Aradhana Das

Advances in Manganese Pollution and Its Bioremediation

The requirement for manganese (Mn) has augmented extensively owing to the intense production of steel and the mounting paucity of natural deposits. The widespread mining, mineral processing, and further human activities have faced a severe consequence in the generation of massive quantity of manganese mining waste residues. The inappropriate supervision and unprocessed liberation of these wastes have resulted in the spread of Mn to the contiguous atmosphere, soil and groundwater pollution, and loads of severe ecological tribulations. Chronic and acute exposure of this metal pollutant leads to lethal consequences and is clinically categorized by the multiple symptoms of neurotoxicity including cognitive and psychiatric symptoms, Parkinson’s disease, manganism, motor system dysfunction, and other neurodegenerative diseases. The advancement of bioremediation technology focuses on accomplishing successful removal of these metal pollutants by increasing the effectiveness of microbes related to metal-solubilizing activities. This chapter describes a complete advance in the research on manganese environmental pollution, manganese compound-induced toxicity, and recent approaches for the microbial remediation of manganese pollutants.

Molecular Identification of Acidophilic Manganese (Mn)-Solubilizing Bacteria from Mining Effluents and Their Application in Mineral Beneficiation

ABSTRACT The study of the microbial ecology in extreme acidic environments has provided an important foundation for the development of mineral biotechnology. The present investigation reports the isolation, identification and molecular characterization of indigenous manganese (Mn) solubilizing acidophilic bacterial strains from mine water samples from Odisha, India. Four morphologically distinct bacterial strains showing visible growth on Mn-supplemented plates of varying pH were isolated and identified. Mn solubilizing ability of the isolates was tested by growing them on Mn-supplemented agar plates. The appearance of lightening around the growing colonies of all the isolates demonstrated their Mn solubilizing ability in the medium. 16 S rRNA sequencing was carried out and the bacterial isolates were taxonomically classified as Enterobacter sp. AMSB1, Bacillus cereus AMSB3, Bacillus nealsonii AMSB4 and Staphylococcus hominis AMSB5. The evolutionary timeline was studied by constructing neighbor-joining phylogenetic trees. The ability of acidophilic microorganisms to solubilize heavy metals is supported by five basic mechanisms which include: enzymatic conversion, metal effluxing, reduction in sensitivity of cellular targets, intra- or extracellular sequestration, and permeability barrier exclusion. Such ecological studies undoubtedly will provide insights into Mn biogeochemical processes occurring in leaching environments. The application of acidophilic microbiology in mineral biorecovery and beneficiation has a large future potential.

Isolation, identification and screening of manganese solubilizing fungi from low grade manganese ore deposits

ABSTRACT The present investigation reports the isolation, molecular identification and screening of manganese (Mn) solubilizing fungal strains from low-grade Mn mine tailings. Six morphologically distinct Mn solubilizing fungal strains were isolated on MnO2-supplemented agar plates with Mn concentration of 0.1% (w/v). The biochemical characterization of the isolated fungal strains was carried out. The molecular identification by internal transcribed spacer (ITS) sequencing identified the strains as Aspergillus terreus, Aspergillus oryzae, Penicillium sp., Penicillium sp., Penicillium daleae and Penicillium sp. with GenBank accession numbers KP309809, KP309810, KP309811, KP309812, KP309813 and KP309814, respectively. The ability of the isolated fungal strains to tolerate and solubilize Mn was investigated by subculturing them on Mn-supplemented plates with concentration ranging from 0.1 to 0.5% (w/v). Mn solubilizing ability of the fungal isolates is possibly due to the mycelia production of biogenerated organic acids such as oxalic acid, citric acid, maleic acid and gluconic acid as revealed by ion chromatography. Our investigation signifies the role of fungi in biotransformation of insoluble Mn oxide.

Comparative Analysis of 16S rRNA Gene Illumina Sequence for Microbial Community Structure in Diverse Unexplored Hot Springs of Odisha, India

ABSTRACT Odisha (East India) is home to several hot springs, of which Atri and Taptapani are the two with variation in temperature and located in the Mahanadi geothermal province having altitude 120 and 1800 ft., respectively, above sea level. Average temperature of Atri hot spring is as higher as 58 ± 5°C as compared to 48 ± 5°C of Taptapani. In-depth analysis of the microbial diversity of these hot springs through 16S rRNA deep sequencing analysis, targeting V3 region was performed using Illumina bar-coded sequencing platform. Existence of higher microbial diversity in Atri hot spring (1662 OTUs; 2708 species) as compared to Taptapani (1561 Operational Taxonomic Units [OTUs]; 2045 species) is supported by higher value of diversity indices for Atri (6.24, Shannon; 0.95, Simpson) than Taptapani (4.03, Shannon; 0.79, Simpson), probably due to favorable influence of environmental parameters around it. Irrespective of the four databases (GREENGENE, M5RNA, Ribosomal Database Project [RDP], and Small Subunit [SSU] databases) used for understanding community structure, the dominant phyla in the Atri hot spring were different from the predominant populations in the Taptapani in terms of percentage representation in different databases. From Principal Coordinates Analysis [PCoA] analysis, Atri and Taptapani metagenome, on comparison with other three metagenomes, were found to be matching with the community structure of hot springs of Gujarat, India, but differed from that of saline desert. Furthermore, predicted functional analysis in both the hot springs were found to be affiliated with carbohydrate, amino acids, energy, vitamins and cofactor, nucleotide, membrane transport metabolic pathways, and the genes involved in them, although their intensity of occurrence was varying as analyzed through PICRUSt and Tax4Fun probably due to physicochemical parameters prevailing around each hot spring. The present study for the first time has revealed the differential microbial community structure and predicted functional diversity of Atri and Taptapani hot springs of Odisha in such a great detail.

De Novo transcriptome assembly of Zingiber officinale cv. Suruchi of Odisha

Zingiber officinale Rosc., known as ginger, is an Asian crop, popularly used in every household kitchen and commercially used in bakery, beverage, food and pharmaceutical industries. The present study deals with de novo transcriptome assembly of an elite ginger cultivar Suruchi by next generation sequencing methodology. From the analysis 10.9 GB raw data was obtained which can be available in NCBI accession number SAMN03761185. We identified 41,969 transcripts using Trinity RNA-Seq from ginger rhizome of Suruchi variety from Odisha. The transcript length varied from 300 bp to 8404 bp with a total length of 3,96,40,526 bp and N50 of 1251 bp. To the best of our knowledge, this is the first transcriptome data of an elite ginger cultivar Suruchi released for Odisha state of India which will help molecular biologists to develop genetic markers for identification of cultivars.

Shift in Cyanobacteria Community Diversity in Hot Springs of India

ABSTRACT Two ecologically distinct tropical sulfur-rich alkaline hot springs, Taptapani at 48°C harboring mesophiles and Atri at 58°C comprising thermophiles situated in the Eastern Ghats foothills of India, differ in their geochemical conditions, and provide an interesting platform to unravel the eco-physiological reasons behind the differential cyanobacterial diversity. The predominance of mesophilic Arthronema (83.81%) in Taptapani and shifting predominance of thermophilic Leptolyngbya (96.25%) in Atri as discovered through 16S rRNA gene Illumina sequencing of their metagenomics DNA as a function of temperature are the intriguing features of the present study. Differential presence of the cyanobacterial community at the phylum level in these two hot springs was found to be correlated with the unequal coexistence of Chloroflexi, Taptapani the non-cyanobacteria members and the possible influence of physiochemical parameters including temperature. Variation in cyanobacterial diversity and composition of these hot springs as revealed through sequence analysis were also evinced by respective differences in richness, evenness, and Shannon diversity indices.

High frequency shoot proliferation from cotyledonary node of Lawsonia inermis L. and validation of their molecular finger printing

An efficient and reproducible protocol for in vitro plant regeneration was developed for Lawsonia inermis L. using cotyledonary node explant derived from axenic seedlings. Highest shoot proliferation frequency (ca 96.6%) was achieved on Murashige and Skoog’s, 1962 (MS) basal medium supplemented with 8.88 μM 6-Benzyladenine (BA) + 2.68 μM Napthalene acetic acid (NAA). Up-scaling of shoots was carried out using in vitro nodes on MS medium supplemented with 4.44 μM BA. So overall, an average of 238 shoots was produced at 75 days. Of the four different forms of cotyledonary node explants evaluated, highest shoot multiplication was observed in cotyledonary node explant with two whole cotyledons. In vitro regenerated shoots were best rooted (ca 34.3 roots / shoot) on ½ MS medium devoid of any growth regulator. The plantlets were successfully acclimated in sand:soil:: 1:1and established in the garden soil. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis revealed a homogeneous amplification profile for all micropropagated plants validating the genetic fidelity of the in vitro-regenerated plants and supporting the regeneration protocol for economic commercial exploitation.

Unraveling Plant-Endophyte Interactions: An Omics Insight

Plants are home to a wide assemblage of nonpathogenic microbial community belonging to different phyla, bacteria, fungi, actinomycetes and viruses, the collective term for which is called endophyte. These endosymbiotic individuals exhibit endophytism principally by assisting in vigor and endurance to host plant and protect them from biotic (pathogenic infections) and abiotic stress (water, heat, nutrient, salinity, and herbivory). In return, these endosymbionts receive energy in the form of carbon from the host tissue. Colonization of endophyte in the internal tissues has been reported almost in every plant examined so far either E. Subudhi (*) · R. K. Sahoo · S. Dey · A. Das · K. Sahoo Centre for Biotechnology, Siksha O Anusandhan Deemed to be University, Bhubaneswar, India e-mail: enketeswarasubudhi@soa.ac.in; rajeshkumarsahoo@soa.ac.in; suchandadey1993@gmail.com; aradhanadas@soa.ac.in; kalpanasahoo@soa.ac.in # Springer Nature Switzerland AG 2018 S. Jha (ed.), Endophytes and Secondary Metabolites, Reference Series in Phytochemistry, https://doi.org/10.1007/978-3-319-76900-4_2-1 1 in intercellular or intracellular mode. The form of relationships established with the host plant may be mutualistic, symbiotic, commensalistic, and trophobiotic. These are either rhizospheric or phyllospheric in origin. To establish such mutualistic relationships between plants and endophytes, certain chemical signals play important role in inducing production of the enhanced amount of secondary metabolites in host plant tissues. These novel metabolites act as a very good source of stress relievers to host and protect from grazing animals. The renewed interest in endophyte is due to the biotechnological relevance of these signal molecules as these have been used as a good source for production of biochemical compounds of industrial importance more specifically in agriculture and medicine. Additionally, their capacity to decontaminate soil bacteria and bring in soil fertility invites huge application in phytoremediation. However, the physiology, biochemistry, and genetics behind such complex interactions, exchange of chemical signals, and their production (the endophytism of plan-microbiome) are still half-understood. With the advent of new efficient analytical technology in molecular biology and genomics, the basic information on the existing diversity, phylogenetic lineage, evolution, and ecophysiological information about these endophytes has been tried to understand. However, the functional gene expression, posttranslational modifications, and protein turnover under various environmental circumstances are only revealed through transcriptome and proteomics analysis. Soon, high-throughput next-generation sequencing technology has remarkably changed the whole scenario of solving the intricate issues entangled with the complexity underlying endophytism. Sequencing of the whole genome of individuals following cultivable method (genomics), multiple host plants and their microbiome (comparative genomics), non-cultivable methods (metagenomics and metatranscriptomics), and microarray has been proved to be potential approaches to unravel the truth behind the plant-endophyte interactions. The present script deals with scopes, prospects, and outcomes of use of these “omics tools” to understand the deep insight into the mechanism of plant host infestation, biological reason behind the mutualism between host and endophytes, exchange of biochemical compounds, enhanced production of secondary metabolite, and host plant ecology.

Genetic diversity analysis of 60 ginger germplasm core accessions using ISSR and SSR markers

Abstract Molecular techniques play a critical role in studies of phylogeny and, thus, have been applied to understand the distribution and extent of genetic variation within and between species. In the present study, a genetic analysis was undertaken using molecular markers (9 ISSR and 13 SSR) on 60 ginger cultivars from different regions of the eastern coast of India (Odisha). The data obtained with 22 polymorphic markers revealed moderate to high diversity in the collection. Both ISSR and SSR markers were efficient in distinguishing all the 60 ginger cultivars. A total of 42 and 160 polymorphic bands were observed with ISSR and SSR markers, respectively. However, SSR markers were observed to be better at displaying average polymorphism (63.29%) than ISSR markers (55%). Analysis of molecular variance results showed that 52 and 66% of the variation occurred among different ginger populations, whereas 48 and 34% of the variation was found within populations, respectively, using ISSR and SSR markers, indicating that ginger cultivars display significant genetic diversity at the population level. Principal coordinates analysis and the dendrogram constructed out of combined data of both markers showed grouping of ginger accessions to their respective area of collection, indicating geographical closeness due to genetic similarity irrespective of the relationship that exists at the morphological level.

Comparative transcriptome analysis of ginger variety Suprabha from two different agro-climatic zones of Odisha

Ginger (Zingiber officinale Rosc.), a well-known member of family Zingiberaceae, is bestowed with number of medicinal properties which is because of the secondary metabolites, essential oil and oleoresin, it contains in its rhizome. The drug yielding potential is known to depend on agro-climatic conditions prevailing at the place cultivation. Present study deals with comparative transcriptome analysis of two sample of elite ginger variety Suprabha collected from two different agro-climatic zones of Odisha. Transcriptome assembly for both the samples was done using next generation sequencing methodology. The raw data of size 10.8 and 11.8 GB obtained from analysis of two rhizomes S1Z4 and S2Z5 collected from Bhubaneswar and Koraput and are available in NCBI accession number SAMN03761169 and SAMN03761176 respectively. We identified 60,452 and 54,748 transcripts using trinity tool respectively from ginger rhizome of S1Z4 and S2Z5. The transcript length varied from 300 bp to 15,213 bp and 8988 bp and N50 value of 1415 bp and 1334 bp respectively for S1Z4 and S2Z5. To the best of our knowledge, this is the first comparative transcriptome analysis of elite ginger cultivars Suprabha from two different agro-climatic conditions of Odisha, India which will help to understand the effect of agro-climatic conditions on differential expression of secondary metabolites.