Biochemical and molecular investigation of non-rhizobial endophytic bacteria as potential biofertilisers

Bakhtiyarifar, Marzieh; Enayatizamir, Naeimeh; Khanlou, Khosro Mehdi

doi:10.1007/s00203-020-02038-z

Cited by 16 publications

(13 citation statements)

References 40 publications

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“…For more than a century, nitrogen-fixing nodules were thought to be uniquely inhabited by rhizobia, and culture-based studies have provided important information about the benefits of rhizobia, including differences in the efficiency of the BNF process among legumes and also between strains of the same host legume, e.g., [ 1 , 2 , 3 , 4 , 5 ]. It was only recently that the first genomic studies reported complex microbial communities inside the nodules [ 25 , 26 , 27 , 28 ], which was confirmed in our study in nodule microbiomes of both soybean and common bean. However, despite evolving as unique ecological niches for nitrogen fixation through the symbiotic relationship between the host legumes and rhizobia, the biological implications of sharing the nodule environment with other bacteria are not well understood yet.…”

Section: Discussionsupporting

confidence: 87%

“…However, despite evolving as unique ecological niches for nitrogen fixation through the symbiotic relationship between the host legumes and rhizobia, the biological implications of sharing the nodule environment with other bacteria are not well understood yet. One hypothesis is that other bacteria living inside the nodules and that probably entered the nodule together with rhizobia are endophytes that can help in plant-growth promotion by other microbial processes, such as the synthesis of phytohormones, antimicrobial molecules, siderophores, mineral solubilization capacity, among others [ 27 , 28 , 29 , 30 ]. As an example of benefit, an interesting study of nodule endophytes performed with Lotus burtii pointed out that in healthy nodules of this legume, Pseudomonas species were the prevalent non-rhizobia, and when used as inoculum infected the plant together with a beneficial Mesorhizobium , but not with an ineffective Rhizobium , benefiting the symbiosis by decreasing the number of ineffective nodules [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

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Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

Bender

Alves²,

Silva³

et al. 2022

IJMS

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Biological nitrogen fixation (BNF) is a key process for the N input in agriculture, with outstanding economic and environmental benefits from the replacement of chemical fertilizers. However, not all symbioses are equally effective in fixing N2, and a major example relies on the high contribution associated with the soybean (Glycine max), contrasting with the low rates reported with the common bean (Phaseolus vulgaris) crop worldwide. Understanding these differences represents a major challenge that can help to design strategies to increase the contribution of BNF, and next-generation sequencing (NGS) analyses of the nodule and root microbiomes may bring new insights to explain differential symbiotic performances. In this study, three treatments evaluated in non-sterile soil conditions were investigated in both legumes: (i) non-inoculated control; (ii) inoculated with host-compatible rhizobia; and (iii) co-inoculated with host-compatible rhizobia and Azospirillum brasilense. In the more efficient and specific symbiosis with soybean, Bradyrhizobium presented a high abundance in nodules, with further increases with inoculation. Contrarily, the abundance of the main Rhizobium symbiont was lower in common bean nodules and did not increase with inoculation, which may explain the often-reported lack of response of this legume to inoculation with elite strains. Co-inoculation with Azospirillum decreased the abundance of the host-compatible rhizobia in nodules, probably because of competitiveness among the species at the rhizosphere, but increased in root microbiomes. The results showed that several other bacteria compose the nodule microbiomes of both legumes, including nitrogen-fixing, growth-promoters, and biocontrol agents, whose contribution to plant growth deserves further investigation. Several genera of bacteria were detected in root microbiomes, and this microbial community might contribute to plant growth through a variety of microbial processes. However, massive inoculation with elite strains should be better investigated, as it may affect the root microbiome, verified by both relative abundance and diversity indices, that might impact the contribution of microbial processes to plant growth.

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Section: Discussionsupporting

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

Bender

Alves²,

Silva³

et al. 2022

IJMS

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“…To validate our hypothesis, the ecological niches of these endophytes, as reported earlier, were correlated with our data. Bacillus endophyticus was first reported as an endophyte of the cotton plant (Reva et al, 2002) and later found as an endophyte of several plants, including sugarcane (Pirhadi et al, 2018), cotton (Vinodkumar et al, 2018), onion (Ibrahim et al, 2020), mung bean, cowpea and soybean nodules (Bakhtiyarifar et al, 2021), Chinese mountain legumes (Pang et al, 2021), groundnut (Pal et al, 2021), medicinal plants like Salvadora persica (Moustafa et al, 2016), Vernonia anthelmintica (Rustamova et al, 2020), Gloriosa superba (Das et al, 2021) and halophyte Salicornia europaea (Zhao et al, 2016). This species was also isolated from wheat rhizosphere (Ibarra‐Villarreal et al, 2021; Verma et al, 2016), sugarcane rhizosphere (Mukhtar et al, 2017), rice phyllosphere (Devarajan Arun et al, 2020), termatorium soil (Chauhan et al, 2016), and honeydew of cotton whitefly (Roopa et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…This species was also isolated from wheat rhizosphere (Ibarra‐Villarreal et al, 2021; Verma et al, 2016), sugarcane rhizosphere (Mukhtar et al, 2017), rice phyllosphere (Devarajan Arun et al, 2020), termatorium soil (Chauhan et al, 2016), and honeydew of cotton whitefly (Roopa et al, 2014). This endophytic bacteria showed plant growth promotion (Danielsson et al, 2007; Devarajan et al, 2021; Figueiredo et al, 2008), antagonism against soil fungal pathogen (Chauhan et al, 2016), drought mitigation (Ibarra‐Villarreal et al, 2021) and salinity stress tolerance (Bakhtiyarifar et al, 2021) upon inoculation to their respective host plants.…”

Section: Discussionmentioning

confidence: 99%

Authentication of putative competitive bacterial endophytes of rice by re-isolation and DNA fingerprinting assay

Devi

Balachandar

2022

Journal of Applied Microbiology

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Aim:The plant-growth-promoting putative competitive endophytes offer significant benefits to sustainable agriculture. The unworthy opportunistic and passenger endophytes are inevitable during the isolation of putative competitive endophytes.This study aimed to discriminate the putative competitive endophytes undoubtedly from the opportunistic and passenger endophytes. Methods and results:The newly isolated endophytes from field-grown rice were inoculated to 5-days old rice seedlings under gnotobiotic conditions. Re-isolation of the inoculated strains from the root surface, inner tissues of the whole plant, root and shoot was performed after 5-days. All the re-isolated colonies were compared with native isolates for homology by BOX-A1R-based repetitive extragenic palindromic-PCR (BOX-PCR) and enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) DNA fingerprints. The results revealed that the putative competitive endophytes (RE25 and RE10) showed positive for re-isolation and BOX and ERIC fingerprints for the whole plant, root and shoot. The opportunistic (RE27 and RE8) and passenger endophytes (RE44 and RE18) failed in re-isolation either from root or shoot. The epiphytes (ZSB15 and Az204) showed negative for endophytic re-isolation and positive for surface colonization. Conclusion:This modified procedure can discriminate the putative competitive endophytes from others.Significance and impact of the study: Eliminating the opportunistic and passenger endophytes and epiphytes early by this method would help develop endophytic inoculants to enhance rice productivity.

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“…With these facts in mind, it is imperative to explore the plant microbe interactions that exist between legumes and the respective microbes. Studies have identified positive plant microbe interactions in arid climate-adapted legumes that make a compelling argument for further exploration and analysis (Bhattacharyya and Jha, 2012;Bahroun et al, 2018;Bakhtiyarifar et al, 2021). All the organisms occurring in these extreme environments, including bacteria, fungi and protozoa, develop intricate survival mechanisms to mitigate abiotic stresses (Khan, et al, 2020a).…”

Section: Introductionmentioning

confidence: 99%

Bacterial bioinoculants adapted for sustainable plant health and soil fertility enhancement in Namibia

Mataranyika

Chimwamurombe

Venturi

et al. 2022

Front. Sustain. Food Syst.

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The increase in dryland agriculture elicits the need to develop sustainable practices that improve crop yield and protect soil fertility. The use of biofertilisers adapted to nutrient deficient soils and arid climates would help achieve this. In this review, the use of plant growth-promoting bacteria is explored as a possible solution to the current state of dryland agriculture and climate change threats to agriculture. Plant microbe interactions form the basis of this review as evidence has shown that these interactions often exist to improve the health of plants. This is achieved by the production of important biochemicals and enzymes like indole acetic acid and amino cyclopropane-1-carboxylate deaminase while also actively protecting plants from pathogens including fungal pathogens. Research, therefore, has shown that these plant-growth promoting bacteria may be exploited and developed into biofertilisers. These biofertilisers are both economically and environmentally sustainable while improving soil quality and crop yield. The literature presented in this review is in context of the Namibian climate and soil profiles.

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Biochemical and molecular investigation of non-rhizobial endophytic bacteria as potential biofertilisers

Cited by 16 publications

References 40 publications

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

Microbiome of Nodules and Roots of Soybean and Common Bean: Searching for Differences Associated with Contrasting Performances in Symbiotic Nitrogen Fixation

Authentication of putative competitive bacterial endophytes of rice by re-isolation and DNA fingerprinting assay

Bacterial bioinoculants adapted for sustainable plant health and soil fertility enhancement in Namibia

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