- Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale
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Sarbjeet Niraula , Meaghan Rose , Woo-Suk Chang
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J. Microbiol. 2022;60(10):986-997. Published online September 27, 2022
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DOI: https://doi.org/10.1007/s12275-022-2363-x
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Microbial communities in the rhizosphere play a crucial role
in determining plant growth and crop yield. A few studies
have been performed to evaluate the diversity and co-occurrence
patterns of rhizosphere microbiomes in soybean (Glycine
max) at a regional scale. Here, we used a culture-independent
method
to compare the bacterial communities of the
soybean rhizosphere between Nebraska (NE), a high-yield
state, and Oklahoma (OK), a low-yield state. It is well known
that the rhizosphere microbiome is a subset of microbes that
ultimately get colonized by microbial communities from the
surrounding bulk soil. Therefore, we hypothesized that differences
in the soybean yield are attributed to the variations in
the rhizosphere microbes at taxonomic, functional, and community
levels. In addition, soil physicochemical properties
were also evaluated from each sampling site for comparative
study. Our result showed that distinct clusters were formed
between NE and OK in terms of their soil physicochemical
property. Among 3 primary nutrients (i.e., nitrogen, phosphorus,
and potassium), potassium is more positively correlated
with the high-yield state NE samples. We also attempted
to identify keystone communities that significantly affected the
soybean yield using co-occurrence network patterns. Network
analysis revealed that communities formed distinct clusters
in which members of modules having significantly positive
correlations with the soybean yield were more abundant in
NE than OK. In addition, we identified the most influential
bacteria for the soybean yield in the identified modules. For
instance, included are class Anaerolineae, family Micromonosporaceae,
genus Plantomyces, and genus Nitrospira in the
most complex module (ME9) and genus Rhizobium in ME23.
This research would help to further identify a way to increase
soybean yield in low-yield states in the U.S. as well as worldwide
by reconstructing the microbial communities in the
rhizosphere.
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Citations
Citations to this article as recorded by  - Interaction of soil microbial communities with soil nutrients, enzymes activity, and allelopathic compounds in flue-cured tobacco continuous monocropping field
Yihong Pan, Tiyuan Xia, Qiulian Peng, Kun Huang, Lijuan Zhou, Guohuan Xiong
Physiological and Molecular Plant Pathology.2026; 141: 103032. CrossRef - Research Progress on Rhizosphere Microbiota for Controlling Soil-Borne Diseases: Mechanisms, Applications, and Challenges
Yong Liu, Xiaofang Sun, Jia Lai, Shugu Wei, Yuzhen Sheng, Yinchao Zhang, Qianfang Zhang, Pengsheng Ye, Ling Huang, Hualan Zeng
Microorganisms.2026; 14(4): 900. CrossRef - Gradient Potassium Application Differentially Regulates Rhizosphere Bacterial and Fungal Communities in Cherry Tomato (Solanum lycopersicum var. cerasiforme)
Chenpeng Gao, Guigui Wan, Ruifeng Cheng, Quansheng Li, Qinglu Fan, Jinxia Cui, Linnan Wu
Plants.2026; 15(10): 1545. CrossRef - Role of rhizosphere specific microbiome in enhancing soybean productivity across contrasting soil and crop management systems
Prem Ranjan, Diptimayhee Das, Vindhya Bundela, Aketi Ramesh, Rakesh Kumar Verma, Raghavendra Nargund, Urmila Manandhar, Rhae Drijber, Rakesh K. Upadhyay, Mahaveer Prasad Sharma
Frontiers in Plant Science.2026;[Epub] CrossRef - Paddy soils with contrasting rice yields harbor distinct microbial networks and candidate key microbes
Do-Hyun Kim, Sang Yoon Kim, Yeomyeong Lee, Sohee Yoon, Hyerin An, Yu-Na Jeon, Jaekyeong Song, Sujin Kim, Jung Seon Kim, Gyeongjun Cho
Applied Soil Ecology.2026; 225: 107166. CrossRef - Cover crops legacy modulates soybean rhizosphere microbiome across phenological stages
Caio César Gomes Freitas, Carolinne Rosa de Carvalho, Rafael Lima Oliveira, Nariane de Andrade, Danilo Ferreira da Silva, Mísia Souza Vieira, Victor Lucas Vieira Prudêncio Araújo, João Henrique dos Santos Ferreira, José Roberto Portugal, Carlos Alexandre
Applied Soil Ecology.2026; 225: 107220. CrossRef - Plant–Microbiome Interactions for Rhizosphere Health: A Three‐Step Framework for Crop Resilience
Wei Qiu, Xiufeng Tang, Qirong Shen, Jun Yuan
Plant, Cell & Environment.2026;[Epub] CrossRef - Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems
Honglei Ren, Huilong Hong, Bire Zha, Sobhi F. Lamlom, Hongmei Qiu, Yongqiang Cao, Rujian Sun, Haorang Wang, Junkui Ma, Hengbin Zhang, Liping Sun, Qing Yang, Changjun Zhou, Xiulin Liu, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Kezhen Zhao, Rongqiang Yuan,
Microbiome.2025;[Epub] CrossRef - Impact of Bacterial Pustule Disease Occurrence on Bacterial and Fungal Communities Within Vegetable Soybean Plants
Choosak Khaengraeng, Wuttichai Mhuantong, Usawadee Chaiprom, Sawita Suwannarat, Nattakorn Kuncharoen, Nutjarin Haewou, Warapon Bunkoed, Tiyakhon Chatnaparat
Plant Pathology.2025; 74(5): 1228. CrossRef - A molecular conveyor belt-associated protein controls the rotational direction of the bacterial type 9 secretion system
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Environmental Research.2025; 286: 122785. CrossRef - Rice-microbiome-metabolite crosstalk: Deciphering the defence signatures of traditional rice landraces against blast (Magnaporthe oryzae)
R. Karan, M.K. Prasannakumar, N. Vamsidharreddy, J. Harish, H.B. Mahesh, C. Manjunatha, K.N. Pallavi, Pramesh Devanna, Selva babu Selvamani, Aditya Narayan Sarangi
Plant Stress.2025; 18: 101084. CrossRef - The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics
Benoit Renaud Martins, Viviane Radl, Krzysztof Treder, Dorota Michałowska, Karin Pritsch, Michael Schloter
FEMS Microbiology Ecology.2024;[Epub] CrossRef - Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Yingying Liu, Dan Wu, Yongjun Kan, Li Zhao, Chang Jiang, Wensheng Pang, Juan Hu, Meilan Zhou
Eurasian Soil Science.2024; 57(3): 446. CrossRef - Analysis of the rhizosphere bacterial diversity of Angelica dahurica var. formosana from different experimental sites and varieties (strains)
Meiyan Jiang, Fei Yao, Yunshu Yang, Yang Zhou, Kai Hou, Yinyin Chen, Dongju Feng, Wei Wu
PeerJ.2023; 11: e15997. CrossRef - Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition
Wanling Wei, Dawei Guan, Mingchao Ma, Xin Jiang, Fenliang Fan, Fangang Meng, Li Li, Baisuo Zhao, Yubin Zhao, Fengming Cao, Huijun Chen, Jun Li
Frontiers in Microbiology.2023;[Epub] CrossRef
- Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum
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Anchana Thaweethawakorn , Dylan Parks , Jae-Seong So , Woo-Suk Chang
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J. Microbiol. 2015;53(8):526-534. Published online July 31, 2015
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DOI: https://doi.org/10.1007/s12275-015-5308-9
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As a nitrogen-fixing bacterium, Bradyrhizobium japonicum
can establish a symbiotic relationship with the soybean plant
(Glycine max). To be a successful symbiont, B. japonicum
must deal with plant defense responses, such as an oxidative
burst. Our previous functional genomics study showed that
carQ (bll1028) encoding extracytoplasmic function (ECF)
sigma factor was highly expressed (107.8-fold induction)
under oxidative stress. Little is known about the underlying
mechanisms of how CarQ responds to oxidative stress. In
this study, a carQ knock-out mutant was constructed using
site-specific mutagenesis to identify the role of carQ in the
oxidative response of B. japonicum. The carQ mutant showed
a longer generation time than the wild type and exhibited
significantly decreased survival at 10 mM H2O2 for 10 min
of exposure. Surprisingly, there was no significant difference
in expression of oxidative stress-responsive genes such as
katG and sod between the wild type and carQ mutant. The
mutant also showed a significant increase in susceptibility to
H2O2 compared to the wild type in the zone inhibition assay.
Nodulation phenotypes of the carQ mutant were distinguishable
compared to those of the wild type, including lower
numbers of nodules, decreased nodule dry weight, decreased
plant dry weight, and a lower nitrogen fixation capability.
Moreover, desiccation of mutant cells also resulted in significantly
lower percent of survival in both early (after 4 h) and
late (after 24 h) desiccation periods. Taken together, this
information will provide an insight into the role of the ECF
sigma factor in B. japonicum to deal with a plant-derived
oxidative burst.
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Citations
Citations to this article as recorded by -
Implication of the σ
E
Regulon Members OmpO and σ
N
in the Δ
ompA
299–356
-Mediated Decrease of Oxidative Stress Tolerance in St
Ren-Hsuan Ku, Li-Hua Li, Yi-Fu Liu, En-Wei Hu, Yi-Tsung Lin, Hsu-Feng Lu, Tsuey-Ching Yang, Silvia T. Cardona
Microbiology Spectrum.2023;[Epub] CrossRef - Identification and Validation of Reference Genes for Expression Analysis in Nitrogen-Fixing Bacteria under Environmental Stress
Dylan Parks, Christian Peterson, Woo-Suk Chang
Life.2022; 12(9): 1379. CrossRef - MostSinorhizobium melilotiExtracytoplasmic Function Sigma Factors Control Accessory Functions
Claus Lang, Melanie J. Barnett, Robert F. Fisher, Lucinda S. Smith, Michelle E. Diodati, Sharon R. Long, Craig D. Ellermeier, Claude Bruand, Sarah Ades, Hans-Martin Fischer
mSphere.2018;[Epub] CrossRef
- Characterization of MocR, a GntR-like transcriptional regulator, in Bradyrhizobium japonicum: its impact on motility, biofilm formation, and soybean nodulation
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May Nyan Taw , Hae-In Lee , Sang-Ho Lee , Woo-Suk Chang
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J. Microbiol. 2015;53(8):518-525. Published online July 31, 2015
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DOI: https://doi.org/10.1007/s12275-015-5313-z
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954
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0
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10
Crossref
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Abstract
PDF
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Bradyrhizobium japonicum is a Gram-negative soil bacterium
that can fix nitrogen into ammonia by developing a
symbiotic relationship with the soybean plant. MocR proteins
make up a subfamily of GntR superfamily, one of the most
widely distributed and prolific groups of the helix-turn-helix
transcription factors. In this study, we constructed a mutant
strain for mocR (blr6977) to investigate its role in cellular
processes and symbiosis in B. japonicum. Although growth
rate and morphology of the mutant were indistinguishable
from those of the wild type, the mutant showed significant
differences in motility and attachment (i.e., biofilm formation)
from the wild type. The mutant displayed a decrease in biofilm
formation, but was more motile than the wild type. The
inactivation of mocR did not affect the number of nodules
on soybean roots, but caused delayed nodulation. Delayed
nodulation intrigued us to study competitiveness of the mutant
infecting soybeans. The mutant was less competitive
than the wild type, indicating that delayed nodulation might
be due to competitiveness. Gene expressions of other MocR
subfamily members were also compared between the wild
type and mutant strains. None of the mocR-like genes examined
in this study were differentially expressed between
both strains.
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Citations
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Peng Zhang, Xiaofang Wu, Lei Ji, Wei Yan, Liping Chen, Zhonghao Lu, Deshun Xu, Yunfeng Zha, Dafang Xu, Fenfen Dong
BMC Genomics.2024;[Epub] CrossRef - The MocR family transcriptional regulator DnfR has multiple binding sites and regulates Dirammox gene transcription in Alcaligenes faecalis JQ135
Si‐Qiong Xu, Xiao Wang, Lu Xu, Ke‐Xin Wang, Yin‐Hu Jiang, Fu‐Yin Zhang, Qing Hong, Jian He, Shuang‐Jiang Liu, Ji‐Guo Qiu
Environmental Microbiology.2023; 25(3): 675. CrossRef - The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus
Yangyang Li, Weidong Sun, Quan Wang, Ying Yu, Ying Wan, Kai Zhou, Rong Guo, Xiangan Han, Zhaoguo Chen, Weihuan Fang, Wei Jiang
Microbial Pathogenesis.2022; 167: 105546. CrossRef - Biological and transcriptional studies reveal VmeL is involved in motility, biofilm formation and virulence in Vibrio parahaemolyticus
Peng-xuan Liu, Xiao-yun Zhang, Quan Wang, Yang-yang Li, Wei-dong Sun, Yu Qi, Kai Zhou, Xian-gan Han, Zhao-guo Chen, Wei-huan Fang, Wei Jiang
Frontiers in Microbiology.2022;[Epub] CrossRef - PrbP modulates biofilm formation in Liberibacter crescens
Lei Pan, Christopher L. Gardner, Reagan Beliakoff, Danilo da Silva, Ran Zuo, Fernando A. Pagliai, Kaylie A. Padgett‐Pagliai, Marcelo L. Merli, Erol Bahadiroglu, Claudio F. Gonzalez, Graciela L. Lorca
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Haozhe Ruan, Haibo Yu, Jianzhong Xu
World Journal of Microbiology and Biotechnology.2020;[Epub] CrossRef - Comparative Genomics of Pseudomonas sp. Strain SI-3 Associated With Macroalga Ulva prolifera, the Causative Species for Green Tide in the Yellow Sea
Huihui Fu, Peng Jiang, Jin Zhao, Chunhui Wu
Frontiers in Microbiology.2018;[Epub] CrossRef - The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism
Angela Tramonti, Caterina Nardella, Martino L. di Salvo, Stefano Pascarella, Roberto Contestabile
The FEBS Journal.2018; 285(21): 3925. CrossRef - Negative Regulation of Ectoine Uptake and Catabolism in Sinorhizobium meliloti: Characterization of the EhuR Gene
Qinli Yu, Hanlin Cai, Yanfeng Zhang, Yongzhi He, Lincai Chen, Justin Merritt, Shan Zhang, Zhiyang Dong, Anke Becker
Journal of Bacteriology.2017;[Epub] CrossRef
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