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Differential capacity of phragmites ecotypes in remediation of inorganic contaminants in coastal ecosystems: Implications for climate change

Akhter N, Aqeel M, Shazia, Irshad MK, Shehnaz MM, Lee SS, et al.

Environ Res, 2024 Apr 15;247:118127.
PMID: 38220075 DOI: 10.1016/j.envres.2024.118127

Remediating inorganic pollutants is an important part of protecting coastal ecosystems, which are especially at risk from the effects of climate change. Different Phragmites karka (Retz) Trin. ex Steud ecotypes were gathered from a variety of environments, and their abilities to remove inorganic contaminants from coastal wetlands were assessed. The goal is to learn how these ecotypes process innovation might help reduce the negative impacts of climate change on coastal environments. The Phragmites karka ecotype E1, found in a coastal environment in Ichkera that was impacted by residential wastewater, has higher biomass production and photosynthetic pigment content than the Phragmites karka ecotypes E2 (Kalsh) and E3 (Gatwala). Osmoprotectant accumulation was similar across ecotypes, suggesting that all were able to successfully adapt to polluted marine environments. The levels of both total soluble sugars and proteins were highest in E2. The amount of glycine betaine (GB) rose across the board, with the highest levels being found in the E3 ecotype. The study also demonstrated that differing coastal habitats significantly influenced the antioxidant activity of all ecotypes, with E1 displaying the lowest superoxide dismutase (SOD) activity, while E2 exhibited the lowest peroxidase (POD) and catalase (CAT) activities. Significant morphological changes were evident in E3, such as an expansion of the phloem, vascular bundle, and metaxylem cell areas. When compared to the E3 ecotype, the E1 and E2 ecotypes showed striking improvements across the board in leaf anatomy. Mechanistic links between architectural and physio-biochemical alterations are crucial to the ecological survival of different ecotypes of Phragmites karka in coastal environments affected by climate change. Their robustness and capacity to reduce pollution can help coastal ecosystems endure in the face of persistent climate change.

Matched MeSH terms: Ecotype*
Fulltext Fine-scale population structure and ecotypes of anadromous Hilsa shad (Tenualosa ilisha) across complex aquatic ecosystems revealed by NextRAD genotyping

Asaduzzaman M, Wahab MA, Rahman MJ, Nahiduzzzaman M, Dickson MW, Igarashi Y, et al.

Sci Rep, 2019 11 05;9(1):16050.
PMID: 31690767 DOI: 10.1038/s41598-019-52465-2

The anadromous Hilsa shad (Tenualosa ilisha) live in the Bay of Bengal and migrate to the estuaries and freshwater rivers for spawning and nursing of the juveniles. This has led to two pertinent questions: (i) do all Hilsa shad that migrate from marine to freshwater rivers come from the same population? and (ii) is there any relationship between adults and juveniles of a particular habitat? To address these questions, NextRAD sequencing was applied to genotype 31,276 single nucleotide polymorphism (SNP) loci for 180 individuals collected from six strategic locations of riverine, estuarine and marine habitats. FST OutFLANK approach identified 14,815 SNP loci as putatively neutral and 79 SNP loci as putatively adaptive. We observed that divergent local adaptations in differing environmental habitats have divided Hilsa shad into three genetically structured ecotypes: turbid freshwater (Western Riverine), clear freshwater (Eastern Riverine) and brackish-saline (Southern Estuarine-Marine). Our results also revealed that genes involved in neuronal activity may have facilitated the juveniles' Hilsa shad in returning to their respective natal rivers for spawning. This study emphasized the application of fundamental population genomics information in strategizing conservation and management of anadromous fish such as Hilsa shad that intersect diverse ecotypes during their life-history stages.

Matched MeSH terms: Ecotype*
Fulltext Genetic Variability, Heritability, and Clustering Pattern Exploration of Bambara Groundnut (Vigna subterranea L. Verdc) Accessions for the Perfection of Yield and Yield-Related Traits

Khan MMH, Rafii MY, Ramlee SI, Jusoh M, Mamun A

Biomed Res Int, 2020;2020:2195797.
PMID: 33415143 DOI: 10.1155/2020/2195797

Bambara groundnut (Vigna subterranea L. Verdc.) is considered an emerging crop for the future and known as a crop for the new millennium. The core intention of this research work was to estimate the variation of landraces of Bambara groundnut considering their 14 qualitative and 27 numerical traits, to discover the best genotype fitted in Malaysia. The findings of the ANOVA observed a highly significant variation (p ≤ 0.01) for all the traits evaluated. There was a substantial variation (7.27 to 41.21%) coefficient value, and 14 out of the 27 numerical traits noted coefficient of variation (CV) ≥ 20%. Yield (kg/ha) disclosed positively strong to perfect high significant correlation (r = 0.75 to 1.00; p ≤ 0.001) with traits like fresh pod weight, dry pod weight, and dry seed weight. The topmost PCV and GCV values were estimated for biomass dry (41.09%) and fresh (40.53%) weight with high heritability (Hb) and genetic advance (GA) Hb = 95.19%, GA = 80.57% and Hb = 98.52%, GA = 82.86%, respectively. The topmost heritability was recorded for fresh pod weight (99.89%) followed by yield (99.75%) with genetic advance 67.95% and 62.03%, respectively. The traits with Hb ≥ 60% and GA ≥ 20% suggested the least influenced by the environment as well as governed by the additive genes and direct selection for improvement of such traits can be beneficial. To estimate the genetic variability among accessions, the valuation of variance components, coefficients of variation, heritability, and genetic advance were calculated. To authenticate the genetic inequality, an unweighted pair group produced with arithmetic mean (UPGMA) and principal component analysis was executed based on their measurable traits that could be a steadfast method for judging the degree of diversity. Based on the UPGMA cluster analysis, constructed five distinct clusters and 44 accessions from clusters II and IV consider an elite type of genotypes that produce more than one ton yield per hectare land with desirable traits. This study exposed an extensive disparity among the landraces and the evidence on genetic relatives will be imperative in using the existing germplasm for Bambara groundnut varietal improvement. Moreover, this finding will be beneficial for breeders to choose the desirable numerical traits of V. subterranea in their future breeding program.

Matched MeSH terms: Ecotype*
Fulltext Evaluation of antioxidant compounds, antioxidant activities, and mineral composition of 13 collected purslane (Portulaca oleracea L.) accessions

Alam MA, Juraimi AS, Rafii MY, Abdul Hamid A, Aslani F, Hasan MM, et al.

Biomed Res Int, 2014;2014:296063.
PMID: 24579078 DOI: 10.1155/2014/296063

The methanolic extracts of 13 accessions of purslane were analyzed for their total phenol content (TPC), total flavonoid contents (TFC), and total carotenoid contents (TCC) and antioxidant activity of extracts was screened using FRAP assay and DPPH radical scavenging methods. The TPC, TFC, and TCC ranged from 0.96 ± 0.04 to 9.12 ± 0.29 mg GAE/g DW, 0.13 ± 0.04 to 1.44 ± 0.08 mg RE/g DW, and 0.52 ± 0.06 to 5.64 ± 0.09 mg (β-carotene equivalent) BCE/g DW, respectively. The DPPH scavenging (IC50) activity varied between 2.52 ± 0.03 mg/mL and 3.29 ± 0.01 mg/mL and FRAP ranged from 7.39 ± 0.08 to 104.2 ± 6.34 μmol TE/g DW. Among all the measured micro- and macrominerals K content was the highest followed by N, Na, Ca, Mg, P, Fe, Zn, and Mn. The overall findings proved that ornamental purslane was richer in antioxidant properties, whereas common purslane possesses more mineral contents than ornamental ones.

Matched MeSH terms: Ecotype*
Ultrastructural aspects of sylvatic dengue virus infection in Vero cell

Fish-Low CY, Abubakar S, Othman F, Chee HY

Malays J Pathol, 2019 Apr;41(1):41-46.
PMID: 31025636

INTRODUCTION: Dengue virus (DENV), the causative agent of dengue disease exists in sylvatic and endemic ecotypes. The cell morphological changes and viral morphogenesis of two dengue ecotypes were examined at the ultrastructural level to identify potential similarities and differences in the surrogate model of enzootic host.
MATERIALS AND METHODS: Vero cells were inoculated with virus at a multiplicity of infection (MOI) of 0.1. Cell cultures were harvested over a time course and processed for transmission electron microscopic imaging.
RESULTS: The filopodia protrusions on cell periphery preceded virus entry. Additionally, sylvatic DENV infection was found spreading slower than the endemic DENV. Morphogenesis of both dengue ecotypes was alike but at different level of efficiency in the permissive cells.
CONCLUSIONS: This is the first ultrastructural study on sylvatic DENV and this comparative study revealed the similarities and differences of cellular responses and morphogenesis of two dengue ecotypes in vitro. The study revealed the weaker infectivity of sylvatic DENV in the surrogate model of enzootic host, which supposed to support better replication of enzootic DENV than endemic DENV.

Matched MeSH terms: Ecotype
Ultrastructural changes of cell morphology and viral morphogenesis of two ecotypes of dengue virus infection in human monocytic U-937 cell

Fish-Low CY, Abu Bakar S, Othman F, Chee HY

Trop Biomed, 2018 Dec 01;35(4):1154-1159.
PMID: 33601863

Dengue virus (DENV) is maintained and circulated in both sylvatic/enzootic and endemic/human cycles and spill over infection of sylvatic DENV into human populations has been reported. Extensive deforestation and increase human activities in forest may increase the risk of human exposure to sylvatic dengue infection and this may become a threat to human. Present study investigated the changes in cell morphology and viral morphogenesis upon infection with sylvatic and endemic ecotypes in human monocytic U-937 cells using transmission electron microscopy. Autophagy, a process that is either pro-viral or anti-viral, was observed in U-937 cells of both infections, however only the replication of endemic DENV was evidenced. An insight into the infection responses of sylvatic progenitors of DENV in susceptible host cells may provide better understanding on dengue emergence in human populations.

Matched MeSH terms: Ecotype
Characterization of a Saccharum spontaneum with a basic chromosome number of x = 10 provides new insights on genome evolution in genus Saccharum

Meng Z, Han J, Lin Y, Zhao Y, Lin Q, Ma X, et al.

Theor Appl Genet, 2020 Jan;133(1):187-199.
PMID: 31587087 DOI: 10.1007/s00122-019-03450-w

KEY MESSAGE: A novel tetraploid S. spontaneum with basic chromosome x = 10 was discovered, providing us insights in the origin and evolution in Saccharum species. Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world's sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, we developed the first set of oligonucleotide (oligo)-based probes based on the S. spontaneum genome (x = 8), which can be used to simultaneously distinguish each of the 64 chromosomes of octaploid S. spontaneum SES208 (2n = 8x = 64) through fluorescence in situ hybridization (FISH). By comparative FISH assay, we confirmed the chromosomal rearrangements of S. spontaneum (x = 8) and S. officinarum (2n = 8x = 80), the main contributors of modern sugarcane cultivars. In addition, we examined a S. spontaneum accession, Np-X, with 2n = 40 chromosomes, and we found that it was a tetraploid with the unusual basic chromosome number of x = 10. Assays at the cytological and DNA levels demonstrated its close relationship with S. spontaneum with basic chromosome number x = 8 (the most common accessions in S. spontaneum), confirming its S. spontaneum identity. Population genetic structure and phylogenetic relationship analyses between Np-X and 64 S. spontaneum accessions revealed that Np-X belongs to the ancient Pan-Malaysia group, indicating a close relationship to S. spontaneum with basic chromosome number of x = 8. This finding of a tetraploid S. spontaneum with basic chromosome number of x = 10 suggested a parallel evolution path of genomes and polyploid series in S. spontaneum with different basic chromosome numbers.

Matched MeSH terms: Ecotype