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Novel Clades (novel + clade)
Selected AbstractsMorphological and Molecular Evidence of Arbuscular Mycorrhizal Fungal Associations in Costa Rican Epiphytic Bromeliads,BIOTROPICA, Issue 2 2005Annette R. Rowe ABSTRACT Arbuscular mycorrhizal fungi influence the growth, morphology, and fitness of a variety of plant species, but little is known of the arbuscular mycorrhizal (AM) fungal associations of plant species in forest canopies. Plant species' associations with AM fungi are most often elucidated by examining the roots for fungal structures; however, morphological data may provide a limited resolution on a plant's mycorrhizal status. We combined a traditional staining technique with a molecular marker (the 18S ribosomal gene) to determine whether or not a variety of epiphytic bromeliads form arbuscular mycorrhizal fungal associations. Using these methods we show that the epiphytic bromeliad Vriesea werkleana forms arbuscular mycorrhizal fungal associations with members of the genus Glomus. AM fungal sequences of this plant species formed three distinct clades nested within a larger Glomus clade; two of the clades did not group with any previously sequenced lineage of Glomus. Novel clades may represent novel species. Although Vriesea werkleana is associated with multiple AM fungal species, each individual plant is colonized by a single lineage. The combination of morphological and molecular methods provides a practical approach to the characterization of the mycorrhizal status of epiphytic bromeliads, and perhaps other tropical epiphytes. [source] Soil CO2 flux and photoautotrophic community composition in high-elevation, ,barren' soilENVIRONMENTAL MICROBIOLOGY, Issue 3 2009Kristen R. Freeman Summary Soil-dominated ecosystems, with little or no plant cover (i.e. deserts, polar regions, high-elevation areas and zones of glacial retreat), are often described as ,barren', despite their potential to host photoautotrophic microbial communities. In high-elevation, subnival zone soil (i.e. elevations higher than the zone of continuous vegetation), the structure and function of these photoautotrophic microbial communities remains essentially unknown. We measured soil CO2 flux at three sites (above 3600 m) and used molecular techniques to determine the composition and distribution of soil photoautotrophs in the Colorado Front Range. Soil CO2 flux data from 2002 and 2007 indicate that light-driven CO2 uptake occurred on most dates. A diverse community of Cyanobacteria, Chloroflexi and eukaryotic algae was present in the top 2 cm of the soil, whereas these clades were nearly absent in deeper soils (2,4 cm). Cyanobacterial communities were composed of lineages most closely related to Microcoleus vaginatus and Phormidium murrayi, eukaryotic photoautotrophs were dominated by green algae, and three novel clades of Chloroflexi were also abundant in the surface soil. During the light hours of the 2007 snow-free measurement period, CO2 uptake was conservatively estimated to be 23.7 g C m,2 season,1. Our study reveals that photoautotrophic microbial communities play an important role in the biogeochemical cycling of subnival zone soil. [source] Detection of glycolate oxidase gene glcD diversity among cultured and environmental marine bacteriaENVIRONMENTAL MICROBIOLOGY, Issue 10 2006W. W. Y. Lau Summary Of eight laboratory cultures of marine ,- and ,- Proteobacteria tested, growth on glycolate as a sole carbon source was detected for only three species: Pseudomonas stutzeri, Oceanimonas doudoroffii and Roseobacter sp. isolate Y3F. Degenerate polymerase chain reaction (PCR) primers were designed to amplify glcD, which encodes the D-subunit of the enzyme glycolate oxidase; glcD could be amplified only from those cultures that grew on glycolate. The PCR primers were used to explore glcD diversity in four field samples collected from different ocean environments: an Atlantic Gulf Stream Ring, sampled above and below the thermocline and two Pacific coastal sites, Parks Bay and San Juan Channel, WA. Environmental glcD sequences belonged to six major bacterial phylogenetic groups, with most sequences forming novel clades with no close relatives. Different patterns of glcD diversity were observed within and between the two nutrient regimes. Comparison of glcD and 16S rDNA diversity and analyses of available bacterial genomes and a metgenomic library from the Sargasso Sea show that glycolate-utilizing potential exists in only a subset of bacteria. Glycolate is produced in marine environments mainly by phytoplankton. Examination of glcD diversity will aid in understanding the influence of phytoplankton on bacterial community structure. [source] Phylogenetic diversity of Synechococcus strains isolated from the East China Sea and the East SeaFEMS MICROBIOLOGY ECOLOGY, Issue 3 2009Dong Han Choi Abstract Phylogenetic relationships among 33 Synechococcus strains isolated from the East China Sea (ECS) and the East Sea (ES) were studied based on 16S rRNA gene sequences and 16S,23S rRNA gene internal transcribed spacer (ITS) sequences. Pigment patterns of the culture strains were also examined. Based on 16S rRNA gene and ITS sequence phylogenies, the Synechococcus isolates were clustered into 10 clades, among which eight were previously identified and two were novel. Half of the culture strains belonged to clade V or VI. All strains that clustered into novel clades exhibited both phycoerythrobilin and phycourobilin. Interestingly, the pigment compositions of isolates belonging to clades V and VI differed from those reported for other oceanic regions. None of the isolates in clade V showed phycourobilin, whereas strains in clade VI exhibited both phycourobilin and phycoerythrobilin, which is in contrast to previous studies. The presence of novel lineages and the different pigment patterns in the ECS and the ES suggests the possibility that some Synechococcus lineages are distributed only in geographically restricted areas and have evolved in these regions. Therefore, further elucidation of the physiological, ecological, and genetic characteristics of the diverse Synechococcus strains is required to understand their spatial and geographical distribution. [source] Avian molecular systematics on the rebound: a fresh look at modern shorebird phylogenetic relationshipsJOURNAL OF AVIAN BIOLOGY, Issue 3 2004Marcel Van Tuinen The study of avian molecular systematics currently lags behind that of mammals in several ways. Little phylogenetic resolution is observed among orders and phylogenetic studies below the ordinal level largely remain based on fast evolving mitochondrial sequences. New papers by Paton et al., Ericson et al., and Thomas et al. provide avian molecular systematics with a badly needed boost. These studies indicate that sampling more taxa and slower evolving nuclear genes yields strong phylogenetic resolution among the major shorebird (order Charadriiformes) families. The new data show surprising overall consensus and converge on certain novel clades. If correct, this newly obtained phylogenetic framework has tremendous implications for our understanding of the evolution of shorebird morphology, ecology and behaviour. [source] | ||||||||||