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Distribution characteristics of fungal communities with depth in paddy fields of three soil types in China
Xu Li , Huanhuan Wang , Xiang Li , Xinyu Li , Huiwen Zhang
J. Microbiol. 2020;58(4):279-287.   Published online February 27, 2020
DOI: https://doi.org/10.1007/s12275-020-9409-8
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  • 14 Web of Science
  • 9 Crossref
AbstractAbstract
Little is known about the distribution of fungal communities with soil depth on relatively large scales. In this study, typical paddy soils in three regions (Hailun, Changshu, and Yingtan) from north to south China were selected to investigate the vertical distribution (0-100 cm) of the fungal community by Illumina MiSeq sequencing, and to identify the main factors influencing the fungal community distribution. The results indicated that the structure of the soil fungal community changed significantly with region and soil depth. Soil fungal taxa such as Zygomycota, Glomeromycota, Saccharomycete, Kazachstania, Mortierella, Massariosphaeria, Hypholoma, and Zopfiella were enriched at depths of 0–20 cm, whereas Dothideomycetes, Microbotryomycetes, Tremellomycetes, Sporobolomyces, Cryptococcus, Rhodotorula, Fusarium, and Pyrenochaetopsis had high relative abundances at 80–100 cm. Variance partitioning analysis indicated that the geographic distance contributed more to the fungal community variation than environmental variables on a large scale. In addition, soil total carbon and nitrogen contents were the main environmental factors driving the vertical distribution of the fungal community in paddy soils.

Citations

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  • Region and Crop Type Influenced Fungal Diversity and Community Structure in Agricultural Areas in Qinghai Province
    Lianyu Zhou, Xuelan Ma, Longrui Wang, Wenjuan Sun, Yu Liu, Yun Ma, Huichun Xie, Feng Qiao
    Agriculture.2023; 14(1): 6.     CrossRef
  • Comparing Sediment Microbial Communities of Arctic Beaver Ponds to Tundra Lakes and Streams
    Kelly C. Shannon, Natasha R. Christman, Byron C. Crump, Michael P. Carey, Joshua Koch, Laura L. Lapham, Jonathan O’Donnell, Brett A. Poulin, Ken D. Tape, Jason A. Clark, Frederick S. Colwell
    Journal of Geophysical Research: Biogeosciences.2023;[Epub]     CrossRef
  • Soil depth as a driver of microbial and carbon dynamics in a planted forest (Pinus radiata) pumice soil
    Alexa K. Byers, Loretta G. Garrett, Charlotte Armstrong, Fiona Dean, Steve A. Wakelin
    SOIL.2023; 9(1): 55.     CrossRef
  • Microbial communities in the diagnostic horizons of agricultural Isohumosols in northeast China reflect their soil classification
    Zhuxiu Liu, Haidong Gu, Qin Yao, Feng Jiao, Junjie Liu, Jian Jin, Xiaobing Liu, Guanghua Wang
    CATENA.2022; 216: 106430.     CrossRef
  • Effects of continuous and rotational cropping practices on soil fungal communities in pineapple cultivation
    Jing Chen, Hui Zeng
    PeerJ.2022; 10: e13937.     CrossRef
  • Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs
    Bunlong Yim, Zeeshan Ibrahim, Lioba Rüger, Minh Ganther, Lorrie Maccario, Søren J. Sørensen, Anna Heintz-Buschart, Mika T. Tarkka, Doris Vetterlein, Michael Bonkowski, Evgenia Blagodatskaya, Kornelia Smalla
    Plant and Soil.2022; 478(1-2): 229.     CrossRef
  • The Effects of Drainage on the Soil Fungal Community in Freshwater Wetlands
    Qingqing Zhao, Junhong Bai, Jia Jia, Guangliang Zhang, Jianing Wang, Yongchao Gao
    Frontiers in Ecology and Evolution.2022;[Epub]     CrossRef
  • Diversity and structure of soil fungal communities unveil the building history of a burial mound of ancient Japan (Tobiotsuka Kofun, Okayama Prefecture)
    Samuele Voyron, Chiara Tonon, Laura Guglielmone, Luisella Celi, Cesare Comina, Hajime Ikeda, Naoko Matsumoto, Daniele Petrella, Joseph Ryan, Kazuhiro Sato, Akira Seike, Ivan Varriale, Jun Yamashita, Sergio E. Favero-Longo, Eleonora Bonifacio
    Journal of Archaeological Science.2022; 146: 105656.     CrossRef
  • Straw retention efficiently improves fungal communities and functions in the fallow ecosystem
    Caifang Zhang, Zhaoli Lin, Youxiong Que, Nyumah Fallah, Muhammad Tayyab, Shiyan Li, Jun Luo, Zichu Zhang, Ahmad Yusuf Abubakar, Hua Zhang
    BMC Microbiology.2021;[Epub]     CrossRef
Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone
Dan Xue , Huai Chen , Xiaolin Luo , Jiuqiang Guan , Yixin He , Xinquan Zhao
J. Microbiol. 2018;56(10):734-743.   Published online August 22, 2018
DOI: https://doi.org/10.1007/s12275-018-8133-0
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  • 28 Crossref
AbstractAbstract
The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.

Citations

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    Qin Li, Yan Tu, Tao Ma, Kai Cui, Jianxin Zhang, Qiyu Diao, Yanliang Bi
    Microorganisms.2023; 11(3): 576.     CrossRef
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    Yuqi Li, Jian Gao, Yihan Xue, Ruolin Sun, Xiaoni Sun, Zhanying Sun, Suozhu Liu, Zhankun Tan, Weiyun Zhu, Yanfen Cheng
    BMC Microbiology.2023;[Epub]     CrossRef
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    Rodrigo Huaiquipán, John Quiñones, Rommy Díaz, Carla Velásquez, Gastón Sepúlveda, Lidiana Velázquez, Erwin A. Paz, Daniela Tapia, David Cancino, Néstor Sepúlveda
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    Ali Mujtaba Shah, Iqra Bano, Izhar Hyder Qazi, Maharach Matra, Metha Wanapat
    Frontiers in Veterinary Science.2023;[Epub]     CrossRef
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    Animals.2023; 13(3): 335.     CrossRef
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    Frontiers in Microbiology.2023;[Epub]     CrossRef
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    Wen Qin, Pengfei Song, Jirong Li, Jiuxiang Xie, Shoudong Zhang
    Sustainability.2022; 14(16): 10263.     CrossRef
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    Xiaojing Cui, Yue Liu, Hao Wu, Qingxiang Meng, Shujie Liu, Shatuo Chai, Lizhuang Hao, Zhenming Zhou
    Frontiers in Veterinary Science.2022;[Epub]     CrossRef
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    Xungang Wang, Tianwei Xu, Xiaoling Zhang, Na Zhao, Linyong Hu, Hongjin Liu, Qian Zhang, Yuanyue Geng, Shengping Kang, Shixiao Xu
    Frontiers in Veterinary Science.2022;[Epub]     CrossRef
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    Yuxin Su, Junhong Su, Fanglin Li, Xiaojing Tian, Zewen Liu, Gongtao Ding, Jialin Bai, Zhuo Li, Zhongren Ma, Maikel P. Peppelenbosch
    Frontiers in Veterinary Science.2022;[Epub]     CrossRef
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    Xiaolong Hu, Yuting Wei, Tianxiang Zhang, Xiaoguo Wang, Yongtao Xu, Weiwei Zhang, Yunlin Zheng, Martha Vives
    Applied and Environmental Microbiology.2022;[Epub]     CrossRef
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    Xinyu Zhou, Mingjuan Gu, Lin Zhu, Di Wu, Miaomiao Yang, Yajie Gao, Xueqiao Wang, Chunling Bai, Zhuying Wei, Lei Yang, Guangpeng Li
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    Z.W. Zhao, Z.Y. Ma, H.C. Wang, C.F. Zhang
    Animal Feed Science and Technology.2022; 283: 115184.     CrossRef
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    Xungang Wang, Linyong Hu, Hongjin Liu, Tianwei Xu, Na Zhao, Xiaoling Zhang, Yuanyue Geng, Shengping Kang, Shixiao Xu
    Animal Bioscience.2021; 34(12): 1921.     CrossRef
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    Chenchen Xu, Wenwen Liu, Baozhong Sun, Songshan Zhang, Shou Zhang, Yuanli Yang, Yuanhua Lei, Lan Chang, Peng Xie, Huayi Suo
    Frontiers in Microbiology.2021;[Epub]     CrossRef
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    Yaling Ma, Hucheng Wang, Chunjie Li
    Journal of Microbiology.2021; 59(8): 718.     CrossRef
  • Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers
    Naren Gaowa, Kevin Panke-Buisse, Shuxiang Wang, Haibo Wang, Zhijun Cao, Yajing Wang, Kun Yao, Shengli Li
    Animals.2020; 10(9): 1712.     CrossRef
  • A Mixed Phytogenic Modulates the Rumen Bacteria Composition and Milk Fatty Acid Profile of Water Buffaloes
    Faiz-ul Hassan, Hossam M. Ebeid, Zhenhua Tang, Mengwei Li, Lijuan Peng, Kaiping Peng, Xin Liang, Chengjian Yang
    Frontiers in Veterinary Science.2020;[Epub]     CrossRef
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    Jian Ma, Yixiao Zhu, Zhisheng Wang, Xiong Yu, Rui Hu, Xueying Wang, Guang Cao, Huawei Zou, Ali Mujtaba Shah, Quanhui Peng, Bai Xue, Lizhi Wang, Suonan Zhao, Xiangying Kong
    Frontiers in Microbiology.2020;[Epub]     CrossRef
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    Qingmiao Ren, Huazhe Si, Xiaoting Yan, Chang Liu, Luming Ding, Ruijun Long, Zhipeng Li, Qiang Qiu
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  • Comparing the Microbial Community in Four Stomach of Dairy Cattle, Yellow Cattle and Three Yak Herds in Qinghai-Tibetan Plateau
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    Frontiers in Microbiology.2019;[Epub]     CrossRef
  • Dynamic Alterations in Yak Rumen Bacteria Community and Metabolome Characteristics in Response to Feed Type
    Chang Liu, Hao Wu, Shujie Liu, Shatuo Chai, Qingxiang Meng, Zhenming Zhou
    Frontiers in Microbiology.2019;[Epub]     CrossRef
Research Support, Non-U.S. Gov't
Improved pipeline for reducing erroneous identification by 16S rRNA sequences using the Illumina MiSeq platform
Yoon-Seong Jeon , Sang-Cheol Park , Jeongmin Lim , Jongsik Chun , Bong-Soo Kim
J. Microbiol. 2015;53(1):60-69.   Published online January 4, 2015
DOI: https://doi.org/10.1007/s12275-015-4601-y
  • 60 View
  • 0 Download
  • 34 Crossref
AbstractAbstract
The cost of DNA sequencing has decreased due to advancements in Next Generation Sequencing. The number of sequences obtained from the Illumina platform is large, use of this platform can reduce costs more than the 454 pyrosequencer. However, the Illumina platform has other challenges, including bioinformatics analysis of large numbers of sequences and the need to reduce erroneous nucleotides generated at the 3􍿁-ends of the sequences. These erroneous sequences can lead to errors in analysis of microbial communities. Therefore, correction of these erroneous sequences is necessary for accurate taxonomic identification. Several studies that have used the Illumina platform to perform metagenomic analyses proposed curating pipelines to increase accuracy. In this study, we evaluated the likelihood of obtaining an erroneous microbial composition using the MiSeq 250 bp paired sequence platform and improved the pipeline to reduce erroneous identifications. We compared different sequencing conditions by varying the percentage of control phiX added, the concentration of the sequencing library, and the 16S rRNA gene target region using a mock community sample composed of known sequences. Our recommended
method
corrected erroneous nucleotides and improved identification accuracy. Overall, 99.5% of the total reads shared 95% similarity with the corresponding template sequences and 93.6% of the total reads shared over 97% similarity. This indicated that the MiSeq platform can be used to analyze microbial communities at the genus level with high accuracy. The improved analysis method recommended in this study can be applied to amplicon studies in various environments using high-throughput reads generated on the MiSeq platform.

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