Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India

A Cyclic Disulfide Diastereomer From Bioactive Fraction of Bruguiera gymnorhiza Shows Anti-Pseudomonas aeruginosa Activity

Pseudomonas aeruginosa is an opportunistic pathogen that commonly causes hospital-acquired infection and is of great concern in immunocompromised patients. The quorum sensing (QS) mechanism of P. aeruginosa is well studied and known to be responsible for pathogenicity and virulence. The QS inhibitor derived from the natural product can be an important therapeutic agent for pathogen control. The present study reports the role of Bruguiera gymnorhiza purified fraction (BG138) in inhibiting virulence factor production, biofilm formation, quorum sensing molecules, and expression of QS-related genes of P. aeruginosa. Structural characterization of BG138 by high resolution mass spectrometry, Fourier transform infrared spectroscopy, 1D (¹H and ¹³C NMR) and 2D NMR reveals that the fraction is a mixture of already known cyclic disulfide diastereomer, namely, brugierol and isobrugierol. The minimum inhibitory concentration (MIC) of BG138 against P. aeruginosa was 32 μg/ml. Biofilm formation was significantly reduced at sub-MIC concentrations of BG138. Scanning electron microscopy analysis reports the concentration-dependent biofilm inhibition and morphological changes of P. aeruginosa. Flow cytometry–based cell viability assay showed that P. aeruginosa cells exhibit increased propidium iodide uptake on treatment with 32 and 64 μg/ml of BG138. At sub-MIC concentrations, BG138 exhibited significant inhibition of virulence factors and reduced swimming and swarming motility of P. aeruginosa. Furthermore, the effect of BG138 on the expression of QS-related genes was investigated by qRT-PCR. Taken together, our study reports the isolation and structural characterization of bioactive fraction BG138 from B. gymnorhiza and its anti-biofilm, anti-virulence, anti-quorum sensing, and cell-damaging activities against P. aeruginosa.

Metabolite profiling of Bruguiera cylindrica reveals presence of potential bioactive compounds

Bruguiera cylindrica parts are commonly used in Chinese and Indian traditional medicine to treat diarrhea, fever, and many ailments. The present study aims non targeted analysis of key secondary metabolites of B. cylindrica by gas chromatography mass spectrometry (GC-MS) and ultra-high performance liquid chromatography hybrid quadrupole-Exactive-Orbitrap high resolution mass spectrometry (UHPLC-Q-Exactive Orbitrap HRMS). GC-MS and UHPLC-Q-Exactive Orbitrap HRMS were utilized for metabolic profiling of ethyl acetate extract of B. cylindrica leaves. Key metabolites in the extract were identified and predicted based on chemical similarity using online databases such as ChemSpider and mzCloud. Thirty-six compounds belonging to different classes of secondary metabolites viz. flavonoids, fatty acids, fatty acid amides, carboxylic acids, and alkaloids were identified in the extract. Pentacyclic triterpenes like betulin, ursolic acid and a tropine, an alkaloid with potential pharmacological and therapeutic activities such as anticancer properties, neuromuscular blockers and antioxidants, were also identified. This study combined GC-MS and UHPLC-Q-Exactive Orbitrap HRMS with available online database for effective and rapid identification of bioactive metabolites in the ethyl acetate extract of mangrove without individual standard application. This is the first report on the HRMS based secondary metabolic profiling of B. cylindrica, with comprehensive map of its biologically important metabolites.

Diversity investigation by application of DNA barcoding: A case study of lepidopteran insects in Xinjiang wild fruit forests, China

To investigate the species diversity of lepidopteran insects in Xinjiang wild fruit forests, establish insect community monitoring systems, and determine the local species pool, we test the applicability of DNA barcoding based on cytochrome c oxidase subunit I (COI) gene for accurate and rapid identification of insect species. From 2017 to 2019, a total of 212 samples with ambiguous morphological identification were selected for DNA barcoding analysis. Five sequence‐based methods for species delimitation (ABGD, BINs, GMYC, jMOTU, and bPTP) were conducted for comparison to traditional morphology‐based identification. In total, 2,422 samples were recorded, representing 143 species of 110 genera in 17 families in Lepidoptera. The diversity analysis showed that the richness indices for Noctuidae was the highest (54 species), and for Pterophoridae, Cossidae, Limacodidae, Lasiocampidae, Pieridae, and Lycaenidae were the lowest (all with 1 species). The Shannon–Wiener species diversity index (H′) and Pielou's evenness (J′) of lepidopteran insects first increased and then decreased across these 3 years, while the Simpson diversity index showed a trend of subtracted then added. For molecular‐based identification, 67 lepidopteran species within 61 genera in 14 families were identified through DNA barcoding. Neighbor‐joining (NJ) analysis showed that conspecific individuals were clustered together and formed monophyletic groups with a high support value, except for Lacanobia contigua (Denis & Schiffermüller, 1775) (Noctuidae: Hadeninae). Sixty‐seven morphospecies were classified into various numbers of MOTUs based on ABGD, BINs, GMYC, jMOTU, and bPTP (70, 96, 2, 71, and 71, respectively). In Xinjiang wild fruit forests, the family with the largest number of species is Noctuidae, followed by Geometridae, Crambidae, and the remaining families. The highest Shannon diversity index is observed for the family Noctuidae. Our results indicate that the distance‐based methods (ABGD and jMOTU) and character‐based method (bPTP) outperform GMYC. BINs is inclined to overestimate species diversity compared to other methods.

Multilocus marker-based delimitation of Salicornia persica and its population discrimination assisted by supervised machine learning approach

The Salicornia L. has been considered one of the most taxonomically challenging genera due to high morphological plasticity, intergradation between related species, and lack of diagnostic features in preserved herbarium specimens. In the United Arab Emirates (UAE), only one species of this genus, Salicornia europaea, has been reported, though investigating its identity at the molecular level has not yet been undertaken. Moreover, based on growth form and morphology variation between the Ras-Al-Khaimah (RAK) population and the Umm-Al-Quwain (UAQ) population, we suspect the presence of different species or morphotypes. The present study aimed to initially perform species identification using multilocus DNA barcode markers from chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA), followed by the genetic divergence between two populations (RAK and UAQ) belonging to two different coastal localities in the UAE. The analysis resulted in high-quality multilocus barcode sequences subjected to species discrimination through the unsupervised OTU picking and supervised learning methods. The ETS sequence data from our study sites had high identity with the previously reported sequences of Salicornia persica using NCBI blast and was further confirmed using OTU picking methods viz., TaxonDNAs Species identifier and Assemble Species by Automatic Partitioning (ASAP). Moreover, matK sequence data showed a non-monophyletic relationship, and significant discrimination between the two populations through alignment-based unsupervised OTU picking, alignment-free Co-Phylog, and alignment & alignment-free supervised learning approaches. Other markers viz., rbcL, trnH-psbA, ITS2, and ETS could not distinguish the two populations individually, though their combination with matK (cpDNA & cpDNA+nrDNA) showed enough population discrimination. However, the ITS2+ETS (nrDNA) exhibited much higher genetic divergence, further splitting both the populations into four haplotypes. Based on the observed morphology, genetic divergence, and the number of haplotypes predicted using the matK marker, it can be suggested that two distinct populations (RAK and UAQ) do exist. Further extensive morpho-taxonomic studies are required to determine the inter-population variability of Salicornia in the UAE. Altogether, our results suggest that S. persica is the species that grow in the present study area in UAE, and do not support previous treatments as S. europaea.

Establishing community-wide DNA barcode references for conserving mangrove forests in China

BACKGROUND

Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering 'blue carbon'. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country's coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification.

RESULTS

To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances.

CONCLUSION

We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

Comparative analyses of sooty mould communities from Brazil and Central Europe

To gain an insight into fungal sooty mould communities on leaves of trees and shrubs in the tropics and in temperate regions, 47 biofilms of the Mata Atlântica rainforest relic and the Caatinga vegetation in the state of Sergipe, Northeast Brazil, and from Central European colline and alpine zones were compared. The four sampling sites clearly differed in composition of their epiphyllous fungal communities. The fungal OTUs from all sites belonged mainly to the Ascomycota, with Dothideomycetes being the dominant class. The core community group consisted of a few site-specific representatives in co-occurrence with the ubiquitous Mycosphaerella tassiana and Aureobasidium pullulans. Most species of the core community were dark pigmented and were accompanied by facultative unpigmented or lightly pigmented species. Among the cultivable fungal species, the proportion of melanised species was significantly more abundant in samples from the two European sites, which supports the theory of thermal melanism. The identity of the host plant had a stronger impact on fungal community composition than the presence of sap-feeding insects.

DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria

Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require both morphological diagnostics and molecular tools, such as DNA barcoding, for correct identification. In particular, the use of the subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding has proven useful in species identification for insects. However, to date, no studies have been carried out on the DNA barcoding of Nigerian butterflies. We evaluated the utility of DNA barcoding applied for the first time to 735 butterfly specimens from southern Nigeria. In total, 699 DNA barcodes, resulting in a record of 116 species belonging to 57 genera, were generated. Our study sample comprised 807 DNA barcodes based on sequences generated from our current study and 108 others retrieved from BOLD. Different molecular analyses, including genetic distance-based evaluation (Neighbor-Joining, Maximum Likelihood and Bayesian trees) and species delimitation tests (TaxonDNA, Automated Barcode Gap Discovery, General Mixed Yule-Coalescent, and Bayesian Poisson Tree Processes) were performed to accurately identify and delineate species. The genetic distance-based analyses resulted in 163 well-separated clusters consisting of 147 described and 16 unidentified species. Our findings indicate that about 90.20% of the butterfly species were explicitly discriminated using DNA barcodes. Also, our field collections reported the first country records of ten butterfly species-Acraea serena, Amauris cf. dannfelti, Aterica galena extensa, Axione tjoane rubescens, Charaxes galleyanus, Papilio lormieri lormeri, Pentila alba, Precis actia, Precis tugela, and Tagiades flesus. Further, DNA barcodes revealed a high mitochondrial intraspecific divergence of more than 3% in Bicyclus vulgaris vulgaris and Colotis evagore. Furthermore, our result revealed an overall high haplotype (gene) diversity (0.9764), suggesting that DNA barcoding can provide information at a population level for Nigerian butterflies. The present study confirms the efficiency of DNA barcoding for identifying butterflies from Nigeria. To gain a better understanding of regional variation in DNA barcodes of this biogeographically complex area, future work should expand the DNA barcode reference library to include all butterfly species from Nigeria as well as surrounding countries. Also, further studies, involving relevant genetic and eco-morphological datasets, are required to understand processes governing mitochondrial intraspecific divergences reported in some species complexes.

Simultaneous Analysis of Vanillin and Coumarin in Mangrove Plants and Commercial Food Products Using UPLC-ESI-MS/MS

Background:

Vanillin is a key constituent of natural vanilla. Usage of natural vanilla is affected due to its high price and limited supply, which leads to the use of artificial vanilla flavoring substances. Coumarin is a commonly encountered adulterant in beverage, food, and cosmetics as a flavoring and fragrance enhancer. However, coumarin has been banned for use as a food additive due to its toxic effects. To comply with the quality of vanillin in food and food products needs to be ensured.

Methods:

A rapid, simple and selective analytical method has been developed and validated using ultra-high performance liquid chromatography-tandem mass spectrometry for quantitative analysis of vanillin and coumarin. We also optimized fragmentation pattern of these metabolites while increasing collision energy to elucidate its structural information. The suitability and robustness of the method was checked by Zorbax Eclipse XDB C8 column (4.6 × 150 mm, 5 μm) using mobile phase comprising of methanol (A) and water with 0.1% formic acid (B) (90:10) with a flow rate 200 μL/min. The separation was achieved within 4.2 min with total run time of 5.0 min. The analysis was done by multiple reaction monitoring using 153/93 and 147/91 pair transition in positive electrospray ionization for vanillin and coumarin respectively.

Results:

The lower limit of quantification of vanillin and coumarin was 0.39 ng/mL and 3.9 ng/mL respectively. The intra and inter-day precisions for vanillin and coumarin were lower than 8.87 and 8.62 whereas, accuracy was within ± 2.13 and ± 1.53 respectively. The vanillin and coumarin was found to be stable under the examined conditions. This method was successfully applied for quantification of vanillin and coumarin in mangrove species and commercial food products.

Conclusion:

The described method and fragmentation pattern could be useful to direct confirmation and quality monitoring of a commercial food products assimilated with vanillin.

Phytochemical Screening, Antimicrobial and Antioxidant Activities of Selected Mangrove Species

Background:

Mangrove plant extracts are used in folkloric medicine as aphrodisiac, sedative, antioxidant, antimicrobial and antimalarial. Screening for antimicrobial, phytochemical and antioxidant activities of fourteen mangroves plant species (Aegiceras corniculatum, Acanthus ilicifolius, Avicennia alba, Avicennia marina, Avicennia officinalis, Bruguiera cylindrica, Bruguiera gymnorhiza, Ceriops tagel, Excoecaria agallocha, Kandelia candel, Rhizophora apiculata, Rhizophora mucronata, Sonneratia alba, and Sonneratia caseolaris) in various solvents are reported in this work.

Methods:

The antimicrobial screening was carried out using agar well diffusion method. In this study, nine pathogenic strains were used, including three Gram-positive and six Gram-negative bacteria. Phytochemical screening, total flavonoids, total phenolic and antioxidant activity was tested by DPPH radical scavenging assay. Four phenolic compounds (gallic acid, vanillin, tannic acid and quercetin) were quantified by LC-MS/MS in selected mangrove species.

Results:

Antimicrobial screening showed Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Pseudomonas aeruginosa were most susceptible to ethyl acetate extract as compared to ethanol and methanol extract. Ethyl acetate extract of Avicennia marina and Bruguiera gymnorhiza showed strong antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Pseudomonas aeruginosa. Phytochemical analysis revealed the presence of saponins, phenolics, flavonoids, alkaloids, tannins, and terpenoids, which was found to be variable as per the solvent used for extraction. In addition, total phenolics and total flavonoids content with different solvents were found in the range of 11.08 to 196.76 mg GAE/g and 12.92 to 110.3 mg QE/g of extract respectively. Moreover, antioxidant capacities expressed in terms of IC50 (mg/mL) showed that methanol extract exhibited higher antioxidant capacity followed by ethanol extract. LC-MS/MS analysis showed gallic acid and tannic acid are present in higher concentration in Aegiceras corniculatum and Sonneratia caseolaris than other species. The vanillin and quercetin were found in the least concentration.

Conclusion:

Mangroves species are rich source of antioxidant, phenolics and antimicrobial compounds.

Selection of reference genes for quantitative real-time PCR analysis in halophytic plant Rhizophora apiculata

Rhizophora apiculata is a halophytic, small mangrove tree distributed along the coastal regions of the tropical and subtropical areas of the world. They are natural genetic reservoirs of salt adaptation genes and offer a unique system to explore adaptive mechanisms under salinity stress. However, there are no reliable studies available on selection and validation of reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) in R. apiculata physiological tissues and in salt stress conditions. The selection of appropriate candidate reference gene for normalization of qRT-PCR data is a crucial step towards relative analysis of gene expression. In the current study, seven genes such as elongation factor 1α (EF1α), Ubiquitin (UBQ), β-tubulin (β-TUB), Actin (ACT), Ribulose1,5-bisphosphate carboxylase/oxygenase (rbcL), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and 18S rRNA (18S) were selected and analyzed for their expression stability. Physiological tissues such as leaf, root, stem, and flower along with salt stress leaf samples were used for selection of candidate reference genes. The high-quality expression data was obtained from biological replicates and further analyzed using five different programs such as geNorm, NormFinder, BestKeeper, Delta Ct and RefFinder. All algorithms comprehensively ranked EF1α followed by ACT as the most stable candidate reference genes in R. apiculata physiological tissues. Moreover, β-TUB and 18S were ranked as moderately stable candidate reference genes, while GAPDH and rbcL were least stable reference genes. Under salt stress, EF1α was comprehensively recommended top-ranked candidate reference gene followed by ACT and 18S. In order to validate the identified most stable candidate reference genes, EF1α, ACT, 18S and UBQ were used for relative gene expression level of sodium/proton antiporter (NHX) gene under salt stress. The expression level of NHX varied according to the internal control which showed the importance of selection of appropriate reference gene. Taken together, this is the first ever systematic attempt of selection and validation of reference gene for qRT-PCR in R. apiculata physiological tissues and in salt stress. This study would promote gene expression profiling of salt stress tolerance related genes in R. apiculata.

Identification of plant species using variable length chloroplast DNA sequences

The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reasonable levels of discrimination. Therefore, new methods for the molecular identification of plants are clearly needed. Here we tested the utility of variable-length sequences in the chloroplast DNA (cpDNA) as a way to identify plant species. The SPInDel (Species Identification by Insertions/Deletions) approach targets hypervariable genomic regions that contain multiple insertions/deletions (indels) and length variability, which are found interspersed with highly conserved regions. The combination of fragment lengths defines a unique numeric profile for each species, allowing its identification. We analysed more than 44,000 sequences retrieved from public databases belonging to 206 different plant families. Four target regions were identified as suitable for the SPInDel concept: atpF-atpH, psbA-trnH, trnL CD and trnL GH. When considered alone, the discrimination power of each region was low, varying from 5.18% (trnL GH) to 42.54% (trnL CD). However, the discrimination power reached more than 90% when the length of some of these regions is combined. We also observed low diversity in intraspecific data sets for all target regions, suggesting they can be used for identification purposes. Our results demonstrate the utility of the SPInDel concept for the identification of plants.