IF 2.2 3区生物学

Fottea Pub Date : 2019-10-30 DOI: 10.5507/FOT.2019.006

Bing Liu, S. Blanco, L. Ector, Zhu-xiang Liu, Juan Ai

引用次数: 7

Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and Limitations¹. 融雪中微藻高通量测序数据评估:改进与局限

IF 2.2 3区生物学

Fottea Pub Date : 2019-10-30 Epub Date: 2019-08-01 DOI: 10.5507/fot.2019.003

Stefanie Lutz, Lenka Procházková, Liane G Benning, Linda Nedbalová, Daniel Remias

{"title":"Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and Limitations1.","authors":"Stefanie Lutz, Lenka Procházková, Liane G Benning, Linda Nedbalová, Daniel Remias","doi":"10.5507/fot.2019.003","DOIUrl":"https://doi.org/10.5507/fot.2019.003","url":null,"abstract":"Melting snow fields are an extremophilic habitat dominated by closely related Chlamydomonadaceae (Chlorophyta). Microscopy-based classification of these cryophilic microalgae is challenging and may not reveal the true diversity. High-throughput sequencing (HTS) allows for a more comprehensive evaluation of the community. However, HTS approaches have been rarely used in such ecosystems and the output of their application has not been evaluated. Furthermore, there is no consensus on the choice for a suitable DNA marker or data processing workflow. We found that the correct placement of taxonomic strings onto OTUs strongly depends on the quality of the reference databases. We improved the assignments of the HST data by generating additional reference sequences of the locally abundant taxa, guided by light microscopy. Furthermore, a manual inspection of all automated OTU assignments, oligotyping of the most abundant 18S OTUs, as well as ITS2 secondary structure analyses were necessary for accurate species assignments. Moreover, the sole use of one marker can cause misleading results, either because of insufficient variability within the locus (18S) or the scarcity of reference sequences (ITS2). Our evaluation reveals that HTS output needs to be thoroughly checked when the studied habitats or organisms are poorly represented in publicly available databases. We recommend an optimized workflow for an improved biodiversity evaluation of not only snow algal communities, but generally 'exotic' ecosystems where similar problems arise. A consistent sampling strategy, two- molecular marker approach, light microscopy-based guidance, generation of appropriate reference sequences and final manual verification of all taxonomic assignments are highly recommended.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2019-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116558/pdf/EMS108597.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38794920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Lagosinema tenuis gen. et sp. nov. (Prochlorotrichaceae, Cyanobacteria): a new brackish water genus from Tropical Africa Lagosinema tenuis gen. et sp. 11 .(原绿藻科，蓝藻门):来自热带非洲的咸淡水新属

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2018.012

S. C. Akagha, J. Johansen, D. Nwankwo, K. Yin

引用次数: 9

Phylogenetically distant clade of Nostoc-like taxa with the description of Minunostoc gen. nov. and Minunostoc cylindricum sp. nov 具有Minunostoc gen. 11和Minunostoc icum sp. nov描述的nostoc -样分类群的系统发育远分支

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2018.013

Fangfang Cai, Xiaochuang Li, Ruozhen Geng, Xin Peng, Renhui Li

{"title":"Phylogenetically distant clade of Nostoc-like taxa with the description of Minunostoc gen. nov. and Minunostoc cylindricum sp. nov","authors":"Fangfang Cai, Xiaochuang Li, Ruozhen Geng, Xin Peng, Renhui Li","doi":"10.5507/FOT.2018.013","DOIUrl":"https://doi.org/10.5507/FOT.2018.013","url":null,"abstract":"Two cyanobacterial strains morphologically identified to the genus Nostoc were isolated from a wet rocky wall in a mid-subtropical region in China, and they were taxonomically and phylogenetically characterized based on the polyphasic approach combining morphological and genetic characteristics. 16S rRNA gene sequence analysis showed that the two strains containing six clones were all >99.6% similar to each other, but had < 94.3% similarities to the existing cyanobacterial genera. The phylogenies based on 16S rRNA and rpoC1 gene sequences indicated that their sequences grouped into a unique and robust cluster with high bootstrap values. This unique cluster was separated from the clade of the 'Nostoc sensu stricto' and the respective clades formed by the morphologically similar genera Mojavia, Desmonostoc, Aliinostoc, Komarekiella and Halotia. The 16S-23S rRNA ITS secondary structure of the both strains exhibited the unique pattern of D1-D1´, Box-B and V3 helix, distinguishing it from the other heterocytous genera. Such a clear cluster leads to the establishment of Minunostoc gen. nov., with the type species as Minunostoc cylindricum sp. nov.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41380860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 30

Revision of the Psammothidium manguinii complex (Bacillariophyta) in the sub-Antarctic Region with the description of four new taxa 亚南极地区沙门藻复合体(硅藻门)的修订及四个新分类群的描述

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2019.001

B. Vijver

引用次数: 5

Three new freshwater species of the genus Achnanthidium (Bacillariophyta, Achnanthidiaceae) from Taiping Lake, China 太平湖阿胶属三新种（硅藻门，阿胶科）

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2018.015

P. Yu, Q. You, J. Kociolek, Quanxi Wang

引用次数: 17

Taxonomic transfer of Gongrosira fluminensis Fritsch (Chaetophorales, Chlorophyceae) to Lithotrichon Darienko et Pröschold (Ulvales, Ulvophyceae) based on morphological observation and phylogenetic analyses 基于形态学观察和系统发育分析的河松（Chaetophorales，Chlorphyceae）向石松Darienko et Pröschold（Ulvales，Ulvohyceae）的分类转移

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2018.014

Benwen Liu, Qinghua Wang, Shuyin Li, Jiao Fang, Guoxiang Liu, Zhengyu Hu

{"title":"Taxonomic transfer of Gongrosira fluminensis Fritsch (Chaetophorales, Chlorophyceae) to Lithotrichon Darienko et Pröschold (Ulvales, Ulvophyceae) based on morphological observation and phylogenetic analyses","authors":"Benwen Liu, Qinghua Wang, Shuyin Li, Jiao Fang, Guoxiang Liu, Zhengyu Hu","doi":"10.5507/FOT.2018.014","DOIUrl":"https://doi.org/10.5507/FOT.2018.014","url":null,"abstract":"One green algal specimen from China was identified as Gongrosira fluminensis Fritsch, due to its unique morphology that pseudoparenchymal basal stratum with rounded or polygonal cells grew into dense little-branched upright threads that reached approximately the same height with specific akinete formation and germination and formed strong cushions without calcification. Examination of the ultrastructural characteristics of plasmodesmata and pyrenoid confirmed that Gongrosira fluminensis Fritsch should be excluded from the order Chaetophorales. The phylogenetic evidence based on DNA sequence data from the nucleus (18S rDNA, ITS rDNA) and chloroplast (tufA) sequences clearly revealed that the Gongrosira fluminensis Fritsch should be classified in the Ulvales (Ulvophyceae) as the new combination species of the genus Lithotrichon Darienko et Proschold, instead of the Chaetophorales (Chlorophyceae). More specimens in conjunction with natural morphological investigation and molecular analyses are required to reevaluate the microfilamentous genus Gongrosira Kutzing and reveal hidden diversities among the Ulvophyceae.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2019-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47245147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

On some common and new cavum-bearing Planothidium (Bacillariophyta) species from freshwater 淡水中几种常见和新的带腔Planothidium（Bacillarophyta）物种的研究

IF 2.2 3区生物学

Fottea Pub Date : 2019-04-01 DOI: 10.5507/FOT.2018.016

C. E. Wetzel, B. Vijver, S. Blanco, L. Ector

引用次数: 13

Quadricoccopsis gen. nov., a new genus of Quadricoccus-like algae in Oocystaceae from China (Trebouxiophyceae, Chlorophyta) 中国乌囊藻科似四角藻属的一个新属——新一代四角藻（Treexiphyceae，Chlorphyta）

IF 2.2 3区生物学

Fottea Pub Date : 2018-11-01 DOI: 10.5507/FOT.2018.005

Xudong Liu, Huan Zhu, Huiyin Song, Benwen Liu, Qinghua Wang, Guoxiang Liu, Zhengyu Hu

{"title":"Quadricoccopsis gen. nov., a new genus of Quadricoccus-like algae in Oocystaceae from China (Trebouxiophyceae, Chlorophyta)","authors":"Xudong Liu, Huan Zhu, Huiyin Song, Benwen Liu, Qinghua Wang, Guoxiang Liu, Zhengyu Hu","doi":"10.5507/FOT.2018.005","DOIUrl":"https://doi.org/10.5507/FOT.2018.005","url":null,"abstract":"Members of Quadricoccus-like algae are characterized by oval to ellipsoid cells adherent to the bowl-shaped or stretched, empty mother cell walls and are common in phytoplankton of inland waters. To date, the morphologically similar genera Quadricoccus and Lobocystis are accepted for this group and the former had been phylogenetic positioned in Oocystaceae. In this study, seven strains of Quadricoccus-like algae were identified and successfully cultured in the laboratory. Light and electron microscope observations and phylogenetic analysis revealed that the strains represent three different species within a new genus, described here as Quadricoccopsis gen. nov. It differed from genus Quadricoccus by characteristically cell adherent mode that two pairs of daughter cells connected to the mother cell remnant respectively by the pole and median portion and distinguished from Lobocystis by variable 2-4-8 autospores, characteristically cell adherent mode and only found in limnetic water. The three new species, described here as Q. simplex, Q. parva and Q. glomerata, differed in cell size, colony morphology and autospore number. Phylogenetic analysis revealed the genus Quadricoccopsis in Oocystaceae and a close relationship with Oocystidium, which is far away from the phylogenetic position of Quadricoccus in one of the granulated clades. The Quadricoccus-like algae were, therefore, proved to be a paraphyly. Furthermore, apart from Planctonema-like algae, the Oocystaceae characteristic cell wall ultrastructure, which is multi-layered with cellulose fibrils in each layer perpendicular to those of the adjoining layer, is not shown again in genus Quadricoccopsis. Different cell wall substructures may be related to the colony formation mechanism. Whether the ultrastructure criterion is applied to all the Oocystaceae needs to be re-evaluated and, further, the definition of this family should be discussed.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45999937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Evolutionary relationships between the varieties of green algae Pediastrum boryanum and P. duplex s.l. (Chlorophyceae, Hydrodictyaceae) 绿藻Pediastrom boryanum和P.duplex s.l.（绿藻科、水藻科）品种的进化关系

IF 2.2 3区生物学

Fottea Pub Date : 2018-11-01 DOI: 10.5507/FOT.2018.004

J. Lenarczyk, M. Saługa

{"title":"Evolutionary relationships between the varieties of green algae Pediastrum boryanum and P. duplex s.l. (Chlorophyceae, Hydrodictyaceae)","authors":"J. Lenarczyk, M. Saługa","doi":"10.5507/FOT.2018.004","DOIUrl":"https://doi.org/10.5507/FOT.2018.004","url":null,"abstract":"The infraspecific relationships of the two most variable species, Pediastrum boryanum and P. duplex s.l. identified on the basis of morphological criteria, have been poorly studied so far. The present study focused on 12 original strains isolated from Polish water bodies and 29 strains from the GenBank database, which represent P. boryanum, P. duplex s.l. varieties and other morphologically similar taxa, against the background of 14 other strains of the family Hydrodictyaceae. In order to estimate the level of congruence between the phylogeny and the classical taxonomic system based on morphological criteria, the strains of P. boryanum and P. duplex s.l., and other morphologically similar taxa were subjected to parallel phylogenetic analyses applying Bayesian and Maximum Likelihood methods to combined molecular data (26S rDNA and rbcL cpDNA) and morphological analyses based on light and scanning electron microscopy, and iconographic documentation of almost all strains published elsewhere. The gene topologies revealed many discrepancies in the morphological features used to delimit the analysed taxa. The polyphyly of both P. boryanum and P. duplex s.l. was confirmed. Pseudopediastrum boryanum var. cornutum (formerly P. boryanum var. cornutum) formed a well supported monophyletic clade, whereas other varieties, including var. boryanum, brevicorne and longicorne, proved to be complex taxa. Previous description of Lacunastrum gracillimum (formerly P. duplex var. gracillimum) was well supported. A clade composed mostly of European strains identified as P. duplex var. rugulosum should be regarded as this taxon, whereas clades containing strains exhibiting P. duplex var. rugulosum-like morphology represent new taxa. Taxonomical changes within both P. boryanum and P. duplex s.l. are required on the basis of a higher number of strains and detailed morphometric data.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44639926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

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