECULAR SYSTEMS BIOLOGY
(2023)
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
Microbiology
Ruonan Wu, Eric M. Bottos, Vincent G. Danna, James C. Stegen, Janet K. Jansson, Michelle R. Davison
Summary: Arctic permafrost thawing leads to the emergence of RNA viruses that target eukaryotic hosts and pose potential threats to humans, animals, and plants. This study identifies a diverse RNA viral community in thawed permafrost samples, showing distinct compositions compared to other habitats. The detection of potential pathogens highlights the importance of environmental reservoirs for RNA viral pathogens, particularly in the context of the ongoing COVID-19 pandemic. Understanding viral-host interactions and the ecological roles of RNA viruses in thawed permafrost is crucial.
Article
Ecology
Zhichao Zhou, Patricia Q. Tran, Alyssa M. Adams, Kristopher Kieft, John A. Breier, Caroline S. Fortunato, Cody S. Sheik, Julie A. Huber, Meng Li, Gregory J. Dick, Karthik Anantharaman
Summary: In globally distributed deep-sea hydrothermal vent plumes, microbiomes are influenced by the redox energy landscapes created by the mixing of hydrothermal vent fluids and seawater. The core microbiome of plumes is defined by sulfur metabolism and drives metabolic connectivity in the microbial community. The impacts of plume biogeochemistry on the oceans and the links between biogeography, evolution, and metabolic connectivity are poorly understood.
Editorial Material
Immunology
Tingtao Chen, Ruonan Wu, Lei Cheng, Qinping Liao, Zhangran Chen
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Ecology
Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman, Karthik Anantharaman
Summary: Deep-sea hydrothermal vents are abundant and have important roles in ocean biogeochemistry. By studying microbial communities in the Guaymas Basin hydrothermal system, we identified key species and their interactions. Metabolic models were used to infer metabolic exchanges and horizontal gene transfer events within the community. Our findings highlight the importance of microbial interactions in driving community structure and organization in hydrothermal plume microbiomes.
ISME COMMUNICATIONS
(2023)