Siderophore-producing bacteria from a sand dune ecosystem and the effect of sodium benzoate on siderophore production by a potential isolate

Screening halotolerant bacteria for their potential as plant growth-promoting and coal-solubilizing agents

The bioconversion of salinized land into healthy agricultural systems by utilizing low-rank coal (LRC) is a strategic approach for sustainable agricultural development. The aims of this study were: (1) to isolate bacterial strains associated with the rhizosphere of native plants in coal-containing soils, (2) to characterize their plant growth-promoting (PGP) and coal-solubilizing capabilities under laboratory conditions and (3) to evaluate their influence on the germination and growth of chia seeds under saline stress. Fourteen bacterial cultures were isolated from the rhizosphere of Artemisia annua L. using culture media containing salt and coal. Based on their PGP activities (nitrogen fixation, phosphate solubilization, siderophore and indole-3-acetic acid production), five strains were selected, belonging to the genera Bacillus, Phyllobacterium, Arthrobacter, and Pseudomonas. Solubilization assays were conducted to confirm the ability of these strains to utilize coal efficiently. Finally, the selected strains were inoculated with chia seeds (Salvia hispanica L.) to evaluate their ameliorating effect under saline stress conditions in coal-containing media. Inoculation with A. subterraneus Y1 resulted in the highest germination and growth metrics of chia seeds. A positive but comparatively weaker response was observed with P. frederiksbergensis AMA1 and B. paramycoides Lb-1 as inoculants. Coal inoculated with halotolerant bacteria can serve as the foundation for humified organic matter in salt-affected environments. The selected halotolerant bacteria enhance coal biotransformation while exhibiting PGP traits.

Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics

Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02809-5.

Potential of Microbial Diversity of Coastal Sand Dunes: Need for Exploration in Odisha Coast of India

Coastal sand dunes are hips and strips formed by sand particles which are eroded and ground rock, derived from terrestrial and oceanic sources. This is considered as a specialized ecosystem characterized by conditions which are hostile for life forms like high salt, low moisture, and low organic matter content. However, dunes are also inhabited by diverse groups of flora, fauna, and microorganisms specifically adapted to these situations. Microbial groups like fungi, bacteria, and actinobacteria are quite abundant in the rhizosphere, phyllosphere, and inside plants which are very much essential for the integration of dunes. Microorganisms in this ecosystem have been found to produce a number of bioactive metabolites which are of great importance to agriculture and industries. Many species of arbuscular mycorrhizal fungi and Rhizobia associated with the roots of dune flora are prolific producers of plant growth promoting biochemicals like indole acetic acid. In addition to that bacteria belonging to Pseudomonas sp., Gammaproteobacteria have been found to have antagonistic activity towards plant pathogens like Rhizoctonia solani, Pythium ultimum, Fusarium oxysporum, and Botrytis cinerea. Many neutrophilic and alkaliphilic eubacterial species, endophytic fungi from dunes have proved their ability for the production of extracellular enzymes like cellulase, pectinase, amylase, protease, tannase, chitinase, etc., which are of great importance to various industries. In this context, it is relevant to observe that the state of Odisha in India has a 480km long coast having numerous sand dunes. These dunes are rich in floral and faunal diversity. However, a comprehensive study is yet to be taken up to explore the microbial diversity and their bioactive potential in this region. The current review sheds light on the enormous potential of sand dune microorganisms in the coast and surfaced the idea and need for such exploration in the state of Odisha, India.

Bacterial siderophores promote plant growth: Screening of catechol and hydroxamate siderophores

The aim of the study was to determine the quality and quantity of siderophores produced by bacteria isolated from plants' roots. The second aim was to determine the effect of siderophores on plants growth (Festuca rubra L. and Brassica napus L.). The study was carried out using bacteria isolated from roots of: Arabidopsis thaliana L., F. rubra, and Agrostis capillaris L., growing on the heavy metals contaminated area. The chrome azurol sulfonate (CAS) test, Arnow's test for catechol siderophores, and Csaksy's test for hydroxamate siderophores were performed. Among the bacteria, 42 isolates (39%) had a positive result in the CAS. Endophytic bacteria were mostly producing the catechol siderophores. It was found that F. rubra is the plant which is linked with the highest number of siderophores producing bacteria. The highest concentration of siderophores was noted for ectorhizospheric bacteria associated with A. thaliana, hyperaccumulating plant. It was found that hydroxamate siderophores are mainly produced by ectorhizosphere and rhizoplane bacteria. The siderophores producing bacteria reduced the toxicity of metals and improved the phytoremediation. Siderophores treatment increased the growth of plants in the biological assay, growing on two different soils: one highly contaminated with heavy metals and the second strongly alkaline soil.

Studies on Siderophore and Pigment Produced by an Adhered Bacterial Strain Halobacillus trueperi MXM-16 from the Mangrove Ecosystem of Goa, India

Mangroves are unique ecosystems in the coastal tropical and subtropical regions of the Earth. The fluctuation in salinity due to tidal action results in a prolific population of adhered halophilic and halotolerant bacteria in this ecosystem. In this study, a pigment producing adhered bacterial strain Halobacillus trueperi MXM-16 was isolated from mangrove plant litter of Goa. This strain was moderately halophilic, Gram positive rod, catalase positive and capable of utilizing sodium benzoate as a source of carbon. H. trueperi MXM-16, produced a siderophore that was hydroxamate in nature. The non-diffusible yellow pigment was a carotenoid and HPLC studies revealed a peak that was indicative of astaxanthin as one of the component. Further studies on the pigment exhibited its ability to chelate iron from the chrome azurol sulphonate medium behaving as an additional mechanism for iron acquisition.

Pigments influence the tolerance of Pseudomonas aeruginosa PAO1 to photodynamically induced oxidative stress

Pseudomonas aeruginosa is an opportunistic pathogen known to be resistant to different classes of antibiotics and disinfectants. P. aeruginosa also displays a certain degree of tolerance to photodynamic therapy (PDT), an alternative antimicrobial approach exploiting a photo-oxidative stress induced by exogenous photosensitizers and visible light. To evaluate whether P. aeruginosa pigments can contribute to its relative tolerance to PDT, we analysed the response to this treatment of isogenic transposon mutants of P. aeruginosa PAO1 with altered pigmentation. In general, in the presence of pigments a higher tolerance to PDT-induced photo-oxidative stress was observed. Hyperproduction of pyomelanin makes the cells much more tolerant to stress caused by either radicals or singlet oxygen generated by different photosensitizers upon photoactivation. Phenazines, pyocyanin and phenazine-1-carboxylic acid, produced in different amounts depending on the cultural conditions, are able to counteract both types of PDT-elicited reactive oxygen species. Hyperproduction of pyoverdine, caused by a mutation in a quorum-sensing gene, rendered P. aeruginosa more tolerant to a photosensitizer that generates mainly singlet oxygen, although in this case the observed tolerance to photo-oxidative stress cannot be exclusively attributed to the presence of the pigment.

Endophytes as producers of peptides: an overview about the recently discovered peptides from endophytic microbes

An endophyte is a fungus or bacterium that lives within a plant in a symbiotic relationship. Extensive colonization of the plant tissue by endophytes creates a barrier effect, where they outcompete and prevent pathogenic organisms from taking hold. This happens by producing secondary metabolites that inhibit the growth of the competitors or pathogens. In this way they play a very important role in the plant defence mechanisms. The metabolites produced by these endophytes fall within a wide range of classes of compounds that include peptides which are the focus of this review. Peptides are increasingly being selected for drug development because they are specific for their targets and have a higher degree of interactions. There have been quite a number of endophytic peptides reported in the recent past indicating that endophytes can be used for the production of peptide based drugs. Molecular screening for NRPS, which shows peptide producing capability, has also shown that endophytes are potential producers of peptides. The presence of NRPS also offers the possibility of genetic modifications which may generate peptides with high pharmacological activities. This review, therefore, aims to show the current status of peptides isolated from endophytic bacteria and fungi in the recent decade. Endophytes as potential sources of peptides according to NRPS studies will also be discussed.

Protein as chemical cue: non-nutritional growth enhancement by exogenous protein in Pseudomonas putida KT2440

Research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. However, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. Here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of Pseudomonas putida KT2440, even when such proteins are not internalized by the cells. The growth enhancement is observed when the exogenous protein is not used as a source of carbon or nitrogen. The data show non-specific nature of the protein inducing growth; growth enhancement was observed irrespective of the protein type. It is shown that growth enhancement is mediated via increased siderophore secretion in response to the exogenous protein, leading to better iron uptake. We highlight the ecological significance of the observation and hypothesize that exogenous proteins serve as chemical cues in the case of P.putida and are perceived as indicator of the presence of competitors in the environment. It is argued that enhanced siderophore secretion in response to exogenous protein helps P.putida establish numerical superiority over competitors by way of enhanced iron assimilation and quicker utilization of aromatic substrates.

Pumping iron to keep fit: modulation of siderophore secretion helps efficient aromatic utilization in Pseudomonas putida KT2440

Studies of biotechnology applications of Pseudomonas putida KT2440 have been predominantly focused on regulation and expression of the toluene degradation (TOL) pathway. Unfortunately, there is limited information on the role of other physiological factors influencing aromatic utilization. In this report, we demonstrate that P. putida KT2440 increases its siderophore secretion in response to the availability of benzyl alcohol, a model aromatic substrate. It is argued that accelerated siderophore secretion in response to aromatic substrates provides an iron ‘boost’ which is required for the effective functioning of the iron-dependent oxygenases responsible for ring opening. Direct evidence for the cardinal role of siderophores in aromatic utilization is provided by evaluation of per capita siderophore secretion and comparative growth assessments of wild-type and siderophore-negative mutant strains grown on an alternative carbon source. Accelerated siderophore secretion can be viewed as a compensatory mechanism in P. putida in the context of its inability to secrete more than one type of siderophore (pyoverdine) or to utilize heterologous siderophores. Stimulated siderophore secretion might be a key factor in successful integration and proliferation of this organism as a bio-augmentation agent for aromatic degradation. It not only facilitates efficient aromatic utilization, but also provides better opportunities for iron assimilation amongst diverse microbial communities, thereby ensuring better survival and proliferation.

Effect of metals on a siderophore producing bacterial isolate and its implications on microbial assisted bioremediation of metal contaminated soils

A bacterial isolate producing siderophore under iron limiting conditions, was isolated from mangroves of Goa. Based on morphological, biochemical, chemotaxonomical and 16S rDNA studies, the isolate was identified as Bacillus amyloliquefaciens NAR38.1. Preliminary characterization of the siderophore indicated it to be catecholate type with dihydroxy benzoate as the core component. Optimum siderophore production was observed at pH 7 in mineral salts medium (MSM) without any added iron with glucose as the carbon source. Addition of NaCl in the growth medium showed considerable decrease in siderophore production above 2% NaCl. Fe(+2) and Fe(+3) below 2 μM and 40 μM concentrations respectively, induced siderophore production, above which the production was repressed. Binding studies of the siderophore with Fe(+2) and Fe(+3) indicated its high affinity towards Fe(+3). The siderophore concentration in the extracellular medium was enhanced when MSM was amended with essential metals Zn, Co, Mo and Mn, however, decreased with Cu, while the concentration was reduced with abiotic metals As, Pb, Al and Cd. Significant increase in extracellular siderophore production was observed with Pb and Al at concentrations of 50 μM and above. The effect of metals on siderophore production was completely mitigated in presence of Fe. The results implicate effect of metals on the efficiency of siderophore production by bacteria for potential application in bioremediation of metal contaminated iron deficient soils especially in the microbial assisted phytoremediation processes.