Qi Zhang, Ling-ling Zheng, Tianli Li, Guoxiang Liu, Lirong Song
The family Radiococcaceae sensu lato, defined as colonial autospore-producing mucilaginous coccoid green algae, is widespread in terrestrial and freshwater habitats. Three species of Radiococcaceae sensu lato, including two Radiococcus species and one Planktosphaeria species, were described from China by light and electron microscopy. A new species of Planktosphaeria, Planktosphaeria hubeiensis sp. nov. was erected based on morphological comparisons and genetic analyses. Our phylogenetic analyses indicated that Radiococcaceae sensu lato is polyphyletic, and separated into three lineages. The Radiococcus species did not cluster into a monophyletic group in phylogenetic analyses; therefore the taxonomy of the genus Radiococcus should be revised in the future.
放射球菌科(Radiococcaceae sensu lato)被定义为产生自孢子的粘液球藻绿藻，广泛存在于陆地和淡水栖息地。利用光镜和电子显微镜对中国产放射球菌科3种，包括2种放射球菌和1种浮游球藻进行了描述。通过形态比较和遗传分析，建立了湖北浮游藻属新种——湖北浮游藻属。我们的系统发育分析表明，放射球菌科具有多系性，可分为三个谱系。在系统发育分析中，放射球菌没有聚在一个单系群中;因此，放射球菌属的分类应在未来进行修订。
{"title":"Morphology and phylogeny of three planktonic Radiococcaceae sensu lato species (Sphaeropleales, Chlorophyceae) from China, including the description of a new species Planktosphaeria hubeiensis sp. nov.","authors":"Qi Zhang, Ling-ling Zheng, Tianli Li, Guoxiang Liu, Lirong Song","doi":"10.5507/fot.2018.009","DOIUrl":"https://doi.org/10.5507/fot.2018.009","url":null,"abstract":"The family Radiococcaceae sensu lato, defined as colonial autospore-producing mucilaginous coccoid green algae, is widespread in terrestrial and freshwater habitats. Three species of Radiococcaceae sensu lato, including two Radiococcus species and one Planktosphaeria species, were described from China by light and electron microscopy. A new species of Planktosphaeria, Planktosphaeria hubeiensis sp. nov. was erected based on morphological comparisons and genetic analyses. Our phylogenetic analyses indicated that Radiococcaceae sensu lato is polyphyletic, and separated into three lineages. The Radiococcus species did not cluster into a monophyletic group in phylogenetic analyses; therefore the taxonomy of the genus Radiococcus should be revised in the future.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47499100","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}
During a survey of the freshwater diatom flora on the sub-Antarctic islands of the southern Indian Ocean, two new Planothidium species were observed, showing some resemblance to Planothidium delicatulum. Therefore, the type material of Achnanthidium delicatulum Kutzing was analysed, a common species in northern hemisphere waterbodies that was later transferred to the genus Planothidium. Additionally the material of Types du Synopsis des Diatomees de Belgique n° 234, designated in 1980 as neotype for Achnanthes delicatula was investigated. This analysis showed that the population in Types n° 234 is not conspecific with Achnanthidium delicatulum but in fact is a population of Planothidium galaicum. Both Planothidium species in the investigated Antarctic material are described as new to science: P. lilianeanum Van de Vijver sp. nov. and P. australodelicatulum Van de Vijver, C.E.Wetzel et Ector sp. nov. The new species can be differentiated based on differences in valve outline, presence of ridges and silica outgrowths on the rapheless valve, the structure of the raphe and the shape and size of the central area. Notes on the ecology and distribution of the new Antarctic species are added. Achnanthidium delicatulum is formally lectotypified.
在对南印度洋亚南极岛屿上的淡水硅藻群落进行调查期间，观察到两种新的扁藻物种，显示出与美味扁藻的一些相似之处。因此，对北半球水体中常见的一种后来被转移到Planothidium属中的美味扁藻（Achanthidium delicatulum Kutzing）的模式物质进行了分析。此外，还对1980年被指定为美味Achnanthes delicatula的新类型的《比利时互变异部概要》234号的材料进行了研究。该分析表明，234型中的种群与美味阿南提姆不是同种，但实际上是一个galaicum Planothidium种群。被调查的南极物质中的两个Planothidium物种都被描述为科学上的新物种：P.lilianeanum Van de Vijver sp.nov.和P.austradelicatulum Van de Vij ver，C.E.Wetzel et Ector sp.nov..新物种可以根据瓣膜轮廓的差异、无缝瓣膜上脊和二氧化硅生长物的存在来区分，中缝的结构以及中央区域的形状和大小。增加了关于南极新物种的生态学和分布的说明。美味阿胶被正式分类。
{"title":"Analysis of the type material of Planothidium delicatulum (Bacillariophyta) with the description of two new Planothidium species from the sub-Antarctic Region","authors":"B. Vijver, C. E. Wetzel, L. Ector","doi":"10.5507/FOT.2018.006","DOIUrl":"https://doi.org/10.5507/FOT.2018.006","url":null,"abstract":"During a survey of the freshwater diatom flora on the sub-Antarctic islands of the southern Indian Ocean, two new Planothidium species were observed, showing some resemblance to Planothidium delicatulum. Therefore, the type material of Achnanthidium delicatulum Kutzing was analysed, a common species in northern hemisphere waterbodies that was later transferred to the genus Planothidium. Additionally the material of Types du Synopsis des Diatomees de Belgique n° 234, designated in 1980 as neotype for Achnanthes delicatula was investigated. This analysis showed that the population in Types n° 234 is not conspecific with Achnanthidium delicatulum but in fact is a population of Planothidium galaicum. Both Planothidium species in the investigated Antarctic material are described as new to science: P. lilianeanum Van de Vijver sp. nov. and P. australodelicatulum Van de Vijver, C.E.Wetzel et Ector sp. nov. The new species can be differentiated based on differences in valve outline, presence of ridges and silica outgrowths on the rapheless valve, the structure of the raphe and the shape and size of the central area. Notes on the ecology and distribution of the new Antarctic species are added. Achnanthidium delicatulum is formally lectotypified.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44709936","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}
A. Saber, J. Mareš, G. Guella, A. Anesi, Lenka Štenclová, M. Cantonati
An interesting population of ulvacean green algae was collected from a limno-rheocrenic, thermal, mineral (chloride, sodium, sulphate) spring known as "Ain Abu Sherouf" in the Siwa Oasis, the Western Desert of Egypt. A detailed combined investigation on its morphotaxonomy, autecology, and a multilocus sequence data set including the chloroplast-encoded rbcL gene and the nuclear-encoded nrDNA SSU and ITS allowed us to identify this population as Ulva flexuosa subsp. paradoxa (syn. Ulva paradoxa, Ulvales, Chlorophyta), although the algal thalli were in average narrower than usual in this taxon. Analysis of the molecular rbcL-ITS sequencing data demonstrated a close phylogenetic relationship of the studied population to two Ulva isolates from Japan and China and their taxonomic status was further discussed. The pigment profiling confirmed chlorophylls and carotenoids typical of the Ulvaceae (lutein, α/β-carotenes, violaxanthin, and neoxanthin). Lipidomic analysis revealed the presence of the monogalactosyl diacylglycerols (MGDG), digalactosyl diacylglycerols (DGDG), sulfoquinovosyl diacylglycerols (SQDG), and diacylglyceryl N,N,N-trimethylhomoserine (DGTS) lipid classes. Presence of the plasma membrane DGTS lipids in remarkable proportion might be an adaptation to this nutrient-poor mineral spring habitat, with relatively low phosphorus values. The lower unsaturation index (UI) values of the plastidial DGDG and SQDG lipids are likely to reflect the need to maintain adequate membrane fluidity in this thermal mineral spring system. This polyphasic study not only extended our little knowledge on the distribution, autecology, and adaptive mechanisms of U. flexuosa subsp. paradoxa in the Saharan habitats of Africa, but also re-assessed and refined the taxonomic and phylogenetic affiliation of previously sampled close relatives from East Asia.
从埃及西部沙漠西瓦绿洲的一个名为“Ain Abu Sherouf”的limno流变、热、矿物（氯化物、钠、硫酸盐）泉中采集了一批有趣的ulvacean绿藻。对其形态分类学、自然生态学以及包括叶绿体编码的rbcL基因和细胞核编码的nrDNA SSU和its在内的多位点序列数据集进行了详细的联合研究，使我们能够将该种群鉴定为弯叶Ulva亚种。paradoxa（即Ulva paradoxa、Ulvales、Chlorophyta），尽管该分类单元的藻类铊平均比平时窄。分子rbcL-ITS测序数据的分析表明，所研究的种群与日本和中国的两个Ulva分离株有着密切的系统发育关系，并进一步讨论了它们的分类地位。色素图谱证实了锦葵科特有的叶绿素和类胡萝卜素（叶黄素、α/β-胡萝卜素、紫花素和新黄质）。脂质组学分析显示存在单半乳糖基二酰基甘油（MGDG）、二半乳糖基双酰基甘油（DGDG）、磺基喹啉基二酰基甘油醇（SQDG）和二酰基甘油N，N，N-三甲基高丝氨酸（DGTS）脂质类别。质膜DGTS脂质的显著比例可能是对这种营养不良、磷值相对较低的矿泉栖息地的适应。塑性DGDG和SQDG脂质的较低不饱和指数（UI）值可能反映了在该热矿泉系统中保持足够的膜流动性的需要。这项多相研究不仅扩展了我们对弯曲木亚种的分布、生态和适应机制的了解。非洲撒哈拉栖息地的悖论，但也重新评估和完善了以前从东亚采样的近亲的分类和系统发育关系。
{"title":"Polyphasic approach to a characteristic Ulva population from a limno-rheocrenic, mineral (chloride, sodium, sulphate) spring in the Siwa Oasis (Western Desert of Egypt)","authors":"A. Saber, J. Mareš, G. Guella, A. Anesi, Lenka Štenclová, M. Cantonati","doi":"10.5507/FOT.2018.008","DOIUrl":"https://doi.org/10.5507/FOT.2018.008","url":null,"abstract":"An interesting population of ulvacean green algae was collected from a limno-rheocrenic, thermal, mineral (chloride, sodium, sulphate) spring known as \"Ain Abu Sherouf\" in the Siwa Oasis, the Western Desert of Egypt. A detailed combined investigation on its morphotaxonomy, autecology, and a multilocus sequence data set including the chloroplast-encoded rbcL gene and the nuclear-encoded nrDNA SSU and ITS allowed us to identify this population as Ulva flexuosa subsp. paradoxa (syn. Ulva paradoxa, Ulvales, Chlorophyta), although the algal thalli were in average narrower than usual in this taxon. Analysis of the molecular rbcL-ITS sequencing data demonstrated a close phylogenetic relationship of the studied population to two Ulva isolates from Japan and China and their taxonomic status was further discussed. The pigment profiling confirmed chlorophylls and carotenoids typical of the Ulvaceae (lutein, α/β-carotenes, violaxanthin, and neoxanthin). Lipidomic analysis revealed the presence of the monogalactosyl diacylglycerols (MGDG), digalactosyl diacylglycerols (DGDG), sulfoquinovosyl diacylglycerols (SQDG), and diacylglyceryl N,N,N-trimethylhomoserine (DGTS) lipid classes. Presence of the plasma membrane DGTS lipids in remarkable proportion might be an adaptation to this nutrient-poor mineral spring habitat, with relatively low phosphorus values. The lower unsaturation index (UI) values of the plastidial DGDG and SQDG lipids are likely to reflect the need to maintain adequate membrane fluidity in this thermal mineral spring system. This polyphasic study not only extended our little knowledge on the distribution, autecology, and adaptive mechanisms of U. flexuosa subsp. paradoxa in the Saharan habitats of Africa, but also re-assessed and refined the taxonomic and phylogenetic affiliation of previously sampled close relatives from East Asia.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44774411","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}
While collecting epiphytic diatom samples from the west coast of Sweden, a small Mastrogloia species has been observed and could not be matched with any of the described taxa. Based on both light and electron microscopes examination, this species has been described as new, Mastogloia wulffii sp. nov. and included in Mastogloia section Sulcatae. This species is very small with valve length not exceeding 16.3 µm. It is characterized by having a narrow, almost straight median depression on both sides of the sternum-raphe, no marginal ridge and with rounded areolae on valve mantle as well as having completely hyaline lateral sterna. A comparison with similar taxa is given. M. wulffii is a marine species growing in moderate numbers on the red alga Polyides rotunda which is widely distributed along the coast of Vrango Island, Sweden.
{"title":"Mastogloia wulffii, a new diatom (Bacillariophyceae) from the west coast of Sweden","authors":"Adil Y. AL-HANDAL, C. Pennesi","doi":"10.5507/FOT.2018.003","DOIUrl":"https://doi.org/10.5507/FOT.2018.003","url":null,"abstract":"While collecting epiphytic diatom samples from the west coast of Sweden, a small Mastrogloia species has been observed and could not be matched with any of the described taxa. Based on both light and electron microscopes examination, this species has been described as new, Mastogloia wulffii sp. nov. and included in Mastogloia section Sulcatae. This species is very small with valve length not exceeding 16.3 µm. It is characterized by having a narrow, almost straight median depression on both sides of the sternum-raphe, no marginal ridge and with rounded areolae on valve mantle as well as having completely hyaline lateral sterna. A comparison with similar taxa is given. M. wulffii is a marine species growing in moderate numbers on the red alga Polyides rotunda which is widely distributed along the coast of Vrango Island, Sweden.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46221627","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}
There are several places in the world where the level of natural radiation is unusually high, such as some regions of Ramsar and Abegarm-e-Mahallat in Iran. Such places are still insufficiently explored in terms of their biodiversity. In this study, strains isolated from six geothermal springs with elevated natural radiation were investigated. The highest concentration of 226Ra were 13,000 Bq.kg-1 in the soil and 130 Bq.l-1 in water respectively. The morphological and molecular analyses revealed, that the strains are not classifiable to any existing taxon. Therefore, they are described as new taxa for science. Based on results of our study, two earlier described species are transferred into newly established genus.
{"title":"New simple trichal cyanobacterial taxa isolated from radioactive thermal springs","authors":"F. Heidari, J. Zima, H. Riahi, T. Hauer","doi":"10.5507/FOT.2017.024","DOIUrl":"https://doi.org/10.5507/FOT.2017.024","url":null,"abstract":"There are several places in the world where the level of natural radiation is unusually high, such as some regions of Ramsar and Abegarm-e-Mahallat in Iran. Such places are still insufficiently explored in terms of their biodiversity. In this study, strains isolated from six geothermal springs with elevated natural radiation were investigated. The highest concentration of 226Ra were 13,000 Bq.kg-1 in the soil and 130 Bq.l-1 in water respectively. The morphological and molecular analyses revealed, that the strains are not classifiable to any existing taxon. Therefore, they are described as new taxa for science. Based on results of our study, two earlier described species are transferred into newly established genus.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47065739","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}
Aydin Kaleli, M. Krzywda, A. Witkowski, C. Riaux-Gobin, C. Solak, I. Zgłobicka, T. Płociński, J. Grzonka, K. Kurzydłowski, A. Car, C. Desrosiers, Y. Kaska, K. Mccartney
The marine diatom Olifantiella Riaux-Gobin et Compere predominantly occurs in tropical Indo-Pacific coral reef environments. The genus has about a dozen validly published taxa and is characterized by transapically elongate striae composed of a macroareola, broad perforated girdle, and tubular buciniportula process of trumpet-shape. The valve mantle of taxa related to the generitype, O. mascarenica, have a canal-shaped structure around the valve at the face / mantle junction, while those to O. gorandiana have a simple mantle or strongly narrow canal and complex buciniportula composed of hollow processes. The geographic distribution of Olifantiella is expanded in this study to include species observed in loggerhead sea turtles scrapes from the Aegean Turkish coast and samples from the Turkish Black Sea and Adriatic Sea coasts. Olifantiella has also been identified in Martinique Island, Caribbean Sea. A transfer of Navicula infirmitata is proposed due to the areola and buciniportula structure, as Olifantiella infirmitata. Further, an application of the Focused Ion Beam (FIB) to a sequential cutting of frustules allows resolution of Olifantiella mascarenica valve ultrastructure.
海洋硅藻Olifantiella Riaux Gobin et Compere主要分布在热带印度-太平洋珊瑚礁环境中。该属有大约12个有效发表的分类群，其特征是由大乳晕、宽穿孔带和喇叭形管状颊口突组成的经根尖伸长的条纹。与该属相关的分类群，即马氏乳杆菌的阀盖在面/地幔交界处的阀盖周围有一个运河状结构，而与戈兰迪亚纳乳杆菌的则有一个简单的地幔或极窄的运河和由中空突起组成的复杂的颊portula。本研究扩大了Olifantiella的地理分布，包括在爱琴海土耳其海岸的红海龟刮伤中观察到的物种，以及土耳其黑海和亚得里亚海海岸的样本。在加勒比海的马提尼克岛也发现了Olifantiella。由于乳晕和颊Portula结构，建议将Navicula weatherita转移为Olifantiella weatherita。此外，将聚焦离子束（FIB）应用于截头体的顺序切割，可以解析马氏Olifantiella瓣膜的超微结构。
{"title":"A new sediment dwelling and epizoic species of Olifantiella (Bacillariophyceae), with an account on the genus ultrastructure based on Focused Ion Beam nanocuts","authors":"Aydin Kaleli, M. Krzywda, A. Witkowski, C. Riaux-Gobin, C. Solak, I. Zgłobicka, T. Płociński, J. Grzonka, K. Kurzydłowski, A. Car, C. Desrosiers, Y. Kaska, K. Mccartney","doi":"10.5507/FOT.2018.007","DOIUrl":"https://doi.org/10.5507/FOT.2018.007","url":null,"abstract":"The marine diatom Olifantiella Riaux-Gobin et Compere predominantly occurs in tropical Indo-Pacific coral reef environments. The genus has about a dozen validly published taxa and is characterized by transapically elongate striae composed of a macroareola, broad perforated girdle, and tubular buciniportula process of trumpet-shape. The valve mantle of taxa related to the generitype, O. mascarenica, have a canal-shaped structure around the valve at the face / mantle junction, while those to O. gorandiana have a simple mantle or strongly narrow canal and complex buciniportula composed of hollow processes. The geographic distribution of Olifantiella is expanded in this study to include species observed in loggerhead sea turtles scrapes from the Aegean Turkish coast and samples from the Turkish Black Sea and Adriatic Sea coasts. Olifantiella has also been identified in Martinique Island, Caribbean Sea. A transfer of Navicula infirmitata is proposed due to the areola and buciniportula structure, as Olifantiella infirmitata. Further, an application of the Focused Ion Beam (FIB) to a sequential cutting of frustules allows resolution of Olifantiella mascarenica valve ultrastructure.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47544306","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}
C. Kilgore, J. Johansen, Truc Mai, T. Hauer, D. Casamatta, C. Sheil
Geitleria was described from a limestone cave in Israel, and subsequently reported from caves of France, Romania, Spain, Florida, Costa Rica, and Cook Islands. It is morphologically unusual in that it has true branching, but no heterocytes. A morphologically distinct species of Geitleria was recently collected from a limestone cave in Great Smoky Mountains National Park, Tennessee, and is herein described as G. appalachiana sp. nov. Sequence data for 16S rRNA and rpoC1 loci for the species were obtained from field material using single filament PCR. Phylogenetic evidence indicates that Geitleria does not belong to any family in the Nostocales containing true-branching genera, i.e. Hapalosiphonaceae, Chlorogloeopsidaceae, and Symphyonemataceae, and consequently Geitleriaceae fam. nov. is established to contain this unique genus.
{"title":"Molecular characterization of Geitleria appalachiana sp. nov. (Nostocales, Cyanobacteria) and formation of Geitleriaceae fam. nov.","authors":"C. Kilgore, J. Johansen, Truc Mai, T. Hauer, D. Casamatta, C. Sheil","doi":"10.5507/FOT.2018.002","DOIUrl":"https://doi.org/10.5507/FOT.2018.002","url":null,"abstract":"Geitleria was described from a limestone cave in Israel, and subsequently reported from caves of France, Romania, Spain, Florida, Costa Rica, and Cook Islands. It is morphologically unusual in that it has true branching, but no heterocytes. A morphologically distinct species of Geitleria was recently collected from a limestone cave in Great Smoky Mountains National Park, Tennessee, and is herein described as G. appalachiana sp. nov. Sequence data for 16S rRNA and rpoC1 loci for the species were obtained from field material using single filament PCR. Phylogenetic evidence indicates that Geitleria does not belong to any family in the Nostocales containing true-branching genera, i.e. Hapalosiphonaceae, Chlorogloeopsidaceae, and Symphyonemataceae, and consequently Geitleriaceae fam. nov. is established to contain this unique genus.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45951179","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}
P. Dvořák, Eva Jahodářová, D. Casamatta, P. Hašler, A. Poulíčková
Cyanobacteria are amongst the most abundant, ubiquitous, ecologically and evolutionarily significant microbes on Earth. Unique among the Bacteria in their capacity to be identified using morphology, understanding the evolutionary relationships and describing the diversity of this lineage is both important and challenging. The advent of modern sequencing technology has proven a boon to those studying cyanobacterial systematics as it has provided copious amounts of sequence data (mainly of the 16S rRNA gene sequence). However, this influx of data has also led to taxonomic confusion and recognition of polyphyly in many genera. Thus, the purpose of this paper is to describe this apparent paradox of increasing data yet poor phylogenetic resolutions by employing the Poisson Tree Process (PTP) algorithm and to propose some ameliorative efforts.
{"title":"Difference without distinction? Gaps in cyanobacterial systematics; when more is just too much","authors":"P. Dvořák, Eva Jahodářová, D. Casamatta, P. Hašler, A. Poulíčková","doi":"10.5507/FOT.2017.023","DOIUrl":"https://doi.org/10.5507/FOT.2017.023","url":null,"abstract":"Cyanobacteria are amongst the most abundant, ubiquitous, ecologically and evolutionarily significant microbes on Earth. Unique among the Bacteria in their capacity to be identified using morphology, understanding the evolutionary relationships and describing the diversity of this lineage is both important and challenging. The advent of modern sequencing technology has proven a boon to those studying cyanobacterial systematics as it has provided copious amounts of sequence data (mainly of the 16S rRNA gene sequence). However, this influx of data has also led to taxonomic confusion and recognition of polyphyly in many genera. Thus, the purpose of this paper is to describe this apparent paradox of increasing data yet poor phylogenetic resolutions by employing the Poisson Tree Process (PTP) algorithm and to propose some ameliorative efforts.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":"18 1","pages":"130-136"},"PeriodicalIF":2.2,"publicationDate":"2018-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47346461","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}
F. Rimet, Nélida Abarca, A. Bouchez, Wolf-Henning Kusber, R. Jahn, M. Kahlert, F. Keck, M. Kelly, D. Mann, A. Piuz, R. Trobajo, K. Tapolczai, V. Vasselon, J. Zimmermann
Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.
{"title":"The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes","authors":"F. Rimet, Nélida Abarca, A. Bouchez, Wolf-Henning Kusber, R. Jahn, M. Kahlert, F. Keck, M. Kelly, D. Mann, A. Piuz, R. Trobajo, K. Tapolczai, V. Vasselon, J. Zimmermann","doi":"10.5507/FOT.2017.013","DOIUrl":"https://doi.org/10.5507/FOT.2017.013","url":null,"abstract":"Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":"18 1","pages":"37-54"},"PeriodicalIF":2.2,"publicationDate":"2018-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41354860","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}
C. Riaux-Gobin, A. Witkowski, A. Igersheim, C. Lobban, Adil Y. AL-HANDAL, P. Compère
Planothidium juandenovense sp. nov. (Bacillariophyta) is described from the marine tropical environments of Juan de Nova I. (Mozambique Channel), Rodrigues I. (Mascarene Archipelago) and from Guam (Northern Mariana Is., Pacific). This small and relatively rare taxon has short multiseriate striae on the sternum valve (SV), hooked raphe valve (RV) terminal raphe endings and no SV cavum or hoof-shaped area. This taxon has similarities with Planothidium delicatulum (Kutz.) Round et Bukht. and Planothidium septentrionale (Ostrup) Round et Bukht. ex Rumrich et al., but also differences: e.g. a relatively narrow and rhombic SV sternum, void of areolae, with vestigial radiate structures and an uninterrupted marginal SV elevated crest or 'crista marginalis'. P. juandenovense sp. nov. is compared to some other Achnanthales with short SV striae. Cocconeis quarnerensis var. lanceolata Jurilj and Planothidium quarnerense f. rhombica (Giffen) comb. nov. may be close to our new taxon.
juandenovense Planothidium sp.nov.（Bacillarophyta）描述自Juan de Nova I.（莫桑比克海峡）、Rodrigues I.（马斯卡群岛）和关岛（北马里亚纳群岛，太平洋）的海洋热带环境。这个小而相对罕见的分类单元在胸骨瓣（SV）上有短的多节纹，钩状中缝瓣（RV）中缝末端，没有SV腔或蹄形区域。该分类单元与圆形和Bukht的美味扁藻（Planothidium delicatulum，Kutz）有相似之处。和Planothidium septentrionale（Ostrup）Round et Bukht。ex Rumrich等人，但也有差异：例如，相对狭窄的菱形SV胸骨，乳晕空洞，具有残余的放射状结构和不间断的边缘SV隆起的嵴或“嵴边缘”。将P.juandenovense sp.nov.与其他一些具有短SV条纹的Achnanthales进行了比较。Quarnernensis var.lanceolata Jurilj和Planothidium quarnerense f.rhombica（Giffen）梳。nov.可能接近我们的新分类单元。
{"title":"Planothidium juandenovense sp. nov. (Bacillariophyta) from Juan de Nova (Scattered Islands, Mozambique Channel) and other tropical environments: A new addition to the Planothidium delicatulum complex","authors":"C. Riaux-Gobin, A. Witkowski, A. Igersheim, C. Lobban, Adil Y. AL-HANDAL, P. Compère","doi":"10.5507/FOT.2017.019","DOIUrl":"https://doi.org/10.5507/FOT.2017.019","url":null,"abstract":"Planothidium juandenovense sp. nov. (Bacillariophyta) is described from the marine tropical environments of Juan de Nova I. (Mozambique Channel), Rodrigues I. (Mascarene Archipelago) and from Guam (Northern Mariana Is., Pacific). This small and relatively rare taxon has short multiseriate striae on the sternum valve (SV), hooked raphe valve (RV) terminal raphe endings and no SV cavum or hoof-shaped area. This taxon has similarities with Planothidium delicatulum (Kutz.) Round et Bukht. and Planothidium septentrionale (Ostrup) Round et Bukht. ex Rumrich et al., but also differences: e.g. a relatively narrow and rhombic SV sternum, void of areolae, with vestigial radiate structures and an uninterrupted marginal SV elevated crest or 'crista marginalis'. P. juandenovense sp. nov. is compared to some other Achnanthales with short SV striae. Cocconeis quarnerensis var. lanceolata Jurilj and Planothidium quarnerense f. rhombica (Giffen) comb. nov. may be close to our new taxon.","PeriodicalId":55149,"journal":{"name":"Fottea","volume":"18 1","pages":"106-119"},"PeriodicalIF":2.2,"publicationDate":"2018-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43344863","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}
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