Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere

AbstractThe plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere are different from the outer soil region (bulk soil). They establish characteristic conditions including microbiota, metabolites, and minerals, and they can directly affect plant growth and development. However, comprehensive insights into those characteristic environments, especially the rhizosphere, and molecular mechanisms of their formation are not well understood. In the present study, we investigated the spatiotemporal dynamics of the root-associated environment in actual field conditions by multi-omics analyses (mineral, microbiome, and transcriptome) of soybean plants. Mineral and microbiome analyses demonstrated a characteristic rhizosphere environment in which most of the minerals were highly accumulated and bacterial communities were distinct from those in the bulk soil. Mantel’s test and co-abundance network analysis revealed that characteristic community structures and dominant bacterial taxa in the rhizosphere significantly interact with mineral contents in the rhizosphere, but not in the bulk soil. Our field multi-omics analysis suggests a rhizosphere-specific close association between the microbiota and mineral environment.

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Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab017 ◽

2021 ◽

Vol 97 (3) ◽

Author(s):

Constantinos Xenophontos ◽

Martin Taubert ◽

W Stanley Harpole ◽

Kirsten Küsel

Keyword(s):

Bacterial Communities ◽

Species Interactions ◽

Phylogenetic Diversity ◽

Molecular Mechanisms ◽

Linear Models ◽

Theory Development ◽

Metabolic Diversity ◽

Community Functioning ◽

Metabolic Functions ◽

Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

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Quantitative Proteomics Reveals that GmENO2 Proteins Are Involved in Response to Phosphate Starvation in the Leaves of Glycine max L.

International Journal of Molecular Sciences ◽

10.3390/ijms22020920 ◽

2021 ◽

Vol 22 (2) ◽

pp. 920

Author(s):

Ling Cheng ◽

Wanling Min ◽

Man Li ◽

Lili Zhou ◽

Chuan-Chih Hsu ◽

...

Keyword(s):

Glycine Max ◽

Molecular Mechanisms ◽

Human Life ◽

Phosphate Starvation ◽

Limiting Factor ◽

Transcriptional Level ◽

Label Free ◽

Promoter Regions ◽

Glycine Max L ◽

Soybean Plants

Soybean (Glycine max L.) is a major crop providing important source for protein and oil for human life. Low phosphate (LP) availability is a critical limiting factor affecting soybean production. Soybean plants develop a series of strategies to adapt to phosphate (Pi) limitation condition. However, the underlying molecular mechanisms responsible for LP stress response remain largely unknown. Here, we performed a label-free quantification (LFQ) analysis of soybean leaves grown under low and high phosphate conditions. We identified 267 induced and 440 reduced differential proteins from phosphate-starved leaves. Almost a quarter of the LP decreased proteins are involved in translation processes, while the LP increased proteins are accumulated in chlorophyll biosynthetic and carbon metabolic processes. Among these induced proteins, an enolase protein, GmENO2a was found to be mostly induced protein. On the transcriptional level, GmENO2a and GmENO2b, but not GmENO2c or GmENO2d, were dramatically induced by phosphate starvation. Among 14 enolase genes, only GmENO2a and GmENO2b genes contain the P1BS motif in their promoter regions. Furthermore, GmENO2b was specifically induced in the GmPHR31 overexpressing soybean plants. Our findings provide molecular insights into how soybean plants tune basic carbon metabolic pathway to adapt to Pi deprivation through the ENO2 enzymes.

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Predominance of soil vs root effect in rhizosphere microbiota reassembly

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz139 ◽

2019 ◽

Vol 95 (10) ◽

Cited By ~ 3

Author(s):

Mengli Zhao ◽

Jun Yuan ◽

Zongzhuan Shen ◽

Menghui Dong ◽

Hongjun Liu ◽

...

Keyword(s):

Bacterial Communities ◽

Disease Incidence ◽

Bulk Soil ◽

Pathogen Population ◽

Root Effect ◽

Rhizosphere Microbiome ◽

Distinct Disease ◽

Pathogenic Microbes ◽

Disease Suppressive Soil ◽

Rhizosphere Community

ABSTRACT Rhizosphere community assembly is simultaneously affected by both plants and bulk soils and is vital for plant health. However, it is still unclear how and to what extent disease-suppressive rhizosphere microbiota can be constructed from bulk soil, and the underlying agents involved in the process that render the rhizosphere suppressive against pathogenic microbes remain elusive. In this study, the evolutionary processes of the rhizosphere microbiome were explored based on transplanting plants previously growing in distinct disease-incidence soils to one disease-suppressive soil. Our results showed that distinct rhizoplane bacterial communities were assembled on account of the original bulk soil communities with different disease incidences. Furthermore, the bacterial communities in the transplanted rhizosphere were noticeably influenced by the second disease-suppressive microbial pool, rather than that of original formed rhizoplane microbiota and homogenous nontransplanted rhizosphere microbiome, contributing to a significant decrease in the pathogen population. In addition, Spearman's correlations between relative abundances of bacterial taxa and the abundance of Ralstonia solanacearum indicated Anoxybacillus, Flavobacterium, Permianibacter and Pseudomonas were predicted to be associated with disease-suppressive function formation. Altogether, our results showed that bulk soil played an important role in the process of assembling and reassembling the rhizosphere microbiome of plants.

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Effect of Two Different Sugarcane Cultivars on Rhizosphere Bacterial Communities of Sugarcane and Soybean Upon Intercropping

Frontiers in Microbiology ◽

10.3389/fmicb.2020.596472 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yue Liu ◽

Huichun Yang ◽

Qi Liu ◽

Xiaowen Zhao ◽

Sasa Xie ◽

...

Keyword(s):

Bacterial Communities ◽

P Uptake ◽

Organic P ◽

Inorganic P ◽

Sugarcane Varieties ◽

P Mineralization ◽

Rhizosphere Environment ◽

Uptake And Transport ◽

Rhizosphere Bacterial Communities ◽

Sugarcane Industry

Intercropping of soybean and sugarcane is an important strategy to promote sustainable development of the sugarcane industry. In fact, our understanding of the interaction between the rhizosphere and bacterial communities in the intercropping system is still evolving; particularly, the influence of different sugarcane varieties on rhizosphere bacterial communities in the intercropping process with soybean, still needs further research. Here, we evaluated the response of sugarcane varieties ZZ1 and ZZ9 to the root bacterial community during intercropping with soybean. We found that when ZZ9 was intercropped with soybean, the bacterial diversity increased significantly as compared to that when ZZ1 was used. ZZ9 played a major role in changing the bacterial environment of the root system by affecting the diversity of rhizosphere bacteria, forming a rhizosphere environment more conducive to the growth of sugarcane. In addition, our study found that ZZ1 and ZZ9 had differed significantly in their utilization of nutrients. For example, nutrients were affected by different functional genes in processes such as denitrification, P-uptake and transport, inorganic P-solubilization, and organic P-mineralization. These results are significant in terms of providing guidance to the sugarcane industry, particularly for the intercropping of sugarcane and soybean in Guangxi, China.

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Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.738129 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jun Zhang ◽

Pengcheng Xing ◽

Mengyu Niu ◽

Gehong Wei ◽

Peng Shi

Keyword(s):

High Throughput Sequencing ◽

Niche Overlap ◽

Spatial Location ◽

Bulk Soil ◽

Community Structures ◽

Potential Predator ◽

Predator Prey ◽

Soybean Plants ◽

Bacteria And Fungi ◽

Potential Interactions

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R2 = 0.37–0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R2 = 0.08–0.09) or cultivar type (R2 = 0.02–0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

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Phospholipid Fatty Acid (PLFA) Analysis of Rhizosphere Bacterial Communities in a Peat Soil

Agrokémia és Talajtan ◽

10.1556/agrokem.51.2002.1-2.15 ◽

2002 ◽

Vol 51 (1-2) ◽

pp. 123-128 ◽

Cited By ~ 5

Author(s):

András Halbritter ◽

T. Mogyoróssy

Keyword(s):

Fatty Acid ◽

Bacterial Communities ◽

Phospholipid Fatty Acid ◽

Plant Root ◽

Peat Soil ◽

Total Lipid Content ◽

Gas Chromatography Mass Spectrometry ◽

Root Cells ◽

Plfa Analysis ◽

Rhizosphere Bacterial Communities

To analyze the rhizosphere bacterial communities in wetlands, the total lipid content was extracted from a peat soil and 4 abundant wetland plant roots ( Typha angustifolia L., Salix cinerea L., Carex pseudocyperus L., Thelypteris palustris Salisb.). The separated phospholipid fraction was further fractionated and derivatized prior to gas chromatography-mass spectrometry (GC-MS) measurement. In the evaluation only the bacteria-specific fatty acids were used in order to neglect fatty acid information derived from plant root cells. Based on these analyses, a high level bacterial concentration was demonstrated in the rhizosphere, and the relative occurrence of aerobe and anaerobe, Gram positive and negative bacteria, methanotrophs, sulphate reducers and Actinobacteria was determined. Through the PLFA analysis the study of bacteria regardless of culturability was possible.

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The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

FEMS Microbiology Letters ◽

10.1093/femsle/fnaa117 ◽

2020 ◽

Vol 367 (15) ◽

Author(s):

Yang Li ◽

Liang Yuan ◽

Sheng Xue ◽

Bingjun Liu ◽

Gang Jin

Keyword(s):

Acid Mine Drainage ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mine Drainage ◽

Plant Root ◽

Bacterial Community Composition ◽

Cellular Processes ◽

Acid Mine ◽

Functional Bacteria ◽

Plant Root System

ABSTRACT This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

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ESCRT-dependent targeting of plasma membrane localized KCa3.1 to the lysosomes

AJP Cell Physiology ◽

10.1152/ajpcell.00120.2010 ◽

2010 ◽

Vol 299 (5) ◽

pp. C1015-C1027 ◽

Cited By ~ 19

Author(s):

Corina M. Balut ◽

Yajuan Gao ◽

Sandra A. Murray ◽

Patrick H. Thibodeau ◽

Daniel C. Devor

Keyword(s):

Plasma Membrane ◽

Molecular Mechanisms ◽

Close Association ◽

Significant Inhibition ◽

Dominant Negative ◽

Human Embryonic Kidney Cells ◽

Endosomal Sorting ◽

Escrt Machinery ◽

Interfering Rna

The number of intermediate-conductance, Ca2+-activated K+ channels (KCa3.1) present at the plasma membrane is deterministic in any physiological response. However, the mechanisms by which KCa3.1 channels are removed from the plasma membrane and targeted for degradation are poorly understood. Recently, we demonstrated that KCa3.1 is rapidly internalized from the plasma membrane, having a short half-life in both human embryonic kidney cells (HEK293) and human microvascular endothelial cells (HMEC-1). In this study, we investigate the molecular mechanisms controlling the degradation of KCa3.1 heterologously expressed in HEK and HMEC-1 cells. Using immunofluorescence and electron microscopy, as well as quantitative biochemical analysis, we demonstrate that membrane KCa3.1 is targeted to the lysosomes for degradation. Furthermore, we demonstrate that either overexpressing a dominant negative Rab7 or short interfering RNA-mediated knockdown of Rab7 results in a significant inhibition of channel degradation rate. Coimmunoprecipitation confirmed a close association between Rab7 and KCa3.1. On the basis of these findings, we assessed the role of the ESCRT machinery in the degradation of heterologously expressed KCa3.1, including TSG101 [endosomal sorting complex required for transport (ESCRT)-I] and CHMP4 (ESCRT-III) as well as VPS4, a protein involved in the disassembly of the ESCRT machinery. We demonstrate that TSG101 is closely associated with KCa3.1 via coimmunoprecipitation and that a dominant negative TSG101 inhibits KCa3.1 degradation. In addition, both dominant negative CHMP4 and VPS4 significantly decrease the rate of membrane KCa3.1 degradation, compared with wild-type controls. These results are the first to demonstrate that plasma membrane-associated KCa3.1 is targeted for lysosomal degradation via a Rab7 and ESCRT-dependent pathway.

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CLE-CLAVATA1 Signaling Pathway Modulates Lateral Root Development under Sulfur Deficiency

Plants ◽

10.3390/plants8040103 ◽

2019 ◽

Vol 8 (4) ◽

pp. 103 ◽

Cited By ~ 8

Author(s):

Wei Dong ◽

Yinghua Wang ◽

Hideki Takahashi

Keyword(s):

Root Development ◽

Lateral Root ◽

Molecular Mechanisms ◽

Plant Root ◽

Root System Architecture ◽

Wild Type ◽

Lateral Root Development ◽

S Deficiency ◽

Cle Peptide ◽

Plant Root System

Plant root system architecture changes drastically in response to availability of macronutrients in the soil environment. Despite the importance of root sulfur (S) uptake in plant growth and reproduction, molecular mechanisms underlying root development in response to S availability have not been fully characterized. We report here on the signaling module composed of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) peptide and CLAVATA1 (CLV1) leucine-rich repeat receptor kinase, which regulate lateral root (LR) development in Arabidopsis thaliana upon changes in S availability. The wild-type seedlings exposed to prolonged S deficiency showed a phenotype with low LR density, which was restored upon sulfate supply. In contrast, the clv1 mutant showed a higher daily increase rate of LR density relative to the wild-type under prolonged S deficiency, which was diminished to the wild-type level upon sulfate supply, suggesting that CLV1 directs a signal to inhibit LR development under S-deficient conditions. CLE2 and CLE3 transcript levels decreased under S deficiency and through CLV1-mediated feedback regulations, suggesting the levels of CLE peptide signals are adjusted during the course of LR development. This study demonstrates a fine-tuned mechanism for LR development coordinately regulated by CLE-CLV1 signaling and in response to changes in S availability.

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