Plant beneficial rhizobacteria community structure changes through developmental stages of peanut and maize

doi:10.1016/j.rhisph.2021.100407

Rhizosphere

Volume 19, September 2021, 100407

https://doi.org/10.1016/j.rhisph.2021.100407 Get rights and content

Highlights

•
Abundance of diazotrophic and phosphate solubilizing bacteria increases during plant development.
•
The growth stage of peanut and maize change rhizobacterial community structure.
•
Bacterial genera associated to beneficial mechanisms of plant growth promotion increases in late plant stages.

Abstract

Our objective in this study was to analyze the structure of the rhizobacterial community during different growth stages of peanut and maize plants. Microcosm assays were performed using pots containing unsterile soil from the peanut growing area of Argentina in which peanut and maize plants were grown during 120 and 100 days, respectively. Four to five samples of rhizospheric soil were obtained at the beginning of the assay, at an early growth stage of each plant and at the end of the assay. Two replicate DNA extractions from rhizospheric soil samples were realized per treatment on both microcosm assays to analyze rhizobacterial community structure by high-throughput sequencing of 16S rRNA gene.

We observed changes in rhizobacteria community structure with crop developmental stages. Community structure changes occurred at several bacteria taxonomic levels, and major changes were observed in later stages. In particular, plant growth promoting bacteria genera were promoted in later stages. Our results indicate plant rhizospheric selection for growth enhancing rhizobacteria during stages of high nutrient demand. In conclusion, the structure of the rhizobacterial communities of peanut and maize are influenced by plant phenological stages, and beneficial bacteria are favoured in late phenological stages.

Introduction

Peanut (Arachis hypogaea L.) is a crop of great economic significance Worldwide reaching its production more than 50M tons in 2018 (Food and Agriculture Organization of the United Nations, 2021). Argentina is one the major producers of this leguminous in the world (Peanut Argentina Chamber, 2018) and approximately 90% of its production is concentrated in the province of Córdoba (Cordoba Cereal Stock-MarketBag Institute, 2018). In addition, peanut crop is usually rotated with maize (Zea mays L.). Argentina is among the main producers and exporters of this crop in the world (Food and Agriculture Organization of the United Nations, 2018) and in the province of Córdoba about 30% of national production of this crop is produced (Argentinian Agroindustry Secretary, 2019).

Soil microbes play key roles in regulating soil fertility, plant health, the cycling of nutrients and the degrading of organic material among others (King, 2014). Within this environment, the rhizosphere is a versatile and dynamic ecological environment of microbe-plant interactions. Effect of root exudates on rhizobacteria are diverse and can be associated with the plant type and development and root branching (Pervaiz et al., 2020; Xu et al., 2021). The root exudates include sugars, amino acids, organic acids, fatty acids, sterols, vitamins, enzymes, flavonones and nucleotides which create a unique environment in the rhizosphere (Badri et al., 2009). Also, the composition of root exudates depends on plant species, phenological plant stage and environmental factors among others (Sessitsch et al., 2012). The quantity and quality of root exudates selectively influence on rhizosphere microbial communities (Dennis et al., 2010).

Many of the bacteria that are found around plant roots have the ability to facilitate plant growth and consequently are called plant growth-promoting bacteria (PGPB). Within PGPB several strains have been used as biofertilizers (Olanrewaju et al., 2017). In peanut and maize producing area of Cordoba, low values of N and P available contents has been reported (9–14 and 5–15 mg kg⁻¹ soil, respectively) (Sainz Rosas et al., 2012; Anzuay et al., 2015). Previous studies indicated that theses soils harbor a heterogenous phosphate solubilizing and nitrogen fixing population (Anzuay et al., 2013, Anzuay et al., 2015).

Since maize and peanut are important crops, representing a cereal and a legume, it would be important to understand the rhizobacterial community structure associated to these plants and their potential change during different plant growth stages. In particular, interest was focused on plant growth promoting bacteria. This study constitutes a descriptive analysis of the rhizobacterial communities that inhabit the agricultural soil of Córdoba. In this sense, the hypothesis of this study was that plant phenological growth stage determines the abundance and diversity of the plant beneficial rhizobacterial community associated to peanut and maize. Thus, the objectives of this study were to analyze in different plant growth stages (1) the abundance of diazotrophic bacteria (DB) and phosphate solubilizing bacteria (PSB) and (2) the rhizobacterial community structure associated with peanut and maize plants.

Section snippets

Microcosm assay

The plant grow support selected for the microcosm assay was soil from the peanut cultivation area of Córdoba: organic matter: 1.92% (Walkley-Black method), pH:7.3 (Potenciometry1:2.5), N: 12.9 μg g⁻¹(phenolsulfonic acid) and P: 13.6 μgg⁻¹ (Bray and Kurtz I method). Approximately 7 kg of unsterilized soil was transferred to superficially disinfected plastic pots (35 cm-diameter, 40 cm height). Disinfected seeds of peanut (cv. granoleico) and maize (NK 910 TD Max hybrid, Syngenta) according to

Dynamics of culturable rhizobacteria associated to peanut and maize in different plants growth stages

Results obtained indicated that the number of the three bacterial populations analyzed varied during plant growth and those changes depended on plant species (Fig. 1). In general, the abundance of CHB and DB was similar in the communities of peanut and maize plants and higher than the number of PSB. For this last population, the count was greater in peanut rhizosphere than in maize rhizosphere (Fig. 1). An increase in the abundance of DB and PSB was observed earlier in both rhizospheres during

Abundance of culturable diazotrophic and phosphate solubilizing bacteria increase during peanut and maize development

As expected, the number of CHB detected in both peanut and maize rhizosphere was higher than the other two bacterial populations analyzed, following in decreasing order DB and PSB. The earlier increase in the number of DB and PSB with respect to CHB observed in both rhizosphere during plant growth suggests that these beneficial bacteria should be attracted by compounds in the plant vegetative stage. It has been reported that root exudates of the plants influence the abundance and composition of

Conclusions

In this study, the most structural changes of the rhizobacterial communities were on the late plant growth stage in which genera related to plant growth promoting bacteria were increased in their relative abundance in the communities of both plants. This increase could be related to the high demands of macronutrients that plants need in the late plant growth stage. The rhizobacterial communities are selected by the plant through the differential root exudate's composition during its different

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

Declaration of Funding statement: This research was supported by Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Secretaría de Ciencia y Técnica de la Universidad Nacional de Río Cuarto (SECYT-UNRC), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT). N.P. is fellowships from CONICET, F.D.M. is professor of UNRC and M.S.A., L.M.L, J.G.A. and T.T. are members of research career of CONICET, Argentina.

This work used computational resources from the

References (64)

D.V. Badri et al.
Rhizosphere chemical dialogues: plant–microbe interactions
Curr. Opin. Biotechnol.
(2009)
J. Cheng et al.
Soil nitrogen leaching decreases as biogas slurry DOC/N ratio increases
Appl. Soil Ecol.
(2017)
Z. Lin et al.
The impact of the soil microbial community and enzyme activity of two earth worm species during the bioremediation of pentachlorophenol-contaminated soils
J. Hazard Mater.
(2016)
E. Pérez et al.
Isolation and characterization of mineral phosphate-solubilizing bacteria naturally colonizing a limonitic crust in the southeastern Venezuelan region
Soil Biol. Biochem.
(2007)
Z.H. Pervaiz et al.
Root microbiome changes with root branching order and root chemistry in peach rhizosphere soil
Rhizosphere
(2020)
J.P. Verma et al.
Evaluation of plant growth promoting activities of microbial strains and their effect on growth and yield of chickpea (Cicer arietinum L.) in India
Soil Biol. Biochem.
(2014)
W. Xu et al.
Peanut (Arachis hypogaea L.) pod and rhizosphere harbored different bacterial communities
Rhizosphere
(2021)
S. Andrews
FastQC: A Quality Control Tool for High Throughput Sequence Data
(2010)
M.S. Anzuay et al.
Genetic diversity of phosphate-solubilizing peanut (Arachis hypogaea L.) associated bacteria and mechanisms involved in this ability
Symbiosis
(2013)
M.S. Anzuay et al.
Beneficial effects of native phosphate solubilizing bacteria on peanut (Arachis hypogaea L.) growth and phosphorus acquisition
Symbiosis
(2015)

M.G. Balzarini et al.

Manual Bashan del Usuario

(2008)

N.A. Bokulich et al.

Quality filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nat. Methods

(2013)

A.M. Bolger et al.

Trimmomatic: a flexible trimmer for Illumina sequence data

Bioinformatics

(2014)

K.J. Boote

Growth stages of peanut (Arachis hypogaea L.)

Peanut Sci.

(1982)

B.J. Campbell

The family Acidobacteriaceae

J.G. Caporaso et al.

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Proc. Natl. Acad. Sci. U.S.A.

(2010)

E.C.P. Catão et al.

Soil Acidobacterial 16S rRNA gene sequences reveal subgroup level differences between savanna-like cerrado and atlantic forest Brazilian biomes

Int. J. Microbiol. ID

(2014)

A. Chao

Non-parametric estimation of the number of classes in a population

Scand. J. Stat.

(1984)

J.M. Chaparro et al.

Rhizosphere microbiome assemblage is affected by plant development

ISME J.

(2014)

M. Chen et al.

Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L.)

PloS One

(2014)

C. Chen et al.

Microbial community composition in a simultaneous nitrification and denitrification bioreactor for domestic wastewater treatment

Earth Environ. Sc.

(2018)

E.J. Chung et al.

Chitinophaga oryziterra esp. nov., isolated from the rhizosphere soil ofrice (Oryza sativaL.)

Int. J. Syst. Evol. Microbiol.

(2012)

M.J. Church

Resource control of bacterial dynamics in the sea

CONACYT

P.G. Dennis et al.

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

FEMS Microbiol. Ecol.

(2010)

J. Döebereiner

Isolation and identification of aerobic nitrogen fixing bacteria from soil and plants

W.L. Du et al.

Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content

Amb. Express

(2016)

B. Fan et al.

Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates

BMC Microbiol.

(2012)

E.L. Figuerola et al.

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale

Environ. Microbiol.

(2015)

Cited by (14)

Root-associated microbiomes are influenced by multiple factors and regulate the growth and quality of Astragalus membranaceus (fisch) Bge. var. mongholicus (Bge.) Hsiao
2022, Rhizosphere
Citation Excerpt :
The above interactions will change with the environment (Edwards et al., 2018). In addition, season is a critical factor for the distribution and dynamic of root-associated microbiomes (Anzuay et al., 2021; Hilton et al., 2018). This study indicated that root-associated microbial communities were differ in June and September.
In this study, the distribution of root-associated microbiomes of Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) was investigated. A. mongholicus has been a generally used perennial herb in China, and it is distributed among five sampling sites in north China. The soil bacterial community composition and diversity of rhizosphere, rhizoplane, endosphere and bulk soil of A. mongholicus in June and September were described by 16S rRNA gene high-throughput sequencing. The results indicated that plant growth variables, root bioactive ingredients and soil properties were different in five sampling sites. The bulk soil bacterial composition of the respective sample was similar, whereas three root-associated microbiomes were different. The bacterial community diversity decreased with the order of bulk soil-rhizosphere-rhizoplane-endosphere, and geographic location (latitude and longitude), climatic factors (mean annual precipitation), soil properties (SOM, AP, TK and AK), and season (summer and autumn) were factors leading to microbiome variation. Likewise, the growth and root bioactive ingredients of A. mongholicus were also comprehensively affected by environmental factors, and were mainly depended on rhizosphere. In brief, this study provided a new theoretical insight into environment–plant–microbiomes interactions in improving the growth and bioactive ingredients of A. mongholicus, which takes on a great significance in the selection of suitable planting sites and management measures of A. mongholicus.
Participation of type VI secretion system in plant colonization of phosphate solubilizing bacteria
2022, Rhizosphere
Citation Excerpt :
Previous studies demonstrated that in this producing area, peanut rhizosphere harbors a high number of enterobacteria belonging to Serratia, Enterobacter, and Pantoea genera with plant growth promoting traits (Taurian et al., 2010; Anzuay et al., 2013). The Enterobacter sp J49 strain is an efficient phosphste solubilizer and a potential P-biofertilizer in microcosmos and field assays (Anzuay et al., 2021; Lucero et al., 2021). Considering that microorganisms possessing a T6SS appear to have a significant competitive advantage within a microbial community (Allsopp et al., 2020) and thus might play an important role in the life style of endophytes, we hypothesized that the T6SS of Enterobacter sp.
In mutualistic endophytic bacteria, the type VI secretion system (T6SS) is related to important functions, such as interbacterial competition, stress response, quorum sensing, biofilm formation, and symbiosis. The presence of T6SS in beneficial endophytic bacterial population associated with different plants suggests that it plays an important role in its interaction with the eucaryotic partner. Within plant promoting bacteria, those with phosphate solubilizing activity constitute a group of great relevance to the rhizosphere as they provide phosphorus to plants. Among them, those with endophytic colonization capacity have survival advantages. The aim of this study was to determine whether the T6SS of a native peanut phosphate solubilizing bacterium is involved in its colonization in this legume. Initially, an in silico analysis looking for genes related to T6SS in the genome of the Enterobacter sp. J49 strain enabled us to identify almost all the tss genes, except for the tssE gene. A T6SS mutant of the Enterobacter sp. J49 strain was obtained by interrupting one of the essential tss genes. Then, the Enterobacter sp. J49-hcp strain was inoculated on peanut plants to analyze its colonization capacity. In addition, properties associated with endophytic colonization were analyzed, such as the formation of biofilms and the production of pectinase and cellulase enzymes. The results obtained indicated a significant decrease in the epiphytic and endophytic colonization of the mutant with respect to the wild strain. It is possible to conclude that T6SS, although not essential, may participate in bacterial colonization, either by accelerating the infection or by promoting other mechanisms involved in it.
Effect of long-term sugar beet cultivation on rhizosphere bacterial diversity, community structure and sugar yield of sugar beet
2022, Rhizosphere
Citation Excerpt :
At present, the sugar beet planting area is about 4 million hectares, and annual global sugar beet production is around 172 million tons, contributing a major part to agricultural production (Dohm et al., 2014; Porcel et al., 2018). Rhizosphere soil microflora is a key component of the soil ecosystem and the driving force of soil nutrient transformation and circulation (Anzuay et al., 2021; Xu et al., 2021). Plant cultivation has a significant impact on the composition of soil bacterial communities in an agroecosystem (Wang et al., 2017).
Long-term sugar beet cultivation in the black soil region of China not only affected sugar beet yield but also influenced rhizosphere soil bacteria. However, the relationship between sugar beet growth and rhizosphere soil bacteria is still indeterminate. Therefore, this study analyzed the sugar beet growth status, rhizosphere soil bacterial diversity, species, and functional composition of long-term cultivation fields (LCF) and initial planting fields (IPF) of sugar beet. The results showed that sugar beet leaf disease in the long-term cultivation fields was significantly aggravated and the sugar beet yield was significantly reduced compared with the initial planting fields. The content of available phosphorus in sugar beet rhizosphere soil and the diversity of the rhizosphere bacterial community were significantly decreased. The Proteobacteria and Actinobacteria were increased, while Acidobacteria were decreased, and the difference in species composition was significant. The abundance of metabolic functions related to nutrient cycling and the abundance of chemoheterotrophy ecological functions was decreased. The bacterial diversity of sugar beet rhizosphere soil was negatively correlated with the leaf disease index and positively correlated with sugar yield. The sugar beet yield was negatively correlated with the abundance of proteobacteria and actinobacteria, while positively correlated with the abundance of acidobacteria, chemoheterotrophy function, and nitrogen fixation function. This study identified the soil reasons for the decline of sugar beet yield in long-term sugar beet cultivation areas and provided a reference basis for improving soil properties and sugar beet productivity.
Metabolic interaction at the level of extracellular amino acids between plant growth-promoting rhizobacteria and plants of alfalfa (Medicago sativa L.)
2022, Rhizosphere
Citation Excerpt :
The production of extracellular effectors is a general strategy for microbial influence on the growth and viability of plants, other microorganisms, and protozoa in these communities. Of particular interest are rhizosphere bacteria that stimulate plant growth (Adeleke et al., 2021; Anzuay et al., 2021). However, the mechanism of the exchange of metabolites between rhizobacteria and plants is not fully understood.
We investigated the relationship between plant growth promoting rhizobacteria (PGPR) and plants at the level of metabolites in the rhizosphere. The study objects were rhizobacteria Bacillus sp. C-21N2 and root exudates of alfalfa (Medicago sativa L.). The strain C-21N2 showed high plant growth promoting (PGP) activity towards alfalfa. During field tests, it was found that the inoculation of seeds with bacteria increases germination by 30%. Moreover, the sowing density increases by 2.1 times and the yield of green mass by 25.2 c/ha compared with control. This study showed that in the rhizhosphere between rhizobacteria and plants there is an active interaction at the level of the exchange of extracellular amino acids. To prove the exchange of extracellular amino acids between PGPR and roots in the rhizosphere, alfalfa roots were immersed in the culture fluid of bacteria. After submerging the roots, of the six amino acids produced by the bacteria, only two remained (asparagine and leucine), the rest were assimilated by the roots. At the same time, three amino acids (valine, alanine and glutamic acid) secreted by the roots of alfalfa were found in the culture liquid of bacteria. That is, the plant roots absorbed the amino acids excreted by the bacteria, and bacteria adsorbed the amino acids excreted by the alfalfa roots. Our findings provide direct experimental evidence that in the rhizosphere between rhizobacteria Bacillus sp. C-21N2 and the alfalfa plants have a metabolic interaction at the level of extracellular amino acids. Also we concluded that the selected strain C-21N2 is a useful bioinoculant, and extracellular amino acids are one of the metabolites that stimulate the growth of alfalfa. The C-21N2 strain should be used in practice in agriculture to increase the productivity of alfalfa.
Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System
2024, International Journal of Molecular Sciences
Biological inoculants and chemical fertilizers application produce differential effects on rhizobacterial community structure associated to peanut (Arachis hypogaea L.) and maize (Zea mays L.) plants
2024, Symbiosis

View all citing articles on Scopus

View full text

Plant beneficial rhizobacteria community structure changes through developmental stages of peanut and maize

Highlights

Abstract

Introduction

Section snippets

Microcosm assay

Dynamics of culturable rhizobacteria associated to peanut and maize in different plants growth stages

Abundance of culturable diazotrophic and phosphate solubilizing bacteria increase during peanut and maize development

Conclusions

Declaration of competing interest

Acknowledgments

Curr. Opin. Biotechnol.

Appl. Soil Ecol.

J. Hazard Mater.

Soil Biol. Biochem.

Rhizosphere

Soil Biol. Biochem.

Rhizosphere

FastQC: A Quality Control Tool for High Throughput Sequence Data

Genetic diversity of phosphate-solubilizing peanut (Arachis hypogaea L.) associated bacteria and mechanisms involved in this ability

Symbiosis

Beneficial effects of native phosphate solubilizing bacteria on peanut (Arachis hypogaea L.) growth and phosphorus acquisition

Symbiosis

Manual Bashan del Usuario

Quality filtering vastly improves diversity estimates from Illumina amplicon sequencing

Nat. Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Bioinformatics

Growth stages of peanut (Arachis hypogaea L.)

Peanut Sci.

The family Acidobacteriaceae

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Proc. Natl. Acad. Sci. U.S.A.

Soil Acidobacterial 16S rRNA gene sequences reveal subgroup level differences between savanna-like cerrado and atlantic forest Brazilian biomes

Int. J. Microbiol. ID

Non-parametric estimation of the number of classes in a population

Scand. J. Stat.

Rhizosphere microbiome assemblage is affected by plant development

ISME J.

Dynamic succession of soil bacterial community during continuous cropping of peanut (Arachis hypogaea L.)

PloS One

Microbial community composition in a simultaneous nitrification and denitrification bioreactor for domestic wastewater treatment

Earth Environ. Sc.

Chitinophaga oryziterra esp. nov., isolated from the rhizosphere soil ofrice (Oryza sativaL.)

Int. J. Syst. Evol. Microbiol.

Resource control of bacterial dynamics in the sea

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

FEMS Microbiol. Ecol.

Isolation and identification of aerobic nitrogen fixing bacteria from soil and plants

Association of running manner with bacterial community dynamics in a partial short-term nitrifying bioreactor for treatment of piggery wastewater with high ammonia content

Amb. Express

Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates

BMC Microbiol.

Crop monoculture rather than agriculture reduces the spatial turnover of soil bacterial communities at a regional scale

Environ. Microbiol.