The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)

Chlorella-like coccoid green algae are widely distributed in many types of habitats such as freshwater, terrestrial and marine. One group of terrestrial microalgae belonging to the Trebouxiophyceae forms the monophyletic lineage of the Watanabea clade. This clade exclusively comprises of ellipsoid and spherical coccoid green algae, which traditionally have been assigned as different species of Chlorella. Within this clade, seven out of ten genera are described mainly based on phylogenetic analyses of SSU and rbcL sequences. Most of the genera are represented by only one or two species that are rarely found in natural samples. In contrast, the genus Chloroidium is widely distributed across different habitats. We investigated 34 new isolates, which were originally assigned as Chloroidium or Chlorella, using an integrative approach. The phylogenetic analyses of SSU and ITS rDNA sequences revealed nine lineages, eight of which were highly supported in all of our bootstrap and Bayesian analyses. The ITS-2/CBC approach clearly demonstrated that these nine lineages represent individual species. The haplotype network analyses revealed that three out of them were widely distributed and showed no preference for any habitat. The comprehensive study of SSU and rbcL datasets also revealed that no clear synapomorphy could be found to support the assigned genus Parachloroidium. As a result of our findings, we proposed that both species belonging to Parachloroidium be transferred to Chloroidium. In addition, we re-established two species originally described by Chodat as new members of Chloroidium (C. lichenum, C. viscosum). Two of the nine lineages (C. antarcticum, C. arboriculum) were newly described in this study.

Download Full-text

Molecular Phylogeny of Unicellular Marine Coccoid Green Algae Revealed New Insights into the Systematics of the Ulvophyceae (Chlorophyta)

Microorganisms ◽

10.3390/microorganisms9081586 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1586

Author(s):

Tatyana Darienko ◽

Cecilia Rad-Menéndez ◽

Christine N. Campbell ◽

Thomas Pröschold

Keyword(s):

Green Algae ◽

Life Histories ◽

Phylogenetic Analyses ◽

Algal Species ◽

Marine Species ◽

Life Cycles ◽

Rdna Sequences ◽

Green Algal ◽

The Family ◽

Chloroplast Formation

Most marine coccoid and sarcinoid green algal species have traditionally been placed within genera dominated by species from freshwater or soil habitats. For example, the genera Chlorocystis and Halochlorococcum contain exclusively marine species; however, their familial and ordinal affinities are unclear. They are characterized by a vegetative cell with lobated or reticulated chloroplast, formation of quadriflagellated zoospores and living epi- or endophytically within benthic macroalgae. They were integrated into the family Chlorochytriaceae which embraces all coccoid green algae with epi- or endophytic life phases. Later, they were excluded from the family of Chlorococcales based on studies of their life histories in culture, and transferred to their newly described order, Chlorocystidales of the Ulvophyceae. Both genera form a “Codiolum”-stage that serves as the unicellular sporophyte in their life cycles. Phylogenetic analyses of SSU and ITS rDNA sequences confirmed that these coccoid taxa belong to the Chlorocystidales, together with the sarcinoid genus Desmochloris. The biflagellated coccoid strains were members of the genus Sykidion, which represented its own order, Sykidiales, among the Ulvophyceae. Considering these results and the usage of the ITS-2/CBC approach revealed three species of Desmochloris, six of Chlorocystis, and three of Sykidion. Three new species and several new combinations were proposed.

Download Full-text

Possible multiple introductions of Cladonia borealis to King George Island

Antarctic Science ◽

10.1017/s0954102012000223 ◽

2012 ◽

Vol 24 (4) ◽

pp. 359-366 ◽

Cited By ~ 5

Author(s):

Chae Haeng Park ◽

Gajin Jeong ◽

Soon Gyu Hong

Keyword(s):

Haplotype Network ◽

Rdna Locus ◽

Rrna Genes ◽

Lsu Rdna ◽

Polar Regions ◽

King George Island ◽

Long Distance ◽

Multiple Introductions ◽

Network Analyses ◽

Rdna Sequences

AbstractMany lichens have extensive distributional ranges covering several climatic zones and are able to colonize extreme habitats, including high alpine and polar regions. Cladonia borealis, one of the dominant lichen species on King George Island, is a cosmopolitan species inhabiting polar, subpolar, and alpine areas. It is usually found on soil, humus, and mosses, and is morphologically highly diverse. To understand the phylogeographic history of C. borealis on King George Island, we compared specimens from there with specimens from Norway and Chile. We conducted phylogenetic and haplotype network analyses of the partial SSU, ITS1-5.8S-ITS2, and partial LSU rDNA sequences including intron sequences in LSU rRNA genes. Nuclear rDNA locus of C. borealis from King George Island was separated into two monophyletic lineages. It is suggested that they originated in multiple independent introduction events after long-distance dispersal from other continents.

Download Full-text

Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters

Antarctic Science ◽

10.1017/s0954102010000477 ◽

2010 ◽

Vol 22 (6) ◽

pp. 727-741 ◽

Cited By ~ 29

Author(s):

Ulrike Ruprecht ◽

H. Thorsten Lumbsch ◽

Georg Brunauer ◽

T.G. Allan Green ◽

Roman Türk

Keyword(s):

Ross Sea ◽

Phylogenetic Analyses ◽

Morphological Characters ◽

Molecular Data ◽

Secondary Chemistry ◽

Bayesian Analyses ◽

Test Species ◽

Rdna Sequences ◽

Continental Antarctica ◽

Nuclear Its

AbstractThe diversity of lichens, especially crustose species, in continental Antarctica is still poorly known. To overcome difficulties with the morphology based species delimitations in these groups, we employed molecular data (nuclear ITS and mitochondrial SSU rDNA sequences) to test species boundaries within the genus Lecidea. Sampling was done along a north–south transect at five different areas in the Ross Sea region (Cape Hallett, Botany Bay to Mount Suess, Taylor Valley, Darwin Area and Mount Kyffin). A total of 153 specimens were collected from 13 localities. Phylogenetic analyses also include specimens from other regions in Antarctica and non-Antarctic areas. Maximum parsimony, maximum likelihood and Bayesian analyses agreed in placing the samples from continental Antarctica into four major groups. Based on this phylogenetic estimate, we restudied the micromorphology and secondary chemistry of these four clades to evaluate the use of these characters as phylogenetic discriminators. These clades are identified as the following species Lecidea cancriformis, L. andersonii as well as the new species L. polypycnidophora Ruprecht & Türk sp. nov. and another previously unnamed clade of uncertain status, referred to as Lecidea sp. (L. UCR1).

Download Full-text

Choricystis and Lewiniosphaera gen. nov. (Trebouxiophyceae Chlorophyta), two different green algal endosymbionts in freshwater sponges

Symbiosis ◽

10.1007/s13199-020-00711-x ◽

2020 ◽

Vol 82 (3) ◽

pp. 175-188

Author(s):

Thomas Pröschold ◽

Tatyana Darienko

Keyword(s):

Green Algae ◽

Phylogenetic Analyses ◽

Wide Distribution ◽

Phylogenetic Position ◽

Freshwater Sponges ◽

Culture Collections ◽

Rdna Sequences ◽

Green Algal ◽

Long Time ◽

A New Species

Associations of freshwater sponges with coccoid green algae have been known for a long time. Two types of coccoid green algae, which are commonly assigned as zoochlorellae, are recognized by morphology: small coccoids (< 3 μm) without pyrenoids and larger Chlorella-like algae (4–6 μm) with pyrenoids. Despite their wide distribution in some freshwater sponges, these green algae were never studied using a combined analysis of morphology and molecular phylogeny. We investigated several endosymbiotic strains isolated from different Spongilla species, which were available in culture collections. Phylogenetic analyses of SSU and ITS rDNA sequences revealed that the strain SAG 211-40a is a member of the Chlorellaceae and represents a new species of the newly erected genus Lewiniosphaera, L symbiontica. The phylogenetic position was confirmed by morphology and ITS-2 barcode. The endosymbionts without pyrenoid were identified as Choricystis parasitica by morphology and phylogenetic analyses. The comparison with free-living strains revealed the recognition of two new Choricystis species, C. krienitzii and C. limnetica, which were confirmed by molecular signatures in V9 region of SSU rDNA and ITS-2 barcode.

Download Full-text

Toward a monograph of non-marine Ulvophyceae using an integrative approach (Molecular phylogeny and systematics of terrestrial Ulvophyceae II.)

Phytotaxa ◽

10.11646/phytotaxa.324.1.1 ◽

2017 ◽

Vol 324 (1) ◽

pp. 1 ◽

Cited By ~ 14

Author(s):

TATYANA DARIENKO ◽

THOMAS PRÖSCHOLD

Keyword(s):

Phylogenetic Diversity ◽

Phylogenetic Analyses ◽

Flagellar Apparatus ◽

Culture Collection ◽

Integrative Approach ◽

Terrestrial Species ◽

Ultrastructural Studies ◽

Filamentous Green Algae ◽

Rdna Sequences ◽

High Degree

Phylogenetic analyses of SSU rDNA sequences have shown that coccoid and filamentous green algae are distributed among all classes of the Chlorophyta. One of these classes, the Ulvophyceae, mostly contains marine seaweeds and microalgae. However, new studies have shown that there are filamentous and sarcinoid freshwater and terrestrial species (including symbionts in lichens) among the Ulvophyceae, but very little is known about these species. Ultrastructural studies of some of them have confirmed that the flagellar apparatus of zoospores (counterclockwise basal body orientation) is typical for the Ulvophyceae. In addition to ultrastructural features, the presence of a “Codiolum”-stage is characteristic of some members of this algal class. We studied more than 50 strains of freshwater and terrestrial ulvophycean microalgae obtained from the different public culture collection and our own isolates using an integrative approach. Three independent lineages of the Ulvophyceae containing terrestrial species were revealed by these methods. Unexpectedly each of these lineages contained several isolates that morphologically developed a high degree of phenotypic plasticity, and included hidden phylogenetic diversity that let us to the description of several new genera and species.

Download Full-text

Gymnopilus minisporus sp. nov., a new species and a new record of the European species G. hybridus from northeast China

Phytotaxa ◽

10.11646/phytotaxa.397.2.3 ◽

2019 ◽

Vol 397 (2) ◽

pp. 159

Author(s):

MENGTING LIU ◽

TOLGOR BAU

Keyword(s):

Northeast China ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Field Work ◽

Internal Transcribed Spacers ◽

Likelihood Methods ◽

Rdna Sequences ◽

Monophyletic Lineage ◽

Maximum Likelihood Methods ◽

Monophyletic Branch

During our field work in northeast China, two species of Gymnopilus, Gymnopilus minisporus sp. nov. and Gymnopilus hybridus, were identified and described based on morphological characteristics and phylogenetic analyses. The main distinguishing characteristic of G. minisporus is the conspicuously small basidiospores. The phylogenetic tree based on internal transcribed spacers of rDNA sequences using Bayesian and Maximum Likelihood methods showed that G. minisporus has an independent monophyletic lineage, and G. hybridus from China and Sweden grouped in a monophyletic branch.

Download Full-text

Micractinium tetrahymenae (Trebouxiophyceae, Chlorophyta), a New Endosymbiont Isolated from Ciliates

Diversity ◽

10.3390/d12050200 ◽

2020 ◽

Vol 12 (5) ◽

pp. 200 ◽

Cited By ~ 2

Author(s):

Thomas Pröschold ◽

Gianna Pitsch ◽

Tatyana Darienko

Keyword(s):

New Species ◽

Green Algae ◽

Aquatic Plant ◽

Phylogenetic Analyses ◽

Integrative Approach ◽

Algal Strain ◽

Anoxic Environments ◽

Phylogenetic Lineages ◽

A New Species ◽

Mixotrophic Ciliates

Endosymbiosis between coccoid green algae and ciliates are widely distributed and occur in various phylogenetic lineages among the Ciliophora. Most mixotrophic ciliates live in symbiosis with different species and genera of the so-called Chlorella clade (Trebouxiophyceae). The mixotrophic ciliates can be differentiated into two groups: (i) obligate, which always live in symbiosis with such green algae and are rarely algae-free and (ii) facultative, which formed under certain circumstances such as in anoxic environments an association with algae. A case of the facultative endosymbiosis is found in the recently described species of Tetrahymena, T. utriculariae, which lives in the bladder traps of the carnivorous aquatic plant Utricularia reflexa. The green endosymbiont of this ciliate belonged to the genus Micractinium. We characterized the isolated algal strain using an integrative approach and compared it to all described species of this genus. The phylogenetic analyses using complex evolutionary secondary structure-based models revealed that this endosymbiont represents a new species of Micractinium, M. tetrahymenae sp. nov., which was further confirmed by the ITS2/CBC approach.

Download Full-text

Molecular analysis of the mitochondrial markers COI, 12S rDNA and 16S rDNA for six species of Iranian scorpions

BMC Research Notes ◽

10.1186/s13104-021-05449-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Parisa Soltan-Alinejad ◽

Javad Rafinejad ◽

Farrokh Dabiri ◽

Piero Onorati ◽

Olle Terenius ◽

...

Keyword(s):

16S Rdna ◽

Phylogenetic Analyses ◽

Coi Gene ◽

Diagnostic Tools ◽

Morphological Identification ◽

Species Determination ◽

Important Species ◽

Mitochondrial Markers ◽

12S Rdna ◽

Rdna Sequences

Abstract Objectives Annually, 1.2 million humans are stung by scorpions and severely affected by their venom. Some of the scorpion species of medical importance have a similar morphology to species with low toxicity. To establish diagnostic tools for surveying scorpions, the current study was conducted to generate three mitochondrial markers, Cytochrome Oxidase I (COI gene), 12S rDNA and 16S rDNA for six species of medically important Iranian scorpions: Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus, M. eupeus, Odontobuthus doriae, and Scorpio maurus. Results Phylogenetic analyses of the obtained sequences corroborated the morphological identification. For the first time, 12S rDNA sequences are reported from Androctonus crassicauda, Hottentotta saulcyi, Mesobuthus caucasicus and M. eupeus and also the 16S rDNA sequence from Hottentotta saulcyi. We conclude that the mitochondrial markers are useful for species determination among these medically important species of scorpions.

Download Full-text

Environmental and Social Risks to Biodiversity and Ecosystem Health—A Bottom-Up, Resource-Focused Assessment Framework

Earth ◽

10.3390/earth2030026 ◽

2021 ◽

Vol 2 (3) ◽

pp. 440-456

Author(s):

Roger A. Pielke ◽

Jimmy Adegoke ◽

Faisal Hossain ◽

Dev Niyogi

Keyword(s):

Ecosystem Function ◽

Ecosystem Health ◽

Interactive System ◽

Integrative Approach ◽

Individual Species ◽

Assessment Framework ◽

Top Down ◽

Bottom Up ◽

Social Risks ◽

Biodiversity And Ecosystem Function

Risks from human intervention in the climate system are raising concerns with respect to individual species and ecosystem health and resiliency. A dominant approach uses global climate models to predict changes in climate in the coming decades and then to downscale this information to assess impacts to plant communities, animal habitats, agricultural and urban ecosystems, and other parts of the Earth’s life system. To achieve robust assessments of the threats to these systems in this top-down, outcome vulnerability approach, however, requires skillful prediction, and representation of changes in regional and local climate processes, which has not yet been satisfactorily achieved. Moreover, threats to biodiversity and ecosystem function, such as from invasive species, are in general, not adequately included in the assessments. We discuss a complementary assessment framework that builds on a bottom-up vulnerability concept that requires the determination of the major human and natural forcings on the environment including extreme events, and the interactions between these forcings. After these forcings and interactions are identified, then the relative risks of each issue can be compared with other risks or forcings in order to adopt optimal mitigation/adaptation strategies. This framework is a more inclusive way of assessing risks, including climate variability and longer-term natural and anthropogenic-driven change, than the outcome vulnerability approach which is mainly based on multi-decadal global and regional climate model predictions. We therefore conclude that the top-down approach alone is outmoded as it is inadequate for robustly assessing risks to biodiversity and ecosystem function. In contrast the bottom-up, integrative approach is feasible and much more in line with the needs of the assessment and conservation community. A key message of our paper is to emphasize the need to consider coupled feedbacks since the Earth is a dynamically interactive system. This should be done not just in the model structure, but also in its application and subsequent analyses. We recognize that the community is moving toward that goal and we urge an accelerated pace.

Download Full-text

Phylogenetic and Haplotype Network Analyses of Diaporthe eres Species in China Based on Sequences of Multiple Loci

Biology ◽

10.3390/biology10030179 ◽

2021 ◽

Vol 10 (3) ◽

pp. 179

Author(s):

Chingchai Chaisiri ◽

Xiangyu Liu ◽

Yang Lin ◽

Yanping Fu ◽

Fuxing Zhu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Elongation Factor ◽

Haplotype Network ◽

Population Diversity ◽

Plant Diseases ◽

Broad Host Range ◽

Internal Transcribed Spacer Region ◽

Chinese Populations ◽

Network Analyses ◽

Haplotype Networks

Diaporthe eres is considered one of the most important causal agents of many plant diseases, with a broad host range worldwide. In this study, multiple sequences of ribosomal internal transcribed spacer region (ITS), translation elongation factor 1-α gene (EF1-α), beta-tubulin gene (TUB2), calmodulin gene (CAL), and histone-3 gene (HIS) were used for multi-locus phylogenetic analysis. For phylogenetic analysis, maximum likelihood (ML), maximum parsimony (MP), and Bayesian inferred (BI) approaches were performed to investigate relationships of D. eres with closely related species. The results strongly support that the D. eres species falls into a monophyletic lineage, with the characteristics of a species complex. Phylogenetic informativeness (PI) analysis showed that clear boundaries could be proposed by using EF1-α, whereas ITS showed an ineffective reconstruction and, thus, was unsuitable for speciating boundaries for Diaporthe species. A combined dataset of EF1-α, CAL, TUB2, and HIS showed strong resolution for Diaporthe species, providing insights for the D. eres complex. Accordingly, besides D. biguttusis, D. camptothecicola, D. castaneae-mollissimae, D. cotoneastri, D. ellipicola, D. longicicola, D. mahothocarpus, D. momicola, D. nobilis, and Phomopsis fukushii, which have already been previously considered the synonymous species of D. eres, another three species, D. henanensis, D. lonicerae and D. rosicola, were further revealed to be synonyms of D. eres in this study. In order to demonstrate the genetic diversity of D. eres species in China, 138 D. eres isolates were randomly selected from previous studies in 16 provinces. These isolates were obtained from different major plant species from 2006 to 2020. The genetic distance was estimated with phylogenetic analysis and haplotype networks, and it was revealed that two major haplotypes existed in the Chinese populations of D. eres. The haplotype networks were widely dispersed and not uniquely correlated to specific populations. Overall, our analyses evaluated the phylogenetic identification for D. eres species and demonstrated the population diversity of D. eres in China.

Download Full-text