Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).

PubMed

Jonathan Shaw, A; Devos, Nicolas; Liu, Yang; Cox, Cymon J; Goffinet, Bernard; Flatberg, Kjell Ivar; Shaw, Blanka

2016-08-01

Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made

Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss)

PubMed Central

Jonathan Shaw, A.; Devos, Nicolas; Liu, Yang; Cox, Cymon J.; Goffinet, Bernard; Flatberg, Kjell Ivar; Shaw, Blanka

2016-01-01

Background and Aims Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided. Methods We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium. Key Results Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two

On the Domene species of China, with descriptions of four new species (Coleoptera, Staphylinidae)

PubMed Central

Feldmann, Benedikt; Peng, Zhong; Li, Li-Zhen

2014-01-01

Abstract Material of the paederine genus Domene Fauvel, 1873 from China is examined. Nine species were identified, four of them described previously, one unnamed (represented exclusively by females), and four are newly described: Domene cultrata sp. n. (Gansu, Hubei, Shaanxi); Domene cuspidata sp. n. (Gansu, Shaanxi, Sichuan); Domene chenae sp. n. (Guangxi); Domene reducta sp. n. (Sichuan). A lectotype is designated for Domene reitteri Koch, 1939; a neotype is designated for Domene chenpengi Li, 1990. Domene dersuuzalai Gusarov, 1992 is placed in synonymy with Domene chenpengi. Previous records of two Japanese species from China are most likely based on misidentifications and considered erroneous. Thus, the Domene fauna of China is currently composed of twelve described species. A key to the Domene species of China is provided. The distributions of eleven species are mapped. PMID:25709524

Water hyacinth Eichhornia crassipes (Mart.) Solms-Laubach dynamics and succession in the Nyanza Gulf of Lake Victoria (east Africa): implications for water quality and biodiversity conservation.

PubMed

Gichuki, John; Omondi, Reuben; Boera, Priscillar; Okorut, Tom; Matano, Ally Said; Jembe, Tsuma; Ofulla, Ayub

2012-01-01

This study, conducted in Nyanza Gulf of Lake Victoria, assessed ecological succession and dynamic status of water hyacinth. Results show that water hyacinth is the genesis of macrophyte succession. On establishment, water hyacinth mats are first invaded by native emergent macrophytes, Ipomoea aquatica Forsk., and Enydra fluctuans Lour., during early stages of succession. This is followed by hippo grass Vossia cuspidata (Roxb.) Griff. in mid- and late stages whose population peaks during climax stages of succession with concomitant decrease in water hyacinth biomass. Hippo grass depends on water hyacinth for buoyancy, anchorage, and nutrients. The study concludes that macrophyte succession alters aquatic biodiversity and that, since water hyacinth infestation and attendant succession are a symptom of broader watershed management and pollution problems, aquatic macrophyte control should include reduction of nutrient loads and implementing multifaceted approach that incorporates biological agents, mechanical/manual control with utilization of harvested weed for cottage industry by local communities.

Nutrient stoichiometry in Sphagnum along a nitrogen deposition gradient in highly polluted region of Central-East Europe.

PubMed

Jiroušek, Martin; Hájek, Michal; Bragazza, Luca

2011-02-01

We investigated the variation of N:P and N:K ratio in ombrotrophic Sphagnum plants along a gradient of atmospheric N deposition from 1 to 2.5 g m(-2) year(-1) in Central-East Europe. The N:P and N:K ratio in Sphagnum capitula increased significantly along the N deposition gradient. Sphagnum species from the Cuspidata section were characterised by significantly lower ratios at low N deposition. When we compared the observed N:P ratios in Sphagnum plants with the values reported in a previous European-wide study, we found a correspondence in nutrient stoichiometry only for a few bogs: higher P concentration in Sphagnum capitula caused a lower N:P ratio in most of the study bogs so that Sphagnum plants still seem N-limited despite their N saturation. Interaction between summer water table decrease and aerial liming of surrounding forests is proposed as an explanation for this discrepancy. Local forestry practice interacting with climate thus alter N:P stoichiometry of Sphagnum along the N deposition gradient. Copyright © 2010 Elsevier Ltd. All rights reserved.

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

PubMed Central

Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

2016-01-01

The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere. PMID:27080869

Plants used traditionally to treat malaria in Brazil: the archives of Flora Medicinal

PubMed Central

Botsaris, Alexandros S

2007-01-01

The archives of Flora Medicinal, an ancient pharmaceutical laboratory that supported ethnomedical research in Brazil for more than 30 years, were searched for plants with antimalarial use. Forty plant species indicated to treat malaria were described by Dr. J. Monteiro da Silva (Flora Medicinal leader) and his co-workers. Eight species, Bathysa cuspidata, Cosmos sulphureus, Cecropia hololeuca, Erisma calcaratum, Gomphrena arborescens, Musa paradisiaca, Ocotea odorifera, and Pradosia lactescens, are related as antimalarial for the first time in ethnobotanical studies. Some species, including Mikania glomerata, Melampodium divaricatum, Galipea multiflora, Aspidosperma polyneuron, and Coutarea hexandra, were reported to have activity in malaria patients under clinical observation. In the information obtained, also, there were many details about the appropriate indication of each plant. For example, some plants are indicated to increase others' potency. There are also plants that are traditionally employed for specific symptoms or conditions that often accompany malaria, such as weakness, renal failure or cerebral malaria. Many plants that have been considered to lack activity against malaria due to absence of in vitro activity against Plasmodium can have other mechanisms of action. Thus researchers should observe ethnomedical information before deciding which kind of screening should be used in the search of antimalarial drugs. PMID:17472740

Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

NASA Astrophysics Data System (ADS)

Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

2016-04-01

The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

Evolution of niche preference in Sphagnum peat mosses.

PubMed

Johnson, Matthew G; Granath, Gustaf; Tahvanainen, Teemu; Pouliot, Remy; Stenøien, Hans K; Rochefort, Line; Rydin, Håkan; Shaw, A Jonathan

2015-01-01

Peat mosses (Sphagnum) are ecosystem engineers-species in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this article, we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary rate of eight niche descriptors and two multivariate niche gradients. We find little to no evidence for phylogenetic signal in most component descriptors of the ionic gradient, but interspecific variation along the hummock-hollow gradient shows considerable phylogenetic signal. We find support for a change in the rate of niche evolution within the genus-the hummock-forming subgenus Acutifolia has evolved along the multivariate hummock-hollow gradient faster than the hollow-inhabiting subgenus Cuspidata. Because peat mosses themselves create some of the ecological gradients constituting their own habitats, the classic microtopography of Sphagnum-dominated peatlands is maintained by evolutionary constraints and the biological properties of related Sphagnum species. The patterns of phylogenetic signal observed here will instruct future study on the role of functional traits in peatland growth and reconstruction. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Taxane recovery from cells of Taxus in micro- and hypergravity

NASA Technical Reports Server (NTRS)

Durzan, D. J.; Ventimiglia, F.; Havel, L.

1998-01-01

Cell suspension cultures of Taxus cuspidata produce taxanes that are released from the outer surface of cells into the culture medium as free and bound alkaloids. Paclitaxel (Taxol (TM)), is an anti-cancer drug in short supply. It has a taxane ring derived from baccatin III and a C-13 phenylisoserine side-chain. This drug is produced over a wide range of gravitational forces. Monoclonal and polyclonal antibodies to paclitaxel, baccatin III, and the C-13 phenylisoserine side chain were combined in multiple-labeling studies to localize taxanes and paclitaxel on cell surfaces or on particles released into the culture medium. Bioreactor vessel design altered the composition of taxanes recovered from cells in simulated microgravity. At 10(-2) and 2x10(-4)g, taxane recovery was reduced but biomass growth and percent paclitaxel was significantly increased. At 1 to 24g, growth was reduced with a significant recovery of total taxanes with low percent paclitaxel. Bound paclitaxel was also localized in endonuclease-rich fragmenting nuclei of individual apoptotic cells. A model is presented comprising TCH (touch) genes encoding enzymes that modify taxane-bearing xylan residues in cell walls, the calcium-sensing of gravitational forces by the cytoplasm, and the predisposition of nuclei to apoptosis. This integrates the adaptive physiological and biochemical responses of drug-producing genomes with gravitational forces.

Comparing Ecological and Genetic Diversity Within the Marine Diatom Genus Pseudo-nitzschia: A Multiregional Synthesis

NASA Astrophysics Data System (ADS)

Hubbard, K.; Bruzek, S.

2016-02-01

The globally distributed marine diatom genus Pseudo-nitzschia consists of approximately 40 species, more than half of which occur in US coastal waters. Here, sensitive genetic tools targeting a variable portion of the internal transcribed spacer 1 (ITS1) region of the rRNA gene were used to assess Pseudo-nitzschia spp. diversity in more than 600 environmental DNA samples collected from US Atlantic, Pacific, and Gulf of Mexico waters. Community-based approaches employed genus-specific primers for environmental DNA fingerprinting and targeted sequencing. For the Gulf of Mexico samples especially, a nested PCR approach (with or without degenerate primers) improved resolution of species diversity. To date, more than 40 unique ITS1 amplicon sizes have been repeatedly observed in ITS1 fingerprints. Targeted sequencing of environmental DNA as well as single chains isolated from live samples indicate that many of these represent novel and known inter- and intra-specific Pseudo-nitzschia diversity. A few species (e.g., P. pungens, P. cuspidata) occur across all three regions, whereas other species and intraspecific variants occurred at local to regional spatial scales only. Generally, species frequently co-occur in complex assemblages, and transitions in Pseudo-nitzschia community composition occur seasonally, prior to bloom initiation, and across (cross-shelf, latitudinal, and vertical) environmental gradients. These observations highlight the dynamic nature of diatom community composition in the marine environment and the importance of classifying diversity at relevant ecological and/or taxonomic scales.

A survey of linyphiid spiders from Xishuangbanna, Yunnan Province, China (Araneae, Linyphiidae)

PubMed Central

Zhao, Qingyuan; Li, Shuqiang

2014-01-01

Abstract Eight new genera and 30 new species are described: Cirrosus gen. n. (type species Cirrosus atrocaudatus sp. n. (♂♀)), Conglin gen. n. (type species Conglin personatus sp. n. (♀)), Curtimeticus gen. n. (type species Curtimeticus nebulosus sp. n. (♂)), Gladiata gen. n. (type species Gladiata fengli sp. n. (♂)), Glebala gen. n. (type species Glebala aspera sp. n. (♂)), Glomerosus gen. n. (type species Glomerosus lateralis sp. n. (♂)), Smerasia gen. n. (type species Smerasia obscurus sp. n. (♂♀)), Vittatus gen. n. (type species Vittatus fencha sp. n. (♂♀)); Batueta cuspidata sp. n. (♂♀), Capsulia laciniosa sp. n. (♂), Dactylopisthes separatus sp. n. (♀), Gongylidiellum bracteatum sp. n. (♀), Houshenzinus xiaolongha sp. n. (♂♀), Laogone bai sp. n. (♂), Laogone lunata sp. n. (♂♀), Maro bulbosus sp. n. (♀), Nasoonaria circinata sp. n. (♂♀), Neriene circifolia sp. n. (♂♀), Oedothorax biantu sp. n. (♀), Oilinyphia hengji sp. n. (♂♀), Paikiniana furcata sp. n. (♂♀), Parameioneta bishou sp. n. (♂♀), Parameioneta multifida sp. n. (♂♀), Parameioneta tricolorata sp. n. (♂♀), Tapinopa undata sp. n. (♂), Theoa bidentata sp. n. (♂♀), Theoa vesica sp. n. (♂♀), Vittatus bian sp. n. (♂♀), Vittatus latus sp. n. (♂♀), Vittatus pan sp. n. (♂♀). The male of Kaestneria bicultrata Chen & Yin, 2000 and the females of Asiagone perforata Tanasevitch, 2014 and Batueta similis Wunderlich & Song, 1995 are described for the first time; photos of Bathyphantes paracymbialis Tanasevitch, 2014 are provided. PMID:25561858

Fungus symbionts colonizing the galleries of the ambrosia beetle Platypus quercivorus.

PubMed

Endoh, Rikiya; Suzuki, Motofumi; Okada, Gen; Takeuchi, Yuko; Futai, Kazuyoshi

2011-07-01

Isolations were made to determine the fungal symbionts colonizing Platypus quercivorus beetle galleries of dead or dying Quercus laurifolia, Castanopsis cuspidata, Quercus serrata, Quercus crispula, and Quercus robur. For these studies, logs from oak wilt-killed trees were collected from Kyoto Prefecture, Japan. Fungi were isolated from the: (1) entrances of beetle galleries, (2) vertical galleries, (3) lateral galleries, and (4) the larval cradle of P. quercivorus in each host tree. Among the fungus colonies which appeared on YM agar plates, 1,219 were isolated as the representative isolates for fungus species inhabiting in the galleries based on their cultural characteristics. The validity of the visual classification of the fungus colonies was checked and if necessary properly corrected using microsatellite-primed PCR fingerprints. The nucleotide sequence of the D1/D2 region of the large subunit nuclear rRNA gene detected 38 fungus species (104 strains) of which three species, i.e., Candida sp. 3, Candida kashinagacola (both yeasts), and the filamentous fungus Raffaelea quercivora were isolated from all the tree species. The two yeasts were most prevalent in the interior of galleries, regardless of host tree species, suggesting their close association with the beetle. A culture-independent method, terminal restriction fragment length polymorphism (T-RFLP) analysis was also used to characterize the fungus flora of beetle galleries. T-RFLP patterns showed that yeast species belonging to the genus Ambrosiozyma frequently occurred on the gallery walls along with the two Candida species. Ours is the first report showing the specific fungi inhabiting the galleries of a platypodid ambrosia beetle.

Recovery kinetics of photochemical efficiency in winter stressed conifers: the effects of growth light environment, extent of the season and species.

PubMed

Verhoeven, Amy S

2013-02-01

Evergreens undergo reductions in maximal photochemical efficiency (F(v)/F(m)) during winter due to increases in sustained thermal energy dissipation. Upon removing winter stressed leaves to room temperature and low light, F(v)/F(m) recovers and can include both a rapid and a slow phase. The goal of this study was to determine whether the rapid component to recovery exists in winter stressed conifers at any point during the season in a seasonally extreme environment. Additional goals were to compare the effects of species, growth light environment and the extent of the winter season on recovery kinetics in conifers. Four species (sun and shade needle) were monitored during the winter of 2007/2008: eastern white pine (Pinus strobus), balsam fir (Abies balsamea), Taxus cuspidata and white spruce (Picea glauca). F(v)/F(m) was measured in the field, and then monitored indoors at room temperature and low light for 6 days. The results showed that all species showed a rapid component to recovery in early winter that disappeared later in the season in sun needles but was present in shade needles on most days monitored during winter. There were differences among species in the recovery kinetics across the season, with pine recovering the most slowly and spruce the most quickly. The results suggest an important role for the rapidly reversible form of energy dissipation in early winter, as well as important differences between species in their rate of recovery in late winter/early spring which may have implications for spring onset of photosynthesis. Copyright © Physiologia Plantarum 2012.

Three-genome mosses: complex double allopolyploid origins for triploid gametophytes in Sphagnum.

PubMed

Karlin, Eric F; Boles, S B; Ricca, M; Temsch, E M; Greilhuber, J; Shaw, A J

2009-04-01

This paper documents the occurrence of allotriploidy (having three differentiated genomes) in gametophytes of two Southern Hemisphere Sphagnum species (S. australe, S. falcatulum). The pattern of microsatellite alleles indicates that both species are composed of a complex of allodiploid and allotriploid gametophytes, with the latter resulting from two allopolyploidization events. No haploid (n = x) gametophytes were found for either species. The ploidal levels suggested by the pattern of microsatellite alleles were confirmed by flow cytometry and Feulgen DNA image densitometry. For both S. australe and S. falcatulum, the respective allodiploid plants (or their ancestors) are one of the parent species of the allotriploid plants. This is the first report of triploidy in Sphagnum gametophytes occurring in nature and also the first report of the presence of three differentiated genomes in any bryophyte. It is also the first report of intersectional allopolyploidy in Sphagnum, with S. australe appearing to have parental species from Sphagnum sections Rigida and Sphagnum, and S. falcatulum having parental species from Sphagnum sections Cuspidata and Subsecunda. In both species, the allotriploid cytotypes were the most prevalent cytotype on the South Island of New Zealand. The pattern of microsatellite alleles shows the presence of two genetically distinct populations of allodiploid S. australe, possibly indicating multiple origins of polyploidy for that allodiploid cytotype. Morphological evidence is also highly indicative of recurrent polyploidy in the allotriploid cytotype of S. falcatulum. Allopolyploidy has clearly played a major evolutionary role in these two Southern Hemisphere taxa. This study, in conjunction with other recent research, indicates that allopolyploidy is a common, if not the predominant, form of polyploidy in Sphagnum.

Desiccation tolerance of Sphagnum revisited: a puzzle resolved.

PubMed

Hájek, T; Vicherová, E

2014-07-01

As ecosystem engineers, Sphagnum mosses control their surroundings through water retention, acidification and peat accumulation. Because water retention avoids desiccation, sphagna are generally intolerant to drought; however, the literature on Sphagnum desiccation tolerance (DT) provides puzzling results, indicating the inducible nature of their DT. To test this, various Sphagnum species and other mesic bryophytes were hardened to drought by (i) slow drying; (ii) ABA application and (iii) chilling or frost. DT tolerance was assessed as recovery of chlorophyll fluorescence parameters after severe desiccation. We monitored the seasonal course of DT in bog bryophytes. Under laboratory conditions, following initial de-hardening, untreated Sphagnum shoots lacked DT; however, DT was induced by all hardening treatments except chilling, notably by slow drying, and in Sphagnum species of the section Cuspidata. In the field, sphagna in hollows and lawns developed DT several times during the growing season, responding to reduced precipitation and a lowered water table. Hummock and aquatic species developed DT only in late autumn, probably as a response to frost. Sphagnum protonemata failed to develop DT; hence, desiccation may limit Sphagnum establishment in drier habitats with suitable substrate chemistry. Desiccation avoiders among sphagna form compact hummocks or live submerged; thus, they do not develop DT in the field, lacking the initial desiccation experience, which is frequent in hollow and lawn habitats. We confirmed the morpho-physiological trade-off: in contrast to typical hollow sphagna, hummock species invest more resources in water retention (desiccation avoidance), while they have a lower ability to develop physiological DT. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

CRYPTIC AND PSEUDO-CRYPTIC DIVERSITY IN DIATOMS-WITH DESCRIPTIONS OF PSEUDO-NITZSCHIA HASLEANA SP. NOV. AND P. FRYXELLIANA SP. NOV.(1).

PubMed

Lundholm, Nina; Bates, Stephen S; Baugh, Keri A; Bill, Brian D; Connell, Laurie B; Léger, Claude; Trainer, Vera L

2012-04-01

A high degree of pseudo-cryptic diversity was reported in the well-studied diatom genus Pseudo-nitzschia. Studies off the coast of Washington State revealed the presence of hitherto undescribed diversity of Pseudo-nitzschia. Forty-one clonal strains, representing six different taxa of the P. pseudodelicatissima complex, were studied morphologically using LM and EM, and genetically using genes from three different cellular compartments: the nucleus (D1-D3 of the LSU of rDNA and internal transcribed spacers [ITSs] of rDNA), the mitochondria (cytochrome c oxidase 1), and the plastids (LSU of RUBISCO). Strains in culture at the same time were used in mating studies to study reproductive isolation of species, and selected strains were examined for the production of the neurotoxin domoic acid (DA). Two new species, P. hasleana sp. nov. and P. fryxelliana sp. nov., are described based on morphological and molecular data. In all phylogenetic analyses, P. hasleana appeared as sister taxa to a clade comprising P. calliantha and P. mannii, whereas the position of P. fryxelliana was more uncertain. In the phylogenies of ITS, P. fryxelliana appeared to be most closely related to P. cf. turgidula. Morphologically, P. hasleana differed from most other species of the complex because of a lower density of fibulae, whereas P. fryxelliana had fewer sectors in the poroids and a higher poroid density than most of the other species. P. hasleana did not produce detectable levels of DA; P. fryxelliana was unfortunately not tested. In P. cuspidata, production of DA in offspring cultures varied from higher than the parent cultures to undetectable. © 2012 Phycological Society of America.

Floriparicapitus, a new genus of lecanicephalidean tapeworm (Cestoda) from sawfishes (Pristidae) and guitarfishes (Rhinobatidae) in the Indo-West Pacific.

PubMed

Cielocha, Joanna J; Jensen, Kirsten; Caira, Janine N

2014-08-01

Floriparicapitus n. gen. (Cestoda: Lecanicephalidea), with Floriparicapitus euzeti n. gen., n. sp. as its type, is erected to house 3 new tapeworm species and 2 known species that are transferred to the new genus, all parasitizing sawfishes and guitarfishes (order Rhinopristiformes) in Indo-Pacific waters. The new genus differs from the 21 valid lecanicephalidean genera in its possession of a large scolex bearing a laterally expanded apical organ in the form of a rugose sheet in combination with a cirrus conspicuously armed with spinitriches and 3 pairs of excretory vessels. It most closely resembles Lecanicephalum, but differs conspicuously in its possession of 3, rather than 1, pair of excretory vessels. Two new species are described from sawfishes: Floriparicapitus euzeti n. sp., from Pristis clavata and Floriparicapitus juliani n. sp. from Pristis pristis, both from Australia. Floriparicapitus plicatilis n. sp. is described from the guitarfish Glaucostegus typus in Australia and the guitarfish Glaucostegus thouin in Malaysian Borneo. Two species formerly assigned to Cephalobothrium are transferred to the new genus; Floriparicapitus variabilis ( Southwell, 1911 ) n. comb. from the sawfish Anoxypristis cuspidata in Sri Lanka and Floriparicapitus rhinobatidis ( Subhapradha, 1955 ) n. comb. from the guitarfish Glaucostegus granulatus in India. The species from guitarfish differ conspicuously from those parasitizing sawfish in their possession of only 4 ( F. plicatilis n. sp.) or 5 (F. rhinobatidis n. comb.) testes per proglottid versus 9 or more in the 3 sawfish-parasitizing species. The latter 3 species differ from one another in scolex width, acetabular size, number of proglottids, and cirrus sac size. As it stands, the new genus appears to be restricted to a subclade of the Rhinopristiformes consisting of the sawfishes and species of Glaucostegus.

Candida kashinagacola sp. nov., C. pseudovanderkliftii sp. nov. and C. vanderkliftii sp. nov., three new yeasts from ambrosia beetle-associated sources.

PubMed

Endoh, Rikiya; Suzuki, Motofumi; Benno, Yoshimi; Futai, Kazuyoshi

2008-10-01

Three new yeast species, Candida kashinagacola (JCM 15019(T) = CBS 10903(T)), C. pseudovanderkliftii (JCM 15025(T) = CBS 10904(T)), and C. vanderkliftii (JCM 15029(T) = CBS 10905(T)) are described on the basis of comparison of nucleotide sequences of large subunit ribosomal DNA D1/D2 region (LSU rDNA D1/D2). The nearest assigned species of the three new species was Candida llanquihuensis. Candida kashinagacola and C. pseudovanderkliftii differed from C. llanquihuensis by 3.8% nucleotide substitution of the region, while C. vanderkliftii did by 4.4%. Three new species differed in a number of physiological and growth characteristics from any previously assigned species and from one another. A phylogenetic tree based on the sequences of LSU rDNA D1/D2 showed that these new species together with Candida sp. ST-246, Candida sp. JW01-7-11-1-4-y2, Candida sp. BG02-7-20-001A-2-1 and C. llanquihuensis form a clade near Ambrosiozyma species. The new species did not assimilate methanol as a sole source of carbon, which supported the monophyly of these non methanol-assimilating species which are closely related to the methylotrophic yeasts. Candida kashinagacola was frequently isolated from the beetle galleries of Platypus quercivorus in three different host trees (Quercus serrata, Q. laurifolia and Castanopsis cuspidata) located in the sourthern part of Kyoto, Japan, thus indicating that this species may be a primary ambrosia fungus of P. quercivorus. On the other hand, C. pseudovanderkliftii and C. vanderkliftii were isolated only from beetle galleries in Q. laurifolia. Candida vanderkliftii was isolated from beetle gallery of Platypus lewisi as well as those of P. quercivorus. Candida pseudovanderkliftii and C. vanderkliftii are assumed to be auxiliary ambrosia fungi of P. quercivorus.

Impact of the Little Ice Age cooling and 20th century climate change on peatland vegetation dynamics in central and northern Alberta using a multi-proxy approach and high-resolution peat chronologies

NASA Astrophysics Data System (ADS)

Magnan, Gabriel; van Bellen, Simon; Davies, Lauren; Froese, Duane; Garneau, Michelle; Mullan-Boudreau, Gillian; Zaccone, Claudio; Shotyk, William

2018-04-01

Northern boreal peatlands are major terrestrial sinks of organic carbon and these ecosystems, which are highly sensitive to human activities and climate change, act as sensitive archives of past environmental change at various timescales. This study aims at understanding how the climate changes of the last 1000 years have affected peatland vegetation dynamics in the boreal region of Alberta in western Canada. Peat cores were collected from five bogs in the Fort McMurray region (56-57° N), at the southern limit of sporadic permafrost, and two in central Alberta (53° N and 55° N) outside the present-day limit of permafrost peatlands. The past changes in vegetation communities were reconstructed using detailed plant macrofossil analyses combined with high-resolution peat chronologies (14C, atmospheric bomb-pulse 14C, 210Pb and cryptotephras). Peat humification proxies (C/N, H/C, bulk density) and records of pH and ash content were also used to improve the interpretation of climate-related vegetation changes. Our study shows important changes in peatland vegetation and physical and chemical peat properties during the Little Ice Age (LIA) cooling period mainly from around 1700 CE and the subsequent climate warming of the 20th century. In some bogs, the plant macrofossils have recorded periods of permafrost aggradation during the LIA with drier surface conditions, increased peat humification and high abundance of ericaceous shrubs and black spruce (Picea mariana). The subsequent permafrost thaw was characterized by a short-term shift towards wetter conditions (Sphagnum sect. Cuspidata) and a decline in Picea mariana. Finally, a shift to a dominance of Sphagnum sect. Acutifolia (mainly Sphagnum fuscum) occurred in all the bogs during the second half of the 20th century, indicating the establishment of dry ombrotrophic conditions under the recent warmer and drier climate conditions.

Palikur traditional roundwood construction in eastern French Guiana: ethnobotanical and cultural perspectives.

PubMed

Ogeron, Clémence; Odonne, Guillaume; Cristinoi, Antonia; Engel, Julien; Grenand, Pierre; Beauchêne, Jacques; Clair, Bruno; Davy, Damien

2018-04-24

Palikur Amerindians live in the eastern part of French Guiana which is undergoing deep-seated changes due to the geographical and economic opening of the region. So far, Palikur's traditional ecological knowledge is poorly documented, apart from medicinal plants. The aim of this study was to document ethnobotanical practices related to traditional construction in the region. A combination of qualitative and quantitative methods was used. Thirty-nine Palikur men were interviewed in three localities (Saint-Georges de l'Oyapock, Regina and Trois-Palétuviers) between December 2013 and July 2014. Twenty-four inventories of wood species used in traditional buildings were conducted in the villages, as well as ethnobotanical walks in the neighboring forests, to complete data about usable species and to determine Linnaean names. After an ethnographic description of roundwood Palikur habitat, the in situ wood selection process of Palikur is precisely described. A total of 960 roundwood pieces were inventoried in situ according to Palikur taxonomy, of which 860 were beams and rafters, and 100 posts in 20 permanent and 4 temporary buildings. Twenty-seven folk species were identified. Sixty-three folk species used in construction were recorded during ethnobotanical walks. They correspond to 263 botanical species belonging to 25 families. Posts in permanent buildings were made of yawu (Minquartia guianensis) (51%) and wakap (Vouacapoua americana) (14%). Beams and rafters were made of wood from Annonaceae (79%) and Lecythidaceae (13%) families. The most frequently used species were kuukumwi priye (Oxandra asbeckii), kuukumwi seyne (Pseudoxandra cuspidata), and pukuu (Xylopia nitida and X. cayennensis). Although the Palikur's relationship with their habitat is undergoing significant changes, knowledge about construction wood is still very much alive in the Oyapock basin. Many people continue to construct traditional buildings alongside modern houses, using a wide array of species

The eastern part of the Fertile Crescent concealed an unexpected route of olive (Olea europaea L.) differentiation.

PubMed

Mousavi, Soraya; Mariotti, Roberto; Bagnoli, Francesca; Costantini, Lorenzo; Cultrera, Nicolò G M; Arzani, Kazem; Pandolfi, Saverio; Vendramin, Giovanni Giuseppe; Torkzaban, Bahareh; Hosseini-Mazinani, Mehdi; Baldoni, Luciana

2017-06-01

Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeo-botanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Ethnomedicinal study of plants used for human ailments in Ankober District, North Shewa Zone, Amhara Region, Ethiopia

PubMed Central

2013-01-01

Background Ankober District has long been inhabited by people who have a long tradition of using medicinal plants to treat human ailments. Overexploitation of medicinal plants coupled with an ever-increasing population growth, deforestation and agricultural land expansion threatens plants in the area. Hence, this study aimed at documenting and analyzing the plant-based ethnomedicinal knowledge of the people in order to preserve the dwindling indigenous knowledge. Methods Ethnobotanical data were collected using semi-structured interviews, focus group discussions, participant observation and walk-in-the-woods. Quantitative approaches were used to determine Informant Consensus Factor (ICF) and Fidelity level (FL) values. Statistical tests were used to compare the indigenous knowledge on medicinal plants among different informant categories. Results A total of 135 medicinal plant species belonging to 128 genera and 71 botanical families were reported to treat human diseases in the District. Families Asteraceae (12 species, 9%) and Fabaceae (10, 7.4%) were found to be best represented in the area. About 44% of preparations were reported to be obtained from roots. Significant difference (P < 0.05) was observed on the mean number of medicinal plants reported by groups of respondents compared within age, literacy level and experience parameters. Highest ICF values were recorded for gastro-intestinal & parasitic and dermatological disease categories (0.70 each) indicating best agreement among informants knowledge on medicinal plants used to treat aliments in these categories. Highest fidelity level values were recorded for Zehneria scabra (95%) and Hagenia abyssinica (93.75%) showing conformity of knowledge on species of best healing potential. Podocarpus falcatus was ranked first in a direct matrix ranking exercise of multipurpose medicinal plants. The output of preference ranking exercise indicated that Olea europaea subsp. cuspidata was the most preferred species to

Human-Forest interfaces in Hugumburda-Gratkhassu National Forest Priority Area, North-eastern Ethiopia.

PubMed

Kidane, Leul; Nemomissa, Sileshi; Bekele, Tamrat

2018-02-23

Traditional management regimes and knowledge systems of forest resources have shaped forests throughout the world where materials from individual species are harvested in a sustainable manner. To comprehend this, the vegetation of Hugumburda-Gratkhassu Forest was described and related to anthropogenic factors. Three ethnobotanical research methods were used to collect indigenous knowledge of the local inhabitants related to conservation and utilization of forest resources. Direct matrix ranking was conducted to discover local attitudes on species preference for multiple use. During this work, the 46 most important tree and shrub species were selected based on recommendations of local guides and key informants to determine the range of uses obtained from each species. Through paired comparison, activities supposed to be the major cause of degradation of the forest were adopted. Pairs of activities were then established from the relation n (n-1)/2. Each respondent was then asked to select an activity that he considered being a major problem to management of the forest. Semi-structured interviews were used to obtain information from sixty local informants to address community attitudes towards forest management and utilization. The result obtained from direct matrix ranking showed; that 20 out of 46 plant species compared had the highest scores and rank, indicating that these species are the most important and are exploited by the local communities for multiple purposes. The paired comparison exercise revealed logging for construction materials to be the major threat to the forest due to cutting of large volume of wood for construction of churches, health centers, schools and new houses. Juniperus procera, Olea europaea ssp. cuspidata, Rhus glutinosa, Ficus sur, Hagenia abyssinica, Cassipourea malosana and Acacia etbaica were the most selected and exploited plant species for these purposes. Survival of protected areas depends on the support of local communities

The implications of ritual practices and ritual plant uses on nature conservation: a case study among the Naxi in Yunnan Province, Southwest China.

PubMed

Geng, Yanfei; Hu, Guoxiong; Ranjitkar, Sailesh; Shi, Yinxian; Zhang, Yu; Wang, Yuhua

2017-10-25

Conservation of biodiversity is primary important of today's critically vulnerable environment. Efficient conservation can be possible only with the long-term participation and understanding of the communities. Ritual beliefs of the indigenous people are one of the important tools to understand the local communities and aid the nature conservation. In this paper, we documented contemporary ritual practices and ritual plant uses among the Naxi people and discussed the importance of traditional knowledge on ritual practice in the conservation of plants in the mountains presenting a case study of the Dongba culture. This study was carried out from July in 2013 to July in 2014. To document and analyze the present state of the ritual plant used by the Naxi people we conducted an ethnobotanical survey. We interviewed local people including Dongba priests using the semi-structured questionnaire. During the field study, we participated in the local religious activities to witness the use of different plants in ritual activities of the Naxi people. We interviewed twenty-two key informants and eleven of them were male. All the specimens of documented species were collected and deposited at the herbarium of Kunming Institute of Botany. The survey results revealed the Naxi people possessed sound knowledge of the traditional ritual plants and great diversity of plants used in many of Naxi rituals and festivals. From the survey, we documented 32 ritual plant species belonging to 24 genera of 17 families used in various ritual activities. The ritual plants were grouped into two categories, namely those burned as incense, and those used for decoration. The incense plants like Olea europaea subsp. cuspidata and Pistacia weinmanniifolia were probably promising natural aromatic resource. Plants of genus Quercus were the most frequently used species. The places for ritual activities were diverse, such as the incense burners inside and outside the house and sacred trees at the

Diversity and toxicity of the diatom Pseudo-nitzschia Peragallo in the Gulf of Maine, Northwestern Atlantic Ocean

PubMed Central

Fernandes, Luciano F.; Hubbard, Katherine A.; Richlen, Mindy L.; Smith, Juliette; Bates, Stephen S.; Ehrman, James; Léger, Claude; Mafra, Luiz L.; Kulis, David; Quilliam, Michael; Libera, Katie; McCauley, Linda; Anderson, Donald M.

2014-01-01

Multiple species in the toxic marine diatom genus Pseudo-nitzschia have been identified in the Northwestern Atlantic region encompassing the Gulf of Maine (GOM), including the Bay of Fundy (BOF). To gain further knowledge of the taxonomic composition and toxicity of species in this region, Pseudo-nitzschia isolates (n=146) were isolated from samples collected during research cruises that provided broad spatial coverage across the GOM and the southern New England shelf, herein referred to as the GOM region, during 2007-2008. Isolates, and cells in field material collected at 38 stations, were identified using electron microscopy (EM). Eight species (P. americana, P. fraudulenta, P. subpacifica, P. heimii, P. pungens, P. seriata, P. delicatissima and P. turgidula), and a novel form, Pseudo-nitzschia sp. GOM, were identified. Species identity was confirmed by sequencing the large subunit of the ribosomal rDNA (28S) and the internal transcribed spacer 2 (ITS2) for six species (36 isolates). Phylogenetic analyses (including neighbor joining, maximum parsimony, and maximum likelihood estimates and ITS2 secondary structure analysis) and morphometric data supported the placement of P. sp. GOM in a novel clade that includes morphologically and genetically similar isolates from Australia and Spain and is genetically most similar to P. pseudodelicatissima and P. cuspidata. Seven species (46 isolates) were grown in nutrient-replete batch culture and aliquots consisting of cells and growth medium were screened by Biosense ASP ELISA to measure total domoic acid (DA) produced (intracellular + extracellular); P. americana and P. heimii were excluded from all toxin analyses as they did not persist in culture long enough for testing. All 46 isolates screened produced DA in culture and total DA varied among species (e.g., 0.04 to 320 ng ml-1 for P. pungens and P. sp. GOM isolates, respectively) and among isolates of the same species (e.g., 0.24 – 320 ng ml-1 for P. sp. GOM). The 15