scholarly journals Using metabarcoding and « Diat.Barcode » database to perfom molecular identification on marine biofilms

2021 ◽  
Vol 4 ◽  
Author(s):  
Raphaëlle Barry-Martinet ◽  
Elora Vedie ◽  
Christine Bressy ◽  
Jean-François Briand
Keyword(s):  
Microscopic Analysis ◽  
Marine Diatom ◽  
Morphological Identification ◽  
Rbcl Gene ◽  
Diatom Species ◽  
Molecular Analyses ◽  
Marine Biofilm ◽  
Freshwater Diatoms ◽  
Artificial Surfaces ◽  
Marine Biofilms

Marine benthic diatoms highly contribute to biofilms formation, playing a crucial role on both living and artificial surfaces ‘colonization (Briand 2017, Salta 2013). However, their microscopic morphological identification is time consuming and requires a high expertise in taxonomy. We therefore decided to look toward molecular analyses and especially metabarcoding. In this study, we determine : (i) if the use of the “Diat.barcode” database, mostly developed for freshwater diatoms (Rimet 2019), is relevant to characterize marine biofilm communities, (ii) if the amplification of degenerated primers targeting the rbcL gene (Vasselon et al. 2017) could improve the diversity of marine diatom biofilms, and (iii) if molecular and morphological analyses could be correlated.A large majority of OTUs (>95%) was affiliated using the “Diat.barcode” database and the pipeline FROGS, with coverage and affinity values above 80%. OTUs tables contained 75% of diatom species already reported from marine environment, with 82% belonging to the pennates group. The use of degenerated primers significantly improved richness and diversity. Moreover, it allowed us to identify taxa that were not present before, as Iconella, Sellaphora and Coronia. Finally, we showed higher richness and diversity, but also a higher repeatability (replicates closeness) leading to a better clustering with metabarcoding. We found differences in terms of biomarkers, but more broadly, we were able to correlate significantly (r = 0,404; p<0.0001) diatom assemblages.While the latest version of “Diat.barcode” database contains only 12.4% species referenced as marine, it appears to be a powerful tool, even on biofilm samples from the Mediterranean, Baltic seas and Indian Ocean. Furthermore, we confirmed the relevance of degenerated primers to amplify a higher diversity of diatoms. Finally, beta-diversity similarity using molecular and microscopic analysis appeared positive, leading to the conclusion that the two methods should be used in a complementary way.

Occurrence of structural aluminum (Al) in marine diatom biological silica: Visible evidence from microscopic analysis

2021 ◽  
Author(s):  
Qian Tian ◽  
Dong Liu ◽  
Peng Yuan ◽  
Mengyuan Li ◽  
Weifeng Yang ◽  
...  
Keyword(s):  
Microscopic Analysis ◽  
Marine Diatom

New species of benthic marine diatoms (Bacillariophyta) from the Western Pacific islands of Guam and Yap

Phytotaxa ◽  
2021 ◽  
Vol 508 (3) ◽  
Author(s):  
CHRISTOPHER S. LOBBAN
Keyword(s):  
Pacific Islands ◽  
Central Area ◽  
Marshall Islands ◽  
Marine Diatom ◽  
Large Species ◽  
Diatom Species ◽  
Cell Interior ◽  
Pennate Diatom ◽  
The Western Pacific ◽  
Benthic Marine Diatoms

In the course of preparation of a major checklist for Yap and ongoing investigations into the benthic marine diatom flora of Micronesia, thirteen new araphid and raphid pennate diatom species have been recognized and are described here. Plagiogramma subatomus is even smaller than P. atomus and the pseudoseptum forms a box with only a small opening toward the cell interior. Licmophora romuli is similar in size and spathulate shape to L. remulus, but the majority of the striae in the lamina lack vimines. L. graphis is exceedingly delicate, pencil-shaped, with apical striae 60–70 in 10 µm. Divergita biformis and D. decipiens are straight species with striae biseriate on the margin, uniseriate on the valve face, differing in the shape and prominence of the sternum and the shape of the valve-face areolae. D. macinnisii (from Marshall Islands, but included here for comparison) is curved, again with the decussate areolar pattern on the mantle, but with single extended areolae along each side of the linear sternum. These characters slightly amend the diagnosis of the genus.  Thalassionema baculum is a very short member of the genus, linear and isopolar. Climaconeis tarangensis is curved and differs from C. riddleae in stria density and areola shape; C. minaegensis is straight, without a stauros or craticular bars, of intermediate length, 228–247 µm. First SEM observations of Climaconeis lorenzii are presented and an updated key to Climaconeis is appended. Parlibellus paschalis is a tube-dwelling species differing from P. delognei is lacking cuniculi and pores in the central area. P. waabensis is a relatively large species, possibly tube-dwelling, that differs from P. delognei in shape and spacing of central striae and from P. berkeleyi in width and stria density. Pleurosigma simulacrum differs in ultrastructural details from P. intermedium. Lastly, Nitzschia tarangensis is a conopeate species, spathulate in profile with ribs along the edge of the valve depression and bordering the raphe, and with pores in the peri-raphe zone.

Toxicities of Irgarol 1051 derivatives, M2 and M3, to two marine diatom species

2019 ◽  
Vol 182 ◽  
pp. 109455 ◽  
Author(s):  
Amy Q. Zhang ◽  
Guang-Jie Zhou ◽  
Michael H.W. Lam ◽  
Kenneth M.Y. Leung
Keyword(s):  
Marine Diatom ◽  
Diatom Species ◽  
Irgarol 1051

scholarly journals Subaxolemmal cytoskeleton in squid giant axon. II. Morphological identification of microtubule- and microfilament-associated domains of axolemma.

1986 ◽  
Vol 102 (5) ◽  
pp. 1710-1725 ◽  
Author(s):  
S Tsukita ◽  
S Tsukita ◽  
T Kobayashi ◽  
G Matsumoto
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Preceding Paper ◽  
Microscopic Analysis ◽  
Giant Axon ◽  
Squid Giant Axon ◽  
Molecular Organization ◽  
Fixation Method ◽  
Morphological Identification

In the preceding paper (Kobayashi, T., S. Tsukita, S. Tsukita, Y. Yamamoto, and G. Matsumoto, 1986, J. Cell Biol., 102:1710-1725), we demonstrated biochemically that the subaxolemmal cytoskeleton of the squid giant axon was highly specialized and mainly composed of tubulin, actin, axolinin, and a 255-kD protein. In this paper, we analyzed morphologically the molecular organization of the subaxolemmal cytoskeleton in situ. For thin section electron microscopy, the subaxolemmal cytoskeleton was chemically fixed by the intraaxonal perfusion of the fixative containing tannic acid. With this fixation method, the ultrastructural integrity was well preserved. For freeze-etch replica electron microscopy, the intraaxonally perfused axon was opened and rapidly frozen by touching its inner surface against a cooled copper block (4 degrees K), thus permitting the direct stereoscopic observation of the cytoplasmic surface of the axolemma. Using these techniques, it became clear that the major constituents of the subaxolemmal cytoskeleton were microfilaments and microtubules. The microfilaments were observed to be associated with the axolemma through a specialized meshwork of thin strands, forming spot-like clusters just beneath the axolemma. These filaments were decorated with heavy meromyosin showing a characteristic arrowhead appearance. The microtubules were seen to run parallel to the axolemma and embedded in the fine three-dimensional meshwork of thin strands. In vitro observations of the aggregates of axolinin and immunoelectron microscopic analysis showed that this fine meshwork around microtubules mainly consisted of axolinin. Some microtubules grazed along the axolemma and associated laterally with it through slender strands. Therefore, we were led to conclude that the axolemma of the squid giant axon was specialized into two domains (microtubule- and microfilament-associated domains) by its underlying cytoskeletons.

scholarly journals Molecular Analyses of Colletotrichum Species from Almond and Other Fruits

2000 ◽  
Vol 90 (6) ◽  
pp. 608-614 ◽  
Author(s):  
Stanley Freeman ◽  
Dror Minz ◽  
Edouard Jurkevitch ◽  
Marcel Maymon ◽  
Ezra Shabi
Keyword(s):  
United States ◽  
Sequence Analysis ◽  
Its Region ◽  
The United States ◽  
Morphological Identification ◽  
Molecular Analyses ◽  
Colletotrichum Species ◽  
Morphological Criteria ◽  
Colletotrichum Spp ◽  
Polymerase Chain

Isolates of Colletotrichum spp. from almond, avocado, and strawberry from Israel and isolates of the pink subpopulation from almond from the United States were characterized by various molecular methods and compared with morphological identification. Taxon-specific primer analysis grouped the avocado isolates within the species C. gloeosporioides and the U.S. almond and Israeli strawberry isolates within the species C. acutatum. However, the Israeli almond isolates, previously identified morphologically as C. gloeosporioides, reacted with C. acutatum-specific primers. Arbitrarily primed polymerase chain reaction and A+T-rich DNA analyses determined that each population from almond and strawberry was distinct and clonal. Sequence analysis of the complete internal transcribed spacer (ITS) region (ITS 1–5.8S–ITS 2) revealed a similarity of between 97.03 and 98.72% among almond isolates from Israel, C. acutatum almond isolates from the United States, and C. acutatum strawberry isolates from Israel. Similarity of the above populations to that of C. gloeosporioides of avocado was between 92.42 and 92.86%. DNA sequence analysis of the entire ITS region supported the phylogeny inferred from the ITS 1 tree of 14 different Colletotrichum species. Although morphological criteria indicated that the Israeli isolates from almond are unique, this population was grouped within the C. acutatum species according to molecular analyses.

scholarly journals Biosynthesis of Silver Nanoparticles UsingAegle marmelos(Bael) Fruit Extract and Its Application to Prevent Adhesion of Bacteria: A Strategy to Control Microfouling

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
A. Nithya Deva Krupa ◽  
Vimala Raghavan
Keyword(s):  
Silver Nanoparticles ◽  
Biological Synthesis ◽  
Isolation And Identification ◽  
Fruit Extract ◽  
Force Microscopy ◽  
Atomic Force ◽  
Marine Biofilm ◽  
Marine Biofilms ◽  
Biosynthesized Agnps ◽  
Rdna Analysis

Marine biofilms formed due to adhesion of bacteria and other microorganisms on submerged surfaces are generally considered to be a major form of microfouling. Subsequent attachment of larvae of higher organisms like barnacles, mussels, and so forth, on marine biofilms, causes macrofouling. Several approaches have been used to prevent micro- and macrofouling. Silver nanoparticles (AgNPs) are known to exhibit strong inhibitory and antimicrobial activity. Biological synthesis of AgNPs is rapidly gaining importance due to its growing success. Hence, the present study is focused on the biosynthesis of AgNPs using fruit extract ofAegle marmelosand its characterization through UV-Vis spectrophotometer, X-ray diffractometer (XRD), Fourier transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM). Further isolation and identification of marine biofilm forming bacteria were carried out through 16S rDNA analysis. The antimicrofouling effect of the biosynthesized AgNPs was tested against marine biofilm forming bacteria and the results suggested that it could effectively inhibit biofilm formation. This preliminary study has proved that AgNPs may be used as antimicrofouling agent for the prevention of biofouling in the early stages.

scholarly journals Occurrence of structural aluminum (Al) in marine diatom biological silica: Visible evidence from microscopic analysis

2021 ◽  
Author(s):  
Qian Tian ◽  
Dong Liu ◽  
Peng Yuan ◽  
Mengyuan Li ◽  
Weifeng Yang ◽  
...  
Keyword(s):  
Focused Ion Beam ◽  
Ion Beam ◽  
Microscopic Analysis ◽  
Atomic Ratio ◽  
Marine Diatom ◽  
Biogeochemical Cycle ◽  
Homogeneous Distribution ◽  
Marine Diatoms ◽  
Mapping Analysis ◽  
Living Diatoms

Abstract. The global marine biogeochemical cycle of aluminum (Al) is believed to be driven by marine diatoms, due to the uptake of dissolved Al (DAl) by living diatoms from surface seawater. The occurrence of Al in diatom biogenic silica (BSi) can inhibit the dissolution of BSi, thus benefiting the effects of the ballast role of diatoms in the biological pump and forming a coupled Si-Al biogeochemical cycle. However, the occurrence mechanism of Al in marine diatoms is still unclear. In particular, whether or not Al is incorporated into the structure of BSi of living diatoms is unrevealed, resulting in difficulties in understanding the biogeochemical behaviors of Al. In this study, Thalassiosira weissflogii, a widely distributed marine diatom in marginal seas, was selected as the model to evaluate the occurrence of structural Al in BSi based on culturing experiments with the addition of DAl. The structural Al in BSi was detected by combining focused ion beam (FIB) scanning electron microscopy and energy dispersive X-ray spectroscopy (EDS) mapping analysis. Direct evidence of structural Al in living BSi was obtained for the first time. The distribution and content of this Al were revealed by the EDS-mapping analysis. The structural Al in the BSi exhibited a homogeneous distribution, and the average Al / Si atomic ratio obtained through the FIB-EDS mapping analysis was 0.011. The effects of structural Al on BSi dissolution-inhibition are discussed based on the content of this Al. The fundamental results indicate the significant contribution of marine diatoms to the biogeochemical migration of marine Al.

scholarly journals Newly Recorded Species of Diatoms in the Source of Han and Nakdong Rivers, South Korea

Phytotaxa ◽  
2019 ◽  
Vol 403 (3) ◽  
pp. 143
Author(s):  
SANG DEUK LEE ◽  
SUK MIN YUN ◽  
PYO YUN CHO ◽  
HYE-WON YANG ◽  
OE JUNG KIM
Keyword(s):  
South Korea ◽  
Diatom Species ◽  
Taxonomic Information ◽  
Floristic Study ◽  
Freshwater Diatoms ◽  
Freshwater Environments ◽  
Taxonomic System

For floristic study on diatoms from the source of Han and Nakdong Rivers, we collected samples in February, April, and July 2016 from Geomryongso and Neodeolsam Ponds, South Korea. Geomryongso and Neodeolsam Ponds are sources of Han and Nakdong Rivers, respectively. Thirty-eight infrageneric taxa of freshwater diatoms were identified in the collected samples from study areas. The diatom species were classified into 25 genera, 17 families, 10 orders, 5 subclasses, and 2 classes based on the taxonomic system proposed by Round et al. (1990). Nine diatom taxa—Achnanthes sinaensis, Achnanthidium atomus, Edtheriotia guizhoiana, Fragilaria recapitellata, Gyrosigma procerum, Navicula nipponica, Pinnularia pseudotabellaria, Pinnularia rabenhorstii, and Platessa barhlsii—were newly recorded, whose taxonomic features have been described; they are indicated by asterisk. We presented the taxonomic information, including the systematics, and dimension in the source of two major rivers in Korea. This study might contribute to the understanding of diversity and flora of diatoms in various freshwater environments in Korea.

Gomphonema bicepiformis sp. nov., a new diatom species (Bacillariophyta) from a stream in Zhejiang, China

Phytotaxa ◽  
2018 ◽  
Vol 375 (4) ◽  
pp. 274 ◽  
Author(s):  
WEI ZHANG ◽  
GUANGXIA SHANG ◽  
JHONE PATRICK KOCIOLEK ◽  
LIQING WANG ◽  
HONGXIN TAN
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
New Species ◽  
Central Region ◽  
Zhejiang Province ◽  
Clean Water ◽  
Diatom Species ◽  
Freshwater Diatoms ◽  
Scanning Electron

During a survey of freshwater diatoms from Shibadukeng stream in the Xianju County, Zhejiang Province, China, a new gomphonemoid species, Gomphonema bicepiformis sp. nov. has been recorded. The new species is diagnosed from all others in the genus based on morphology as observed with both light and scanning electron microscopy. Valves of Gomphonema bicepiformis are lanceolate with a gibbous central region. The headpole is broadly rounded, clearly capitate and the footpole is also broadly rounded, capitate. The axial area is wide, lanceolate-rhombic, broad at mid-valve, reaching 3/4 of the total breadth. There are circular to irregularly-shaped depressions in the axial area on the exterior of the valve surface often appearing as light spots in LM. The new species was compared with G. biceps, G. obstipum, G. manubrium, G. pyrenaicum, G. guayabense and G. nipponica, all of which resemble Gomphonema bicepiformis in outline, but differ from the new species in specific details of size, striae density, and extent of the axial area. This species occurs in relatively low conductivity and clean water in Zhejiang, China.

Streblocladia (Rhodomelaceae) in New Zealand: recognition of a new species

Phytotaxa ◽  
2018 ◽  
Vol 374 (1) ◽  
pp. 41
Author(s):  
MYUNG SOOK KIM ◽  
BYEONGSEOK KIM ◽  
MI YEON YANG ◽  
ROBERTA D’ARCHINO ◽  
JUDY E. SUTHERLAND ◽  
...  
Keyword(s):  
New Species ◽  
New Zealand ◽  
Strong Support ◽  
Red Alga ◽  
Morphological Evidence ◽  
Rbcl Gene ◽  
Monophyletic Clade ◽  
Molecular Analyses ◽  
A New Species ◽  
Rbcl Gene Sequences

The genus Streblocladia was described by early European collectors based on S. neglecta, a marine red alga from southern New Zealand currently treated as a taxonomic synonym of Streblocladia glomerulata. In New Zealand, Streblocladia includes two species and has always been considered distinct. To analyse the phylogenetic relationships of this genus with other Polysiphonia sensu lato, we conducted a molecular-assisted investigation using plastid rbcL gene sequences of recent collections of Streblocladia from New Zealand, as well as morphological observations. The molecular analyses indicated that Streblocladia species form a monophyletic clade sister to P. rhododactyla with strong support. The Streblocladia clade is clearly separated from other species of Polysiphonia sensu lato. Species of Streblocladia are characterized by sympodially branched, corticated main axes, the absence of vegetative trichoblasts, and spermatangial branches that are unilaterally arranged and replace the whole trichoblast. As a result, the New Zealand endemic Polysiphonia rhododactyla is transferred to the genus Streblocladia on the basis of genetic and morphological evidence and compared with the two other species from New Zealand, S. glomerulata and S. muelleriana.

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