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Zheng D, Zou L, Zou J, Li Q, Lu S. Refining taxonomic identification of microalgae through molecular and genetic evolution: a case study of Prorocentrum lima and Prorocentrum arenarium. Microbiol Spectr 2024; 12:e0236723. [PMID: 38572997 PMCID: PMC11064606 DOI: 10.1128/spectrum.02367-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/08/2024] [Indexed: 04/05/2024] Open
Abstract
Species delimitation based on lineage definition has become increasingly popular. However, these methods have been limited, especially for species that lack genomic data and are morphologically similar. The trickiest part for the species identification is that the interspecific and intraspecific boundaries are vague. Taking Prorocentrum (Dinophyta) as an example, analysis of cell morphology, growth, and toxin synthesis in both species of P. lima and P. arenarium does not provide a reliable basis for species delineation. However, through phylogenetic and genetic distance analyses of their ITS and LSU sequences, establishment of evolutionary tree based on orthologous gene sequences, and combining the results of automatic barcode gap discovery and Poisson tree processes models, it was sustained that P. arenarium does not belong to the P. lima complex and should be considered as an independent species. Interspecies genetic evolution analysis revealed that P. lima and P. arenarium may contribute to evolutionary direction that favors combating reverse environmental factors. In P. lima, viral invasion may be one of the reasons for its large genome size. In the study, P. lima complex has been selected as an example to enhance the taxonomic identification of microalgae through molecular and genetic evolution, offering valuable insights into refining taxonomic identification and promoting microbial biodiversity research in other species.IMPORTANCEMicroalgae, especially the species known as Prorocentrum, have received significant attention due to their ability to trigger harmful algal blooms and produce toxins. However, the boundaries between species and within species are ambiguous. Clear and comprehensive species delineation indicates that Prorocentrum arenarium should be considered as an independent species, separate from the Prorocentrum lima complex. Improving the classification and identification of microalgae through molecular and genetic evolution will provide reference points for other cryptic species. Prorocentrum occupy multiple ecological niches in marine environments, and studying their evolutionary direction contributes to understanding their ecological adaptations and community succession.
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Affiliation(s)
- Danlin Zheng
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Ligong Zou
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Jian Zou
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Qun Li
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
| | - Songhui Lu
- College of Life Science and Technology, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Jinan University, Guangzhou, China
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Abraham JS, Somasundaram S, Maurya S, Sood U, Lal R, Toteja R, Makhija S. Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. FEMS MICROBES 2024; 5:xtae003. [PMID: 38450097 PMCID: PMC10917447 DOI: 10.1093/femsmc/xtae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.
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Affiliation(s)
- Jeeva Susan Abraham
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Sripoorna Somasundaram
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Ravi Toteja
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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Ezugwu BU, Bala JD, Abioye OP, Oyewole OA. Phycoremediation of crude oil polluted water from selected water sources in Ogoniland, Rivers State, Nigeria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:111916-111935. [PMID: 37544945 DOI: 10.1007/s11356-023-29004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/22/2023] [Indexed: 08/08/2023]
Abstract
Crude oil exploitation in the Niger Delta, particularly in Ogoniland, brought environmental devastation occasioned by petroleum pollution, as farmlands and water sources were destroyed. This study was designed to remediate crude oil contaminated water obtained from water sources in Ogoniland using two green algal species. Thirty water samples were collected from eight different water sources. The samples were analysed for total petroleum hydrocarbon (TPH) using gas chromatography/flame ionization detector (GC/FID). Algal samples were collected from Ogba River and at wetland in Military Hospital Benin, Edo State, Nigeria. The algal samples were identified, screened, optimized and grown in Bold basal medium. Results obtained from the determination of TPH showed that the infiltrated pond (Exc) sample site had the highest concentration among all the sites sampled with 198.8329 μg/L, R2 with 134.1296 μg/L, R1 with 108.9394 μg/L, R3 with 105.8011 μg/L, R4 with 98.442 8 μg/L, the hand-dug wells (Wll) had 9.6586 μg/L while the borehole (Bhl) had the lowest with 1.8310 μg/L. It was deduced that pollution of water sources was principally because of pollutants washed from the soil environment into the open surface water sources via run-off rather than through the seepage from the underground aquifers, incriminating illegal oil mining and artisanal refining. Results obtained from the analysis of algal growth medium indicated that the two algal species were able to absorb the hydrocarbon contaminants, albeit at different rates, corresponding with the algal growth rate. Analysis of algal biomass after 4 weeks of remediation showed that from the initial 10.27 μg/20 mL added to the growth medium, the highest TPH mean value of 0.490 μg/20 mL was extracted from Ulothrix zonata (F.Weber & Mohr) Kützing biomass grown in Exc compared to 0.344 μg/20 mL of TPH extracted from Chlorella sorokiniana Shihira & R.W.Krauss grown in the same sample site. Also, Ulothrix zonata had higher TPH yield 0.023 μg/20 mL in Bhl compared to Chlorella sorokiniana 0.021 μg/20 mL of TPH from the same water source. This result indicated Ulothrix zonata had superior TPH phycoremediation ability to Chlorella sorokiniana. While the present study calls for deployment of the algal species for field trial, it is strongly recommended that crude oil pollution should be discouraged.
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Affiliation(s)
- Basil Utazi Ezugwu
- Department of Microbiology, School of Life Sciences, Federal University of Technology, Niger State, Minna, Nigeria
| | - Jeremiah David Bala
- Department of Microbiology, School of Life Sciences, Federal University of Technology, Niger State, Minna, Nigeria
- African Center of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Niger State, Minna, Nigeria
| | - Olabisi Peter Abioye
- Department of Microbiology, School of Life Sciences, Federal University of Technology, Niger State, Minna, Nigeria
| | - Oluwafemi Adebayo Oyewole
- Department of Microbiology, School of Life Sciences, Federal University of Technology, Niger State, Minna, Nigeria.
- African Center of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Niger State, Minna, Nigeria.
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Nikulin VY, Nikulin AY, Gontcharov AA, Bagmet VB, Abdullin SR. Oogamochlamys kurilensis sp. nov. (Chlorophyta, Volvocales) from the Soils of Iturup Island (Sakhalin Region, Russia). PLANTS (BASEL, SWITZERLAND) 2023; 12:3350. [PMID: 37836090 PMCID: PMC10574126 DOI: 10.3390/plants12193350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
A strain of oogamous biflagellate green alga was isolated during a study on soil algal diversity in the Russian Far East (Sakhalin Region, Iturup Island) and examined using an integrative approach. Phylogenetic analyses, based on the SSU rDNA gene, resolved the new strain as a part of the RL clade (sensu Watanabe and Nakada) within Oogamochlamydinia (Volvocales, Chlorophyceae). The strain was similar to members of the genus Oogamochlamys (parietal and massive cup-shaped chloroplasts; two apical contractile vacuoles), but was, however, distinguished from them based on the size and shape of the mature vegetative cells, the flagellar length, the presence of only one pyrenoid in both the mature vegetative cells and the zoospores, the anterior nucleus position, and the spermatozoids' shape. Although a concept of the genus Oogamochlamys has been compromised in recent phylogenetic analysis based on the SSU rDNA sequence data and its likely affinity to anisogamous Chlamydomonas allensworthii, we described the strain from Iturup Island as Oogamochlamys kurilensis sp. nov.
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Affiliation(s)
- Vyacheslav Yu. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159, 100-Letia Vladivostoka Prospect, Vladivostok 690022, Russia; (A.A.G.); (V.B.B.); (S.R.A.)
| | - Arthur Yu. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 159, 100-Letia Vladivostoka Prospect, Vladivostok 690022, Russia; (A.A.G.); (V.B.B.); (S.R.A.)
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Fathy WA, Techen N, Elsayed KNM, Essawy EA, Tawfik E, Alwutayd KM, Abdelhameed MS, Hammouda O, Ross SA. Applying an internal transcribed spacer as a single molecular marker to differentiate between Tetraselmis and Chlorella species. Front Microbiol 2023; 14:1228869. [PMID: 37680531 PMCID: PMC10482269 DOI: 10.3389/fmicb.2023.1228869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/04/2023] [Indexed: 09/09/2023] Open
Abstract
In the realm of applied phycology, algal physiology, and biochemistry publications, the absence of proper identification and documentation of microalgae is a common concern. This poses a significant challenge for non-specialists who struggle to identify numerous eukaryotic microalgae. However, a promising solution lies in employing an appropriate DNA barcoding technique and establishing comprehensive databases of reference sequences. To address this issue, we conducted a study focusing on the molecular characterization and strain identification of Tetraselmis and Chlorella species, utilizing the internal transcribed spacer (ITS) barcode approach. By analyzing the full nuclear ITS region through the Sanger sequencing approach, we obtained ITS barcodes that were subsequently compared with other ITS sequences of various Tetraselmis and Chlorella species. To ensure the reliability of our identification procedure, we conducted a meticulous comparison of the DNA alignment, constructed a phylogenetic tree, and determined the percentage of identical nucleotides. The findings of our study reveal the significant value of the ITS genomic region as a tool for distinguishing and identifying morphologically similar chlorophyta. Moreover, our results demonstrate that both the ITS1 and ITS2 regions are capable of effectively discriminating isolates from one another; however, ITS2 is preferred due to its greater intraspecific variation. These results underscore the indispensability of employing ITS barcoding in microalgae identification, highlighting the limitations of relying solely on morphological characterization.
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Affiliation(s)
- Wael A. Fathy
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
- Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Natascha Techen
- National Centre for Natural Products Research, Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Khaled N. M. Elsayed
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Ehab A. Essawy
- Biochemistry Division, Department of Chemistry, Faculty of Science, Helwan University, Helwan, Egypt
| | - Eman Tawfik
- Department of Botany and Microbiology, Faculty of Science, Helwan University, Helwan, Egypt
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohamed S. Abdelhameed
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Ola Hammouda
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Samir A. Ross
- Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged, Hungary
- Division of Pharmacognosy, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, MS, United States
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Badr AA, Fouad WM. Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples. PLoS One 2023; 18:e0285913. [PMID: 37418475 PMCID: PMC10328328 DOI: 10.1371/journal.pone.0285913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/03/2023] [Indexed: 07/09/2023] Open
Abstract
The vast diversity of microalgae imposes the challenge of identifying them through the most common and economical identification method, morphological identification, or through using the more recent molecular-level identification tools. Here we report an approach combining enrichment and metagenomic molecular techniques to enhance microalgae identification and identify microalgae diversity from environmental water samples. From this perspective, we aimed to identify the most suitable culturing media and molecular approach (using different primer sets and reference databases) for detecting microalgae diversity. Using this approach, we have analyzed three water samples collected from the River Nile on several enrichment media. A total of 37 microalgae were identified morphologically to the genus level. While sequencing the three-primer sets (16S rRNA V1-V3 and V4-V5 and 18S rRNA V4 region) and aligning them to three reference databases (GG, SILVA, and PR2), a total of 87 microalgae were identified to the genus level. The highest eukaryotic microalgae diversity was identified using the 18S rRNA V4 region and alignment to the SILVA database (43 genera). The two 16S rRNA regions sequenced added to the eukaryotic microalgae identification, 26 eukaryotic microalgae. Cyanobacteria were identified through the two sequenced 16S rRNA regions. Alignment to the SILVA database served to identify 14 cyanobacteria to the genera level, followed by Greengenes, 11 cyanobacteria genera. Our multiple-media, primer, and reference database approach revealed a high microalgae diversity that would have been overlooked if a single approach had been used over the other.
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Affiliation(s)
- Amal A. Badr
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Walid M. Fouad
- Biotechnology Graduate Program, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
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Pikoli MR. ANALYSIS OF NEW PRIMER PAIR CANDIDATES OF rbcL GENE FOR IDENTIFICATION OF MICROALGAE SCENEDESMACEAE. BIOLINK (JURNAL BIOLOGI LINGKUNGAN INDUSTRI KESEHATAN) 2023. [DOI: 10.31289/biolink.v9i2.7918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Scenedesmaceae is one of the microalgae groups that has been widely studied as promising biodiesel feedstock. Its morphological identification is often confused by environmental changes, so it requires molecular identification as well. The current study aimed to obtain primer pair candidates that identify the Scenedesmaceae based on the rbcL gene. The research used bioinformatics tools, which harvested rbcL protein sequence data, performed multiple sequence alignments, and designed primers based on conserved and less-conserved regions. The best left and right primers selected based on sequence length, melting temperature, 3' end stability, number of hairpins, and self-dimers, were paired, and three candidates were obtained. The three pairs were examined based on melting temperature difference, number of hetero-dimers, length of amplified nucleotide product, number of hits, and number of genera captured from the GenBank. Sce-16 (F, 5'-TGGTCGTGCTGTTTATGAATGT-3' and 1_RL, 5'-TGCCAAACATGAATACCACCA-3'), which is back-translated according to Hariotina sp. (AOY36008.1), is the most preferred candidate compared to the other two pairs after discussing their advantages and disadvantages. In the future, the proposed primer candidate needs to be validated through in vitro amplification with some optimizations to eliminate potential weaknesses.
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Werba JA, Phong AC, Brar L, Frempong-Manso A, Oware OV, Kolasa J. Interactions between two functionally distinct aquatic invertebrate herbivores complicate ecosystem- and population-level resilience. PeerJ 2022; 10:e14103. [PMID: 36225899 PMCID: PMC9549887 DOI: 10.7717/peerj.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/01/2022] [Indexed: 01/21/2023] Open
Abstract
Resilience, the capacity for a system to bounce-back after a perturbation, is critical for conservation and restoration efforts. Different functional traits have differential effects on system-level resilience. We test this experimentally in a lab system consisting of algae consumed by zooplankton, snails, or both, using an eutrophication event as a perturbation. We examined seston settlement load, chlorophyll-a and ammonium concentration as gauges of resilience. We find that Daphnia magna increased our measures of resilience. But this effect is not consistent across ecosystem measures; in fact, D. magna increased the difference between disturbed and undisturbed treatments in seston settlement loads. We have some evidence of shifting reproductive strategy in response to perturbation in D. magna and in the presence of Physa sp. These shifts correspond with altered population levels in D. magna, suggesting feedback loops between the herbivore species. While these results suggest only an ambiguous connection between functional traits to ecosystem resilience, they point to the difficulties in establishing such a link: indirect effects of one species on reproduction of another and different scales of response among components of the system, are just two examples that may compromise the power of simple predictions.
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Affiliation(s)
- Jo A. Werba
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Lakhdeep Brar
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | | | | | - Jurek Kolasa
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Martin JL, Santi I, Pitta P, John U, Gypens N. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.
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Shan S, Xu L, Chen K, Tong M, Wang X. A rapid fluorescence approach on differentiation of typical dinoflagellate of East China Sea. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121216. [PMID: 35429857 DOI: 10.1016/j.saa.2022.121216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/20/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Detecting the marine phytoplankton by the means of absorption or fluorescence spectra were successfully deployed in the past decades, however, the differentiation are mainly limited in levels of class, such as bacillariophytas, dinophytas, raphidophytes, chlorophytes, cyanobacteria, etc. which are characterized by their specific composition of photosynthetic pigments. To further differentiate the typical dinoflagellate Prorocentrum donghaiense, Amphidinium carterae, Scrippsiella trochoidea, Karenia mikimotoi out of the common diatom Skeletonema costatum and haptonema Phaeocystis globosa at East China Sea, a rapid 3D-fluorescence method equipped with CHEMTAX model were conducted. Initial fluorescence excitation spectra of each algal species (under variable environmental conditions) were captured by 3D-fluorometer first. Then fingerprints of each algae were characterized by ten-point discrete excitation spectrum with the excitation wavelengths of 405, 420, 435, 470, 490, 505, 535, 555, 570 and 590 nm, which closely reflecting the difference of photosynthetic pigments. By equipping with CHEMTAX model, the standard spectra and norm spectra were constructed for FS-CHEMTAX (Fluorescence spectra-CHEMTAX) model to further identify the algal species and estimate the cell density. The developed method performed a better way of identifying the toxic species Amphidinium carterae, Phaeocystis globosa, and Karenia mikimotoi out of the non-toxic ones, with the identification accuracy rates of 83.3%, 90% and 100%, in monocultures, and 77.8%, 90% and 100%, in the bi-mixed cultures, respectively. Meanwhile, the detection limits for the three toxic species were found as low as 250, 1,400 and 120 cells/mL. The concentrations estimated are in good agreement with the microscopic cell counts for all the algae groups (correlation coefficients (R2) exceed 0.8). The relative error of predict concentration was lowest for small cells, i.e., Phaeocystis globosa (10.0%) and Amphidinium carterae (21.1%), but the highest for big cells, i.e. Karenia mikimotoi (41.8%) when the target algae become the dominant species. The overall concentration detection error was no more than one order of magnitude, indicating that this method could provide an important technical support for monitoring the related harmful algal blooms.
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Affiliation(s)
- Shihan Shan
- Ocean College, Zhejiang University, Zhoushan, Zhejiang 316021, China; Key Laboratory of Ocean Observation-Imaging Testbed of Zhejiang Province, Zhejiang University, Zhoushan, Zhejiang 316021, China
| | - Lei Xu
- Zhejiang Veelang Environment Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Ke Chen
- Zhejiang Veelang Environment Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan, Zhejiang 316021, China.
| | - Xiaoping Wang
- Ocean College, Zhejiang University, Zhoushan, Zhejiang 316021, China; The Engineering Research Center of Oceanic Sensing Technology and Equipment, Ministry of Education, Zhoushan, Zhejiang 316021, China; Key Laboratory of Ocean Observation-Imaging Testbed of Zhejiang Province, Zhejiang University, Zhoushan, Zhejiang 316021, China
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Babich O, Dolganyuk V, Andreeva A, Katserov D, Matskova L, Ulrikh E, Ivanova S, Michaud P, Sukhikh S. Isolation of Valuable Biological Substances from Microalgae Culture. Foods 2022; 11:foods11111654. [PMID: 35681404 PMCID: PMC9180597 DOI: 10.3390/foods11111654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/18/2022] Open
Abstract
Methods for purifying, detecting, and characterizing protein concentrate, carbohydrates, lipids, and neutral fats from the microalgae were developed as a result of research. Microalgae were collected from natural sources (water, sand, soil of the Kaliningrad region, Russia). Microalgae were identified based on morphology and polymerase chain reaction as Chlorella vulgaris Beijer, Arthrospira platensis Gomont, Arthrospira platensis (Nordst.) Geitl., and Dunaliella salina Teod. The protein content in all microalgae samples was determined using a spectrophotometer. The extracts were dried by spray freeze drying. Pressure acid hydrolysis with 1% sulfuric acid was determined to be the most effective method for extracting carbohydrates from microalgae biomass samples. The highest yield of carbohydrates (more than 56%) was obtained from A. platensis samples. The addition of carbohydrates to the cultivation medium increased the accumulation of fatty acids in microalgae, especially in Chlorella. When carbohydrates were introduced to nutrient media, neutral lipids increased by 10.9%, triacylglycerides by 10.9%, fatty acids by 13.9%, polar lipids by 3.1%, unsaponifiable substances by 13.1%, chlorophyllides by 12.1%, other impurities by 8.9% on average for all microalgae. It was demonstrated that on average the content of myristic acid increased by 10.8%, palmitic acid by 10.4%, oleic acid by 10.0%, stearic acid by 10.1%, and linoleic acid by 5.7% in all microalgae samples with the addition of carbohydrates to nutrient media. It was established that microalgae samples contained valuable components (proteins, carbohydrates, lipids, fatty acids, minerals). Thereby the study of the composition of lipids and fatty acids in microalgae, as well as the influence of carbohydrates in the nutrient medium on lipid accumulation, is a promising direction for scientific research in the fields of physiology, biochemistry, biophysics, genetics, space biology and feed additive production.
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Affiliation(s)
- Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
| | - Vyacheslav Dolganyuk
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
- Department of Bionanotechnology, Kemerovo State University, Krasnaya Street 6, Kemerovo 650043, Russia
| | - Anna Andreeva
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
| | - Dmitriy Katserov
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
| | - Liudmila Matskova
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
| | - Elena Ulrikh
- Institute of Agroengineering and Food System, Kaliningrad State Technical University, Soviet Avenue 1, Kaliningrad 236022, Russia;
| | - Svetlana Ivanova
- Natural Nutraceutical Biotesting Laboratory, Kemerovo State University, Krasnaya Street 6, Kemerovo 650043, Russia
- Department of General Mathematics and Informatics, Kemerovo State University, Krasnaya Street 6, Kemerovo 650043, Russia
- Correspondence: (S.I.); (P.M.); Tel.: +7-384-239-6832 (S.I.); +33-47-340-7425 (P.M.)
| | - Philippe Michaud
- Institut Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000 Clermont-Ferrand, France
- Correspondence: (S.I.); (P.M.); Tel.: +7-384-239-6832 (S.I.); +33-47-340-7425 (P.M.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (V.D.); (A.A.); (D.K.); (L.M.); (S.S.)
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12
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Selective feeding of three bivalve species on the phytoplankton community in a marine pond revealed by high-throughput sequencing. Sci Rep 2022; 12:6163. [PMID: 35418129 PMCID: PMC9007993 DOI: 10.1038/s41598-022-08832-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/04/2022] [Indexed: 11/18/2022] Open
Abstract
The study of the selective feeding of bivalves is necessary in order to improve our understanding of bivalve growth and development, which helps to better define the roles of bivalves in their ecosystems. Little information is currently available on the feeding preferences of bivalves in natural waters, since all diets are provided as single or mixed algae in experiments. In this study, high-throughput sequencing of the 23S rRNA gene was performed to explore differences in the feeding selectivity of Mercenaria mercenaria, Meretrix meretrix and Ruditapes philippinarum during different stages of their culturing to reveal their feeding preferences in natural waters. We found that the three bivalve species had different preferential selection of phytoplankton genera, indicating specific selection and avoidance of particular types of algae during their development in aquaculture. M. mercenaria was the most selective of the bivalves, followed by M. meretrix and then R. philippinarum. With the growth of M. mercenaria and M. meretrix, more kinds of phytoplankton could be ingested. In addition, high-throughput sequencing showed that some picophytoplankton including Synechococcus, Microchloropsis, and Chrysochromulina were dominant in the hepatopancreas samples obtained from these three bivalves. Therefore, the importance of these pico-sized algae in bivalve diets should be reassessed.
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13
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Dave N, Varadavenkatesan T, Singh RS, Giri BS, Selvaraj R, Vinayagam R. Evaluation of seasonal variation and the optimization of reducing sugar extraction from Ulva prolifera biomass using thermochemical method. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:58857-58871. [PMID: 33544343 PMCID: PMC8541971 DOI: 10.1007/s11356-021-12609-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/18/2021] [Indexed: 04/15/2023]
Abstract
Green macroalgae comprise significant amount of structural carbohydrates for their conversion to liquid biofuels. However, it generally relies on species characteristics and the variability in seasonal profile to determine its route for bioprocessing. Hence, this study was conducted to analyze the indigenous marine macroalgal strain (Ulva prolifera) with respect to periodic trend and reducing sugar extraction. Consequently, in our investigation, the monthly variation in sugar profile and bioethanol yield was assessed between the monsoon and post-monsoon seasons, of which relatively high reducing sugar and fermentative bioethanol yield of about 0.152 ± 0.009 g/gdw and 6.275 ± 0.161 g/L was obtained for the October-month isolate (MITM10). Thereafter, the biochemical profile of this collected biomass (MITM10) revealed carbohydrate 34.98 ± 3.30%, protein 12.45 ± 0.49%, and lipid 1.93 ± 0.07%, respectively, on dry weight basis. Of these, the total carbohydrate fraction yielded the maximum reducing sugar of 0.156 ± 0.005 g/gdw under optimal conditions (11.07% (w/v) dosage, 0.9 M H2SO4, 121°C for 50 min) for thermal-acid hydrolysis. Furthermore, the elimination of polysaccharides was confirmed using the characterization techniques scanning electron microscopy (SEM) and Fourier transform infrared (FT-IR) spectroscopy. Therefore, the present thermochemical treatment method provides a species-specific novel strategy to breakdown the macroalgal cell wall polysaccharides that enhances sugar extraction for its utilization as an efficient bioenergy resource.
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Affiliation(s)
- Niyam Dave
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| | - Ram Sharan Singh
- Department of Chemical Engineering and Technology, Indian Institute of Technology (IIT-BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Balendu Shekher Giri
- The Centre for Energy and Environmental Sustainability, Lucknow, 226001, Uttar Pradesh, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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14
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Abstract
A number of technological challenges need to be overcome if algae are to be utilized for commercial fuel production. Current economic assessment is largely based on laboratory scale up or commercial systems geared to the production of high value products, since no industrial scale plant exits that are dedicated to algal biofuel. For macroalgae (‘seaweeds’), the most promising processes are anaerobic digestion for biomethane production and fermentation for bioethanol, the latter with levels exceeding those from sugar cane. Currently, both processes could be enhanced by increasing the rate of degradation of the complex polysaccharide cell walls to generate fermentable sugars using specifically tailored hydrolytic enzymes. For microalgal biofuel production, open raceway ponds are more cost-effective than photobioreactors, with CO2 and harvesting/dewatering costs estimated to be ~50% and up to 15% of total costs, respectively. These costs need to be reduced by an order of magnitude if algal biodiesel is to compete with petroleum. Improved economics could be achieved by using a low-cost water supply supplemented with high glucose and nutrients from food grade industrial wastewater and using more efficient flocculation methods and CO2 from power plants. Solar radiation of not <3000 h·yr−1 favours production sites 30° north or south of the equator and should use marginal land with flat topography near oceans. Possible geographical sites are discussed. In terms of biomass conversion, advances in wet technologies such as hydrothermal liquefaction, anaerobic digestion, and transesterification for algal biodiesel are presented and how these can be integrated into a biorefinery are discussed.
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15
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Silva M, Seijas P, Otero P. Exploitation of Marine Molecules to Manage Alzheimer's Disease. Mar Drugs 2021; 19:md19070373. [PMID: 34203244 PMCID: PMC8307759 DOI: 10.3390/md19070373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases are sociosanitary challenges of today, as a result of increased average life expectancy, with Alzheimer’s disease being one of the most prevalent. This pathology is characterized by brain impairment linked to a neurodegenerative process culminating in cognitive decline and behavioral disorders. Though the etiology of this pathology is still unknown, it is usually associated with the appearance of senile plaques and neurofibrillary tangles. The most used prophylaxis relies on anticholinesterase drugs and NMDA receptor antagonists, whose main action is to relieve symptoms and not to treat or prevent the disease. Currently, the scientific community is gathering efforts to disclose new natural compounds effective against Alzheimer’s disease and other neurodegenerative pathologies. Marine natural products have been shown to be promising candidates, and some have been proven to exert a high neuroprotection effect, constituting a large reservoir of potential drugs and nutraceutical agents. The present article attempts to describe the processes of extraction and isolation of bioactive compounds derived from sponges, algae, marine bacteria, invertebrates, crustaceans, and tunicates as drug candidates against AD, with a focus on the success of pharmacological activity in the process of finding new and effective drug compounds.
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Affiliation(s)
- Marisa Silva
- MARE—Marine and Environmental Sciences Centre, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal;
- Department of Plant Biology, Faculty of Science, University of Lisbon, Campo Grande, 1749-016 Lisbon, Portugal
| | - Paula Seijas
- Department of Pharmacology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Paz Otero
- Department of Pharmacology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
- Department of Production and Characterization of Novel Foods, Institute of Food Science Research (CIAL), Campus of International Excellence UAM+CSIC, 28049 Madrid, Spain
- Nutrition and Bromatology Group, CITACA, Faculty of Food Science and Technology, University of Vigo, Ourense Campus, 32004 Ourense, Spain
- Correspondence: or
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16
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Pinto R, Vilarinho R, Carvalho AP, Moreira JA, Guimarães L, Oliva-Teles L. Raman spectroscopy applied to diatoms (microalgae, Bacillariophyta): Prospective use in the environmental diagnosis of freshwater ecosystems. WATER RESEARCH 2021; 198:117102. [PMID: 33882320 DOI: 10.1016/j.watres.2021.117102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Diatom species are good pollution bioindicators due to their large distribution, fast response to changes in environmental parameters and different tolerance ranges. These organisms are used in ecological water assessment all over the world using autoecological indices. Such assessments commonly rely on the taxonomic identification of diatom species-specific shape and frustule ornaments, from which cell counts, species richness and diversity indices can be estimated. Taxonomic identification is, however, time-consuming and requires years of expertise. Additionally, though the diatom autoecological indices are region-specific, they are often applied indiscriminately across regions. Raman spectroscopy is a simpler, fast and label-free technique that can be applied to environmental diagnosis with diatoms. However, this approach has been poorly explored. This work reviews Raman spectroscopy studies involving the structure, location and conformation of diatom cell components and their variation under different conditions. A critical appreciation of the pros and cons of its application to environmental diagnosis is also given. This knowledge provides a strong foundation for the development of environmental protocols using Raman spectroscopy in diatoms. Our work aims at stimulating further research on the application of Raman spectroscopy as a tool to assess physiological changes and water quality under a changing climate.
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Affiliation(s)
- Raquel Pinto
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Rui Vilarinho
- IFIMUP, Department of Physics and Astronomy, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n. 4169-007, Porto, Portugal
| | - António Paulo Carvalho
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - J Agostinho Moreira
- IFIMUP, Department of Physics and Astronomy, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n. 4169-007, Porto, Portugal
| | - Laura Guimarães
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - Luís Oliva-Teles
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
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17
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Jacobs-Palmer E, Gallego R, Cribari K, Keller AG, Kelly RP. Environmental DNA Metabarcoding for Simultaneous Monitoring and Ecological Assessment of Many Harmful Algae. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.612107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Harmful algae can have profound economic, environmental, and social consequences. As the timing, frequency, and severity of harmful algal blooms (HABs) change alongside global climate, efficient tools to monitor and understand the current ecological context of these taxa are increasingly important. Here we employ environmental DNA metabarcoding to identify patterns in a wide variety of potentially harmful algae and associated ecological communities in the Hood Canal of Puget Sound in Washington State, USA. Tracking trends of occurrence in a series of water samples over a period of 19 months, we find algal sequences from genera with harmful members in a majority of samples, suggesting that these groups are routinely present in local waters. We report patterns in variants of the economically important genus Pseudo-nitzschia (of which some members produce domoic acid; family Bacillariaceae), as well as multiple potentially harmful algal taxa previously unknown or poorly documented in the region, including a cold-water variant from the genus Alexandrium (of which some members produce saxitoxin; family Gonyaulacaceae), two variants from the genus Karlodinium (of which some members produce karlotoxins; family Kareniaceae), and one variant from the parasitic genus Hematodinium (family Syndiniaceae). We then use data on environmental variables and the biological community surrounding each algal taxon to illustrate the ecological context in which they are commonly found. Environmental DNA metabarcoding thus simultaneously (1) alerts us to potential new or cryptic occurrences of algae from harmful genera, (2) expands our knowledge of the co-occurring conditions and species associated with the growth of these organisms in changing marine environments, and (3) suggests a pathway for multispecies monitoring and management moving forward.
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18
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Amina M, Al Musayeib NM, Alarfaj NA, El-Tohamy MF, Al-Hamoud GA. Facile multifunctional-mode of fabricated biocompatible human serum albumin/reduced graphene oxide/ Cladophora glomeratananoparticles for bacteriostatic phototherapy, bacterial tracking and antioxidant potential. NANOTECHNOLOGY 2021; 32:315301. [PMID: 33794506 DOI: 10.1088/1361-6528/abf457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
To overcome multi-drug resistance in microbes, highly efficient antimicrobial substances are required that have a controllable antibacterial effect and are biocompatible. In the present study, an efficient phototherapeutic antibacterial agent, human serum albumin (HSA)/reduced graphene oxide (rGO)/Cladophora glomeratabionanocomposite was synthesized by the incorporation of rGO nanoparticles with HSA, forming protein-rGO, and decorated with a natural freshwater seaweedCladophora glomerata. The prepared HSA/rGO/Cladophora glomeratabionanocomposite was characterized by spectroscopic (UV-vis, FTIR, XRD and Raman) and microscopic (TEM and SEM) techniques. The as-synthesized bionanocomposite showed that sunlight/NIR irradiation stimulated ROS-generating dual-phototherapic effects against antibiotic-resistant bacteria. The bionanocomposite exerted strong antibacterial effects (above 96 %) against amoxicillin-resistantP. aeruginosaandS. aureus, in contrast to single-model-phototherapy. The bionanocomposite not only generated abundant ROS for killing bacteria, but also expressed a fluorescence image for bacterial tracking under sunlight/NIR irradiation. Additionally, the bionanocomposite displayed pronounced antioxidant activity.
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Affiliation(s)
- Musarat Amina
- Department of Pharmacognosy, Pharmacy College, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nawal M Al Musayeib
- Department of Pharmacognosy, Pharmacy College, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nawal A Alarfaj
- Department of Chemistry, College of Science, King Saud University, PO Box 22452, Riyadh 11451, Saudi Arabia
| | - Maha F El-Tohamy
- Department of Chemistry, College of Science, King Saud University, PO Box 22452, Riyadh 11451, Saudi Arabia
| | - Gadah A Al-Hamoud
- Department of Pharmacognosy, Pharmacy College, King Saud University, Riyadh 11451, Saudi Arabia
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19
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Ballesteros I, Terán P, Guamán-Burneo C, González N, Cruz A, Castillejo P. DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1920296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Isabel Ballesteros
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Paulina Terán
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | | | - Nory González
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Alejandra Cruz
- Ingeniería en Biotecnología. Facultad de Ingenierías y Ciencias Aplicadas, Universidad de las Américas, Quito, Ecuador
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
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20
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Castro MS, Barbosa FG, Guimarães PS, Martins CDMG, Zanette J. A scientometric analysis of ecotoxicological studies with the herbicide atrazine and microalgae and cyanobacteria as test organisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25196-25206. [PMID: 33453026 DOI: 10.1007/s11356-020-12213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Atrazine (ATZ) is one of the most widely used herbicides in the world. A scientometric study was conducted to analyze the evolution of research on ATZ. The study also looked at the use of microalgae and cyanobacteria as biological models for toxicity tests during the period from 1959 to 2019, in the category of toxicology of Web of Science. The results show an increase in the number of scientific publications mainly in the USA, Canada, and China. The majority of papers was published in journals with high impact factors, demonstrating the relevance of such studies. About 83% of the studies aimed to evaluate the effect of ATZ on non-target organisms. From those, 7.5% included microalgae and cyanobacteria. The majority of them worked with chlorophyceae to perform toxicity bioassays of ATZ and analyze its sublethal effects. The gaps identified by this analysis included a small number of collaborations between research groups from different countries; the number of studies with terrestrial organisms, which are larger in comparison to aquatic organisms; and the fact that none of the studies with ATZ and microalgae was performed in the field. These findings can point out to researchers and funding agencies the gaps in knowledge on the toxic effects of ATZ and guide the development of new research projects as well as environmental policies.
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Affiliation(s)
- Muryllo Santos Castro
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, 96203-900, Brazil
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Av. Itália Km 8, Rio Grande, RS, 96203-900, Brazil
| | - Fabiana Gonçalves Barbosa
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Av. Itália Km 8, Rio Grande, RS, 96203-900, Brazil
| | - Pablo Santos Guimarães
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Av. Itália Km 8, Rio Grande, RS, 96203-900, Brazil
| | - Camila De Martinez Gaspar Martins
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, 96203-900, Brazil
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Av. Itália Km 8, Rio Grande, RS, 96203-900, Brazil
| | - Juliano Zanette
- Programa de Pós-graduação em Biologia de Ambientes Aquáticos Continentais, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande (FURG), Rio Grande, RS, 96203-900, Brazil.
- Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande (FURG), Av. Itália Km 8, Rio Grande, RS, 96203-900, Brazil.
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21
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A Comparison of DNA Metabarcoding and Microscopy Methodologies for the Study of Aquatic Microbial Eukaryotes. DIVERSITY 2021. [DOI: 10.3390/d13050180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The procedures and methodologies employed to study microbial eukaryotic plankton have been thoroughly discussed. Two main schools exist—one insisting on classic microscopy methodologies and the other supporting modern high-throughput sequencing (DNA metabarcoding). However, few studies have attempted to combine both these approaches; most studies implement one method while ignoring the other. This work aims to contribute to this discussion and examine the advantages and disadvantages of each methodology by comparing marine plankton community results from microscopy and DNA metabarcoding. The results obtained by the two methodologies do not vary significantly for Bacillariophyta, although they do for Dinoflagellata and Ciliophora. The lower the taxonomic level, the higher the inconsistency between the two methodologies for all the studied groups. Considering the different characteristics of microscopy-based identification and DNA metabarcoding, this work underlines that each method should be chosen depending on the aims of the study. DNA metabarcoding provides a better estimate of the taxonomic richness of an ecosystem while microscopy provides more accurate quantitative results regarding abundance and biomass. In any case, the combined use of the two methods, if properly standardized, can provide much more reliable and accurate results for the study of marine microbial eukaryotes.
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22
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Ignatenko ME, Selivanova EA, Khlopko YA, Khlopko YA, Yatsenko-Stepanova TN. Algal and cyanobacterial diversity in saline rivers of the Elton Lake Basin (Russia) studied via light microscopy and next-generation sequencing. BIOSYSTEMS DIVERSITY 2021. [DOI: 10.15421/012108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Naturally saline rivers are known in various regions of the world. Saline rivers with a salinity gradient from the source to the mouth are particularly interesting, because the range of salinity is the structure-forming factor of the hydrobiont assemblage. Such rivers are represented by saline rivers of the Elton Lake Basin in Volgograd region of Russia (the Bolshaya Samoroda River and the Malaya Samoroda River). Herein, we analyzed taxonomic structure and species diversity of microalgae and Cyanobacteria of the saline rivers flowing into the Elton Lake by light microscopy and next-generation sequencing. The differences and possible causes of inconsistencies in the results obtained by these methods are discussed. In total, 91 taxa of microorganisms were identified by integrated approach in the assemblages of microalgae and Cyanobacteria in the middle course of the Bolshaya Samoroda River, and 60 taxa – in the river mouth. The species diversity of those assemblages in the hypersaline Malaya Samoroda River was lower: 27 taxa from the middle course and 23 taxa from the mouth. Next-generation sequencing allowed us to refine and expand the list of microalgae taxa in the studied saline rivers due to detection of species which were hard to identify, low-abundance taxa, as well as extremely small-cell forms. Some discrepancies between the data obtained by light microscopy and next-generation sequencing indicate the advantage of simultaneous use of both methods for study of the algae communities. Such a comprehensive approach provides the most accurate and correct list of taxa added with the morphological descriptions and 18S rRNA and 16S rRNA partial sequences. Generally, 18 taxa have been recorded for the first time in the Bolshaya Samoroda River, belonging to the phyla Chlorophyta (Borodinellopsis sp., Chlorochytrium lemnae Cohn, Caespitella sp., Halochlorococcum sp., Tetraselmis cordiformis (H. J. Carter) F. Stein), Ochrophyta (Pseudocharaciopsis ovalis (Chodat) D. J. Hibberd, Characiopsis sp., Poterioochromonas stipitata Scherffel, Chrysolepidomonas sp.), Euglenozoa (Euglena bucharica I. Kisselev, Lepocinclis tripteris (Dujardin) B. Marin & Melkonian, Phacus orbicularis K. Hübner, P. parvulus G. A. Klebs), Cryptophyta (Hemiselmis cryptochromatica C. E. Lane & J. M. Archibald, Rhodomonas sp., Hanusia phi J. A. Deane), Haptophyta (Pavlova sp.), Cyanobacteria (Johanseninema constrictum (Szafer) Hasler, Dvorák & Poulícková). Seven taxa have been detected for the first time in the algal and cyanobacterial assemblages of the Malaya Samoroda River from the phyla Chlorophyta (Tetraselmis cordiformis, T. arnoldii (Proschkina-Lavrenko) R. E. Norris, Hori & Chihara, T. tetrathele (West) Butcher, Pyrobotrys elongatus Korshikov), Cryptophyta (Hanusia phi), and Cyanobacteria (Synechococcus elongatus (Nägeli) Nägeli, Oscillatoria simplicissima Gomont).
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Screening of native microalgae species for carbon fixation at the vicinity of Malaysian coal-fired power plant. Sci Rep 2020; 10:22355. [PMID: 33339883 PMCID: PMC7749181 DOI: 10.1038/s41598-020-79316-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 12/02/2022] Open
Abstract
Global warming has become a serious issue nowadays as the trend of CO2 emission is increasing by years. In Malaysia, the electricity and energy sector contributed a significant amount to the nation’s CO2 emission due to fossil fuel use. Many research works have been carried out to mitigate this issue, including carbon capture and utilization (CCUS) technology and biological carbon fixation by microalgae. This study makes a preliminary effort to screen native microalgae species in the Malaysian coal-fired power plant’s surrounding towards carbon fixation ability. Three dominant species, including Nannochloropsis sp., Tetraselmis sp., and Isochrysis sp. were identified and tested in the laboratory under ambient and pure CO2 condition to assess their growth and CO2 fixation ability. The results indicate Isochrysis sp. as the superior carbon fixer against other species. In continuation, the optimization study using Response Surface Methodology (RSM) was carried out to optimize the operating conditions of Isochrysis sp. using a customized lab-scale photobioreactor under simulated flue gas exposure. This species was further acclimatized and tested under actual flue gas generated by the power plant. Isochrysis sp. had shown its capability as a carbon fixer with CO2 fixation rate of 0.35 gCO2/L day under actual coal-fired flue gas exposure after cycles of acclimatization phase. This work is the first to demonstrate indigenous microalgae species' ability as a carbon fixer under Malaysian coal-fired flue gas exposure. Thus, the findings shall be useful in exploring the microalgae potential as a biological agent for carbon emission mitigation from power plants more sustainably.
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TYREE MEREDITHA, BISHOP IANW, HAWKINS CHARLESP, MITCHELL RICHARD, SPAULDING SARAHA. Reduction of taxonomic bias in diatom species data. LIMNOLOGY AND OCEANOGRAPHY, METHODS 2020; 18:271-279. [PMID: 34025297 PMCID: PMC8139252 DOI: 10.1002/lom3.10350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/28/2020] [Indexed: 05/30/2023]
Abstract
Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts five elements of sample preparation, taxon identification and enumeration, and quality control (QC) samples. We used six independent datasets to assess the effect of the adjustments on analytical outcomes. The first dataset was produced by five analysts from three laboratories following a standard protocol (Charles et al. 2002). The remaining datasets were produced by 2-3 analysts in 1-3 laboratories following a revised protocol. The revised protocol included the following modifications: 1) use of Battarbee settling chambers to prepare coverslips, 2) development of coordinated pre-count voucher floras based on morphological operational taxonomic units (mOTUs), 3) random assignment of samples to analysts, 4) post-count identification and documentation of taxa, and 5) increased QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.
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Affiliation(s)
- MEREDITH A. TYREE
- Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Campus Box 450, Boulder, CO 80309-0450 USA
| | - IAN W. BISHOP
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI, USA
| | - CHARLES P. HAWKINS
- Department of Watershed Sciences, Western Center for Monitoring and Assessment of Freshwater Ecosystems, and the Ecology Center, Utah State University, 5210 Old Main Hill, Logan, UT 84322-5210, USA
| | | | - SARAH A. SPAULDING
- Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Campus Box 450, Boulder, CO 80309-0450 USA
- United States Geological Survey, University of Colorado Boulder, Campus Box 450 Boulder CO 80309-0450 USA
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Hu Y, Gao MZ, Huang P, Zhou HL, Ma YB, Zhou MY, Cheng SY, Xie HG, Lv ZY. Taxonomic integrative and phylogenetic identification of the first recorded Triatoma rubrofasciata in Zhangzhou, Fujian Province and Maoming, Guangdong Province, China. Infect Dis Poverty 2019; 8:70. [PMID: 31409377 PMCID: PMC6693202 DOI: 10.1186/s40249-019-0579-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most species of Triatominae live exclusively in Latin America. However, one species, Triatoma rubrofasciata, has been recorded in the Americas as well as in various port areas in Africa and Asia. An increasing number of T. rubrofasciata have been reported in southern China in recent years. However, the origin of this invasive insect vector in China remains unknown, therefore, accurate identification and phylogenetic analysis of the bugs are urgently needed. METHODS A total of seven triatomine insect specimens were found and collected from Maoming City, Guangdong Province, China (GDMM) and Zhangzhou City, Fujian Province, China (FJZZ), respectively. The obtained insect vector specimens were observed under a dissecting microscope for morphological classification and then the genomic DNA was extracted, and the 16S ribosomal RNA (rRNA), 28S rRNA as well as cytochrome oxidase subunit I (COI) genes of the species were amplified and sequenced. Subsequently, molecular phylogenetic analyses based on multiple alignments of the above genes were conducted in order to identify the species and determine the phylogenetic origin approximation accurately. RESULTS The triatomine insects collected from GDMM and FJZZ were identified as Triatoma rubrofasciata using morphological and genetic analyses. All of the Chinese T. rubrofasciata captured in FJZZ, GDMM and other localities in southern China, together with a Vietnamese and Brazilian strain, formed a new, cohesive clade. T. rubrofasciata in GDMM and FJZZ are likely derived from strains found in Vietnam or Brazil. CONCLUSIONS To the best of our knowledge, this is the first record of the invasive insect T. rubrofasciata, which is likely derived from strains native to Vietnam or Brazil, in both Maoming City, Guangdong Province and Zhangzhou City, Fujian Province of China. A comparison of the DNA sequences of the 16 s rRNA, 28 s rRNA and COI genes confirmed the specific identification of T. rubrofasciata, and its potential origin in China is based on the phylogenetic analyses undertaken in this study. More targeted interventions and improved entomological surveillance are urgently needed to control the spread of this haematophagous insect in China.
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Affiliation(s)
- Yue Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Min-Zhao Gao
- Department of Gastroenterology of the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Ping Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Hong-Li Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Yu-Bin Ma
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Min-Yu Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Shao-Yun Cheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China
| | - Han-Guo Xie
- Fujian Center for Disease Control and Prevention, Fuzhou, 350001, China.
| | - Zhi-Yue Lv
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, 510080, China.
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Zieger SE, Seoane S, Laza-Martínez A, Knaus A, Mistlberger G, Klimant I. Spectral Characterization of Eight Marine Phytoplankton Phyla and Assessing a Pigment-Based Taxonomic Discriminant Analysis for the in Situ Classification of Phytoplankton Blooms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:14266-14274. [PMID: 30451494 DOI: 10.1021/acs.est.8b04528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Early stage identification of harmful algal blooms (HABs) has gained significance for marine monitoring systems over the years. Various approaches for in situ classification have been developed. Among them, pigment-based taxonomic classification is one promising technique for in situ characterization of bloom compositions, although it is yet underutilized in marine monitoring programs. To demonstrate the applicability and importance of this powerful approach for monitoring programs, we combined an ultra low-cost and miniaturized multichannel fluorometer with Fisher's linear discriminant analysis (LDA). This enables the real-time characterization of algal blooms at order level based on their spectral properties. The classification capability of the algorithm was examined with a leave-one-out cross validation of 53 different unialgal cultures conducted in terms of standard statistical measures and independent figures of merit. The separation capability of the linear discriminant analysis was further successfully examined in mixed algal suspensions. Besides this, the impact of the growing status on the classification capability was assessed. Further, we provide a comprehensive study of spectral features of eight different phytoplankton phyla including an extensive study of fluorescence excitation spectra and marker pigments analyzed via HPLC. The analyzed phytoplankton species belong to the phyla of Cyanobacteria, Dinophyta (Dinoflagellates), Bacillariophyta (Diatoms), Haptophyta, Chlorophyta, Ochrophyta, Cryptophyta, and Euglenophyta.
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Affiliation(s)
- Silvia E Zieger
- Optical Sensors Group, Institute of Analytical Chemistry and Food Chemistry , Graz University of Technology , Graz , Austria
| | - Sergio Seoane
- Plant biology and Ecology Department, Faculty of Science and Technology , University of the Basque Country (UPV/EHU) , Leioa 48940 , Spain
| | - Aitor Laza-Martínez
- Plant biology and Ecology Department, Faculty of Science and Technology , University of the Basque Country (UPV/EHU) , Leioa 48940 , Spain
| | - Anna Knaus
- Optical Sensors Group, Institute of Analytical Chemistry and Food Chemistry , Graz University of Technology , Graz , Austria
| | - Günter Mistlberger
- Optical Sensors Group, Institute of Analytical Chemistry and Food Chemistry , Graz University of Technology , Graz , Austria
| | - Ingo Klimant
- Optical Sensors Group, Institute of Analytical Chemistry and Food Chemistry , Graz University of Technology , Graz , Austria
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Rippin M, Borchhardt N, Williams L, Colesie C, Jung P, Büdel B, Karsten U, Becker B. Genus richness of microalgae and Cyanobacteria in biological soil crusts from Svalbard and Livingston Island: morphological versus molecular approaches. Polar Biol 2018. [DOI: 10.1007/s00300-018-2252-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Pandey LK, Bergey EA, Lyu J, Park J, Choi S, Lee H, Depuydt S, Oh YT, Lee SM, Han T. The use of diatoms in ecotoxicology and bioassessment: Insights, advances and challenges. WATER RESEARCH 2017; 118:39-58. [PMID: 28419896 DOI: 10.1016/j.watres.2017.01.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 06/07/2023]
Abstract
Diatoms are regularly used for bioassessment and ecotoxicological studies in relation to environmental and anthropogenic disturbances. Traditional taxonomical diatom parameters (cell counts, biovolume estimates, species richness, diversity indices and metrics using sensitive and tolerant diatom species) are regularly used for these studies. In the same context, very less focus was given on new endpoints of diatoms (life-forms, nuclear anomalies, alteration in photosynthetic apparatus shape, motility, lipid bodies, size reduction and deformities), in spite of their numerous merits, such as, their easiness, quickness, cheapness, global acceptation and no especial training in diatom taxonomy. In this review we analyzed 202 articles (from lab and field studies), with the aim to investigate the bioassessment and ecotoxicological advancement taken place in diatom research especially in terms of exploring new endpoints along with the traditional taxonomical parameters in a perspective which can greatly enhance the evaluation of fluvial ecosystem quality for biomonitoring practices.
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Affiliation(s)
- Lalit K Pandey
- Institute of Green Environmental Research Center, 169, Gaetbeol-ro, Yeonsu-gu, Incheon 21999, South Korea; Department of Marine Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea
| | - Elizabeth A Bergey
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jie Lyu
- Division of Life Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea
| | - Jihae Park
- Division of Life Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University Global Campus, 119, Songdomunwha-ro, Yeonsu-gu, Incheon 21985, South Korea
| | - Soyeon Choi
- Division of Life Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea
| | - Hojun Lee
- Department of Marine Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea
| | - Stephen Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University Global Campus, 119, Songdomunwha-ro, Yeonsu-gu, Incheon 21985, South Korea
| | - Young-Tae Oh
- Institute of Public Health and Environment, 471, Seohae-daero, Jung-gu, Incheon 22320, Republic of Korea
| | - Sung-Mo Lee
- Institute of Public Health and Environment, 471, Seohae-daero, Jung-gu, Incheon 22320, Republic of Korea
| | - Taejun Han
- Department of Marine Sciences, Incheon National University, 119, Academy-ro, Yeonsu-gu, Incheon 22012, South Korea; Ghent University Global Campus, 119, Songdomunwha-ro, Yeonsu-gu, Incheon 21985, South Korea.
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Algal Community Membership of Estuarine Mudflats from the Savannah River, United States. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2016. [DOI: 10.3390/jmse4010011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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da Silva WJ, Jahn R, Ludwig TAV, Hinz F, Menezes M. Typification and taxonomic status re-evaluation of 15 taxon names within the species complex Cymbellaaffinis/tumidula/turgidula (Cymbellaceae, Bacillariophyta). PHYTOKEYS 2015; 53:1-25. [PMID: 26312038 PMCID: PMC4547021 DOI: 10.3897/phytokeys.53.4782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 07/02/2015] [Indexed: 06/04/2023]
Abstract
Specimens belonging to the Cymbellaaffinis / Cymbellatumidula / Cymbellaturgidula species complex have many taxonomic problems, due to their high morphological variability and lack of type designations. Fifteen taxon names of this complex, distributed in five species, were re-evaluated concerning their taxonomic status, and lectotypified based on original material. In addition to light microscopy, some material was analyzed by electron microscopy. Four new combinations are proposed in order to reposition infraspecific taxa.
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Affiliation(s)
- Weliton José da Silva
- Labfico, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biodiversidade Vegetal, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil
| | - Regine Jahn
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Thelma Alvim Veiga Ludwig
- Departamento de Botânica, Setor de Ciências Biológicas, Centro Politécnico, Universidade Federal do Paraná, Curitiba, Brazil
| | - Friedel Hinz
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Mariângela Menezes
- Labfico, Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Garey AL, Smock LA. Principles for the Development of Contemporary Bioassessment Indices for Freshwater Ecosystems. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2015. [DOI: 10.1007/978-3-319-14212-8_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Smucker NJ, Drerup SA, Vis ML. Roles of benthic algae in the structure, function, and assessment of stream ecosystems affected by acid mine drainage. JOURNAL OF PHYCOLOGY 2014; 50:425-436. [PMID: 26988317 DOI: 10.1111/jpy.12184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/20/2014] [Indexed: 06/05/2023]
Abstract
Tens of thousands of stream kilometers worldwide are degraded by a legacy of acid loads, high metal concentrations, and altered habitat caused by acid mine drainage (AMD) from abandoned underground and surface mines. As the primary production base in streams, the condition of algal-dominated periphyton communities is particularly important to nutrient cycling, energy flow, and higher trophic levels. Here, we synthesize current knowledge regarding how AMD-associated stressors affect (i) algal communities and their use as ecological indicators, (ii) their functional roles in stream ecosystems, and (iii) how these findings inform management decisions and evaluation of restoration effectiveness. A growing body of research has found ecosystem simplification caused by AMD stressors. Species diversity declines, productivity decreases, and less efficient nutrient uptake and retention occur as AMD severity increases. New monitoring approaches, indices of biological condition, and attributes of algal community structure and function effectively assess AMD severity and effectiveness of management practices. Measures of ecosystem processes, such as nutrient uptake rates, extracellular enzyme activities, and metabolism, are increasingly being used as assessment tools, but remain in their infancy relative to traditional community structure-based approaches. The continued development, testing, and implementation of functional measures and their use alongside community structure metrics will further advance assessments, inform management decisions, and foster progress toward restoration goals. Algal assessments will have important roles in making progress toward improving and sustaining the water quality, ecological condition, and ecosystem services of streams in regions affected by the legacy of unregulated coal mining.
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Affiliation(s)
- Nathan J Smucker
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, U.S. Environmental Protection Agency, Narragansett, Rhode Island, USA
| | - Samuel A Drerup
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
| | - Morgan L Vis
- Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
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Stevenson J. Ecological assessments with algae: a review and synthesis. JOURNAL OF PHYCOLOGY 2014; 50:437-61. [PMID: 26988318 DOI: 10.1111/jpy.12189] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/20/2014] [Indexed: 05/24/2023]
Abstract
Algae have been used for a century in environmental assessments of water bodies and are now used in countries around the world. This review synthesizes recent advances in the field around a framework for environmental assessment and management that can guide design of assessments, applications of phycology in assessments, and refinements of those applications to better support management decisions. Algae are critical parts of aquatic ecosystems that power food webs and biogeochemical cycling. Algae are also major sources of problems that threaten many ecosystems goods and services when abundances of nuisance and toxic taxa are high. Thus, algae can be used to indicate ecosystem goods and services, which complements how algal indicators are also used to assess levels of contaminants and habitat alterations (stressors). Understanding environmental managers' use of algal ecology, taxonomy, and physiology can guide our research and improve its application. Environmental assessments involve characterizing ecological condition and diagnosing causes and threats to ecosystems goods and services. Recent advances in characterizing condition include site-specific models that account for natural variability among habitats to better estimate effects of humans. Relationships between algal assemblages and stressors caused by humans help diagnose stressors and establish targets for protection and restoration. Many algal responses to stressors have thresholds that are particularly important for developing stakeholder consensus for stressor management targets. Future research on the regional-scale resilience of algal assemblages, the ecosystem goods and services they provide, and methods for monitoring and forecasting change will improve water resource management.
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Affiliation(s)
- Jan Stevenson
- Department of Zoology and Center for Water Sciences, Michigan State University, East Lansing, Michigan, 48824, USA
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