Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions

Polívková, Markéta; Šuman, Jáchym; Strejcek, Michal; Kracmarova, Martina; Hradilová, Miluše; Filipová, Alena; Cajthaml, Tomáš; Macek, Tomáš; Uhlík, Ondřej

doi:10.1016/j.apsoil.2018.02.002

Cited by 20 publications

(10 citation statements)

References 87 publications

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“…Acidothermus is a monospecic genus described as thermophilic, acidophilic, and cellulolytic bacterium which can also degrade chitin [2, 3]. However, there are previous reports of genus Acidothermus being enriched in the salinized rhizosphere of Tamarixparviflora [4]. It was also observed that the pond sediment exhibited 308 genera ( Supplementary data 2 ) out of which 46.9% of the genus were unclassified indicating the potential novel genus yet to be discovered.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine

Radhakrishnan

Imchen

Kaari

et al. 2018

Preprint

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44Metagenomic analysis holds immense potential for identifying rare and uncharacterized 45 microorganisms from many ecological habitats. Actinobacteria have been proved to be an 46 excellent source of novel antibiotics for several decades. The present study was designed to 47 delineate and understand the bacterial diversity with special focus on Actinobacteria from pond 48 sediment collected from Sanjeeviraya Hanuman Temple, Ayyangarkulam, Kanchipuram, Tamil 49 Nadu, India. The sediment had an average temperature (25.32%), pH (7.13), salinity (0.960 50 mmhos/cm) and high organic content (10.7%) posing minimal stress on growth condition of the 51 microbial community. Subsequent molecular manipulations, sequencing and bioinformatics 52 analysis of V3 and V4 region of 16S rRNA metagenomics analysis confirmed the presence of 40 53 phyla, 100 classes, 223 orders, 319 families and 308 genera in the sediment sample dominated by 54 56(1.63%). Among the Actinobacteria phylum, Acidothermus (29.68%) was the predominant genus 57 followed by Actinospica (17.65%), Streptomyces (14.64%), Nocardia (4.55%) and Sinomonas 58 (2.9%). Culture-dependent isolation of Actinobacteria yielded all strains of similar morphology 59 to that of Streptomyces genus which clearly indicating that the traditional based technique is 60 incapable of isolating majority of the non-Streptomyces or the so called rare Actinobacteria. 61 Although Actinobacteria were among the dominant phylum, a close look at the species level 62 indicated that only 15.2% within the Actinobacterial phylum could be assigned to cultured 63 species. This leaves a vast majority of the Actinobacterial species yet to be explored with 64 possible novel metabolites have special pharmaceutical and industrial application. It also 65 indicates that the microbial ecology of pond sediment is neglected fields which need attention. 66 67 metabolites 68 It is estimated that only 1% of microbes in the natural environment are culturable under 70 laboratory conditions [46]. More than 88% of culturable isolates belong to four phyla known as 71 Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes [47]. However, uncultivated 72 bacteria possess a great diversity of enzymes adaptable to different environmental conditions 73 which could serve as a prolific source of novel bioactive compounds with industrial and 74 pharmaceutical applications. Metagenomics is a tool to study massive microbial communities 75 prevailing in the environment in its natural state irrespective of its uncultivable properties. This 76technique has not only helped to overcome the barriers of culture dependent techniques but also 77 identified rare microorganisms [23]. It also provides a wide and unbiased view of the potential 78 microbial functions in a single snapshot with high resolution contributing immensely to the 79 global microbial diversity studies from different ecosystem and their potential ecological 80 functions [27]. On the other hand, there have been several reports on the widespread distribution...

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Section: Discussionmentioning

confidence: 99%

Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine

Radhakrishnan

Imchen

Kaari

et al. 2018

Preprint

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“…Reconditioning PCR products were purified using AMPure XP Beads (Agencourt, Beckman Coulter, Brea, CA, United States) following the manufacturer’s instructions and pooled together for sequencing. Pyrosequencing was performed unidirectionally from the forward primer using a GS FLX + system with Titanium reagents (Roche, Germany) as described elsewhere ( Polivkova et al, 2018 ). An analogous procedure was applied to total community DNA, which was isolated prior to the construction of SIP microcosms ( Uhlik et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

et al. 2021

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In this study, the diversity of bphA genes was assessed in a 13C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with 13C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.

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“…Acidothermus is a monospecific genus described as thermophilic, acidophilic, and cellulolytic bacterium which can also degrade chitin [2,3]. However, there are previous reports of genus Acidothermus being enriched in the salinized rhizosphere of Tamarixparviflora [4]. It was also observed that the pond sediment exhibited 308 genera (Supplementary data 2) out of which 46.9% of the genus were unclassified indicating the potential novel genus yet to be discovered.…”

Section: Pond Sediment Microbial Community Structurementioning

confidence: 98%

Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine

et al. 2020

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Metagenomic analysis holds immense potential for identifying rare and uncharacterized microorganisms from many ecological habitats. Actinobacteria have been proved to be an excellent source of novel antibiotics for several decades. The present study was designed to delineate and understand the bacterial diversity with special focus on Actinobacteria from pond sediment collected from Sanjeeviraya Hanuman Temple, Ayyangarkulam, Kanchipuram, Tamil Nadu, India. The sediment had an average temperature (25.32%), pH (7.13), salinity (0.960 mmhos/cm) and high organic content (10.7%) posing minimal stress on growth condition of the microbial community. Subsequent molecular manipulations, sequencing and bioinformatics analysis of V3 and V4 region of 16S rRNA metagenomics analysis confirmed the presence of 40 phyla, 100 classes, 223 orders, 319 families and 308 genera in the sediment sample dominated by Acidobacteria (18.14%), Proteobacteria (15.13%), Chloroflexi (12.34), Actinobacteria (10.84%), Cyanobacteria (5.58%), Verrucomicrobia (3.37%), Firmicutes (2.28%), and, Gemmatimonadetes (1.63%). Among the Actinobacteria phylum, Acidothermus (29.68%) was the predominant genus followed by Actinospica (17.65%), Streptomyces (14.64%), Nocardia (4.55%) and Sinomonas (2.9%). Culture-dependent isolation of Actinobacteria yielded all strains of similar morphology to that of Streptomyces genus which clearly indicating that the traditional based technique is incapable of isolating majority of the non-Streptomyces or the so called rare Actinobacteria.Although Actinobacteria were among the dominant phylum, a close look at the species level indicated that only 15.2% within the Actinobacterial phylum could be assigned to cultured species. This leaves a vast majority of the Actinobacterial species yet to be explored with possible novel metabolites have special pharmaceutical and industrial application. It also indicates that the microbial ecology of pond sediment is neglected fields which need attention..

show abstract

Diversity of root-associated microbial populations of Tamarix parviflora cultivated under various conditions

Cited by 20 publications

References 87 publications

Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine

Metagenomic Insights Unveil the Dominance of Undescribed Actinobacteria in Pond Ecosystem of an Indian Shrine

Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone

Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine

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