Article

Molecular Identification and In Vitro Plant Growth-Promoting Activities of Culturable Potato (Solanum tuberosum L.) Rhizobacteria in Tanzania

Authors:
  • The Nelson Mandela African Institutation of Science and Technology
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Abstract

The present study investigated the diversity of culturable rhizobacteria associated with potato (S. tuberosum L.) in Tanzania and assessed their in vitro plant growth-promoting (PGP) activities to deduce their potential as biofertilizers. Potato rhizosphere soil and tuber samples (54 samples in total) were collected from 9 villages in three different agro-ecological regions in Tanzania. A total of 145 rhizobacterial isolates were obtained, 52 of which were selected and identified by partial 16S rRNA gene sequences and screened for various PGP traits in vitro including qualitative and quantitative solubilization of phosphorus (P), zinc (Zn) and potassium (K), nitrogen (N2) fixation and production of ammonia (NH3) in nitrogen-free medium, and indole-3-acetic acid (IAA), gibberellic acids (GA) and siderophores production. The results showed that the isolates were all Gammaproteobacteria, belonging to 4 families (Enterobacteriaceae, Yersiniaceae, Pseudomonadaceae and Morganellaceae) and 9 genera (Enterobacter, Klebsiella, Serratia, Pseudomonas, Morganella, Buttiauxella, Pantoea and Cedecea). Significant differences (P < 0.05) were observed for all assessed PGP abilities of the external and endophytic rhizobacterial isolates except for quantitative siderophore production and qualitative P and K solubilization for the external rhizobacteria and production of IAA and GA for the endophytic rhizobacteria. Among the best PGP isolates which can be exploited for biofertilization of the potato were Klebsiella pneumoniae KIBS1, K. grimontii LUTS10, Serratia liquefaciens KIBT1, Enterobacter ludwigii KIBS10 and Citrobacter freundii MWALS6. Comparative evaluation of PGP abilities of these two groups of isolates revealed significant differences (P < 0.05) only for NH3 and IAA production and qualitative K solubilization.

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... SBP-8 produced 10 µg/ml GA after 72 h in nutrient broth (Singh et al., 2015). Klebsiella grimontii LUTS1 isolated from the rhizospheric soil produced 150 µg/ ml GA in the nutrient broth after 96 h (Aloo et al., 2021). The application of bacterial cultures producing plant growth promoting hormone production stimulates the plant growth. ...
... A PGPR isolate Klebsiella pneumoniae from chickpea rhizosphere produced 1.00 µmol/ml ammonia after 96 h (Mazumdar et al., 2018). Aloo et al. (2021) reported two plant growth-promoting Klebsiella grimontii strains LUTS1 and LUTS1 produced 1.31 and 1.16 µmol/ml ammonia, respectively. Ammonia build-up in the soil can indorses plant growth and cause an alkaline environment that inhibits the growth of several plant pathogens (Masclaux-Daubresse et al., 2010). ...
... Rhizospheric Klebsiella variicola solubilized 513 μg/ml phosphate after 72 h (Kusale et al., 2021). The rhizospheric PGPB Klebsiella grimontii LUTS and Klebsiella grimontii LUTS10 were able to solubilize 66.20 and 160.74 µg/ml tri-calcium phosphate, respectively after 10 days (Aloo et al., 2021). Zhong et al., 2021 revealed that by phosphate solubilization decreased the pH of the medium from 7.0 to 4.7. ...
Article
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A natural bacterial isolate from fermented panchagavya named as PG-64, exhibits multiple plant growth-promoting traits. This Gram-negative bacteria was identified as Klebsiella sp. PG-64 by 16S rRNA gene sequencing. The Klebsiella sp. PG-64 has shown production of indole acetic acid (106.0 µg/ml), gibberellic acid (20.0 µg/ml), ammonia (7.12 µmol/ml), exopolysaccharide (2.04% w/v) and phosphate solubilization (106.0 µg/ml). It produced 437 µg/ml IAA with 0.75% (w/v) L-tryptophan supplementation and was increased to 575 µg/ml in a laboratory-scale fermenter. The PG-64 has shown tolerance to abiotic stress conditions like pH (5.0–12.0), temperature (28–46 °C), salt (0.5–10.0% w/v NaCl) and osmotic resistance (1–10% w/v PEG-6000). The PG-64 also produced 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (0.3 ng α-ketobutyrate/mg protein/h) indicating its potential for drought tolerance. Owing to its diverse properties, the effect of Klebsiella sp. PG-64 on Vigna radiata (Mung bean) was examined. The seeds treated with PG-64 culture showed 92% germination with a good seedling vigour index (202). In the pot study, Vigna radiata growth showed 2.23, 1.55, 2.00, 1.65, 1.73, 1.88, 5.00, 5.00, 1.57 times increase in primary root length, dry root weight, root hair numbers, leaf width, leaf numbers, leaf area, fruits number, flower number and chlorophyll content, respectively after 75 days. The application of Klebsiella sp. PG-64 culture resulted in substantial growth enhancement of Vigna radiata. The Klebsiella sp. PG-64 has multiple plant growth-promoting properties along with capabilities to tolerate abiotic stresses, making it a promising liquid biofertilizer contender for various crops.
... Successful applications of phosphate-solubilizing bacteria were carried out for many important crops such as wheat (Kumar et al. 2014), mung bean (Biswas et al. 2018), rapeseed (Valetti et al. 2018), tomatoes (Nassal et al. 2018), and potato (Aloo et al. 2020). ...
... The quantification of these compounds suggested that the B.A10 strain is the most productive (Table 1). Similarly, Aloo et al. (2020) showed that S. liquefaciens can produce IAA and Ahmad et al. (2008) showed the ability of Achromobacter spanius bacteria to produce IAA. ...
... Moreover, El-Esawi et al. (2018 showed that Serratia liquefaciens could enhance maize growth under normal and high salinity conditions. Aloo et al. (2020) also showed that S. liquefaciens isolated from potato rhizosphere is a PGPR which can be exploited as biofertilizer. Likewise, Achromobacter spanius inoculation was able to increase the growth of sugarcane plants under greenhouse conditions (Santos and Rigobelo 2021). ...
Article
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The beneficial effect of compost and compost tea on plant growth and protection is mainly associated with the microbial diversity and the presence of bacteria with plant growth–promoting effect. PGPR are considered as eco-friendly bio-fertilizers that may reduce the use of chemical pesticides and fertilizers. Three composts (AT, A10, and A30) were previously prepared from industrial wastes (olive mill wastewater, olive pomace, coffee ground, and phosphogypsum). In the present study, we isolated three bacterial strains from the compost teas. The phylogenetic identification of these bacterial strains (B.AT, B.A10, and B.A30) showed that they correspond to Serratia liquefaciens (B.AT and B.A10) and Achromobacter spanius (B.A30) species. A further characterization of the PGPR traits of these bacteria showed that they produce siderophore, exopolysaccharides, and IAA. Their effect on potato plant growth, yields, and tuber quality was performed under field culture conditions. Results showed that these strains can be characterized as PGPR, the best effect on potato plant growth was observed with Serratia liquefaciens (B.AT), the best yield and tuber quality was observed with Serratia liquefaciens (B.A10) while bacterial treatment with Achromobacter spanius (B.A30) is a Cd-tolerant PGPR.
... Numerous and recent studies on the rhizosphere, mycorrhizosphere, and endo-rhizosphere of the potato reveals the presence of a diverse and dense microbial community. This microbial community constitutes a rich source of plant growthpromoting rhizobacteria and biocontrol agents (Aloo et al. 2020). Its beneficial effects would be related to the activity of microbial siderophores, antibiotics, biosynthesis of surfactants and phytohormones, competition for nutrients, mycoparasitism, induced systemic resistance, phage-therapy, quorum sensing, and construction of transgenic lines (Diallo et al. 2011). ...
... Among the best isolates which can be exploited for bio fertilization of the potato were Klebsiella pneumoniae KBS1, K. grimontii LUTS10, Serratia liquefaciens KIBT1, Enterobacter ludwigii KIBS10, and Citrobacter freundii MWALS6. Comparative evaluation of strain abilities of these groups of isolates revealed significant differences only for NH3 and IAA production and qualitative K solubilization (Aloo et al. 2020). ...
Chapter
Harvest and postharvest management determine not only that potato reaches its maximum storage potential (genetically defined) but also the organoleptic, nutritional, and functional quality maintenance of the final product. The potato must be harvested in endodormancy state. After harvest and before storage, curing occurs (15-20 °C and 90-95% HR for 5-10 days) and periderm is formed to protects tubers from dehydration and pathogens entry. During storage, temperature management allows to prolong dormancy (2-4 °C) and reduce metabolic activity, which reaches minimum values between 4-5 °C. However, the storage temperature will depend on potato destination since it is sensitive to cold and when stored below 4 °C, glucose and fructose levels increase, and it would not be suitable for frying (non-enzymatic browning). Potato is a source of beneficial compounds such as vitamins, polyphenols, anthocyanins, carotenoids, and minerals. More than 50% of the marketed potato is destined for industrial processing (frozen or minimally processed) and is consumed in several forms: fried, steamed and/or microwaved. The suitability of the potato genetic material for these preparations depends fundamentally on the dry matter content, determined genetically and on the reducing sugars, mainly dependent on the storage conditions. Processing prior cooking and cooking itself determine changes at the functional quality, in some cases reducing or increasing compounds. This chapter reviews the main aspects of potato postharvest from harvest, postharvest practices, and storage. Aspects related to organoleptic and functional quality linked to the genetic material characteristics, and to the storage and processing conditions, are also addressed.
... Numerous and recent studies on the rhizosphere, mycorrhizosphere, and endo-rhizosphere of the potato reveals the presence of a diverse and dense microbial community. This microbial community constitutes a rich source of plant growthpromoting rhizobacteria and biocontrol agents (Aloo et al. 2020). Its beneficial effects would be related to the activity of microbial siderophores, antibiotics, biosynthesis of surfactants and phytohormones, competition for nutrients, mycoparasitism, induced systemic resistance, phage-therapy, quorum sensing, and construction of transgenic lines (Diallo et al. 2011). ...
... Among the best isolates which can be exploited for bio fertilization of the potato were Klebsiella pneumoniae KBS1, K. grimontii LUTS10, Serratia liquefaciens KIBT1, Enterobacter ludwigii KIBS10, and Citrobacter freundii MWALS6. Comparative evaluation of strain abilities of these groups of isolates revealed significant differences only for NH3 and IAA production and qualitative K solubilization (Aloo et al. 2020). ...
Chapter
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Microbial diversity has been found to be associated with the plant systems and beneficial properties of agricultural microbiomes, which improve crop sustainability. This chapter is a review of the microbiota associated with potato crop and their use in sustainable production systems. The chapter highlights the plant microbiome's importance in the potato production system and potato adaptation to its biotic environment, including its productivity benefits. Thus, it is possible to visualize the response of the potato microbiota to the environment and the complex interactions in the ecosystem, and the development of new agricultural practices that include the management of specific microbiomes for potato crop production. The data presented here reinforces the idea that the microbiome should be considered as an important strategy to reach sustainability in potato crops, as the use of growth-promoting microorganisms in potatoes can help reduce the vulnerability of the crop, increasing the level of sustainability at the farm level.
... After aligning by BLASTn, we considered the coverage similarity and E-value for selecting the bacteria. Many authors (Aloo et al., 2021;Rossmann et al., 2012) reported that some bacteria of Pseudomonas, Bacillus, Enterobacteriaceae, Serratia, Pantoea, and Enterobacter genus were found in the region of the rhizosphere and these are benefical to plants. However, the genus Bacillus, Priestia, Paraburkholderia, Rhizobium, Pseudarthrobacter, Arthrobacter, Agrobacterium, Rhodanobacter, and Flavobacterium were screened by our research. ...
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Overpopulation in world has created immense pressure on agricultural land to increase crops production by using excess chemical fertilizers, pesticides, and plant growth regulators. Nowadays, biofertilizer is one of the best concerns of research interest for sustainable development in agriculture and environment. About 30 soil bacteria were isolated from three different locations in Bangladesh by growing on nitrogen-free selective media and primarily had been categorized based on colony features. However, to short out the biofertilizer and biocontrol potential bacteria several assay had been conducted including nitrogen-fixing assay, ammonia production assay, phosphate solubilizing assay, IAA production assay, siderophores production assay, amylase production assay, biocontrol assay, and seed germination bioassay. Different species of Rhizobium, Bacillus, Paraburkholderia, Priestia, Arthrobacter, Pseudarthrobacter, Rhodanobacter, Flavobacterium, Mucilaginibacter, and Sphingomonas were identified by analyzing 16S rRNA gene partial sequence analysis by BLASTn that revealed many of these act as biofertilizer. Moreover, the antibiotic resistance tests of biofertilizer potential isolates and all others intensive data analysis in respect of biofertilizer functionality revealed that Paraburkholderia sacchari is the best while Priestia megaterium, Bacillus zanthoxyli, Arthrobacter globiformis, and Bacillus wiedmannii have also the potentiality to be biofertilizer. The outcome will help the researchers and industries to develop biofertilizer for crops plant.
... For their part, Aldayel and Khalifa (2021) identified Pseudomonas mon teilii in rhizospheric soil samples of tomato (Solanum lycopersicum L.) with 99.86% homologous regions by sequencing the 16s rRNA gene and applying the universal primers 27F and 1494R; the results evidenced that this strain significantly promoted primary root length, stem and leaf number in Eruca sativa (arugula) and Raphanus sativus (radish), growing under 1,000 mg kg -1 salt stress conditions. Finally, Aloo et al., (2020), investigated the diversity of cultivable rhizobacteria asso ciated with potato (Solanum tu berosum L.) in Tanzania; of the 152 isolates obtained, 52 of them were selected for molecular identification based on preliminary screening for PGP activities; thus for PCR amplification, primers 27F and 1492R were used; The results showed that the isolates were all Gammaproteobacteria, belonging to four families (Enterobacteriaceae, Yersiniaceae, Pseudomonadaceae and Morganellaceae) and nine genera (Enterobacter, Klebsiella, Serratia, Pseudomonas, Morganella, Buttiaux ella, Pantoea and Cedecea). ...
Article
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The excessive use of agrochemicals and poor agricultural practices have increased the negative effects on soil and crop biodiversity. In that sense, there is a need to identify potential bacteria by molecular techniques for sustainable agricultural production. The objective of this article was to develop a systematic and bibliometric mapping of the research carried out applying molecular techniques in soil microbiology for the identification of bacteria with agricultural potential. A search for research related to molecular techniques used for the identification of bacteria with agricultural potential was carried out in the Web of Science and Scopus databases, which were classified and analyzed by means of the R studio software. The origin, theoretical reference, bibliometric study and networks on the proposed topic were analyzed from the research obtained. A total of 527 researches related to molecular techniques used for the identification of bacteria with agricultural potential were reported, increasing by 52.75% in the last five years, with an annual growth rate of 17.4%, with India standing out as the country with the highest number of publications, contributing 25% of researches worldwide. Sequencing and PCR are the most common techniques to identify potential microorganisms, being Bacillus, Pseudomonas, Enterobacter and Acinetobacter the most frequent bacterial genera to be identified due to mechanisms used to favor sustainable agricultural production systems.
... Identifying microbial species is very relevant because the beneficial activity is characteristic of certain species [14]. Bacterial species found in this work belonging to the genera Enterobacter, Pantoea, Pseudomonas, and Serratia have been successfully studied as PGPM in several crops [4,5,8,[38][39][40][41][42][43][44][45][46][47][48][49]. In the case of Pseudomonas allii, it has also been reported as a plant pathogen responsible for soft rot in onions [50]; even though the plants in this study did not show disease symptoms, further experiments must be performed at later stages of plant development to determine their safety. ...
Article
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Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29–176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40–69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06–51.32%), leaf diameter (25.43–82.91%), and fresh weight (54.18–85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.
... Although N 2 -fixation potential is widely investigated among the symbiotic legume-Rhizobium interactions, reports show that nitrogenase genes occur in diverse bacterial taxa [98], and non-leguminous plants can also host N 2 -fixing bacterial strains [33,99,100]. This implies that other plant-microbe interactions can similarly be important. ...
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Agricultural intensification continues in Africa in attempts to meet the rising food demands of the equally rising population. However, most arable lands in the region are characterized by nutrient deficiency and over-reliance on synthetic fertilizers which consequently contributes to increased production costs, environmental pollution, and global warming. Decades of research on plant-rhizobacterial interactions have led to the formulation and commer-cialization of rhizobacterial biofertilizers globally for sustainable soil and crop health. Nevertheless, this promising technology has not received much attention in Africa and remains largely unexplored due to several constraints. This article discusses the practical applications of rhizobacterial biofertilizers for sustainable crop production in sub-Saha-ran Africa. The challenges of soil infertility and the use of conventional synthetic fertilizers in crop production in Africa are critically evaluated. An overview of the potential of rhizobacteria as biofertilizers and alternatives to synthetic fertilizers for soil fertility and crop productivity in the continent is also provided. The advantages that these biofertiliz-ers present over their synthetic counterparts and the status of their commercialization in the African region are also assessed. Finally, the constraints facing their formulation, commercialization, and utilization and the prospects of this promising technology in the region are deliberated upon. Such knowledge is valuable towards the full exploitation and adoption of this technology for sustainable agriculture for Africa's food security.
... Ten rhizobacterial cultures that had previously isolated from potato rhizosphere soils growing in various regions in Tanzania and identified using their 16S rRNA gene sequences (Aloo et al. 2020) were selected for the present study. The strains, sources, and species of these rhizobacterial cultures are displayed in Table 1. ...
Chapter
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The global rise in human population has led to the intensification of agricultural activities to meet the ever-rising food demand. The potato (Solanum tuberosum L.) is a crop with the potential to tackle food security issues in developing countries due to its short growth cycle and high nutrient value. However, its cultivation is heavily dependent on artificial fertilizers for yield maximization which culminates in global warming and other environmental problems. There is need, therefore, for its alternative fertilization technologies to mitigate climate change. This study evaluated the potential of indigenous rhizobacteria for potato cropping in Tanzania. Ten potato rhizobacterial isolates belonging to Enterobacter, Klebsiella, Citrobacter, Serratia, and Enterobacter genera were obtained from a previous collection from different agro-ecological areas in Tanzania. The isolates were characterized culturally, microscopically, biochemically, and by their carbohydrate utilization patterns. Their in vitro plant growth-promoting (PGP) traits such as nitrogen fixation, solubilization of phosphates, potassium, and zinc, and production of siderophores, indole acetic acid, and gibberellic acids were then evaluated. Lastly, sterilized potato seed tubers were bacterized with the inoculants and grown in pots of sterile soil in a screen-house using untreated plants as a control experiment. The potato rhizobacterial isolates had varying characteristics and showed varying in vitro PGP activities. The screen-house experiment also showed that the rhizobacterial treatments significantly (p < 0.05) enhanced different parameters associated with potato growth by up to 91% and established the potential of most of the isolates as alternative biofertilizers in potato cropping systems in Tanzania.
Chapter
Root-associated microbiomes (RAMs) have a substantial effect on plant growth and defense systems. RAMs connect with roots to promote plant development and yield, retain root architecture, protect plants from infections, biotic and abiotic stresses, and enhance nutrient absorption. The rhizosphere is home to a diverse spectrum of microbial populations. Microbiome engineering is a powerful tool for promoting plant development and supporting biocontrol systems by fortifying plants with advantageous microorganisms and suppressing the growth of pathogens. Employing rhizosphere engineering measures to encourage the formation of beneficial microbial communities while minimizing detrimental counterparts addresses the current need in a sustainable manner. The ultimate goal is to create edaphic conditions that promote healthy plant development. Microbiome engineering has potential as a long-term agricultural strategy that promotes reliable plant-microbe connections for higher crop productivity and disease resistance.
Chapter
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The excessive use of agrochemicals and poor agricultural practices have increased the negative effects on soil and crop biodiversity. In that sense, there is a need to identify potential bacteria by molecular techniques for sustainable agricultural production. The objective of this article was to develop a systematic and bibliometric mapping of the research carried out applying molecular techniques in soil microbiology for the identification of bacteria with agricultural potential. A search for research related to molecular techniques used for the identification of bacteria with agricultural potential was carried out in the Web of Science and Scopus databases, which were classified and analyzed by means of the R studio software. The origin, theoretical reference, bibliometric study and networks on the proposed topic were analyzed from the research obtained. A total of 527 researches related to molecular techniques used for the identification of bacteria with agricultural potential were reported, increasing by 52.75% in the last five years, with an annual growth rate of 17.4%, with India standing out as the country with the highest number of publica tions, contributing 25% of researches worldwide. Sequencing and PCR are the most common techniques to identify potential microorganisms, being Bacillus, Pseudomonas, Enterobacter and Acinetobacter the most frequent bacterial genera to be identified due to mechanisms used to favor sustainable agricultural production systems.
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Bioremediation among many cleanup technologies, considered an attractive and affordable remediation technology with no side effects on agroenvironment, is adopted to circumvent polluted soils making ecologically disturbed soils cultivable again. Soil microbes spanning different genera and groups evade the toxicity of various environmental contaminants like heavy metals, pesticides, and hydrocarbons. Biofertilizer organisms, among soil microbiomes, have been used in the management of abiotic and biotic stresses and as a formulation to optimize yields and quality of food crops. The exploitation of soil microbes both as pollution alleviating agents (bioremediation) and as crop stimulants (biofertilizers) has provided solutions to both the challenges of environmental stresses and expensive chemical fertilizers. Considering the impactful role of biofertilizers in soil amelioration and plant growth promotion, the priority of current research has been directed toward finding unexplored microbes with dual features as bioremediating materials and as biofertilizers. Despite the growing interest in biofertilizer-based remediation technology, the full potential of this technology has not yet been realized. Recent developments in bacterial biofertilizer (especially nitrogen and phosphate biofertilizers)-based bioremediation of polluted soils and sustainable crop production are reviewed. Here, the microbial formulations, biofertilizer-based strategies for stress management, and their prospects for sustainable crop production are surveyed and presented. Collectively, the information provided herein is desirable to fully explore the bioremediation potential of bacterial biofertilizers and is likely to generate interest for adoption and application of this microbiological technology for remediation of contaminated soils vis-à-vis crop production under both conventional and stressful conditions to satisfy global “food and feed” demands.
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Conventional agriculture relies heavily on chemical pesticides and fertilizers to control plant pests and diseases and improve production. Nevertheless, the intensive and prolonged use of agrochemicals may have undesirable consequences on the structure, diversity, and activities of soil microbiomes, including the beneficial plant rhizobacteria in agricultural systems. Although literature continues to mount regarding the effects of these chemicals on the beneficial plant rhizobacteria in agricultural systems, our understanding of them is still limited, and a proper account is required. With the renewed efforts and focus on agricultural and environmental sustainability, understanding the effects of different agrochemicals on the beneficial plant rhizobacteria in agricultural systems is both urgent and important to deduce practical solutions towards agricultural sustainability. This review critically evaluates the effects of various agrochemicals on the structure, diversity, and functions of the beneficial plant rhizobacteria in agricultural systems and propounds on the prospects and general solutions that can be considered to realize sustainable agricultural systems. This can be useful in understanding the anthropogenic effects of common and constantly applied agrochemicals on symbiotic systems in agricultural soils and shed light on the need for more environmentally friendly and sustainable agricultural practices.
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Low soybean yields in western Kenya have been attributed to low soil fertility despite much work done on nitrogen (N) and phosphorus (P) nutrition leading to suspicion of other nutrient limitations. To investigate this, a nutrient omission trial was set up in the greenhouse at the University of Eldoret-Kenya to diagnose the nutrients limiting soybean production in Acrisols from Masaba central and Butere sub-Counties, and Ferralsols from Kakamega (Shikhulu and Khwisero sub-locations) and Butula sub-Counties and to assess the effect of liming on soil pH and soybean growth. The experiment was laid out in a completely randomized design with ten treatments viz; positive control (complete), negative control (distilled water), complete with lime, complete with N, minus macronutrients P, potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S) and with, micro-nutrients boron (B), molybdenum (Mo), manganese (Mn), copper (Cu) and zinc (Zn) omitted. Visual deficiency symptoms observed included interveinal leaf yellowing in Mg omission and N addition and dark green leaves in P omission. Nutrients omission resulted in their significantly low concentration in plant tissues than the complete treatment. Significantly (P 0.05) lower shoot dry weights (SDWs) than the complete treatment were obtained in different treatments; omission of K and Mg in Masaba and Shikhulu, Mg in Khwisero, K in Butere and, P, Mg and K in Butula. Nitrogen significantly improved SDWs in soils from Kakamega and Butula. Liming significantly raised soil pH by 9, 13 and 11% from 4.65, 4.91 and 4.99 in soils from Masaba, Butere and Butula respectively and soybean SDWs in soils from Butere. The results show that, poor soybean growth was due to K, Mg and P limitation and low pH in some soils. The results also signify necessity of application of small quantities of N for initial soybean use.
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In this study, chickpea plant (Cicer arietinum) rhizobacteria were screened for plant growth promoting traits and among the isolated PGPR, a potent strain RS26 was selected for further studies. The strain was non-pathogenic to human as determined by its inability to produce hemolysin and was identified by morphological, biochemical and 16S rRNA analysis as Klebsiella pneumoniae RS26. RS26 was found to be capable of N2 fixation, ammonia production, phosphate solubilisation and IAA production. Time dependent analysis of ammonia production revealed that RS26 produced 15.21 µg/ml of NH3 at 72 h of incubation. IAA production by the strain enhanced in presence of tryptophan and was maximum (15 µg/ml) at 48 h of incubation. Phosphate solubilisation was negatively correlated with the medium pH and maximum phosphorus solubilisation (29µg/ml) was observed after 7 days of incubation.
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The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant–plant and plant–microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground ‘signalomics’, and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial – and priming events.
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Endophytic bacteria represents a unique class of bacteria that can colonize interior tissues of plant and provide a range of benefits to the plant similar to those provided by the rhizospheric bacteria. Certain endophytic bacteria can provide nitrogen to the plants through biological nitrogen fixation, which is an important source of nitrogen input in agriculture and represents a promising substitute for chemical fertilizers, and are known as endophytic diazotrophic bacteria. Besides fixing nitrogen, endophytic bacteria can produce plant growth hormones like auxin and gibberellin, help in nutrient uptake, and increase the plant’s tolerance to biotic and abiotic stresses. Various direct and indirect methods have been used to quantify the amount of nitrogen fixed by these bacteria, including the acetylene reduction assay, which is a quick but indirect method, and the 15N isotopic dilution assay, which is a robust and accurate method. Research on endophytic diazotrophic bacteria has come a long way, and in this chapter, we have briefly discussed the mechanisms of biological nitrogen fixation and methods to quantify the fixed nitrogen along with reviewing recent studies focused on evaluating the role of endophytic diazotrophic bacteria in promoting plant growth in both native and nonnative crop hosts.
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The nitrogen fixing bacterial group known as rhizobia are very important and are used as biological fertilizers for two main purposes; one is to fulfil the nutritional requirements of increasingly populated world and other to overcome the problems arising due to chemical fertilizers. Rhizobial bioformulations are in the market since more than a century and can be the solution for deficiency of nitrogen in our food and soils. Rhizobia maintain the soil fertility along with higher crop yields due to the capability of biological nitrogen fixation (BNF). Currently, various types of rhizobial biofertilizers are commercially available in the market all over the world for agricultural purposes. These can be solid carrier based formulations (organic and inorganic), liquid formulations (with and without additives), synthetic polymer based formulations or metabolite based formulations, but there still is a great room for improvement. However, over the years there have been subtle changes in the rhizobial inoculants in terms of production and application.
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Groundnut is an economically important symbiotic-fixing legume that contributes 100–190 kg N ha⁻¹ to a cropping system. In this study, groundnut-nodulating native rhizobia in South African soils were isolated from root nodules. Genetic analysis of isolates was assessed using restriction fragment length polymorphism (RFLP)-PCR of the intergenic spacer (IGS) region of 16S-23S rDNA. A total of 26 IGS types were detected with band sizes ranging from 471 to 1,415 bp. The rhizobial isolates were grouped into five main clusters with Jaccard similarity coefficients of 0.00 − 1.00, and 35 restriction types in a UPGMA dendrogram. Partial sequence analysis of the 16S rDNA, IGS of 16S rDNA-23S rDNA, atpD, gyrB, gltA, glnII and symbiotic nifH and nodC regions obtained for representative isolates of each RFLP-cluster showed that these native groundnut-nodulating rhizobia were phylogenetically diverse, thus confirming the extent of promiscuity of this legume. Concatenated gene sequence analysis showed that most isolates did not align with known type strains, and may represent new species from South Africa. This underscored the high genetic variability associated with groundnut Rhizobium and Bradyrhizobium in South African soils, and the possible presence of a reservoir of novel groundnut-nodulating Bradyrhizobium and Rhizobium in the country.
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Endophytic bacteria from roots and leaves of rice plants were isolated and identified in order to select the diazotrophs and improve their nitrogen-fixing abilities. The nitrogen-fixing endophytes were identified by PCR amplification of the nifH gene fragment. For this purpose, two isolates, Enterobacter cloacae RCA25 and Klebsiella variicola RCA26, and two model bacteria (Herbaspirillum seropedicae z67 and Sinorhizobium fredii NGR234) were transformed to increase the biosynthesis of the main plant auxin indole-3-acetic acid (IAA). A significant increase in the production of IAA was observed for all strains. When the expression of nifH gene and the activity of the nitrogenase enzyme were analyzed in liquid cultures, we found that they were positively affected in the IAA-overproducing endophytes as compared to the wild-type ones. Rice plants inoculated with these modified strains showed a significant upregulation of the nitrogenase activity when plants infected with the wild-type strains were used as reference. Similar results were obtained too with common bean plants infected with the S. fredii NGR234 strain. These findings suggest that IAA overproduction improves nitrogen-fixing apparatus of endophytic bacteria both in liquid cultures and in inoculated host plants. The present study highlights new perspectives to enhance nitrogen-fixing ability in non-legume crops. These strains could be used as bioinoculants to improve the growth and the yield of agricultural crops, offering an alternative to the use of chemical nitrogen fertilizers.
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Global population increases and climate change pose a challenge to worldwide crop production. There is a need to intensify agricultural production in a sustainable manner and to find solutions to combat abiotic stress, pathogens, and pests. Plants are associated with complex microbiomes, which have an ability to promote plant growth and stress tolerance, support plant nutrition, and antagonize plant pathogens. The integration of beneficial plant-microbe and microbiome interactions may represent a promising sustainable solution to improve agricultural production. The widespread commercial use of the plant beneficial microorganisms will require a number of issues addressed. Systems approach using microscale information technology for microbiome metabolic reconstruction has potential to advance the microbial reproducible application under natural conditions.
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In this communication, the diversity and beneficial characteristics of endophytic bacteria have been studied in Simmondsia chinensis that has industrial importance because of the quality of its seed oil. Endophytes were isolated (N = 101) from roots of the jojoba plants collected, of which eight were identified by partial sequencing of the 16S rDNA gene. The isolated bacteria were Bacillus sp., Methylobacterium aminovorans, Oceanobacillus kimchi, Rhodococcus pyridinivorans and Streptomyces sp. All isolates had at least one positive feature, characterizing them as potential plant growth promoting bacteria. In this study, R. pyridinivorans and O. kimchi are reported as plant growth promoters.
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Phosphorus is an essential element for all life forms. Phosphate solubilizing bacteria are capable of converting phosphate into a bioavailable form through solubilization and mineralization processes. Hence in the present study a phosphate solubilizing bacterium, PSB-37, was isolated from mangrove soil of the Mahanadi river delta using NBRIP-agar and NBRIP-BPB broth containing tricalcium phosphate as the phosphate source. Based on phenotypic and molecular characterization , the strain was identified as Serratia sp. The maximum phosphate solubilizing activity of the strain was determined to be 44.84 lg/ml, accompanied by a decrease in pH of the growth medium from 7.0 to 3.15. During phosphate solubilization, various organic acids, such as malic acid (237 mg/l), lactic acid (599.5 mg/l) and acetic acid (5.0 mg/l) were also detected in the broth culture through HPLC analysis. Acid phosphatase activity was determined by performing p-nitrophenyl phosphate assay (pNPP) of the bacterial broth culture. Optimum acid phosphatase activity was observed at 48 h of incubation (76.808 U/ml), temperature of 45 °C (77.87 U/ml), an agitation rate of 100 rpm (80.40 U/ml), pH 5.0 (80.66 U/ml) and with glucose as a original carbon source (80.6 U/ml) and ammonium sulphate as a original nitrogen source (80.92 U/ml). Characterization of the partially purified acid phosphatase showed maximum activity at pH 5.0 (85.6 U/ml), temperature of 45 °C (97.87 U/ml) and substrate concentration of 2.5 mg/ml (92.7 U/ml). Hence the present phosphate solubilizing and acid phosphatase production activity of the bacterium may have probable use for future industrial, agricultural and biotechnological application.
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Klebsiella species known to exhibit important PGP traits like solubilization of phosphate, phytohormone production and good germination potential. In present study, based on the Phosphate solubilization and IAA production bacterial strain VRE36 was selected among the isolates collected from different sugarcane cultivar rhizosphere growing near Bardoli area for characterization and molecular identification through 16S rRNA gene sequence, which confirms the isolate as Klebsiella pneumoniae. The phosphate solubilization index of the isolate recorded was 3.9 and quantitative estimation reveals 17.4±1.78µg/ml release of phosphate in NBRIP broth. The high amount of IAA produced was 45.32±2.46µg/ml after 96 hour incubation at 37 °C. In seed germination assay with V radiate, C tetragonoloba and V unguiculata, treatments with bacteria were supported good plant height, dry weight and fresh weight when compared with controls. Maximum percentage of germination was recorded in V radiate (97.78%). The improved seedling parameters of the inoculated crop seeds indicated the potential of this isolate to be used in a bio-fertilizer formulation for sustainable production.
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Potato (Solanum tuberosum L.) is a widely planted crop. The primary obstacles for potato production are the high demands of fertilizers and the occurrence of widespread diseases. Traditional intensively managed agroecosystems depend on fertilizers and biocides, which could induce soil degradation and environmental problems. This review emphasizes the effects of inoculating crops with plant growthpromoting bacteria, endophytes, especially arbuscular mycorrhizal fungi (AMF), as well as the potential application of these microbes in the establishment of a sustainable potatoes cultivation system. We concluded that it is worth to isolate the most efficient microbial strains during the process of microbial diversity investigations. And it is also worth to apply flavonoids and other stimulators to promoter beneficial microbes growth since emerging evidence implies that these compounds can stimulate native mycorrhizal activity and subsequent potato yield. In summary, more practical application of biofertilizers and bio-control methods should be encouraged to facilitate potato production.
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Plant Growth Promoting Bacteria (PGPB) are considered a promising approach to replace the conventional agricultural practices, since they have been shown to affect plant nutrient-acquisition processes by influencing nutrient availability in the rhizosphere and/or those biochemical processes determining the uptake at root level of nitrogen (N), phosphorus (P), and iron (Fe), that represent the major constraints for crop productivity worldwide. We have isolated novel bacterial strains from the rhizosphere of barley (Hordeum vulgare L.) and tomato (Solanum lycopersicon L.) plants, previously grown in hydroponic solution (either Fe deficient or Fe sufficient) and subsequently transferred onto an agricultural calcareous soil. PGPB have been identified by molecular tools and characterized for their capacity to produce siderophores and indole-3-acetic acid (IAA), and to solubilize phosphate. Selected bacterial isolates, showing contemporarily high levels of the three activities investigated, were finally tested for their capacity to induce Fe reduction in cucumber roots.two isolates, from barley and tomato plants under Fe deficiency, significantly increased the root Fe-chelate reductase activity; interestingly, another isolate enhanced the reduction of Fe-chelate reductase activity in cucumber plant roots, although grown under Fe sufficiency.
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Plant growth promoting rhizobacteria (PGPR) shows an important role in the sustainable agriculture industry. The increasing demand for crop production with a significant reduction of synthetic chemical fertilizers and pesticides use is a big challenge nowadays. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth through either a direct or indirect mechanism. The mechanisms of PGPR include regulating hormonal and nutritional balance, inducing resistance against plant pathogens, and solubilizing nutrients for easy uptake by plants. In addition, PGPR show synergistic and antagonistic interactions with microorganisms within the rhizosphere and beyond in bulk soil, which indirectly boosts plant growth rate. There are many bacteria species that act as PGPR, described in the literature as successful for improving plant growth. However, there is a gap between the mode of action (mechanism) of the PGPR for plant growth and the role of the PGPR as biofertilizer—thus the importance of nano-encapsulation technology in improving the efficacy of PGPR. Hence, this review bridges the gap mentioned and summarizes the mechanism of PGPR as a biofertilizer for agricultural sustainability.
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Plant growth-promoting rhizobacteria (PGPR) may provide a biological alternative to fix atmospheric N2 and delay N remobilisation in maize plant to increase crop yield, based on an understanding that plant-N remobilisation is directly correlated to its plant senescence. Thus, four PGPR strains were selected from a series of bacterial strains isolated from maize roots at two locations in Malaysia. The PGPR strains were screened in vitro for their biochemical plant growth-promoting (PGP) abilities and plant growth promotion assays. These strains were identified as Klebsiella sp. Br1, Klebsiella pneumoniae Fr1, Bacillus pumilus S1r1 and Acinetobacter sp. S3r2 and a reference strain used was Bacillus subtilis UPMB10. All the PGPR strains were tested positive for N2 fixation, phosphate solubilisation and auxin production by in vitro tests. In a greenhouse experiment with reduced fertiliser-N input (a third of recommended fertiliser-N rate), the N2 fixation abilities of PGPR in association with maize were determined by 15N isotope dilution technique at two harvests, namely, prior to anthesis (D50) and ear harvest (D65). The results indicated that dry biomass of top, root and ear, total N content and bacterial colonisations in non-rhizosphere, rhizosphere and endosphere of maize roots were influenced by PGPR inoculation. In particular, the plants inoculated with B. pumilus S1r1 generally outperformed those with the other treatments. They produced the highest N2 fixing capacity of 30.5% (262 mg N2 fixed plant-1) and 25.5% (304 mg N2 fixed plant-1) of the total N requirement of maize top at D50 and D65, respectively. N remobilisation and plant senescence in maize were delayed by PGPR inoculation, which is an indicative of greater grain production. This is indicated by significant interactions between PGPR strains and time of harvests for parameters on N uptake and at. % 15Ne of tassel. The phenomenon is also supported by the lower N content in tassels of maize treated with PGPR, namely, B. pumilus S1r1, K. pneumoniae Fr1, B. subtilis UPMB10 and Acinetobacter sp. S3r2 at D65 harvest. This study provides evidence that PGPR inoculation, namely, B. pumilus S1r1 can biologically fix atmospheric N2 and provide an alternative technique, besides plant breeding, to delay N remobilisation in maize plant for higher ear yield (up to 30.9%) with reduced fertiliser-N input.
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Rhizosphere engineering with beneficial plant growth promoting bacteria offers great promise for sustainable crop yield. Potato is an important food commodity that needs large inputs of nitrogen and phosphorus fertilizers. To overcome high fertilizer demand (especially nitrogen), five bacteria, i.e., Azospirillum sp. TN10, Agrobacterium sp. TN14, Pseudomonas sp. TN36, Enterobacter sp. TN38 and Rhizobium sp. TN42 were isolated from the potato rhizosphere on nitrogen-free malate medium and identified based on their 16S rRNA gene sequences. Three strains, i.e., TN10, TN38, and TN42 showed nitrogen fixation (92.67–134.54 nmol h⁻¹mg⁻¹ protein), while all showed the production of indole-3-acetic acid (IAA), which was significantly increased by the addition of L-tryptophan. Azospirillum sp. TN10 produced the highest amount of IAA, as measured by spectrophotometry (312.14 μg mL⁻¹) and HPLC (18.3 μg mL⁻¹). Inoculation with these bacteria under axenic conditions resulted in differential growth responses of potato. Azospirillum sp. TN10 incited the highest increase in potato fresh and dry weight over control plants, along with increased N contents of shoot and roots. All strains were able to colonize and maintain their population densities in the potato rhizosphere for up to 60 days, with Azospirillum sp. and Rhizobium sp. showing the highest survival. Plant root colonization potential was analyzed by transmission electron microscopy of root sections inoculated with Azospirillum sp. TN10. Of the five test strains, Azospirillum sp. TN10 has the greatest potential to increase the growth and nitrogen uptake of potato. Hence, it is suggested as a good candidate for the production of potato biofertilizer for integrated nutrient management.
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Low soybean yields in western Kenya have been attributed to low soil fertility despite much work done on nitrogen (N) and phosphorus (P) nutrition leading to suspicion of other nutrient limitations. To investigate this, a nutrient omission trial was set up in the greenhouse at the University of Eldoret-Kenya to diagnose the nutrients limiting soybean production in Acrisols from Masaba central and Butere sub-Counties, and Ferralsols from Kakamega (Shikhulu and Khwisero sub-locations) and Butula sub-Counties and to assess the effect of liming on soil pH and soybean growth. The experiment was laid out in a completely randomized design with ten treatments viz; positive control (complete), negative control (distilled water), complete with lime, complete with N, minus macronutrients P, potassium (K), calcium (Ca), magnesium (Mg) and sulphur (S) and with, micro-nutrients boron (B), molybdenum (Mo), manganese (Mn), copper (Cu) and zinc (Zn) omitted. Visual deficiency symptoms observed included interveinal leaf yellowing in Mg omission and N addition and dark green leaves in P omission. Nutrients omission resulted in their significantly low concentration in plant tissues than the complete treatment. Significantly (P≤ 0.05) lower shoot dry weights (SDWs) than the complete treatment were obtained in different treatments; omission of K and Mg in Masaba and Shikhulu, Mg in Khwisero, K in Butere and, P, Mg and K in Butula. Nitrogen significantly improved SDWs in soils from Kakamega and Butula. Liming significantly raised soil pH by 9, 13 and 11% from 4.65, 4.91 and 4.99 in soils from Masaba, Butere and Butula respectively and soybean SDWs in soils from Butere. The results show that, poor soybean growth was due to K, Mg and P limitation and low pH in some soils. The results also signify necessity of application of small quantities of N for initial soybean use.
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Zinc (Zn) is an important micronutrient and its adequate supply is considered indispensable for growth, development and normal functioning of plants. Recent reports reveal that more than 70% of Pakistani soils are Zn deficient. ZnSO4, containing 33% Zn, is commonly used, but only 4-8% of the total applied Zn is available to plants while remaining gets fixed into soil. Contrarily, zinc oxide is a cheaper and insoluble source which contains 80% Zn. However, zinc solubilizing bacteria could be used to solubilize insoluble sources of zinc (ZnO). Keeping in view the above stated problem, the present study was conducted for isolation, screening, identification and characterization of efficient zinc solubilizing bacteria for improving growth of maize. Several bacteria were isolated from rhizosphere of maize through dilution plate technique. The selected bacterial isolates, capable of solubilizing ZnO, were further screened for their plant growth promoting activity under axenic conditions. Out of ten bacterial isolates, AZ6 was found best strain on the basis of maximum zinc solubilization potential and growth promotion of maize. The selected bacterium was identified as Bacillus sp. AZ6 (Accession # KT221633). Bacillus sp. AZ6 had different growth promoting attributes and also ability to produce organic acids.
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Plant growth promoting rhizobacteria (PGPR) have immense potential application in sustainable agriculture as ecofriendly biofertilizers and biopesticides. The present study was undertaken to explore the potential of such microorganisms from the rhizosphere of tea [Camellia sinensis (L.) O. Kuntze] for the overall improvement in growth and productivity of tea, which is the most important crop of this region. Isolation and testing of bacteria for PGPR activities revealed that a large number of them showed such activities. Of which three were selected for various studies. The selected bacteria were Bacillus amyloliquefaciens, Serratia marcescens and B. pumilus. These bacteria showed positive PGPR traits in vitro, such as, phosphate solubilization, siderophore production, antagonism to pathogens and IAA production. 16S rDNA sequencing of the bacteria was done and their phylogenetic relationships determined. Under in vivo conditions, thePGPR enhanced the seedling growth of tea varieties in the nursery as well as in the field. Plant growth promotion was determined in terms of increase in number of leaves, their biomass and number of shoots. In order to determine the tolerance of bacteria to insecticides, in vitro tests were conducted, which indicated that PGPR could tolerate more than 100times the concentration applied in the field. Sustainability of the applied bacteria in soil was tested by PTA-ELISA and Dot immunobinding assay using polyclonal antibodies raised against the PGPR. Certain bioformulations of the PGPR in talc powder, saw dust and rice husk also been prepared and their viability tested. The bacteria showed good survivability even up to 9 months of storage. Application of the PGPR led to enhancement in activities of defense related enzymes, such as, phenyl alanine ammonia lyase, peroxidase, chitinase and α-1,3-glucanase, in tea leaves. Total phenols also increased quantitatively. It is evident from the present study that application of PGPR in the soil lead to biopriming ofthe plantsthrough induced systemic resistance and other mechanisms.
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Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.
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The use of plant growth promoting bacterial inoculants as live microbial biofertilizers provides a promising alternative to chemical fertilizers and pesticides. Inorganic phosphate solubilization is one of the major mechanisms of plant growth promotion by plant associated bacteria. This involves bacteria releasing organic acids into the soil which solubilize the phosphate complexes converting them into ortho-phosphate which is available for plant up-take and utilization. The study presented here describes the ability of endophytic bacteria to produce gluconic acid (GA), solubilize insoluble phosphate, and stimulate the growth of Pisum sativum L. plants. This study also describes the genetic systems within three of these endophyte strains thought to be responsible for their effective phosphate solubilizing abilities. The results showed that many of the endophytic strains produced GA (14–169 mM) and have moderate to high phosphate solubilization capacities (~400–1300 mg L⁻¹). When inoculated into P. sativum L. plants grown in soil under soluble phosphate limiting conditions, the endophytes that produced medium-high levels of GA displayed beneficial plant growth promotion effects.
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This book contains 17 chapters providing details on decision tools that use linear programming to determine recommendations specific to a farmer's context intended to maximize profit from fertilizer use in sub-saharan Africa. Chapter 1 and 2 discusses the principles and approach, and spatial analysis of fertilizer use optimization, respectively. Chapter 3 covers integrated soil fertility management in sub-Saharan Africa. Further, Chapters 4 to 16 explore optimizing fertilizer use within an integrated soil fertility management framework in countries in sub-Saharan Africa, including: Burkina Faso, Ethiopia, Ghana, Kenya, Mali, Malawi, Mozambique, Niger, Nigeria, Rwanda, Tanzania, Uganda, and Zambia. Finally, Chapter 17 describes the process of enabling fertilizer use optimization in sub-Saharan Africa.
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Potato (Solanum tuberosum L.) is one of the most important food crops worldwide but its cultivation is affected by numerous challenges including pests, diseases and high fertiliser requirements which have associated environmental problems. The exploitation of plant rhizospheres and their associated rhizobacterial interactions has gathered momentum worldwide in search of environmentally-friendly approaches to crop cultivation. A lot of literature exists on rhizobacterial associations and their biofertilisation or bioprotection roles in many plants. However, very scanty information is available on rhizobacterial functions and communities of the potato, an indication that they are still understudied. In this regard, more research is needed to understand and exploit them for the successful application of rhizobacteria-based technology in potato cropping. This review updates our knowledge of the beneficial rhizobacteria of the potato and documents their roles in its bioprotection, phytostimulation and biofertilisation while highlighting their potential in enhancing its production and productivity. The future prospects regarding the research on these important potato microflora are further discussed as a guide and a baseline for future research on them. This review shows that rhizobacteria-based technology is a viable option for potato biofertilisation and bioprotection and could be the missing link in its sustainable cropping. The adoption and full exploitation of this technology can be fast-tracked if we increase our understanding of the subject matter.
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One of the premium qualities of Phosphate solubilizing bacteria is to solubilize insoluble phosphorus to make it available for plant roots to be engrossed. To check the ability for phosphate solubilization, production of indole acetic acid, antagonistic activity against fungal pathogen and intrinsic antibiotic resistance phosphorous solubilizing bacterial isolates were isolated and screened. In total, 12 PSB were found rod shaped cells being gram negative. Different levels of antibiotic resistance were observed by rhizobacterial isolates against four antibiotics (Ampicillin, Kanamycin, Tetracycline and Streptomycin 25, 30, 30 and 10 μg/mL respectively). The isolates S7 and S20 showed antifungal activity against Fusarium oxysporum. Conversion of insoluble phosphorous Ca3(PO4) into IAA was observed by all PSB Isolates. Two phosphorous solubilizing bacterial isolates sequences were submitted in NCBI database. Conclusively, good antifungal activity with greater ability to solubilize insoluble phosphorus can be achieved by combine application of rhizobacterial isolates with S22. Further, it is an eco-friendly and cost effective strategy to improve crop production.
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Conventional agricultural practices often rely on synthetic fertilizers and pesticides which have immense and adverse effects on humans, animals and environments. To minimize these effects, scientists world over are now deeply engaged in finding alternative approaches for crop production which are less dependent on chemical inputs. One such approach is the use of rhizospheric bacteria as vital components of soil fertility and plant growth promotion (PGP) through their direct and indirect processes in plant rhizospheres. Among the most studied rhizobacteria are the Bacilli, particularly for production of antibiotics, enzymes and siderophores all of which are important aspects of PGP. Despite this, little information is available especially on their potentiality in crop production and their direct application only involves a few species, leaving a majority of these important rhizobacteria exploited. This paper gives an overview of the unique properties of Bacilli rhizobacteria as well as their different PGP mechanisms that if mined can lead to their successful application and agricultural sustainability. It further points out the missing aspects with regards to these important rhizobacteria that should be considered for future research. This information will be useful in analyzing the PGP abilities of Bacilli rhizobacteria with an aim of fully mining their potential for crop production and environmental sustainability.
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Agriculture is a complex network interaction among soil-plant-microbes. There is an urgent need for an ecologically compatible, environment-friendly tech- nique in agriculture system that might be able to provide adequate supply of essen- tial nutrients for the alarming growing rate of human populations through qualitative and quantitative improvement of agricultural products. Conventional agriculture plays a crucial role to fulfill the increasing food demands of a growing human popu- lation, which has also led to enhancing the use of pesticides and chemical fertilizers. Improvement in agricultural sustainability requires optimal use and management of soil fertility which rely on soil microbiological processes and soil biodiversity. An understanding of microbial diversity perspectives in agriculture is important and useful to arrive at measures that can act as indicators of soil quality, soil health, and plant productivity. In this context, microorganisms present in soils have multiple plant growth-promoting (PGP) activities such as IAA (indole-3-acetic acid), hydro- gen cyanide (MCM) and siderophore production, ACC deaminase activity, and nitro- gen fixation and nutrient solubilization (P, K, and Zn). Efficient plant growth-promoting microorganisms (PGPMs) solubilize the nutrients in soil and facilitate absorption by plants and consequently enhance the plant growth and yield. PGPMs also sustain the soil fertility, soil health, and nutrient mobilization efficiency under sustainable agriculture. © Springer Nature Singapore Pte Ltd. 2018. All rights reserved.
Article
Inoculation of microorganisms to improve crop yields and minimize the use of chemical fertilizers is a promising sustainable strategy. The objective of this study was to isolate and identify bacteria from the rhizosphere of rapeseed plants able to solubilize phosphate and promote the growth of this crop. We isolated 40 different bacterial morphotypes which were phenotypically and genotypically characterized. Fourteen isolates (37.8%) were able to solubilize phosphate, 9 of them being epiphytic and 5 endophytic. In greenhouse experiments 7 of these isolates increased shoot dry weight, reaching values similar to those of fertilized plants. Additionally, we determined that survival, growth and biofilm formation ability of these bacteria were not affected by rapeseed root exudates. All the phosphate solubilizing strains able to promote plant growth under greenhouse conditions, with the exception of Bacillus sp. LTAD-52, also increase rapeseed yield (from 21 to 44%) in field trials.
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A metal resistant bacterium was isolated from the rhizosphere of Kair ‘Capparis decidua’ and screened for its phytoextraction ability under gradient metal stress conditions. Based on 16S rDNA analysis, the strain was identified as Enterobacter ludwigii. Among the plant growth promoting traits, isolate showed the ACC (1-aminocyclopropane-1-carboxylate) deaminase activity, production of indole-3-acetic acid in tryptophan supplemented medium and solubilize the inorganic phosphate. The isolate was resistant to heavy metals like zinc (Zn), nickel (Ni), copper (Cu), and cadmium (Cd). The fatty acid adaptation of isolate growing at different concentration of Zn (100–300 mg kg⁻¹) was also studied, which indicated that metal concentration strongly influenced the fatty acid composition of bacterium, particularly by increasing the unsaturated fatty acids. Furthermore, inoculation with the test isolate was found to significantly (p < 0.01) increase the various growth parameters of wheat plants and also improve the photosynthetic pigments. In addition, inoculation with isolate resulted in significant (p < 0.01) increase in the Zn content in wheat plant under metal stress. Moreover, bacterial application significantly (p < 0.01) increased the various compatible solutes such as proline content (30–65%), total soluble sugar (9–49%), and decreased the malondialdehyde (MDA) content (38–47%) as compared to control, illustrating its protective effect under metal induced oxidative stress. Inoculation with test isolate also increased the total protein content in range of 16–52%. Our work revealed that metal resistant plant growth promoting rhizobacterium could be exploited as microbial mediated phytoremediation of metal polluted soils.
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The present study focuses on the isolation of three phosphate solubilizing bacteria (PSB), PSB1, PSB2 and PSB3 from the gut of earthworm Metaphire posthuma. The three stains were identified as Bacillus megaterium (MF 589715), Staphylococcus haemolyticus (MF 589716) and Bacillus licheniformis (MF 589720) through 16 S rRNA gene sequencing and biochemical characterization. The strains showed resistance to the metals Cu and Zn at significant concentrations and could solubilize phosphate even in the presence of metals. Maximum phosphate was solubilized by strain PSB3 with a production of 222 ± 2.0 mg L⁻¹ soluble phosphate followed by PSB1 (213.7 ± 1.3 mg L⁻¹) and PSB2 (193.5 ± 1.5 mg L⁻¹) at 96 h of incubation. The strains were able to produce indole acetic acid (IAA) in presence of L-tryptophan and possessed ammonium ion production potential in the order PSB3 > PSB1 > PSB2 (P < 0.05). The sterilized seeds of mung beans (Vigna radiata) displayed greater germination rate and higher growth under bacterium-enriched conditions. The effect on seed germination traits by the isolated strains followed the order of PSB3 > PSB1 > PSB2 (P < 0.05). Our results suggest that the three isolated PSB strains from earthworm gut possess intrinsic abilities of growth promotion, metal resistance and solubilization of phosphate which could be exploited for plant growth promotion and bioremediation even under metal-stress conditions.
Chapter
Agriculture is a complex network interaction among soil-plant-microbes. There is an urgent need for an ecologically compatible, environment-friendly technique in agriculture system that might be able to provide adequate supply of essential nutrients for the alarming growing rate of human populations through qualitative and quantitative improvement of agricultural products. Conventional agriculture plays a crucial role to fulfill the increasing food demands of a growing human population, which has also led to enhancing the use of pesticides and chemical fertilizers. Improvement in agricultural sustainability requires optimal use and management of soil fertility which rely on soil microbiological processes and soil biodiversity. An understanding of microbial diversity perspectives in agriculture is important and useful to arrive at measures that can act as indicators of soil quality, soil health, and plant productivity. In this context, microorganisms present in soils have multiple plant growth-promoting (PGP) activities such as IAA (indole-3-acetic acid), hydrogen cyanide (HCN) and siderophore production, ACC deaminase activity, and nitrogen fixation and nutrient solubilization (P, K, and Zn). Efficient plant growth-promoting microorganisms (PGPMs) solubilize the nutrients in soil and facilitate absorption by plants and consequently enhance the plant growth and yield. PGPMs also sustain the soil fertility, soil health, and nutrient mobilization efficiency under sustainable agriculture.
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In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.
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The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential.
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Chemicals in the form of fertilizers and pesticides have been used in boosting agricultural productivity and crop protection since years. The adverse effects such as environmental toxicity and long residual action resulting from excessive use of these chemicals have prompted the search for nontoxic eco-friendly biological agents. Microbes have emerged as eco-friendly alternate to achieve enhanced plant productivity and protection. Microorganisms colonize rhizosphere/interior of the plant, thereby promoting growth of plants by increasing the availability of essential nutrients such as nitrogen and phosphorus and providing growth regulators. Microbes and their supplements also provide protection against various pests and pathogens. Biofertilizers and biopesticides serve as an eco-friendly substitute to toxic chemicals and form an important component of integrated nutrient management system. Efficiency of both biopesticides and biofertilizers can be increased by molecular approaches. The present chapter highlights the role of biofertilizers and biopesticides in crop improvement and hence achievement of sustainable agriculture.
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Multi-strain inoculants have increased potential to accomplish a diversity of plant needs, mainly attributed to its multi-functionality. This work evaluated the ability of a mixture of three bacteria to colonize and induce a beneficial response on the pasture crop annual ryegrass. Pseudomonas G1Dc10 and Paenibacillus G3Ac9 were previously isolated from annual ryegrass and were selected for their ability to perform multiple functions related to plant growth promotion. Sphingomonas azotifigens DSMZ 18530T was included due to nitrogen fixing ability. The effects of the bacterial mixture were assessed in gnotobiotic plant inoculation assays and compared with single and dual inoculation treatments. Triple inoculation with 3 × 10⁸ bacteria significantly increased plant dry weight and leaf pigments, indicating improved photosynthetic performance. Plant lipid biosynthesis was enhanced by 65%, mainly due to the rise of linolenic acid, an omega-3 fatty acid with high dietary value. Electrolyte leakage, an indicator of plant membrane stability under stress, was decreased pointing to a beneficial effect by inoculation. Plants physiological condition was more favoured by triple inoculation than by single, although benefits on biomass were only evident relative to non-inoculated plants. The colonization behaviour and coexistence in plant tissues were assessed using FISH and GFP-labelling, combined with confocal microscopy and a cultivation-based approach for quantification. The three strains occupied the same sites, localizing preferentially along root hairs and in stem epidermis. Endophytic colonization was observed as bacteria entered root and stem inner tissues. This study reveals the potential of this mixture of strains for biofertilization, contributing to improve crop productivity and nutritional value.
Article
Siderophore producing rhizobacteria beneficially affect plant growth by providing available iron to plants. In this study, bacteria were isolated from the rhizosphere of canola (Brassica napus L.) plants grown in the central fields in Iran, for presence of siderophore-producing bacteria. A total of 45 distinct isolates were found to produce siderophore using qualitative Chrome-Azurol S (CAS)-agar assay. Of them, ten isolates, based on the highest halo diameter/colony diameter ratios were selected to quantify the rate of siderophore production using chrome azurol sulfonate (CAS)-liquid assay. A variety of biochemical assays was used to determine the type(s) of siderophores produced by each of the ten isolates. The best isolates, based on production of the highest rates of either hydroxamates or carboxylates, were identified and used in further studies. Based on 16 S ribosomal ribonucleic acid (rRNA) sequence analysis and a variety of phenotypic properties, the isolates were identified as Micrococcus yunnanensis YIM 65004 (T) and Stenotrophomonas chelatiphaga LPM-5 (T). We also studied the plant growth promoting effect of the most promising isolates (YIM 65004 and LPM-5) on canola and maize plants under greenhouse conditions. The results of this study showed M. yunnanensis and S. chelatiphaga increased gain weight and iron (Fe) content of roots and shoots significantly, in comparison with control indicating beneficial effects of these rhizobacteria on plant growth and development. This study reports M. yunnanensis and S. chelatiphaga, as new records for Iran. The latter is reported for the first time from plant (canola) rhizosphere. Besides, the ability of both M. yunnanensis and S. chelatiphaga to produce siderophores is documented for the first time.
Article
In the present investigation, there were 143 Zinc solubilizing bacterial isolates obtained from rice rhizosphere soil samples using Tris-mineral salt growth medium supplemented with insoluble source of zinc such as Zinc Oxide (ZnO) and Zinc Carbonate (ZnCO3) individually. Among the ZSB isolates, there was maximum zinc solubilizing halo zone observed with the isolate AGM3 followed by AGM9 both on ZnO and ZnCO3 amended solid tris-mineral salt growth medium with the diameter of 13.21 mm, 10.71 mm and 11.74 mm, 7.90 mm respectively. Similarly, in broth assay, the AGM3 showed high value of zinc solubilization than AGM9 in both ZnO and ZnCO3 supplemented medium with a value of 36.54 μg Zn ml-1, 35.40 μg Zn ml-1 and 33.14 μg Zn ml-1, 32.69 μg Zn ml-1 respectively. The SEM images of AGM3 exhibited better solubility of ZnO than ZnCO3. Both AGM3 and AGM9 bacterial isolates were confirmed as Acinetobacter sp. through biochemical and 16S rRNA gene analysis. IAA productivity of isolate AGM3 showed highest at a level of 45.61 μg mL-1 than AGM9 at 37.27 μg mL-1. In pot experiment, among the all treatments, the combined use of AGM3 and AGM9 with ZnO and ZnCO3 resulted maximum in plant growth. The assay of fractionation of soil zinc after harvest showed an increase in exchangeable zinc, manganese oxide found bound zinc, crystalline and amorphours bound zinc and a decrease organically complexed and carbonate bound zinc compared to untreated control.
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The plant holobiont comprises the plant and its associated microbiota, which interact with each other and determine holobiont functioning and plant performance. We have started to understand the complexity of the involved microorganisms and their interactions, however, we need more research on plant-microbiome interactions to understand holobiont functioning. By 2020 we expect that our knowledge on these interactions will have considerably increased facilitating crop management practices based on the interactions of the plant holobiont.
Article
Zinc plays a pivotal role in physiological and biochemical functions of the plants. Both quantitative and qualitative yield of the plants are strongly dependent on this micronutrient. Supplementation of zinc in the form of synthetic fertilizer is proved to be inappropriate due to its unavailability to plants. This crisis can be prevented by the identification of rhizospheric micro-organisms which has the potential to transform various unavailable forms of the metal to available forms. In the present study about thirty five zinc solubilizing bacteria were isolated from eight different agricultural fields (banana, chilli, field bean, ground nut, maize, sugarcane, sorghum and tomato) in and around Coimbatore district of Tamil Nadu. Five isolates were selected as best strains based on their solubilization efficacy in the qualitative estimation. The selected five isolates were identified using 16S rRNA as Stenotrophomonas maltophilia (ZSB-1), Mycobacterium brisbanense (ZSB-10), Enterobacter aerogenes (ZSB-13), Pseudomonas aeruginosa (ZSB-22) and Xanthomonas retroflexus (ZSB-23). These strains were subjected to further studies such as quantitative estimation, influence of the isolates on the pH of the medium and production of gluconic acid as well as IAA. Of the five bacterial isolates, Pseudomonas aeruginosa showed maximum solubilization of zinc in the broth and also maximum decrease in the pH from 7 to 3.3 and recorded highest IAA production. HPLC analysis of gluconic acid production by the selected isolates indicated their potential to solubilize zinc.
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New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data.
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A Gram-stain negative, motile, rod-shaped bacterium, designated strain YIM Hb-3(T), was isolated from the stem of a tobacco plant. The strain was observed to form convex, circular and yellow-colored colonies. The predominant respiratory quinone was identified as Q-8. The major fatty acids (>5 %) detected were C16:1ω7c and/or C16:1ω6c (summed feature 3), C16:0, C17:0cyclo, C18:1ω7c and/or C18:1ω6c (summed feature 8), C14:03-OH and/or iso-C16:1I (summed feature 2), C14:0 and C12:0. The genomic DNA G+C content was determined to be 54.8 mol%. Phylogenetic trees based on 16S rRNA gene sequences and multilocus sequence analysis showed that strain YIM Hb-3(T) had the closest phylogenetic relationship with Enterobacter mori LMG 25706(T). DNA-DNA relatedness value between strain YIM Hb-3(T) and E. mori LMG 25706(T) was 46.9 ± 3.8 %. On the basis of phenotypic and chemotaxonomic data, phylogenetic analysis, and DNA-DNA relatedness value, strain YIM Hb-3(T) is considered to represent a novel species of the genus Enterobacter, for which the name Enterobacter tabaci sp. nov. is proposed. The type strain is YIM Hb-3(T) (=KACC 17832(T) =KCTC 42694(T)).
Article
Ten mustard rhizobacterial isolates that utilize 1-aminocyclopropane-1-carboxylate (ACC) as sole nitrogen source were screened for plant growth-promoting traits. These isolates enhanced root elongation significantly and minimized ethylene synthesis in wheat seedlings under induced cadmium stress condition. The presence of acdS gene coding for ACC deaminase was tested through gene-specific PCR amplification and further confirmed by nucleic acid hybridization. acdS gene from isolates Ps 2-3 and Ps 7-12 selected on the basis of wheat growth promotion was cloned and sequenced. Sequence analysis showed an open reading frame of 1017 bp encoding a complete polypeptide with an identity of 86.4 % between each other and sharing 84–95 % similarity with the earlier reported acdS genes. The deduced protein sequences were highly conserved and shared a 95.2 % homology at the amino acid level. Eight and thirteen new amino acid residues were found in the protein sequence of Ps 2-3 and Ps 7-12 with variation in numbers of different peptidase acting sites and protein motifs. Based on 16S rDNA sequencing, the isolates Ps 2-3 and Ps 7-12 were identified as Pseudomonas sp. and Pseudomonas fluorescens, respectively.