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Jiang Y, Mo XY, Liu LT, Lai GZ, Qiu GW. Changes in the Arbuscular Mycorrhizal Fungal Community in the Roots of Eucalyptus grandis Plantations at Different Ages in Southern Jiangxi, China. J Fungi (Basel) 2024; 10:404. [PMID: 38921389 PMCID: PMC11204516 DOI: 10.3390/jof10060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/25/2024] [Accepted: 06/01/2024] [Indexed: 06/27/2024] Open
Abstract
Eucalyptus roots form symbiotic relationships with arbuscular mycorrhizal (AM) fungi in soil to enhance adaptation in challenging environments. However, the evolution of the AM fungal community along a chronosequence of eucalypt plantations and its relationship with soil properties remain unclear. In this study, we evaluated the tree growth, soil properties, and root AM fungal colonization of Eucalyptus grandis W. Hill ex Maiden plantations at different ages, identified the AM fungal community composition by high-throughput sequencing, and developed a structural equation model among trees, soil, and AM fungi. Key findings include the following: (1) The total phosphorus (P) and total potassium (K) in the soil underwent an initial reduction followed by a rise with different stand ages. (2) The rate of AM colonization decreased first and then increased. (3) The composition of the AM fungal community changed significantly with different stand ages, but there was no significant change in diversity. (4) Paraglomus and Glomus were the dominant genera, accounting for 70.1% and 21.8% of the relative abundance, respectively. (5) The dominant genera were mainly influenced by soil P, the N content, and bulk density, but the main factors were different with stand ages. The results can provide a reference for fertilizer management and microbial formulation manufacture for eucalyptus plantations.
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Affiliation(s)
- Yao Jiang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.J.); (X.-Y.M.)
| | - Xiao-Yong Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.J.); (X.-Y.M.)
| | - Li-Ting Liu
- Jiangxi Academy of Forestry, Nanchang 330000, China;
| | - Guo-Zhen Lai
- Jiangxi Academy of Forestry, Nanchang 330000, China;
| | - Guo-Wei Qiu
- Jinpenshan Forest Farm, Xinfeng 341600, China;
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2
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Phillips JD, Griswold CK, Young RG, Hubert N, Hanner RH. A Measure of the DNA Barcode Gap for Applied and Basic Research. Methods Mol Biol 2024; 2744:375-390. [PMID: 38683332 DOI: 10.1007/978-1-0716-3581-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.
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Affiliation(s)
- Jarrett D Phillips
- School of Computer Science, University of Guelph, Guelph, ON, Canada.
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
| | - Cortland K Griswold
- School of Computer Science, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Robert G Young
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Nicolas Hubert
- UMR ISEM (IRD, UM, CNRS), Université de Montpellier, Montpellier, France
| | - Robert H Hanner
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Kulizin P, Vodeneeva E, Martynenko N, Sharagina E, Okhapkin A. Alien Algae Species Invasions in Humic Rivers within Weakly Human Impact Basin. Life (Basel) 2023; 14:61. [PMID: 38255675 PMCID: PMC10817329 DOI: 10.3390/life14010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/24/2024] Open
Abstract
Increasing anthropogenic influence and climate change are leading to significant transformations in living conditions for indigenous representatives of aquatic communities. The problem of alien species invasions is actively discussed in the example of large rivers and water reservoirs, but medium and small rivers with weak anthropogenic influence have been insufficiently studied in this aspect. With the help of analysis of literary data and the results of our own long-term observations of phytoplankton using morphological and molecular genetic methods in some left-bank Volga tributaries, we identified six invasive species of different taxonomic groups of algae, with a predominance of diatoms. The relevance of using both traditional and modern approaches to identifying invasive algae species is revealed. Such invasive species as Thalassiosira incerta, T. faurii, Skeletonema subsalsum, Unruhdinium kevei, and Gonyostomum semen were part of planktonic communities; the benthic species Plagiotropis lepidoptera var. proboscidea sometimes reached a significant level of development (up 6 to 44% from total biomass) in plankton. It was demonstrated that some algae species have firmly taken the position of dominants and subdominants in planktonic algae communities. The expansion of alien representatives of microphytobenthos was noted in the Volga River basin for the first time. For Gonyostomum semen, its European origin was revealed, for plankton and benthic diatom-Ponto-Caspian. Our study showed that the processes of invasion and subsequent development of alien species take place in habitats with weak anthropogenic influence, which is likely determined by the hydrological, hydrochemical, and climatic changes in river basins and the high adaptive capabilities of invasive species.
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Affiliation(s)
- Pavel Kulizin
- Laboratory of Water Ecosystems, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603022, Russia; (E.V.); (E.S.)
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Avenue, Moscow 119071, Russia
| | - Ekaterina Vodeneeva
- Laboratory of Water Ecosystems, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603022, Russia; (E.V.); (E.S.)
| | - Nikita Martynenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Avenue, Moscow 119071, Russia
| | - Ekaterina Sharagina
- Laboratory of Water Ecosystems, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603022, Russia; (E.V.); (E.S.)
| | - Alexander Okhapkin
- Laboratory of Water Ecosystems, Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603022, Russia; (E.V.); (E.S.)
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4
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Setta SP, Lerch S, Jenkins BD, Dyhrman ST, Rynearson TA. Oligotrophic waters of the Northwest Atlantic support taxonomically diverse diatom communities that are distinct from coastal waters. JOURNAL OF PHYCOLOGY 2023; 59:1202-1216. [PMID: 37737069 DOI: 10.1111/jpy.13388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/23/2023] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Diatoms are important components of the marine food web and one of the most species-rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the genera Bacteriastrum, Haslea, Hemiaulus, Pseudo-nitzschia, and Nitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems.
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Affiliation(s)
- Samantha P Setta
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
| | - Sarah Lerch
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Bethany D Jenkins
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
- College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, Palisades, New York, USA
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, USA
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, USA
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Hernanz-Torrijos M, Ortega MJ, Úbeda B, Bartual A. Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages. Mar Drugs 2023; 21:571. [PMID: 37999395 PMCID: PMC10672285 DOI: 10.3390/md21110571] [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: 09/13/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.
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Affiliation(s)
- María Hernanz-Torrijos
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
| | - María J. Ortega
- Departamento de Química Orgánica, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain;
| | - Bárbara Úbeda
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
| | - Ana Bartual
- Instituto Universitario de Investigaciones Marinas (INMAR), Campus de Excelencia Internacional del Mar (CEI-MAR), Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-T.); (B.Ú.)
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, 11510 Cádiz, Spain
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Kulikovskiy M, Glushchenko A, Kezlya E, Kuznetsova I, Kociolek JP, Maltsev Y. The Genus Pinnularia Ehrenberg (Bacillariophyta) from the Transbaikal Area (Russia, Siberia): Description of Seven New Species on the Basis of Morphology and Molecular Data with Discussion of the Phylogenetic Position of Caloneis. PLANTS (BASEL, SWITZERLAND) 2023; 12:3552. [PMID: 37896016 PMCID: PMC10610464 DOI: 10.3390/plants12203552] [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: 08/30/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Seven Pinnularia species from the Transbaikal area, Russia, are described as new for science. These are P. baicalgenkalii, P. baicalflexuosa, P. microfrauenbergiana, P. pergrunowii, P. siberiosinistra, P. baicalodivergens, and P. baicalislandica. All species are described by original LM and SEM microphotographs and molecular phylogeny. We provide comparisons between the taxa and document variability in the features found in the species. The number of Pinnularia species in the Transbaikal area is the largest number of species of the genus anywhere in the world.
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Affiliation(s)
- Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Anton Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Elena Kezlya
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - Irina Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
| | - John Patrick Kociolek
- Museum of Natural History, Henderson Building, 15th and Broadway, Boulder, CO 80309, USA;
| | - Yevhen Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia; (A.G.); (E.K.); (I.K.); (Y.M.)
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Juchem DP, Schimani K, Holzinger A, Permann C, Abarca N, Skibbe O, Zimmermann J, Graeve M, Karsten U. Lipid degradation and photosynthetic traits after prolonged darkness in four Antarctic benthic diatoms, including the newly described species Planothidium wetzelii sp. nov. Front Microbiol 2023; 14:1241826. [PMID: 37720158 PMCID: PMC10500929 DOI: 10.3389/fmicb.2023.1241826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/08/2023] [Indexed: 09/19/2023] Open
Abstract
In polar regions, the microphytobenthos has important ecological functions in shallow-water habitats, such as on top of coastal sediments. This community is dominated by benthic diatoms, which contribute significantly to primary production and biogeochemical cycling while also being an important component of polar food webs. Polar diatoms are able to cope with markedly changing light conditions and prolonged periods of darkness during the polar night in Antarctica. However, the underlying mechanisms are poorly understood. In this study, five strains of Antarctic benthic diatoms were isolated in the field, and the resulting unialgal cultures were identified as four distinct species, of which one is described as a new species, Planothidium wetzelii sp. nov. All four species were thoroughly examined using physiological, cell biological, and biochemical methods over a fully controlled dark period of 3 months. The results showed that the utilization of storage lipids is one of the key mechanisms in Antarctic benthic diatoms to survive the polar night, although different fatty acids were involved in the investigated taxa. In all tested species, the storage lipid content declined significantly, along with an ultrastructurally observable degradation of the chloroplasts. Surprisingly, photosynthetic performance did not change significantly despite chloroplasts decreasing in thylakoid membranes and an increased number of plastoglobules. Thus, a combination of biochemical and cell biological mechanisms allows Antarctic benthic diatoms to survive the polar night.
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Affiliation(s)
- Desirée P. Juchem
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Katherina Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Andreas Holzinger
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
| | - Charlotte Permann
- Department of Botany, Functional Plant Biology, University of Innsbruck, Innsbruck, Austria
| | - Nélida Abarca
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Oliver Skibbe
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Jonas Zimmermann
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin, Germany
| | - Martin Graeve
- Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research, Ecological Chemistry, Bremerhaven, Germany
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
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Kezlya E, Tseplik N, Kulikovskiy M. Genetic Markers for Metabarcoding of Freshwater Microalgae: Review. BIOLOGY 2023; 12:1038. [PMID: 37508467 PMCID: PMC10376359 DOI: 10.3390/biology12071038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023]
Abstract
The metabarcoding methods for studying the diversity of freshwater microalgae and routine biomonitoring are actively used in modern research. A lot of experience has been accumulated already, and many methodological questions have been solved (such as the influence of the methods and time of sample conservation, DNA extraction and bioinformatical processing). The reproducibility of the method has been tested and confirmed. However, one of the main problems-choosing a genetic marker for the study-still lacks a clear answer. We analyzed 70 publications and found out that studies on eukaryotic freshwater microalgae use 12 markers (different nuclear regions 18S and ITS and plastids rbcL, 23S and 16S). Each marker has its peculiarities; they amplify differently and have various levels of efficiency (variability) in different groups of algae. The V4 and V9 18S and rbcL regions are used most often. We concentrated especially on the studies that compare the results of using different markers and microscopy. We summarize the data on the primers for each region and on how the choice of a marker affects the taxonomic composition of a community.
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Affiliation(s)
- Elena Kezlya
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Natalia Tseplik
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 127276 Moscow, Russia
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Yakoviichuk A, Krivova Z, Maltseva S, Kochubey A, Kulikovskiy M, Maltsev Y. Antioxidant Status and Biotechnological Potential of New Vischeria vischeri (Eustigmatophyceae) Soil Strains in Enrichment Cultures. Antioxidants (Basel) 2023; 12:654. [PMID: 36978902 PMCID: PMC10045218 DOI: 10.3390/antiox12030654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
The functional state of enrichment cultures of the Eustigmatophycean strains Vischeria vischeri MZ-E3 and MZ-E4 after 25-day cultivation in the BBM medium was studied. The concentrations of chlorophyll a, total carotenoids, protein, vitamins A and E, fatty acid peroxidation product content, an antioxidant enzyme, and succinate dehydrogenase activity were measured. MZ-E3 succinate dehydrogenase activity was significantly higher by 2.21 times; the MZ-E4 strain had 2.94 times higher glutathione peroxidase activity. The MZ-E3 antioxidant activity index and the MZ-E3 unsaturation of fatty acids were 1.3 and 1.25 times higher than the MZ-E4. The retinol and α-tocopherol content of the MZ-E3 was 28.6% and 38.76% higher than MZ-E4. The main fatty acid profile differences were the 3.46-fold and 3.92-fold higher stearic and eicosapentaenoic acid content in the MZ-E4 biomass. MZ-E3 had higher antioxidant, energy, and metabolic and photosynthetic status than MZ-E4. The antioxidant status of the studied strains showed the dependence of the adaptive mechanisms of each, associated with differences in the ecological conditions of the biotopes from which they were isolated. These strains are promising for producing α-tocopherol and biomass enriched with omega-3 and omega-6 fatty acids.
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Affiliation(s)
- Aleksandr Yakoviichuk
- Faculty of Natural Sciences, A. Makarenko Melitopol State University, Melitopol 72312, Russia
| | - Zinaida Krivova
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow 127276, Russia
| | - Svetlana Maltseva
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow 127276, Russia
| | - Angelica Kochubey
- Faculty of Natural Sciences, A. Makarenko Melitopol State University, Melitopol 72312, Russia
| | - Maxim Kulikovskiy
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow 127276, Russia
| | - Yevhen Maltsev
- Laboratory of Molecular Systematics of Aquatic Plants, K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow 127276, Russia
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Fei X, Huang X, Li Z, Li X, He C, Xiao S, Li Y, Zhang X, Deng X. Effect of marker-free transgenic Chlamydomonas on the control of Aedes mosquito population and on plankton. Parasit Vectors 2023; 16:18. [PMID: 36653886 PMCID: PMC9847121 DOI: 10.1186/s13071-022-05647-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND More than half of the world's population suffers from epidemic diseases that are spread by mosquitoes. The primary strategy used to stop the spread of mosquito-borne diseases is vector control. Interference RNA (RNAi) is a powerful tool for controlling insect populations and may be less susceptible to insect resistance than other strategies. However, public concerns have been raised because of the transfer of antibiotic resistance marker genes to environmental microorganisms after integration into the recipient genome, thus allowing the pathogen to acquire resistance. Therefore, in the present study, we modified the 3-hydroxykynurenine transaminase (3hkt) and hormone receptor 3 (hr3) RNAi vectors to remove antibiotic resistance marker genes and retain the expression cassette of the inverse repeat sequence of the 3hkt/hr3 target gene. This recombinant microalgal marker-free RNAi insecticide was subsequently added to the suburban water in a simulated-field trial to test its ability to control mosquito population. METHODS The expression cassette of the 3hkt/hr3 inverted repeat sequence and a DNA fragment of the argininosuccinate lyase gene without the ampicillin resistance gene were obtained using restriction enzyme digestion and recovery. After the cotransformation of Chlamydomonas, the recombinant algae was then employed to feed Aedes albopictus larvae. Ten and 300 larvae were used in small- and large-scale laboratory Ae.albopictus feeding trials, respectively. Simulated field trials were conducted using Meishe River water that was complemented with recombinant Chlamydomonas. Moreover, the impact of recombinant microalgae on phytoplankton and zooplankton in the released water was explored via high-throughput sequencing. RESULTS The marker-free RNAi-recombinant Chlamydomonas effectively silenced the 3hkt/hr3 target gene, resulting in the inhibition of Ae. albopictus development and also in the high rate of Ae. albopictus larvae mortality in the laboratory and simulated field trials. In addition, the results confirmed that the effect of recombinant Chlamydomonas on plankton in the released water was similar to that of the nontransgenic Chlamydomonas, which could reduce the abundance and species of plankton. CONCLUSIONS The marker-free RNAi-recombinant Chlamydomonas are highly lethal to the Ae. albopictus mosquito, and their effect on plankton in released water is similar to that of the nontransgenic algal strains, which reduces the abundance and species of plankton. Thus, marker-free recombinant Chlamydomonas can be used for mosquito biorational control and mosquito-borne disease prevention.
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Affiliation(s)
- Xiaowen Fei
- grid.443397.e0000 0004 0368 7493Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Xiaodan Huang
- grid.443397.e0000 0004 0368 7493Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Zhijie Li
- grid.443397.e0000 0004 0368 7493Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Xinghan Li
- grid.509158.0Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science and Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China
| | - Changhao He
- grid.443397.e0000 0004 0368 7493Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Sha Xiao
- grid.443397.e0000 0004 0368 7493Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, China
| | - Yajun Li
- grid.509158.0Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science and Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China ,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou, China
| | - Xiuxia Zhang
- grid.509158.0Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science and Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China ,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou, China
| | - Xiaodong Deng
- grid.509158.0Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science and Key Laboratory of Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou, China ,Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-Resources, Haikou, China ,grid.453499.60000 0000 9835 1415Zhanjiang Experimental Station, CATAS, Zhanjiang, China
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11
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Jeong M, Wang Y, Kim JI, Shin W. Multigene phylogeny reveals a cryptic diversity in the genus Dinobryon (Chrysophyceae) with integrative description of five new species. FRONTIERS IN PLANT SCIENCE 2023; 14:1150814. [PMID: 37143890 PMCID: PMC10151809 DOI: 10.3389/fpls.2023.1150814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/23/2023] [Indexed: 05/06/2023]
Abstract
Introduction The genus Dinobryon is one of the most recognizable chrysophyte genera, characterized by dendroid colonies with a biflagellate inside each cellulosic lorica. The representative forms of lorica are cylindrical, conical, vase, or funnel shaped, with undulation on the lorica wall. Traditionally, the morphological characteristics of the lorica and the colony organization have been used for the delimitation of Dinobryon species. Methods To understand the taxonomy and phylogeny of colonial Dinobryon species, we performed molecular and morphological studies using 39 unialgal cultures and 46 single colony isolations from environmental specimens collected in Korea. We used a nuclear internal transcript spacer (ITS1-5.8S-ITS2) to find the genetic diversity of Dinobryon from environmental samples and a combined dataset from six gene sequences (nuclear SSU and LSU rRNA, plastid LSU rRNA, rbcL and psaA, and mitochondrial CO1 genes) for phylogenetic analysis. Results and discussion We found 15 different lineages based on the genetic diversity of the nuclear ITS sequences. The phylogenetic tree of the colonial species based on the combined multigene dataset were divided into 18 subclades, including five new species, each with unique molecular signatures for the E23-5 helix of the V4 region in the nuclear SSU rRNA and the E11-1 helix of D7b, and the E20-1 helix of D8 regions in the nuclear LSU rRNA. Morphological studies were focused on lorica dimension and shape, and stomatocyst morphology. The Dinobryon species showed similarities or differences in lorica morphologies between and within species, and also differences in lorica size between culture and environmental samples. Five Dinobryon species formed distinctive stomatocysts, their stomatocyst morphologies, including collar structure, surface ornamentation, and cyst shape, showed unique characteristics in each species and were useful for identification. Here, we propose five new species based on morphological and molecular evidences: D. cylindricollarium, D. exstoundulatum, D. inclinatum, D. similis, and D. spinum.
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Affiliation(s)
| | | | - Jong Im Kim
- *Correspondence: Jong Im Kim, ; Woongghi Shin,
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12
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Antil S, Abraham JS, Sripoorna S, Maurya S, Dagar J, Makhija S, Bhagat P, Gupta R, Sood U, Lal R, Toteja R. DNA barcoding, an effective tool for species identification: a review. Mol Biol Rep 2023; 50:761-775. [PMID: 36308581 DOI: 10.1007/s11033-022-08015-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/07/2022] [Indexed: 02/01/2023]
Abstract
DNA barcoding is a powerful taxonomic tool to identify and discover species. DNA barcoding utilizes one or more standardized short DNA regions for taxon identification. With the emergence of new sequencing techniques, such as Next-generation sequencing (NGS), ONT MinION nanopore sequencing, and Pac Bio sequencing, DNA barcoding has become more accurate, fast, and reliable. Rapid species identification by DNA barcodes has been used in a variety of fields, including forensic science, control of the food supply chain, and disease understanding. The Consortium for Barcode of Life (CBOL) presents various working groups to identify the universal barcode gene, such as COI in metazoans; rbcL, matK, and ITS in plants; ITS in fungi; 16S rRNA gene in bacteria and archaea, and creating a reference DNA barcode library. In this article, an attempt has been made to analyze the various proposed DNA barcode for different organisms, strengths & limitations, recent advancements in DNA barcoding, and methods to speed up the DNA barcode reference library construction. This study concludes that constructing a reference library with high species coverage would be a major step toward identifying species by DNA barcodes. This can be achieved in a short period of time by using advanced sequencing and data analysis methods.
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Affiliation(s)
- Sandeep Antil
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | | | - S Sripoorna
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Jyoti Dagar
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Pooja Bhagat
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, New Delhi, Delhi, 110 021, India
| | - Utkarsh Sood
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Rup Lal
- The Energy and Resources Institute, IHC Complex, New Delhi, 110003, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, New Delhi, Delhi, India.
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13
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Lobus NV, Glushchenko AM, Osadchiev AA, Maltsev YI, Kapustin DA, Konovalova OP, Kulikovskiy MS, Krylov IN, Drozdova AN. Production of Fluorescent Dissolved Organic Matter by Microalgae Strains from the Ob and Yenisei Gulfs (Siberia). PLANTS (BASEL, SWITZERLAND) 2022; 11:3361. [PMID: 36501400 PMCID: PMC9735766 DOI: 10.3390/plants11233361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/09/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Dissolved organic matter (DOM) is an important component of aquatic environments; it plays a key role in the biogeochemical cycles of many chemical elements. Using excitation-emission matrix fluorescence spectroscopy, we examined the fluorescent fraction of DOM (FDOM) produced at the stationary phase of growth of five strains of microalgae sampled and isolated from the Ob and Yenisei gulfs. Based on the morphological and molecular descriptions, the strains were identified as diatoms (Asterionella formosa, Fragilaria cf. crotonensis, and Stephanodiscus hantzschii), green microalgae (Desmodesmus armatus), and yellow-green microalgae (Tribonema cf. minus). Three fluorescent components were validated in parallel factor analysis (PARAFAC): one of them was characterized by protein-like fluorescence (similar to peak T), two others, by humic-like fluorescence (peaks A and C). The portion of fluorescence intensity of humic compounds (peak A) to the total fluorescence intensity was the lowest (27 ± 5%) and showed little variation between species. Protein-like fluorescence was most intense (45 ± 16%), but along with humic-like fluorescence with emission maximum at 470 nm (28 ± 14%), varied considerably for different algae strains. The direct optical investigation of FDOM produced during the cultivation of the studied algae strains confirms the possibility of autochthonous production of humic-like FDOM in the Arctic shelf regions.
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Affiliation(s)
- Nikolay V. Lobus
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Anton M. Glushchenko
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Alexander A. Osadchiev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskiy Prospect 36, 117997 Moscow, Russia
| | - Yevhen I. Maltsev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Dmitry A. Kapustin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Olga P. Konovalova
- Marine Research Center at Lomonosov Moscow State University, Leninskie Gory 1, 119992 Moscow, Russia
| | - Maxim S. Kulikovskiy
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276 Moscow, Russia
| | - Ivan N. Krylov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1 bldg. 3, 119234 Moscow, Russia
| | - Anastasia N. Drozdova
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovskiy Prospect 36, 117997 Moscow, Russia
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14
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Sterling AR, Kirk RD, Bertin MJ, Rynearson TA, Borkman DG, Caponi MC, Carney J, Hubbard KA, King MA, Maranda L, McDermith EJ, Santos NR, Strock JP, Tully EM, Vaverka SB, Wilson PD, Jenkins BD. Emerging harmful algal blooms caused by distinct seasonal assemblages of a toxic diatom. LIMNOLOGY AND OCEANOGRAPHY 2022; 67:2341-2359. [PMID: 36636629 PMCID: PMC9827834 DOI: 10.1002/lno.12189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 03/09/2022] [Accepted: 06/12/2022] [Indexed: 06/10/2023]
Abstract
Diatoms in the Pseudo-nitzschia genus produce the neurotoxin domoic acid. Domoic acid bioaccumulates in shellfish, causing illness in humans and marine animals upon ingestion. In 2017, high domoic acid levels in shellfish meat closed shellfish harvest in Narragansett Bay, Rhode Island for the first and only time in history, although abundant Pseudo-nitzschia have been observed for over 60 years. To investigate whether an environmental factor altered endemic Pseudo-nitzschia physiology or new domoic acid-producing strain(s) were introduced to Narragansett Bay, we conducted weekly sampling from 2017 to 2019 and compared closure samples. Plankton-associated domoic acid was quantified by LC-MS/MS and Pseudo-nitzschia spp. were identified using a taxonomically improved high-throughput rDNA sequencing approach. Comparison with environmental data revealed a detailed understanding of domoic acid dynamics and seasonal multi-species assemblages. Plankton-associated domoic acid was low throughout 2017-2019, but recurred in fall and early summer maxima. Fall domoic acid maxima contained known toxic species as well as a novel Pseudo-nitzschia genotype. Summer domoic acid maxima included fewer species but also known toxin producers. Most 2017 closure samples contained the particularly concerning toxic species, P. australis, which also appeared infrequently during 2017-2019. Recurring Pseudo-nitzschia assemblages were driven by seasonal temperature changes, and plankton-associated domoic acid correlated with low dissolved inorganic nitrogen. Thus, the Narragansett Bay closures were likely caused by both resident assemblages that become toxic depending on nutrient status as well as the episodic introductions of toxic species from oceanographic and climatic shifts.
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Affiliation(s)
- Alexa R. Sterling
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Riley D. Kirk
- Department of Biomedical and Pharmaceutical SciencesCollege of Pharmacy, University of Rhode IslandKingstonRhode Island
| | - Matthew J. Bertin
- Department of Biomedical and Pharmaceutical SciencesCollege of Pharmacy, University of Rhode IslandKingstonRhode Island
| | - Tatiana A. Rynearson
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - David G. Borkman
- Rhode Island Department of Environmental ManagementOffice of Water ResourcesProvidenceRhode Island
| | - Marissa C. Caponi
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Jessica Carney
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - Katherine A. Hubbard
- Fish and Wildlife Research InstituteFlorida Fish and Wildlife Conservation CommissionSt. PetersburgFlorida
- Woods Hole Center for Oceans and Human HealthWoods Hole Oceanographic InstitutionWoods HoleMassachusetts
| | - Meagan A. King
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Lucie Maranda
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - Emily J. McDermith
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Nina R. Santos
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - Jacob P. Strock
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
| | - Erin M. Tully
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
- College of Earth, Ocean and Atmospheric SciencesOregon State UniversityCorvallisOregon
| | - Samantha B. Vaverka
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Patrick D. Wilson
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
| | - Bethany D. Jenkins
- Department of Cell and Molecular BiologyUniversity of Rhode IslandKingstonRhode Island
- Graduate School of OceanographyUniversity of Rhode IslandNarragansettRhode Island
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15
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Bíró T, Duleba M, Földi A, Kiss KT, Orgoványi P, Trábert Z, Vadkerti E, Wetzel CE, Ács É. Metabarcoding as an effective complement of microscopic studies in revealing the composition of the diatom community – a case study of an oxbow lake of Tisza River (Hungary) with the description of a new Mayamaea species. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.87497] [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
Diatoms are valuable bioindicators and their traditional classification and identification are mainly based on the morphological characteristics of their frustules. However, in recent years, DNA-based methods have been proposed and are rapidly growing in the scientific literature as a complementary tool to assess the ecological status of freshwaters. Diatom-based ecological status assessment uses indices calculated from sensitivity and tolerance values as well as relative abundance of species. Correct assessment requires an accurate identification of species. In the present study, diatom assemblages of an oxbow lake were investigated using light and scanning electron microscopy as well as metabarcoding using rbcL marker, and the identification results were compared, intending to match barcode sequences of species that are currently missing in the diatom reference database. The investigated oxbow is an important wetland for bird conservation, although it is impacted by land use. Taxon lists based on morphology and metabarcoding considerably differed when bioinformatics analysis involved DADA2 pipeline with Diat.barcode database. Previously unknown sequence variants of four pennate species were found with additional BLAST search. Using phylogeny and p-distance calculations sequences could be matched to three small-celled naviculoid species that were found under a microscope. One of them was found to be a new species of the genus Mayamaea and was described as a new species, Mayamaea ectorii. Additionally, spatial distribution maps for several small-celled naviculoid species are provided for the Hungarian territory.
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16
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Glushchenko AM, Maltsev YI, Kociolek JP, Kuznetsova IV, Kulikovskiy MS. Molecular and Morphological Investigations of Two Giant Diatom Cymbella Species from the Transbaikal Area (Russia, Siberia) with Comments on Their Distributions. PLANTS 2022; 11:plants11182445. [PMID: 36145844 PMCID: PMC9506225 DOI: 10.3390/plants11182445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/25/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022]
Abstract
For the first time, a giant diatom species of the genus Cymbella from Lake Baikal was studied using molecular methods. Molecular and morphological investigations allowed to us to described one new species, Cymbella baicalaspera Glushchenko, Kulikovskiy and Kociolek sp. nov. This species is both morphologically similar and phylogenetically close to a second giant Cymbella species that we investigated here, identified by us as Cymbella himalaspera Jüttner and Van de Vijver in Jüttner et al. 2010. This species was first described from Nepal on the basis of a morphological investigation. Small morphological differences exist between the type population and specimens from Lake Baikal, but otherwise the two are identical. These very interesting results show that some Baikalian diatoms can be distributed more widely and are not only endemic to this ancient lake. Similarity between Cymbella baicalaspera sp. nov. and Cymbella himalaspera on the basis of both morphological features and their close phylogenetic relationships suggested by molecular data indicate they are sister species and an example of sympatric speciation. These results also suggest an early development of a species flock. This species group warrants additional research in terms of. their diversification and biogeography.
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Affiliation(s)
- Anton M. Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Yevhen I. Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - John Patrick Kociolek
- Museum of Natural History, Henderson Building, 15th and Broadway, Boulder, CO 80309, USA
| | - Irina V. Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Maxim S. Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
- Correspondence: ; Tel.: +7-916-456-43-70; Fax: +7-499-678-54-20
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17
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Glushchenko A, Kezlya E, Maltsev Y, Genkal S, Kociolek JP, Kulikovskiy M. Description of the Soil Diatom Sellaphora terrestris sp. nov. (Bacillariophyceae, Sellaphoraceae) from Vietnam, with Remarks on the Phylogeny and Taxonomy of Sellaphora and Systematic Position of Microcostatus. PLANTS 2022; 11:plants11162148. [PMID: 36015452 PMCID: PMC9415725 DOI: 10.3390/plants11162148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/12/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
In material isolated from soils of Cát Tiên National Park, we isolated four strains that were assigned to the genus Sellaphora. Identification was carried out on the basis of morphological and molecular studies. We proposed a new species named Sellaphora terrestris sp. nov. An evolutionary distance matrix, based on the 18S rDNA gene including the V4 domain, showed the new species shared 94.1–97.2% similarities with other Sellaphora sequences. The new species is morphologically similar to species previously identified as representatives of the genus Microcostatus.
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Affiliation(s)
- Anton Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Elena Kezlya
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Yevhen Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
| | - Sergei Genkal
- Papanin Institute for Biology of Inland Waters RAS, IBIW RAS, Borok, 152742 Yaroslavl Region, Russia
| | - John Patrick Kociolek
- Museum of Natural History, Henderson Building, 15th and Broadway, Boulder, CO 80309, USA
| | - Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., 127276 Moscow, Russia
- Correspondence: ; Tel.: +7-916-456-43-70; Fax: +7-499-678-54-20
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18
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Phylogeny and Fatty Acid Profiles of New Pinnularia (Bacillariophyta) Species from Soils of Vietnam. Cells 2022; 11:cells11152446. [PMID: 35954290 PMCID: PMC9368540 DOI: 10.3390/cells11152446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
We studied the morphology, ultrastructure, and phylogeny of eight soil diatom strains assigned to the Pinnularia genus. Six of these strains, identified by us as new species, are described for the first time. We provide a comprehensive comparison with related species and include ecological data. Molecular phylogeny reconstruction using 18S rDNA and rbcL affiliates the new strains with different subclades within Pinnularia, including ‘borealis’, ‘grunowii’ and ‘stomatophora’. We also studied the fatty acid profiles in connection with the emerging biotechnological value of diatoms as a source of lipids. Stearic (36.0–64.4%), palmitic (20.1–30.4%), and palmitoleic (up to 20.8%) acids were the dominant fatty acids in the algae cultured on Waris-H + Si medium. High yields of saturated and monounsaturated fatty acids position the novel Pinnularia strains as a promising feedstock for biofuel production.
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Prelle LR, Schmidt I, Schimani K, Zimmermann J, Abarca N, Skibbe O, Juchem D, Karsten U. Photosynthetic, Respirational, and Growth Responses of Six Benthic Diatoms from the Antarctic Peninsula as Functions of Salinity and Temperature Variations. Genes (Basel) 2022; 13:genes13071264. [PMID: 35886047 PMCID: PMC9324188 DOI: 10.3390/genes13071264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Temperature and salinity are some of the most influential abiotic parameters shaping biota in aquatic ecosystems. In recent decades, climate change has had a crucial impact on both factors—especially around the Antarctic Peninsula—with increasing air and water temperature leading to glacial melting and the accompanying freshwater increase in coastal areas. Antarctic soft and hard bottoms are typically inhabited by microphytobenthic communities, which are often dominated by benthic diatoms. Their physiology and primary production are assumed to be negatively affected by increased temperatures and lower salinity. In this study, six representative benthic diatom strains were isolated from different aquatic habitats at King George Island, Antarctic Peninsula, and comprehensively identified based on molecular markers and morphological traits. Photosynthesis, respiration, and growth response patterns were investigated as functions of varying light availability, temperature, and salinity. Photosynthesis−irradiance curve measurements pointed to low light requirements, as light-saturated photosynthesis was reached at <70 µmol photons m−2 s−1. The marine isolates exhibited the highest effective quantum yield between 25 and 45 SA (absolute salinity), but also tolerance to lower and higher salinities at 1 SA and 55 SA, respectively, and in a few cases even <100 SA. In contrast, the limnic isolates showed the highest effective quantum yield at salinities ranging from 1 SA to 20 SA. Almost all isolates exhibited high effective quantum yields between 1.5 °C and 25 °C, pointing to a broad temperature tolerance, which was supported by measurements of the short-term temperature-dependent photosynthesis. All studied Antarctic benthic diatoms showed activity patterns over a broader environmental range than they usually experience in situ. Therefore, it is likely that their high ecophysiological plasticity represents an important trait to cope with climate change in the Antarctic Peninsula.
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Affiliation(s)
- Lara R. Prelle
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Ina Schmidt
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Katherina Schimani
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Nelida Abarca
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Oliver Skibbe
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, 14163 Berlin, Germany; (K.S.); (J.Z.); (N.A.); (O.S.)
| | - Desiree Juchem
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, Albert-Einstein-Strasse 3, University of Rostock, 18057 Rostock, Germany; (L.R.P.); (I.S.); (D.J.)
- Correspondence:
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Parsy A, Guyoneaud R, Lot MC, Baldoni-Andrey P, Périé F, Sambusiti C. Impact of salinities, metals and organic compounds found in saline oil & gas produced water on microalgae and cyanobacteria. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113351. [PMID: 35255251 DOI: 10.1016/j.ecoenv.2022.113351] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
This work evaluates the impact of salinity and the toxicity of some metals and organic compounds commonly found in produced waters on the growth of model photosynthetic organisms. Five strains of marine microalgae and one cyanobacteria (i.e. Dunaliella salina, Nannochloropsis oceanica, Tetraselmis suecica, Picochlorum costavermella, Coccomyxa simplex and Synechococcus rubescens) were tested in microplates as well as the freshwater Chlorella vulgaris selected as reference. Results revealed that D.salina was able to growth at high salinity (up to 135 g·L-1). Copper was the most toxic metal for all strains (half maximal effective concentration between 0.1 and 10 mg·L-1) except for D.salina and C.simplex. These two strains were the most resistant to all metals tested. All organic compounds presented half maximal effective concentration above 10 mg·L-1, none of them being very toxic for the studied microorganisms. P.costavermella and C.simplex were the most resistant strains to organic compounds. Looking at tolerance to salinity, metals and organic compounds, D.salina appeared to be the best choice for biomass production in produced waters. In addition, growths in 80% artificial produced water supplemented with f medium confirm the feasibility to use this medium to produce biomass.
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Affiliation(s)
- Aurélien Parsy
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Environmental Microbiology and Chemistry, UMR 5254, 64000 Pau, France; TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS IPREM, Environmental Microbiology and Chemistry, UMR 5254, 64000 Pau, France
| | - Marie-Claire Lot
- TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Patrick Baldoni-Andrey
- TotalEnergies, PERL - Pôle D'Etudes et de Recherche de Lacq, Pôle Economique 2, BP 47 - RD 817, 64170 Lacq, France
| | - Frédéric Périé
- TotalEnergies, CSTJF - Avenue Larribau, 64018 Pau, France
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21
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Zhao JY, Geng HX, Zhang QC, Li YF, Kong FZ, Yan T, Zhou MJ, Yang D, Yuan Y, Yu RC. Green Tides in the Yellow Sea Promoted the Proliferation of Pelagophyte Aureococcus anophagefferens. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3056-3064. [PMID: 35133807 DOI: 10.1021/acs.est.1c06502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Harmful algal blooms formed by fast-growing, ephemeral macroalgae have expanded worldwide, yet there is limited knowledge of their potential ecological consequences. Here, we select intense green tides formed by Ulva prolifera in the Yellow Sea, China, to examine the ecological consequences of these blooms. Using 28-isofucosterol in the surface sediment as a biomarker of green algae, we identified the settlement region of massive floating green algae in the area southeast of the Shandong Peninsula in the southern Yellow Sea. The responses of the phytoplankton assemblage from the deep chlorophyll-a maximum layer were then resolved using high-throughput sequencing. We found striking changes in the phytoplankton community in the settlement region after an intensive green tide in 2016, characterized by a remarkable increase in the abundance of the pelagophyte Aureococcus anophagefferens, the causative species of ecosystem disruptive brown tides. Our study strongly suggests that the occurrence of massive macroalgal blooms may promote blooms of specific groups of microalgae through alteration of the marine environment.
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Affiliation(s)
- Jia-Yu Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui-Xia Geng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yi-Fan Li
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tian Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Ming-Jiang Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Dezhou Yang
- CAS Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongquan Yuan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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22
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Vannoni M, Créach V, Ryder D, Sheahan D. Resilience of a microphytobenthos community from the Severn Estuary, UK, to chlorination: A mesocosm approach. MARINE POLLUTION BULLETIN 2022; 176:113443. [PMID: 35217420 DOI: 10.1016/j.marpolbul.2022.113443] [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: 05/17/2021] [Revised: 02/03/2022] [Accepted: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The Severn Estuary is a large macrotidal estuary which includes an extensive mudflat with microphytobenthos (MPB) playing a key role in the ecosystem. This study evaluated the impact of chlorination at two different dosing levels (0.05 and 0.5 mg/l as total residual oxidants, TRO, representative of potential concentrations in the mixing zone and within the cooling water systems of a power station) on a MPB community representative of the Severn Estuary. Biomass and diversity were not negatively impacted while physiology was partially affected at the beginning of the experiment, and it recovered towards the end of the experiment. Further investigations for diversity are needed to consolidate our findings. In conclusion our results show that MPB is resilient to chlorination up to a concentration of 0.5 mg/l which is much higher (>10 times) than what might be expected near the chlorinated discharges for most coastal power stations.
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Affiliation(s)
- Marta Vannoni
- CEFAS, Pakefield Road, Lowestoft NR33 0HT, Suffolk, UK.
| | | | - David Ryder
- CEFAS, Barrack Road, Weymouth DT4 8UB, Dorset, UK.
| | - Dave Sheahan
- CEFAS, Pakefield Road, Lowestoft NR33 0HT, Suffolk, UK.
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23
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Morpho-physiological adaptations of Leptocylindrus aporus and L. hargravesii to phosphate limitation in the northern Adriatic. Sci Rep 2022; 12:2687. [PMID: 35177689 PMCID: PMC8854398 DOI: 10.1038/s41598-022-06062-5] [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: 07/28/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
The northern Adriatic is highly productive and shallow area characterized by numerous spatio-temporal gradients (e.g. nutrients, salinity, temperature). It is strongly influenced by numerous freshwater inputs, mainly from Po river. Its current systems as well as Po river, generates gradients of phosphate availability with an expressed N/P imbalance and phosphate limitation. A number of recent studies characterized these gradients as major factors affecting abundance and composition of microphytoplankton communities. Focus of this study is on two Leptocylindrus species, Leptocylindrus aporus (F.W. French & Hargraves) D. Nanjappa & A. Zingone 2013 and Leptocylindrus hargravesii D. Nanjappa & A. Zingone 2013. Species belonging to Leptocylindrus genus are frequently observed and have high abundances and also high contributions to the microphytoplankton community in this area. We focused on their morphological and physiological responses to phosphate limitation in situ and also performed in vitro experiments. In this study we report data on species specific growth rates under phosphorus (P) deplete and P rich conditions, localization and characteristics of alkaline phosphate activity, phosphate uptake rates as well as their morphological differences in P deplete versus P rich conditions. Our in vitro experiments showed that both Leptocylindrus species morphologically reacted similarly to phosphorus depletion and showed significantly elongated pervalvar axis in P depleted conditions if compared to P rich conditions. Also average chain lengths increased when in P depleted conditions. Two previously mentioned adaptations indicate their tendency to increase cellular surface areas available for alkaline phosphatase. Chlorophyll fluorescence of both species significantly decreased in P depleted medium. Although both species morphologically reacted similarly, our experiment demonstrated significant differences in physiological reactions to P depleted conditions.
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24
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Schulte NO, Khan AL, Smith EW, Zoumplis A, Kaul D, Allen AE, Adams BJ, McKnight DM. Blowin' in the wind: Dispersal, structure, and metacommunity dynamics of aeolian diatoms in the McMurdo Sound region, Antarctica. JOURNAL OF PHYCOLOGY 2022; 58:36-54. [PMID: 34817069 DOI: 10.1111/jpy.13223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
Diatom metacommunities are structured by environmental, historical, and spatial factors that are often attributed to organism dispersal. In the McMurdo Sound region (MSR) of Antarctica, wind connects aquatic habitats through delivery of inorganic and organic matter. We evaluated the dispersal of diatoms in aeolian material and its relation to the regional diatom metacommunity using light microscopy and 18S rRNA high-throughput sequencing. The concentration of diatoms ranged from 0 to 8.76 * 106 valves · g-1 dry aeolian material. Up to 15% of whole cells contained visible protoplasm, indicating that up to 3.43 * 104 potentially viable individuals could be dispersed in a year to a single 2 -cm2 site. Diatom DNA and RNA was detected at each site, reinforcing the likelihood that we observed dispersal of viable diatoms. Of the 50 known morphospecies in the MSR, 72% were identified from aeolian material using microscopy. Aeolian community composition varied primarily by site. Meanwhile, each aeolian community was comprised of morphospecies found in aquatic communities from the same lake basin. These results suggest that aeolian diatom dispersal in the MSR is spatially structured, is predominantly local, and connects local aquatic habitats via a shared species pool. Nonetheless, aeolian community structure was distinct from that of aquatic communities, indicating that intrahabitat dispersal and environmental filtering also underlie diatom metacommunity dynamics. The present study confirms that a large number of diatoms are passively dispersed by wind across a landscape characterized by aeolian processes, integrating the regional flora and contributing to metacommunity structure and landscape connectivity.
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Affiliation(s)
- Nicholas O Schulte
- Institute of Arctic and Alpine Research, University of Colorado, Campus Box 450, Boulder, Colorado, 80309, USA
| | - Alia L Khan
- Department of Environmental Sciences, Western Washington University, Bellingham, Washington, 98225, USA
| | - Emma W Smith
- Division of the Biological Sciences, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Angela Zoumplis
- Scripps Institution of Oceanography, University of California, La Jolla, California, USA
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Drishti Kaul
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Andrew E Allen
- Scripps Institution of Oceanography, University of California, La Jolla, California, USA
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, 92037, USA
| | - Byron J Adams
- Department of Biology, Evolutionary Ecology Laboratories and Monte L. Bean Museum, Brigham Young University, Provo, Utah, 84602, USA
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Campus Box 450, Boulder, Colorado, 80309, USA
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25
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Tseplik ND, Maltsev YI, Glushchenko AM, Kuznetsova IV, Genkal SI, Gusev ES, Kulikovskiy MS. Achnanthidiumgladius sp. nov. (Bacillariophyceae) - a new monoraphid diatom species from Indonesia. PHYTOKEYS 2021; 187:129-140. [PMID: 35068971 PMCID: PMC8709835 DOI: 10.3897/phytokeys.187.73913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
A new monoraphid diatom species Achnanthidiumgladius sp. nov. is described from Indonesia. The description is based on molecular data (18SV4), morphological analysis and comparison with similar species. According to molecular data, Achnanthidiumgladius sp. nov. is closely related to Achnanthidiumminutissimum. Morphologically, the new species differs from similar species by the absence of a fascia on raphe valve, cell size, and striae density and pattern. The new species is only known from the type locality in Indonesia. Comparison with close related species is given.
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Affiliation(s)
- Natalia D. Tseplik
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Yevhen I. Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Anton M. Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Irina V. Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Sergei I. Genkal
- I.D. Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl, Nekouz, Borok, 152742, Russia
| | - Evgeniy S. Gusev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Maxim S. Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
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26
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Morales EA, Wetzel CE, Ector L. New and poorly known "araphid" diatom species (Bacillariophyta) from regions near Lake Titicaca, South America and a discussion on the continued use of morphological characters in "araphid" diatom taxonomy. PHYTOKEYS 2021; 187:23-70. [PMID: 35002365 PMCID: PMC8688410 DOI: 10.3897/phytokeys.187.73338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Based on two Andean Altiplano samples and on light and scanning electron microscopy analyses, we present six new species of "araphid" diatoms in the genus Pseudostaurosira, P.aedes sp. nov., P.frankenae sp. nov., P.heteropolaris sp. nov., P.oblonga sp. nov., P.occulta sp. nov., and P.pulchra sp. nov. Additional data are provided for four other known taxa, Nanofrustulumcataractarum, N.rarissimum, P.sajamaensis and P.vulpina, the latter species corresponding to a stat. nov. based on a variety of P.laucensis. Each taxon is described morphologically and compared with closely related published taxa, using characters such as axial area, virgae, vimines, areolar shape, volae, internal striae depositions, spines, flaps and apical pore fields, which are not usually used for species distinction within the genus. It is our intention that the detailed morphological descriptions of each taxon and the elaborate comparative tables we provide serve as a basis for correction of neo and paleo-databases for the Altiplano to produce a better account of autecological data and ecological change in the region. Some arguments for our continued use of a morphologically based approach are given in the context of rapid environmental degradation in the Andes and the difficulties in applying molecular approaches in countries such as Bolivia.
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Affiliation(s)
- Eduardo A. Morales
- Water Laboratory, University of Évora, P.I.T.E. Rua da Barba Rala No. 1, 7005–345 Évora, Portugal
- Institute of Earth Sciences – ICT, University of Évora, Rua Romão Ramalho n°. 59, 7000–671 Évora, Portugal
| | - Carlos E. Wetzel
- Observatory for Climate, Environment and Biodiversity (OCEB), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
| | - Luc Ector
- Observatory for Climate, Environment and Biodiversity (OCEB), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, 4422 Belvaux, Luxembourg
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27
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Glushchenko A, Gusev E, Maltsev Y, Kociolek JP, Kuznetsova I, Kulikovskiy M. Cymbopleuranatellia - a new species from Transbaikal area (Russia, Siberia) described on the basis of molecular and morphological investigation. PHYTOKEYS 2021; 183:95-105. [PMID: 34744474 PMCID: PMC8548289 DOI: 10.3897/phytokeys.183.72285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
A new cymbelloid diatom species from the genus Cymbopleura (Krammer) Krammer is described on the basis of molecular and morphological investigations. Cymbopleuranatellia Glushchenko, Kulikovskiy & Kociolek, sp. nov. is, on the basis of results with molecular data, close to C.naviculiformis (Auerswald ex Heiberg) Krammer. The two species differ both by molecular distance and morphological features. Morphologically, C.natellia sp. nov. is compared with several other species in the genus. This work is a pioneer investigation of cymbelloid taxa using molecular tool from Transbaikal area.
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Affiliation(s)
- Anton Glushchenko
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, RussiaК.А. Timiryazev Institute of Plant Physiology RAS, IPP RASMoscowRussia
| | - Evgeniy Gusev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, RussiaК.А. Timiryazev Institute of Plant Physiology RAS, IPP RASMoscowRussia
| | - Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, RussiaК.А. Timiryazev Institute of Plant Physiology RAS, IPP RASMoscowRussia
| | - John Patrick Kociolek
- University of Colorado, Boulder; University of Colorado Museum of Natural History, Boulder, Colorado, 80309, USAUniversity of Colorado, BoulderBoulderUnited States of America
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USAUniversity of Colorado Museum of Natural HistoryBoulderUnited States of America
| | - Irina Kuznetsova
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, RussiaК.А. Timiryazev Institute of Plant Physiology RAS, IPP RASMoscowRussia
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, RussiaК.А. Timiryazev Institute of Plant Physiology RAS, IPP RASMoscowRussia
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28
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Lipid accumulation by Coelastrella multistriata (Scenedesmaceae, Sphaeropleales) during nitrogen and phosphorus starvation. Sci Rep 2021; 11:19818. [PMID: 34615938 PMCID: PMC8494790 DOI: 10.1038/s41598-021-99376-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
A novel freshwater strain of Coelastrella multistriata MZ-Ch23 was discovered in Tula region, Russia. The identification is based on morphological features, phylogenetic analysis of SSU rDNA gene and ITS1-5.8S rDNA-ITS2 region and predicted secondary structure of the ITS2. Phylogenetic analysis places the novel strain in the "core" Coelastrella clade within the Chlorophyceae. This is the first record of Coelastrella multistriata in the algal flora of Russia. Cultivation experiments were carried out to evaluate growth dynamics of the newly identified strain and the impact of nitrogen and/or phosphorus depletion on the fatty acid profiles and lipid productivity. On the fully supplemented Bold's basal medium and under phosphorus-depleted conditions as well, the fatty acid profiles were dominated by α-linolenic acid (29.4-38.1% of total fatty acids). Depletion of either nitrogen or both nitrogen and phosphorus was associated with increased content of oleic acid (32.9-33.7%) and linoleic acid (11.9%). Prolongation of the growth to two months (instead of 25 days) resulted in increased content and diversity of very long-chain fatty acids including saturated species. The total very long-chain fatty acid content of 9.99% achieved in these experiments was 1.9-12.3-fold higher than in stress experiments. The highest variation was observed for oleic acid (3.4-33.7%). The novel strain showed the ability to accumulate lipids in amounts up to 639.8 mg L-1 under nitrogen and phosphorus starvation, which exceeds the previously obtained values for most Coelastrella strains. Thus, the newly identified MZ-Ch23 strain can be considered as a potential producer of omega-3 fatty acids on fully supplemented Bold's basal medium or as a source of biomass with high content of saturated and monounsaturated fatty acids after nitrogen and phosphorus starvation.
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29
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Nistal-García A, García-García P, García-Girón J, Borrego-Ramos M, Blanco S, Bécares E. DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147410. [PMID: 33971606 DOI: 10.1016/j.scitotenv.2021.147410] [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: 11/25/2020] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.
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Affiliation(s)
| | - Pedro García-García
- Genetic Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - Jorge García-Girón
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
| | - María Borrego-Ramos
- Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
| | - Saúl Blanco
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain; Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
| | - Eloy Bécares
- Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain; Institute of Environment, Natural Resources and Biodiversity, La Serna, 58, 24007 León, Spain.
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30
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Schäffer AA, McVeigh R, Robbertse B, Schoch CL, Johnston A, Underwood BA, Karsch-Mizrachi I, Nawrocki EP. Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation. BMC Bioinformatics 2021; 22:400. [PMID: 34384346 PMCID: PMC8359073 DOI: 10.1186/s12859-021-04316-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. Results To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa. Conclusion Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.
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Affiliation(s)
- Alejandro A Schäffer
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Richard McVeigh
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Anjanette Johnston
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Beverly A Underwood
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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31
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Vaulot D, Geisen S, Mahé F, Bass D. pr2-primers: An 18S rRNA primer database for protists. Mol Ecol Resour 2021; 22:168-179. [PMID: 34251760 DOI: 10.1111/1755-0998.13465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023]
Abstract
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R-based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set (https://app.pr2-primers.org). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France.,Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.,Nanjing Agricultural University, Nanjing, China
| | - Frédéric Mahé
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.,Department of Life Sciences, The Natural History Museum, London, UK
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Gillmore ML, Golding LA, Chariton AA, Stauber JL, Stephenson S, Gissi F, Greenfield P, Juillot F, Jolley DF. Metabarcoding Reveals Changes in Benthic Eukaryote and Prokaryote Community Composition along a Tropical Marine Sediment Nickel Gradient. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2021; 40:1894-1907. [PMID: 33751674 DOI: 10.1002/etc.5039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
The Southeast Asia and Melanesia region has extensive nickel (Ni)-rich lateritic regoliths formed from the tropical weathering of ultramafic rocks. As the global demand for Ni continues to rise, these lateritic regoliths are increasingly being exploited for their economic benefit. Mining of these regoliths contributes to the enrichment of coastal sediments in trace metals, especially Ni. The present study used high-throughput sequencing (metabarcoding) to determine changes in eukaryote (18s v7 recombinant DNA [rDNA] and diatom-specific subregion of the 18s v4 rDNA) and prokaryote (16s v4 rDNA) community compositions along a sediment Ni concentration gradient offshore from a large lateritized ultramafic regolith in New Caledonia (Vavouto Bay). Significant changes in the eukaryote, diatom, and prokaryote community compositions were found along the Ni concentration gradient. These changes correlated most with the dilute-acid extractable concentration of Ni in the sediments, which explained 26, 23, and 19% of the variation for eukaryote, diatom, and prokaryote community compositions, respectively. Univariate analyses showed that there was no consistent change in indices of biodiversity, evenness, or richness. Diatom richness and diversity did, however, decrease as sediment acid extractable-Ni concentrations increased. Threshold indicator taxa analysis was conducted separately for each of the 3 targeted genes to detect changes in taxa whose occurrences decreased or increased along the acid extractable-Ni concentration gradient. Based on these data, 46 mg acid extractable-Ni/kg was determined as a threshold value where sensitive species began to disappear. In the case of the estuarine sediments offshore from lateritized ultramafic regolith in New Caledonia, this is recommended as an interim threshold value until further lines of evidence can contribute to a region-specific Ni sediment quality guideline value. Environ Toxicol Chem 2021;40:1894-1907. © 2021 SETAC.
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Affiliation(s)
- Megan L Gillmore
- School of Earth, Atmosphere and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
| | - Lisa A Golding
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
| | - Anthony A Chariton
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Jenny L Stauber
- Commonwealth Scientific and Industrial Research Organisation Land and Water, Lucas Heights, New South Wales, Australia
| | - Sarah Stephenson
- Commonwealth Scientific and Industrial Research Organisation Oceans and Atmosphere, Lucas Heights, New South Wales, Australia
| | - Francesca Gissi
- School of Earth, Atmosphere and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
- Commonwealth Scientific and Industrial Research Organisation Oceans and Atmosphere, Lucas Heights, New South Wales, Australia
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation Energy, North Ryde, New South Wales, Australia
| | - Farid Juillot
- Institut de Recherche pour le Developpement, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Noumea, New Caledonia
| | - Dianne F Jolley
- School of Earth, Atmosphere and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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De Luca D, Piredda R, Sarno D, Kooistra WHCF. Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets. THE ISME JOURNAL 2021; 15:1931-1942. [PMID: 33589768 PMCID: PMC8245484 DOI: 10.1038/s41396-021-00895-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/23/2020] [Accepted: 01/14/2021] [Indexed: 12/21/2022]
Abstract
Marine protists have traditionally been assumed to be lowly diverse and cosmopolitan. Yet, several recent studies have shown that many protist species actually consist of cryptic complexes of species whose members are often restricted to particular biogeographic regions. Nonetheless, detection of cryptic species is usually hampered by sampling coverage and application of methods (e.g. phylogenetic trees) that are not well suited to identify relatively recent divergence and ongoing gene flow. In this paper, we show how these issues can be overcome by inferring phylogenetic haplotype networks from global metabarcoding datasets. We use the Chaetoceros curvisetus (Bacillariophyta) species complex as study case. Using two complementary metabarcoding datasets (Ocean Sampling Day and Tara Oceans), we equally resolve the cryptic complex in terms of number of inferred species. We detect new hypothetical species in both datasets. Gene flow between most of species is absent, but no barcoding gap exists. Some species have restricted distribution patterns whereas others are widely distributed. Closely related taxa occupy contrasting biogeographic regions, suggesting that geographic and ecological differentiation drive speciation. In conclusion, we show the potential of the analysis of metabarcoding data with evolutionary approaches for systematic and phylogeographic studies of marine protists.
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Affiliation(s)
- Daniele De Luca
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biology, Botanical Garden of Naples, University of Naples Federico II, Naples, Italy
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Diana Sarno
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Wiebe H C F Kooistra
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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Bonfantine KL, Trevathan-Tackett SM, Matthews TG, Neckovic A, Gan HM. Dumpster diving for diatom plastid 16S rRNA genes. PeerJ 2021; 9:e11576. [PMID: 34249491 PMCID: PMC8255066 DOI: 10.7717/peerj.11576] [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: 09/15/2020] [Accepted: 05/18/2021] [Indexed: 11/20/2022] Open
Abstract
High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.
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Affiliation(s)
- Krista L Bonfantine
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Ty G Matthews
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Ana Neckovic
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,GeneSEQ Sdn Bhd, Rawang, Selangor, Malaysia
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Bininda-Emonds ORP. 18S rRNA variability maps reveal three highly divergent, conserved motifs within Rotifera. BMC Ecol Evol 2021; 21:118. [PMID: 34112085 PMCID: PMC8194223 DOI: 10.1186/s12862-021-01845-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 18S rRNA is a major component of the small subunit of the eukaryotic ribosome and an important phylogenetic marker for many groups, often to the point of being the only marker available for some. A core structure across eukaryotes exists for this molecule that can help to inform about its evolution in different groups. Using an alignment of 18S rDNA for Rotifera as traditionally recognized (=Bdelloidea, Monogononta, and Seisonacea, but not Acanthocephala), I fitted sequences for three exemplar species (Adineta vaga, Brachionus plicatilis, and Seison nebaliae, respectively) to the core structure and used these maps to reveal patterns of evolution for the remainder of this diverse group of microscopic animals. RESULTS The obtained variability maps of the 18S rRNA molecule revealed a pattern of high diversity among the three major rotifer clades coupled with strong conservation within each of bdelloids and monogononts. A majority of individual sites (ca. 60%) were constant even across rotifers as a whole with variable sites showing only intermediate rates of evolution. Although the three structural maps each showed good agreement with the inferred core structure for eukaryotic 18S rRNA and so were highly similar to one another at the secondary and tertiary levels, the overall pattern is of three highly distinct, but conserved motifs within the group at the primary sequence level. A novel finding was that of a variably expressed deletion at the 3' end of the V3 hypervariable region among some bdelloid species that occasionally extended into and included the pseudoknot structure following this region as well as the central "square" of the 18S rRNA molecule. Compared to other groups, levels of variation and rates of evolution for 18S rRNA in Rotifera roughly matched those for Gastropoda and Acanthocephala, despite increasing evidence for the latter being a clade within Rotifera. CONCLUSIONS The lack of comparative data for comparable groups makes interpretation of the results (i.e., very low variation within each of the three major rotifer clades, but high variation between them) and their potential novelty difficult. However, these findings in combination with the high morphological diversity within rotifers potentially help to explain why no clear consensus has been reached to date with regard to the phylogenetic relationships among the major groups.
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Affiliation(s)
- Olaf R P Bininda-Emonds
- AG Systematics and Evolutionary Biology, IBU-Faculty V, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Strasse 9-11, 26111, Oldenburg, Germany.
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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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Tseplik ND, Maltsev YI, Glushchenko AM, Kuznetsova IV, Genkal SI, Kociolek JP, Kulikovskiy MS. Achnanthidium tinea sp. nov. - a new monoraphid diatom (Bacillariophyceae) species, described on the basis of molecular and morphological approaches. PHYTOKEYS 2021; 174:147-163. [PMID: 33776528 PMCID: PMC7979678 DOI: 10.3897/phytokeys.174.60337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
A new monoraphid diatom species Achnanthidium tinea Tseplik, Kulikovskiy, Kociolek & Maltsev, sp. nov. is described from Indonesia. The species is described on the basis of molecular and morphological analyses. According to molecular data the new species belongs to the clade that includes strains of Achnanthidium minutissimum, Achnanthidium saprophilum and Achnanthidium digitatum. Morphologically, the new species differs quite significantly from other species of the same genus because of linear-elliptic valves with almost parallel sides and strongly radiate striae and a butterfly-shaped fascia on the raphe valve. The morphology and phylogeny of the new species are discussed, and thoughts on the current state of the taxonomy of the genus Achnanthidium are expressed. Our work shows the importance of using molecular data in diatom systematics and also demonstrates the need to investigate rarely studied regions of our planet.
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Affiliation(s)
- Natalia D. Tseplik
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Yevhen I. Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Anton M. Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Irina V. Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Sergei I. Genkal
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl, Nekouz, Borok, 152742, Russia
| | - John Patrick Kociolek
- University of Colorado Museum of Natural History, Broadway, Boulder, CO 80302, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Maxim S. Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
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Liu Y, Chen Z, Gao Y, Zou J, Lu S, Zhang L. Identifying the Source Organisms Producing Paralytic Shellfish Toxins in a Subtropical Bay in the South China Sea. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3124-3135. [PMID: 33566578 DOI: 10.1021/acs.est.0c06991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Identifying the exact phytoplanktonic sources of paralytic shellfish toxins (PSTs) is crucial for monitoring and preventing the buildup of toxin pollution, especially for causative species occurring at low levels. Phytoplankton and shellfish samples were simultaneously collected from representative mariculture zones in Daya Bay, China. Low concentration/low toxicity PSTs predominated with N-sulfocarbamoyl toxins 1, 2 (C1/2) being detected in phytoplankton (≤6.25 pmol L-1) and shellfish (≤0.21 μg STXeq g-1), which pose a potential risk of seafood poisoning. High-throughput sequencing of the phytoplankton samples based on 18S rDNA V4 regions identified 93 genera in 445 operational taxonomic units (OTUs). Five OTUs were assigned to Alexandrium hiranoi, Ambicodamus leei, Alexandrium pacificum, Alexandrium minutum, and an uncertain Alexandrium sp. A. pacificum and A. minutum are candidate PST producers and observed under the light microscope with densities of 66-972 cells L-1. Three strains of toxigenic species were successfully isolated and identified as A. pacificum and A. minutum based on their 18S rDNA V4 regions. The predominant toxins in A. pacificum were C1/2 (43.9-53.6 fmol cell-1) and resembled the toxins found in field samples predominated with C1/2. A. minutum produced only gonyautoxins 2/3 (8.03 fmol cell-1). Therefore, A. pacificum was identified as the predominant PST contributor in this area. This research makes a valuable contribution to the understanding of the traceability of phycotoxins in marine waters.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhenfan Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yue Gao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Jian Zou
- Research Center of Harmful Algae and Marine Biology, Jinan University, Guangzhou 510632, China
| | - Songhui Lu
- Research Center of Harmful Algae and Marine Biology, Jinan University, Guangzhou 510632, China
| | - Li Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou 510301, China
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Yu RC, Zhang QC, Liu Y, Chen ZF, Geng HX, Dai L, Lin ZR, Tang WJ, Kong FZ, Yan T, Zhou MJ. The dinoflagellate Alexandrium catenella producing only carbamate toxins may account for the seafood poisonings in Qinhuangdao, China. HARMFUL ALGAE 2021; 103:101980. [PMID: 33980430 DOI: 10.1016/j.hal.2021.101980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
An outbreak of paralytic shellfish poisoning, recorded in April 2016 in Qinhuangdao China, was suspected to be caused by a toxic species in genus Alexandrium. Shortly after the poisoning outbreak, shellfish and net-concentrated phytoplankton samples were collected from the Bohai Sea, and analysed using high performance liquid chromatography coupled with fluorescence detection. Paralytic shellfish toxins (PSTs) were detected in both phytoplankton and shellfish samples, with similar toxin profiles dominated by carbamate toxins. High throughput sequencing data for phytoplankton samples collected previously in the coastal waters of Qinhuangdao were then analysed, and 8 operational taxonomic units (OTUs) were assigned to Alexandrium affine, A. andersonii/A. ostenfeldii, A. catenella, A. fraterculus, A. hiranoi/A. pseudogonyaulax, A. margalefii, A. pacificum and A. pohangense, among which A. catenella, A. pacificum and A. ostenfeldii could be potential producers of PSTs. During a cruise in 2019, three isolates of Alexandrium were established by cyst germination, and identified as A. catenella based on the sequences of the 28S ribosomal RNA gene (28S rDNA) D1-D2 region. Interestingly, all the three strains had the same toxin profile consisting of gonyautoxins 1, 3, 4 (GTX1, 3, 4) and neosaxitoxin (NEO). The toxin profile is similar to those of phytoplankton samples collected previously in the coastal waters of Qinhuangdao, but remarkably different from the general toxin profile of A. catenella dominated by N-sulfocarbamoyl toxins C1-2 in the Bohai Sea and the Yellow Sea. The results suggest that A. catenella is most likely to be the causative species of the poisoning outbreak in Qinhuangdao. As far as we know, this is the first report of A. catenella in the Bohai Sea producing PSTs dominated by high potent gonyautoxins GTX1-4. Occurrence of the highly toxic A. catenella will increase the risk of paralytic shellfish poisoning, which necessitates in-depth mechanism studies and increasing monitoring efforts.
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Affiliation(s)
- Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Yang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Zhen-Fan Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Hui-Xia Geng
- Changjiang River Estuary Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Li Dai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo-Ru Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Jiao Tang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Tian Yan
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Ming-Jiang Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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Majaneva S, Ringvold H, Johansen E, Østensen MA, Hosia A. Hiding in plain sight- Euplokamis dunlapae (Ctenophora) in Norwegian waters. JOURNAL OF PLANKTON RESEARCH 2021; 43:257-269. [PMID: 33814975 PMCID: PMC8009683 DOI: 10.1093/plankt/fbab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Cydippid ctenophores of genus Euplokamis have been rarely reported from the north-east Atlantic in the scientific literature. The conspicuous lack of previous records is likely attributable to methodological constraints detrimental to sampling ctenophores, including the use of plankton nets and preservation of samples as well as poor identification literature and a lack of taxonomic expertise on gelatinous zooplankton. Here, we have compiled published and novel records as well as documented diver observations, of Euplokamis spp. in Norwegian waters. Despite scant earlier reports, our data suggest that the genus Euplokamis is widely distributed and relatively common along the entire Norwegian coast, including Svalbard. Euplokamis was recorded from samples taken from several hundred meters depth to surface, from fjords as well as offshore. Most of the observations reported in this study are from the period between April and July, whereas specimens have been found nearly throughout the year. Specimens from Norwegian waters were morphologically most similar to Euplokamis dunlapae, and conservative 18S rDNA sequences of some specimens had a 100% match with an E. dunlapae specimen from Friday Harbor, USA, the type locality for the species. However, the morphological and molecular variation of Euplokamis demonstrates the need for systematic global sampling of multiple individuals of many ctenophore species.
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Affiliation(s)
- Sanna Majaneva
- Department for Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø NO-9037, Norway
| | | | - Ellie Johansen
- Trondhjem Biological Station, Department of Biology, Norwegian University of Science and Technology, Trondheim NO-7491, Norway
| | - Mari-Ann Østensen
- Trondhjem Biological Station, Department of Biology, Norwegian University of Science and Technology, Trondheim NO-7491, Norway
| | - Aino Hosia
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen NO-5020, Norway
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Maltsev Y, Maltseva S, Kociolek JP, Jahn R, Kulikovskiy M. Biogeography of the cosmopolitan terrestrial diatom Hantzschia amphioxys sensu lato based on molecular and morphological data. Sci Rep 2021; 11:4266. [PMID: 33608589 PMCID: PMC7896094 DOI: 10.1038/s41598-021-82092-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/11/2021] [Indexed: 12/02/2022] Open
Abstract
Until now, the reported diversity of representatives from the genus Hantzschia inhabiting soils from different parts of Eurasia was limited to the few species H. amphioxys, H. elongata and H. vivax and some of their infraspecific taxa. We have studied the morphology, ultrastructure and phylogeny of 25 soil diatom strains, which according to published description would be assigned to “H. amphioxys sensu lato” using 18S rDNA, 28S rDNA and rbcL. We show that strains are made up of seven different species of Hantzschia, including five new for science. Five strains were identified as H. abundans. This species has a slight curvature of the raphe near its external proximal ends. Four of the examined strains were represented by different populations of H. amphioxys and their morphological characteristics fully correspond with its isolectotype and epitype. The main specific features of this species include 21–25 striae in 10 μm, 6–11 fibulae in 10 μm, 40–50 areolae in 10 μm and internal proximal raphe endings bent in opposite directions. H. attractiva sp. nov., H. belgica sp. nov., H. parva sp. nov., H. pseudomongolica sp. nov. and H. stepposa sp. nov. were described based on differences in the shape of the valves, significant differences in dimensions, a lower number of striae and areolae in 10 μm and the degree and direction of deflection of the internal central raphe endings. Based on the study of the morphological variability and phylogeny of soil Hantzschia-species from different geographical locations we conclude that while some species such as H. amphioxys are truly cosmopolitan in their distributions, some sympatric populations of pseudocryptic taxa exist in the Holarctic.
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Affiliation(s)
- Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, Russia, 127276.
| | - Svetlana Maltseva
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, Russia, 127276
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Regine Jahn
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, Russia, 127276
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Zhang J, Zhou Y, Vieira DN, Cao Y, Deng K, Cheng Q, Zhu Y, Zhang J, Qin Z, Ma K, Chen Y, Huang P. An efficient method for building a database of diatom populations for drowning site inference using a deep learning algorithm. Int J Legal Med 2021; 135:817-827. [PMID: 33392655 DOI: 10.1007/s00414-020-02497-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
Seasonal or monthly databases of the diatom populations in specific bodies of water are needed to infer the drowning site of a drowned body. However, existing diatom testing methods are laborious, time-consuming, and costly and usually require specific expertise. In this study, we developed an artificial intelligence (AI)-based system as a substitute for manual morphological examination capable of identifying and classifying diatoms at the species level. Within two days, the system collected information on diatom profiles in the Huangpu and Suzhou Rivers of Shanghai, China. In an animal experiment, the similarities of diatom profiles between lung tissues and water samples were evaluated through a modified Jensen-Shannon (JS) divergence measure for drowning site inference, reaching a prediction accuracy of 92.31%. Considering its high efficiency and simplicity, our proposed method is believed to be more applicable than existing methods for seasonal or monthly water monitoring of diatom populations from sections of interconnected rivers, which would help police narrow the investigation scope to confirm the identity of an immersed body.
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Affiliation(s)
- Ji Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China
| | - Yuanyuan Zhou
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China.,Department of Forensic Medicine, Inner Mongolia Medical University, Huhhot, Inner Mongolia, People's Republic of China
| | - Duarte Nuno Vieira
- Department of Forensic Medicine, Ethics and Medical Law, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Yongjie Cao
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Kaifei Deng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China
| | - Qi Cheng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Yongzheng Zhu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Jianhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China
| | - Zhiqiang Qin
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China
| | - Kaijun Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, People's Republic of China.
| | - Yijiu Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China.
| | - Ping Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, People's Republic of China.
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Jeong M, Kim JI, Nam SW, Shin W. Molecular Phylogeny and Taxonomy of the Genus Spumella (Chrysophyceae) Based on Morphological and Molecular Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:758067. [PMID: 34764972 PMCID: PMC8577464 DOI: 10.3389/fpls.2021.758067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 05/08/2023]
Abstract
The genus Spumella, established by Cienkowsky in 1870, is characterized by omnivory, two (rarely three) flagella, a short stick-like structure beneath the flagella, a threadlike stalk, cell division via constriction and cyst formation. Since the first phylogenetic study of Spumella-like flagellates, their paraphyly has consistently been shown, with separation into several genera. More recently, Spumella was carefully investigated using molecular and morphological data to propose seven new species. Classification of this genus and knowledge of its species diversity remain limited because Spumella-like flagellates are extremely difficult to identify based on limited morphological characters. To understand the phylogeny and taxonomy of Spumella, we analyzed molecular and morphological data from 47 strains, including 18 strains isolated from Korean ponds or swamps. Nuclear SSU, ITS and LSU rDNA data were used for maximum likelihood and Bayesian analyses. The molecular data divided the strains into 15 clades, including seven new lineages, each with unique molecular signatures for nuclear SSU rRNA from the E23-2 to E23-5 domains, the spacer between the E23-8 and E23-9 domains of the V4 region and domain 29 of the V5 region. Our results revealed increased species diversity in Spumella. In contrast to the molecular phylogeny results, the taxa showed very similar cell morphologies, suggesting morphological convergence into simple nanoflagellates to enable heterotrophy. Three new species produced stomatocysts in culture. Aspects of stomatocyst morphology, including collar structure, surface ornamentation, and cyst shape, were very useful in differentiating the three species. The general ultrastructure of Spumella bureschii strain Baekdongje012018B8 and S. benthica strain Hwarim032418A5 showed the typical chrysophyte form for the leucoplast, a vestigial chloroplast surrounded by four envelope membranes, supporting the hypothesis that Spumella evolved from a phototroph to a heterotroph via the loss of its photosynthetic ability. Seven new species are proposed: S. benthica, S. communis, S. longicolla, S. oblata, S. rotundata, S. similis, and S. sinechrysos.
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Affiliation(s)
- Minseok Jeong
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Seung Won Nam
- Nakdonggang National Institute of Biological Resources, Sangju-si, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
- *Correspondence: Woongghi Shin,
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Kulikovskiy M, Maltsev Y, Glushchenko A, Kuznetsova I, Kapustin D, Gusev E, Lange-Bertalot H, Genkal S, Kociolek JP. Gogorevia, a New Monoraphid Diatom Genus for Achnanthes exigua and Allied Taxa (Achnanthidiaceae) Described on the Basis of an Integrated Molecular and Morphological Approach. JOURNAL OF PHYCOLOGY 2020; 56:1601-1613. [PMID: 32871027 DOI: 10.1111/jpy.13064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
A new diatom genus, Gogorevia, is described on the basis of an integrated molecular and morphological investigation. Two species are described from Vietnam: the generitype, G. rinatii sp. nov., and G. ovalis sp. nov. These species share many morphological features with Achnanthes exigua and allied taxa that were previously transferred to the genera Achnanthidium or Lemnicola. Our current molecular investigation shows that Gogorevia is distinct and phylogenetically removed from the above-mentioned genera. Morphologically, Gogorevia differs from Achnanthidium and Lemnicola by the shape of the valves, possessing uniseriate striae, raphe morphology, and the presence of an evident sternum. The recently described species Lemnicola uniseriata is transferred to Gogorevia on the basis that it possesses the same morphological features and phylogenetic position as other members of the genus.
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Affiliation(s)
- Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Yevhen Maltsev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Anton Glushchenko
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Irina Kuznetsova
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Dmitry Kapustin
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Evgeniy Gusev
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Horst Lange-Bertalot
- K.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, 35 Botanicheskaya St., Moscow, 127276, Russia
| | - Sergei Genkal
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Yaroslavl, Nekouz, Borok, Russia
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
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Liu M, Zhao Y, Sun Y, Li Y, Wu P, Zhou S, Ren L. Comparative study on diatom morphology and molecular identification in drowning cases. Forensic Sci Int 2020; 317:110552. [PMID: 33147546 DOI: 10.1016/j.forsciint.2020.110552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
In the field of criminal investigations, in the event that a body is found in water, the ability to differentiate whether the cause of death was drowning or the body was murdered then dumped into water elsewhere is difficult but important for case detection. Detecting diatoms in human organs can be used to effectively identify if the cause of death was drowning. At present, diatom detection methods are roughly divided into morphological and molecular detection methods, but both methods have different limitations. In this study, a total of 79 samples from 23 victims in 19 known drowning deaths were collected. The diatom morphological identification combined with DNA metabarcoding technology was used to compare the reliability of the diatom detection method. Microscopic observations revealed that the positive detection rate of diatoms was 52.6 %, 26.3 % and 58.8 % respectively in the kidney, liver and lung samples. DNA metabarcoding analysis found that the positive detection rate of diatoms was 31.6 %, 31.6 % and 35.3 % respectively in kidney, liver and lung samples. When compared with barcode BacirbcL, barcode 18S605 detected more diatoms, while diatoms in BacirbcL were more consistent with environmental samples. The comparative analysis found that microscopic observations were not highly correlated with the identification results of DNA barcoding technology. There were no obvious differences in the effect of internal organs on diatom enrichment, and different organs should be tested at the same time. At present, the DNA barcode reference sequence is gravely insufficient and has many errors, which leads to restrictions in the application of this technology, resulting in many OTU not being accurately identified. This explains why the success rate of molecular identification is not higher than that of microscopic identification. Construction of a reliable diatom DNA barcode reference sequence database is an urgent task for drowning forensics.
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Affiliation(s)
- Mengyan Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China; Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Yi Zhao
- Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Yuzhe Sun
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanan Li
- Forensic Judicial Appraisal Center of Beijing Public Security Bureau, Beijing, 100192, China
| | - Ping Wu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Liang Ren
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
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46
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Mann DG, Trobajo R, Sato S, Li C, Witkowski A, Rimet F, Ashworth MP, Hollands RM, Theriot EC. Ripe for reassessment: A synthesis of available molecular data for the speciose diatom family Bacillariaceae. Mol Phylogenet Evol 2020; 158:106985. [PMID: 33059066 DOI: 10.1016/j.ympev.2020.106985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/21/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023]
Abstract
The Bacillariaceae is a very species-rich family of raphid diatoms and includes the large and taxonomically difficult genus Nitzschia, whose species are often small-celled and finely structured and have few discrete morphological characters visible in the light microscope. The classification of Nitzschia is still mostly based on one developed in the second half of the 19th century by Grunow, who separated the genus into a series of sections largely on cell shape and symmetry, the position of the raphe, transverse extension of the fibulae, and folding of the valve. We assembled and analysed single-gene and concatenated alignments of nSSU, nLSU, rbcL, psbC and cox1 to test Grunow's and subsequent classifications and to examine selected morphological characters for their potential to help define monophyletic groups. The maximum likelihood trees were equivocal as to monophyly of the family itself but showed good support for each of eight main clades of Bacillariaceae, three of which corresponded more or less to existing genera (Hantzschia, Cylindrotheca and Bacillaria). The other five main clades and some subclades comprised groups of Nitzschia species or assemblies of Nitzschia species with other genera (Pseudo-nitzschia, Fragilariopsis, Neodenticula, Tryblionella, Psammodictyon). Relationships between most of the eight main clades were not resolved robustly but all analyses recovered Nitzschia as non-monophyletic. The Grunowian classification of Nitzschia into sections was not supported, though in some respects (e.g. treatment of sigmoid species) it is better than subsequent reclassifications. Several of the main clades and subclades are cryptic (lacking morphological synapomorphies) and homoplasy is common in both light microscopical and ultrastructural characters (to the extent that organisms initially assigned to the same species sometimes prove to belong to a different main clade). Nevertheless, some characters, including the structure of the raphe canal and girdle, seem to be sufficiently conservative evolutionarily to give a provisional estimate of relationships if molecular data are unavailable. No new formal classifications are proposed but various options are explored and research needs identified.
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Affiliation(s)
- David G Mann
- Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 Sant Carles de la Ràpita, Catalunya, Spain; Royal Botanic Garden Edinburgh (RBGE), Edinburgh EH3 5LR, UK.
| | - Rosa Trobajo
- Marine and Continental Waters, Institute for Food and Agricultural Research and Technology (IRTA), Crta de Poble Nou Km 5.5, E-43540 Sant Carles de la Ràpita, Catalunya, Spain.
| | - Shinya Sato
- Fukui Prefectural University, 1-1 Gakuen-cho, Obama, Fukui 917-0003, Japan
| | - Chunlian Li
- Institute of Marine and Environmental Sciences, University of Szczecin, and Natural Sciences Research and Educational Center, University of Szczecin, Mickiewicza 16a, PL-70-383 Szczecin, Poland; Ecological Institute, South China Normal University, 510631 Guangzhou, China
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, and Natural Sciences Research and Educational Center, University of Szczecin, Mickiewicza 16a, PL-70-383 Szczecin, Poland
| | - Frédéric Rimet
- UMR CARRTEL, Savoie Mont-Blanc University, INRAE, 75bis avenue de Corzent, CS50511, F-74203 Thonon-les-Bains, France
| | - Matt P Ashworth
- UTEX Culture Collection of Algae, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Ruth M Hollands
- Royal Botanic Garden Edinburgh (RBGE), Edinburgh EH3 5LR, UK
| | - Edward C Theriot
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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Novis PM, Sales RE, Gordon K, Manning N, Duleba M, Ács É, Dressler M, Schallenberg M. Lindavia intermedia (Bacillariophyceae) and Nuisance lake Snow in New Zealand: Chitin Content and Quantitative PCR Methods to Estimate Cell Concentrations and Expression of Chitin Synthase 1. JOURNAL OF PHYCOLOGY 2020; 56:1232-1244. [PMID: 32396981 DOI: 10.1111/jpy.13014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Lake snow, caused by the freshwater centric diatom Lindavia intermedia, has become problematic in several large, oligotrophic New Zealand lakes over the past decade. Macroaggregates produced by L. intermedia foul fishing lines, intake screens, and water filters, and have a negative impact on recreational values. It was confirmed that the fibers constituting lake snow are composed of chitin, two chitin synthase genes (chs1 and 2) from L. intermedia were characterized, new qPCR-based tools to quantify the abundance of the species and measure expression of chs2 relative to the reference gene act1 (the product of which has cytoskeletal functions) were developed. The strong heterogeneity and mucilaginous nature of lake snow samples create particular difficulties for calibrations of gene or transcript copy numbers with cell densities and obtaining high yields of mRNA. However, data collected from four lakes during November 2018 and February and May 2019 show that abundance of L. intermedia is always high when lake snow is also abundant, but that a full range of L. intermedia abundance can occur when lake snow is absent, suggesting that chitin production is not obligate in L. intermedia. This result is consistent with the available data for chs2 expression, which suggest higher transcription when lake snow is abundant. Lake snow production by L. intermedia therefore requires an as yet undetermined stimulus independent of cell abundance.
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Affiliation(s)
- Phil M Novis
- Allan Herbarium, Manaaki Whenua - Landcare Research, P.O. Box 69040, Lincoln, 7640, New Zealand
| | - Ruth E Sales
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Keith Gordon
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Nathan Manning
- Otago Regional Council, 14 Rogers St, Cromwell, 9310, New Zealand
| | - Mónika Duleba
- MTA Centre for Ecological Research, Danube Research Institute, 1113, Budapest, Hungary
| | - Éva Ács
- MTA Centre for Ecological Research, Danube Research Institute, 1113, Budapest, Hungary
| | - Mirko Dressler
- Department of Allgemeine u. Spezielle Botanik, Universität Rostock, Wismarsche Str. 44/45, 18051, Rostock, Germany
| | - Marc Schallenberg
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
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Schenk J, Höss S, Brinke M, Kleinbölting N, Brüchner-Hüttemann H, Traunspurger W. Nematodes as bioindicators of polluted sediments using metabarcoding and microscopic taxonomy. ENVIRONMENT INTERNATIONAL 2020; 143:105922. [PMID: 32663713 DOI: 10.1016/j.envint.2020.105922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/04/2020] [Accepted: 06/20/2020] [Indexed: 05/19/2023]
Abstract
The use of bioindicator species is a widely applied approach to evaluate ecological conditions, and several indices have been designed for this purpose. To assess the impact of pollution, especially in sediments, a pollution-sensitive index based on nematodes, one of the most abundant and species-rich groups of metazoa, was developed. The NemaSPEAR[%] index in its original form relies on the morphological inspection of nematode species. The application of a morphologically based NemaSPEAR[%] at the genus-level was previously validated. The present study evaluated a NemaSPEAR[%] index based on metabarcoding of nematode communities and tested the potential of fragments from the 28S rDNA, 18S rDNA and cytochrome c oxidase subunit I (COI) genes. In general, molecular-based results tended to show a poorer condition than morphology-based results for the investigated sites. At the genus level, NemaSPEAR[%] values based on morphological data strongly correlated with those based on molecular data for both the 28S rDNA and the 18S rDNA gene fragments (R2 = 0.86 and R2 = 0.74, respectively). Within the dominant genera (>3%) identified by morphology, 68% were detected by at least one of the two ribosomal markers. At the species level, however, concordance was less pronounced, as there were several deviations of the molecular from the morphological data. These differences could mostly be attributed to shortcomings in the reference database used in the molecular-based assignments. Our pilot study shows that a molecularly based, genus-level NemaSPEAR[%] can be successfully applied to evaluate polluted sediment. Future studies need to validate this approach further, e.g. with bulk extractions of whole meiofaunal communities in order to circumvent time-consuming nematode isolation. Further database curation with abundant NemaSPEAR[%] species will also increase the applicability of this approach.
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Affiliation(s)
- Janina Schenk
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
| | - Sebastian Höss
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany; Ecossa, Giselastrasse 6, 82319 Starnberg, Germany.
| | - Marvin Brinke
- Federal Institute of Hydrology (BfG), Mainzer Tor 1, 56068 Koblenz, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.
| | | | - Walter Traunspurger
- Department of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany.
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Vinayak V. Chloroplast gene markers detect diatom DNA in a drowned mice establishing drowning as a cause of death. Electrophoresis 2020; 41:2144-2148. [PMID: 32969082 DOI: 10.1002/elps.202000100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/27/2020] [Accepted: 09/08/2020] [Indexed: 11/12/2022]
Abstract
Diatoms are unicellular microalgae with cell wall made up of rigid silica found in all open water bodies. They thus resist degradation and hence are important tool to diagnose cause of death in drowned bodies. The nitric acid digestion method practiced conventionally in forensic science laboratories has limitations due to manual error. Plant chloroplast genes found in diatoms such as ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL-3P) and rbcL, universal plastidic amplicon (UPA), and photosynthesis I P700 apoprotein chlorophyll Al (psaA), which play an important role in photosystems I and II of photosynthesis, are tested to diagnose drowning in experimental mice. It was seen that psaA-2 showed amplification at 150 bp in all biological samples. The sequences of psaA-2 gene marker showed 100% proximity to Thalassiosira weissflogii and rbcL-3P showed 99% resemblance to Pseudo-nitzschia multiseries. On the other hand, in postmortem drowned biological samples, the chloroplast-based gene marker failed to show any amplification.
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Affiliation(s)
- Vandana Vinayak
- Diatom Nanoengineering and Metabolism Lab (DNM), School of Applied Sciences, Dr. Hari Singh Gour Central University, Sagar, India
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50
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Gubelit YI, Grossart HP. New Methods, New Concepts: What Can Be Applied to Freshwater Periphyton? Front Microbiol 2020; 11:1275. [PMID: 32670226 PMCID: PMC7328189 DOI: 10.3389/fmicb.2020.01275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.
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Affiliation(s)
- Yulia I. Gubelit
- Laboratory of Freshwater Hydrobiology, Zoological Institute, Russian Academy of Science, Saint Petersburg, Russia
| | - Hans-Peter Grossart
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Experimental Limnology, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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