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1

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

Penton, C. Ryan, Gupta, Vadakattu V. S. R., Yu, Julian, Tiedje, James M.

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 1.71 MB

english, 2016

2

Soil fungal and bacterial responses to conversion of open land to short rotation woody biomass crops

Xue, Chao, Penton, C. Ryan, Zhang, Bangzhou, Zhao, Mengxin, Rothstein, David E., Mladenoff, David J., Forrester, Jodi A., Shen, Qirong, Tiedje, James M.

Journal:

Year:

2015

Language:

english

File:

PDF, 886 KB

english, 2015

3

Inducing the rhizosphere microbiome by biofertilizer application to suppress banana Fusarium wilt disease

Fu, Lin, Penton, C. Ryan, Ruan, Yunze, Shen, Zongzhuan, Xue, Chao, Li, Rong, Shen, Qirong

Journal:

Soil Biology and Biochemistry

Year:

2017

Language:

english

File:

PDF, 1.34 MB

english, 2017

4

Suppression of banana Panama disease induced by soil microbiome reconstruction through an integrated agricultural strategy

Shen, Zongzhuan, Xue, Chao, Penton, C. Ryan, Thomashow, Linda S., Zhang, Na, Wang, Beibei, Ruan, Yunze, Li, Rong, Shen, Qirong

Journal:

Soil Biology and Biochemistry

Year:

2018

Language:

english

File:

PDF, 2.66 MB

english, 2018

5

Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon

Sul, Woo Jun, Asuming-Brempong, Stella, Wang, Qiong, Tourlousse, Dieter M., Penton, C. Ryan, Deng, Ye, Rodrigues, Jorge L.M., Adiku, Samuel G.K., Jones, James W., Zhou, Jizhong, Cole, James R., Tiedje

Journal:

Soil Biology and Biochemistry

Year:

2013

Language:

english

File:

PDF, 1.52 MB

english, 2013

6

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing

Penton, C. Ryan, Gupta, V. V. S. R., Tiedje, James M., Neate, Stephen M., Ophel-Keller, Kathy, Gillings, Michael, Harvey, Paul, Pham, Amanda, Roget, David K., Vinatzer, Boris Alexander

Journal:

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

7

Soil depth and crop determinants of bacterial communities under ten biofuel cropping systems

Zhang, Bangzhou, Penton, C. Ryan, Xue, Chao, Quensen, John F., Roley, Sarah S., Guo, Jiarong, Garoutte, Aaron, Zheng, Tianling, Tiedje, James M.

Journal:

Soil Biology and Biochemistry

Year:

2017

Language:

english

File:

PDF, 3.85 MB

english, 2017

8

Alterations in soil fungal community composition and network assemblage structure by different long-term fertilization regimes are correlated to the soil ionome

Xue, Chao, Ryan Penton, C., Zhu, Chen, Chen, Huan, Duan, Yinghua, Peng, Chang, Guo, Shiwei, Ling, Ning, Shen, Qirong

Journal:

Biology and Fertility of Soils

Year:

2017

Language:

english

File:

PDF, 1.90 MB

english, 2017

9

Biochar application influences microbial assemblage complexity and composition due to soil and bioenergy crop type interactions

Yu, Julian, Deem, Lauren M., Crow, Susan E., Deenik, Jonathan L., Penton, C. Ryan

Journal:

Soil Biology and Biochemistry

Year:

2018

Language:

english

File:

PDF, 953 KB

english, 2018

10

Effect of LSU and ITS genetic markers and reference databases on analyses of fungal communities

Xue, Chao, Hao, Yuewen, Pu, Xiaowei, Ryan Penton, C., Wang, Qiong, Zhao, Mengxin, Zhang, Bangzhou, Ran, Wei, Huang, Qiwei, Shen, Qirong, Tiedje, James M.

Journal:

Biology and Fertility of Soils

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

11

Reshaping the rhizosphere microbiome by bio-organic amendment to enhance crop yield in a maize-cabbage rotation system

Qiao, Cece, Penton, C. Ryan, Xiong, Wu, Liu, Chao, Wang, Roufei, Liu, Zhengyang, Xu, Xu, Li, Rong, Shen, Qirong

Journal:

Applied Soil Ecology

Year:

2019

Language:

english

File:

PDF, 1.38 MB

english, 2019

12

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil

Yu, Julian, Pavia, Michael J., Deem, Lauren M., Crow, Susan E., Deenik, Jonathan L., Penton, Christopher Ryan

Journal:

Frontiers in Microbiology

Year:

2020

File:

PDF, 1.30 MB

2020

13

Enzyme activity responses to nutrient loading in subtropical wetlands

C. Ryan Penton, Susan Newman

Journal:

Biogeochemistry

Year:

2007

Language:

english

File:

PDF, 508 KB

english, 2007

14

Importance of sub-surface rhizosphere-mediated coupled nitrification–denitrification in a flooded agroecosystem in Hawaii

Penton, C. Ryan, Deenik, Jonathan L., Popp, Brian N., Bruland, Gregory L., Engstrom, Pia, St. Louis, Derek, Tiedje, James

Journal:

Soil Biology and Biochemistry

Year:

2013

Language:

english

File:

PDF, 970 KB

english, 2013

15

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH

Zhang, Bangzhou, Penton, C. Ryan, Xue, Chao, Wang, Qiong, Zheng, Tianling, Tiedje, James M., Lovell, C. R.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 2.14 MB

english, 2015

16

Assessing Nitrogen Transformations in a Flooded Agroecosystem Using the Isotope Pairing Technique and Nitrogen Functional Gene Abundances

Penton, C. Ryan, Deenik, Jonathan L., Popp, Brian N., Bruland, Gregory L., Engstrom, Pia, Mueller, Jaclyn, Worden, Andrew, Tiedje, James M.

Journal:

Year:

2014

Language:

english

File:

PDF, 985 KB

english, 2014

17

Enzyme Activity Responses to Nutrient Loading in Subtropical Wetlands

C. Ryan Penton and Susan Newman

Journal:

Biogeochemistry

Year:

2007

Language:

english

File:

PDF, 2.13 MB

english, 2007

18

Manipulating the banana rhizosphere microbiome for biological control of Panama disease

Xue, Chao, Ryan Penton, C., Shen, Zongzhuan, Zhang, Ruifu, Huang, Qiwei, Li, Rong, Ruan, Yunze, Shen, Qirong

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.01 MB

english, 2015

19

Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter

Penton, C. Ryan, Johnson, Timothy A., Quensen, John F., Iwai, Shoko, Cole, James R., Tiedje, James M.

Journal:

Frontiers in Microbiology

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

20

Erratum: Corrigendum: Manipulating the banana rhizosphere microbiome for biological control of Panama disease

Xue, Chao, Ryan Penton, C., Shen, Zongzhuan, Zhang, Ruifu, Huang, Qiwei, Li, Rong, Ruan, Yunze, Shen, Qirong

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 97 KB

english, 2015

21

Banana Fusarium Wilt Disease Incidence Is Influenced by Shifts of Soil Microbial Communities Under Different Monoculture Spans

Shen, Zongzhuan, Penton, C. Ryan, Lv, Nana, Xue, Chao, Yuan, Xianfu, Ruan, Yunze, Li, Rong, Shen, Qirong

Journal:

Microbial Ecology

Year:

2017

Language:

english

File:

PDF, 2.54 MB

english, 2017

22

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra

Liang, Junyi, Xia, Jiangyang, Shi, Zheng, Jiang, Lifen, Ma, Shuang, Lu, Xingjie, Mauritz, Marguerite, Natali, Susan M, Pegoraro, Elaine, Penton, C Ryan, Plaza, César, Salmon, Verity G, Celis, Gerardo,

Journal:

Global Change Biology

Year:

2018

Language:

english

File:

PDF, 1.68 MB

english, 2018

23

NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

Penton, C. Ryan, Yang, Caiyun, Wu, Liyou, Wang, Qiong, Zhang, Jin, Liu, Feifei, Qin, Yujia, Deng, Ye, Hemme, Christopher L., Zheng, Tianling, Schuur, Edward A. G., Tiedje, James, Zhou, Jizhong

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 2.69 MB

english, 2016

24

More replenishment than priming loss of soil organic carbon with additional carbon input

Liang, Junyi, Zhou, Zhenghu, Huo, Changfu, Shi, Zheng, Cole, James R., Huang, Lei, Konstantinidis, Konstantinos T., Li, Xiaoming, Liu, Bo, Luo, Zhongkui, Penton, C. Ryan, Schuur, Edward A. G., Tiedje,

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.12 MB

english, 2018

25

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol

Yu, Julian, Deem, Lauren M., Crow, Susan E., Deenik, Jonathan, Penton, C. Ryan

Journal:

Applied and Environmental Microbiology

Year:

2019

File:

PDF, 1.40 MB

2019

26

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol

Yu, Julian, Deem, Lauren M., Crow, Susan E., Deenik, Jonathan, Penton, C. Ryan

Journal:

Applied and Environmental Microbiology

Year:

2019

Language:

english

File:

PDF, 1.40 MB

english, 2019

27

Key extracellular enzymes triggered high-efficiency composting associated with bacterial community succession

Qiao, Cece, Ryan Penton, C., Liu, Chao, Shen, Zongzhuan, Ou, Yannan, Liu, Zhengyang, Xu, Xu, Li, Rong, Shen, Qirong

Journal:

Bioresource Technology

Year:

2019

Language:

english

File:

PDF, 1.59 MB

english, 2019

28

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon

Hale, Lauren, Feng, Wenting, Yin, Huaqun, Guo, Xue, Zhou, Xishu, Bracho, Rosvel, Pegoraro, Elaine, Penton, C. Ryan, Wu, Liyou, Cole, James, Konstantinidis, Konstantinos T., Luo, Yiqi, Tiedje, James M.

Journal:

The ISME Journal

Year:

2019

Language:

english

File:

PDF, 1.69 MB

english, 2019

29

Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon

Hale, Lauren, Feng, Wenting, Yin, Huaqun, Guo, Xue, Zhou, Xishu, Bracho, Rosvel, Pegoraro, Elaine, Penton, C. Ryan, Wu, Liyou, Cole, James, Konstantinidis, Konstantinos T., Luo, Yiqi, Tiedje, James M.

Journal:

The ISME Journal

Year:

2019

File:

PDF, 1.69 MB

2019

30

Deciphering Underlying Drivers of Disease Suppressiveness Against Pathogenic Fusarium oxysporum

Ou, Yannan, Penton, C. Ryan, Geisen, Stefan, Shen, Zongzhuan, Sun, Yifei, Lv, Nana, Wang, Beibei, Ruan, Yunze, Xiong, Wu, Li, Rong, Shen, Qirong

Journal:

Frontiers in Microbiology

Year:

2019

Language:

english

File:

PDF, 8.87 MB

english, 2019

31

Deciphering Underlying Drivers of Disease Suppressiveness Against Pathogenic Fusarium oxysporum

Ou, Yannan, Penton, C. Ryan, Geisen, Stefan, Shen, Zongzhuan, Sun, Yifei, Lv, Nana, Wang, Beibei, Ruan, Yunze, Xiong, Wu, Li, Rong, Shen, Qirong

Journal:

Frontiers in Microbiology

Year:

2019

File:

PDF, 8.87 MB

2019

32

Soil quality shapes the composition of microbial community stress response and core cell metabolism functional genes

Finn, Damien, Yu, Julian, Penton, C. Ryan

Journal:

Applied Soil Ecology

Year:

2020

File:

PDF, 1.16 MB

2020

33

Patterns of fungal community succession triggered by C/N ratios during composting

Qiao, Cece, Ryan Penton, C., Liu, Chao, Tao, Chengyuan, Deng, Xuhui, Ou, Yannan, Liu, Hongjun, Li, Rong

Journal:

Journal of Hazardous Materials

Year:

2020

File:

PDF, 2.09 MB

2020

34

Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt

Yuan, Jun, Wen, Tao, Zhang, He, Zhao, Mengli, Penton, C. Ryan, Thomashow, Linda S., Shen, Qirong

Journal:

The ISME Journal

Year:

2020

File:

PDF, 4.44 MB

2020