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Nathalie Amacker, Edward A D Mitchell, Benoît J D Ferrari, Nathalie Chèvre
An ever-increasing diversity of potentially toxic chemical compounds are being developed and released into the environment as a result of human activities (e.g. agriculture, drugs, and cosmetics). Among these, pesticides have been shown to affect non-targeted wildlife since the 1960s. A range of ecotoxicological tests are used to assess the toxicity of pesticides on various model organisms. However most model organisms are metazoans, while the majority of Eukaryotes are unicellular microorganisms known as protists...
March 1, 2018: Chemosphere
Jonathan W Leff, Richard D Bardgett, Anna Wilkinson, Benjamin G Jackson, William J Pritchard, Jonathan R De Long, Simon Oakley, Kelly E Mason, Nicholas J Ostle, David Johnson, Elizabeth M Baggs, Noah Fierer
There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa)...
March 9, 2018: ISME Journal
Carolina Valença Barbosa, Magali Muniz Barreto, Rosemary de Jesus Andrade, Fernando Sodré, Claudia Masini d'Avila-Levy, José Mauro Peralta, Ricardo Pereira Igreja, Heloisa Werneck de Macedo, Helena Lucia Carneiro Santos
BACKGROUND: Intestinal parasitic infections are considered a serious public health problem and widely distributed worldwide, mainly in urban and rural environments of tropical and subtropical countries. Globally, soil-transmitted helminths and protozoa are the most common intestinal parasites. Blastocystis sp. is a highly prevalent suspected pathogenic protozoan, and considered an unusual protist due to its significant genetic diversity and host plasticity. METHODOLOGY/MAIN FINDINGS: A total of 294 stool samples were collected from inhabitants of three rural valleys in Rio de Janeiro, Brazil...
2018: PloS One
Daria Tashyreva, Galina Prokopchuk, Jan Votýpka, Akinori Yabuki, Aleš Horák, Julius Lukeš
Diplonemids represent a hyperdiverse and abundant yet poorly studied group of marine protists. Here we describe two new members of the genus Diplonema (Diplonemea, Euglenozoa), Diplonema japonicum sp. nov. and Diplonema aggregatum sp. nov., based on life cycle, morphology, and 18S rRNA gene sequences. Along with euglenozoan apomorphies, they contain several unique features. Their life cycle is complex, consisting of a trophic stage that is, following the depletion of nutrients, transformed into a sessile stage and subsequently into a swimming stage...
March 6, 2018: MBio
Riley E Steele, Nawaf A Nasser, R Timothy Patterson, Braden R B Gregory, Helen M Roe, Eduard G Reinhardt
Arcellinida (testate lobose amoebae), a group of benthic protists, were examined from 46 sediment-water interface samples collected from oligotrophic Oromocto Lake, New Brunswick, Canada. To assess (1) assemblage homogeneity at a sub-meter spatial scale and (2) the necessity for collecting samples from multiple stations during intra-lake surveys; multiple samples were collected from three stations (quadrats 1, 2, and 3) across the north basin of Oromocto Lake, with quadrat 1 (n = 16) being the furthest to the west, quadrat 2 (n = 15) situated closer to the center of the basin, and quadrat 3 (n = 15) positioned 300 m south of the mouth of Dead Brook, an inlet stream...
March 4, 2018: Microbial Ecology
David Bass, Christopher van der Gast, Serena Thomson, Sigrid Neuhauser, Sally Hilton, Gary D Bending
Microbial communities closely associated with the rhizosphere can have strong positive and negative impacts on plant health and growth. We used a group-specific amplicon approach to investigate local scale drivers in the diversity and distribution of plasmodiophorids in rhizosphere/root and bulk soil samples from oilseed rape (OSR) and wheat agri-systems. Plasmodiophorids are plant- and stramenopile-associated protists including well known plant pathogens as well as symptomless endobiotic species. We detected 28 plasmodiophorid lineages (OTUs), many of them novel, and showed that plasmodiophorid communities were highly dissimilar and significantly divergent between wheat and OSR rhizospheres and between rhizosphere and bulk soil samples...
2018: Frontiers in Microbiology
Patrick T West, Alexander J Probst, Igor V Grigoriev, Brian C Thomas, Jillian F Banfield
Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k-mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation and prediction of metabolic potential...
March 1, 2018: Genome Research
Liang Huo, Ping Zhang, Chenxi Li, Kashif Rahim, Xiaoran Hao, Biyun Xiang, Xudong Zhu
Circular RNAs (circRNAs), a novel class of ubiquitous and intriguing noncoding RNA, have been found in a number of eukaryotes but not yet basidiomycetes. In this study, we identified 73 circRNAs from 39.28 million filtered RNA reads from the basidiomycete Cryptococcus neoformans JEC21 using next-generation sequencing (NGS) and the bioinformatics tool circular RNA identification (CIRI). Furthermore, mapping of newly found circRNAs to the genome showed that 73.97% of the circRNAs originated from exonic regions, whereas 20...
February 26, 2018: Genes
Ran Li, Nianzhi Jiao, Alan Warren, Dapeng Xu
Protists make up an important component of aquatic ecosystems, playing crucial roles in biogeochemical processes on local and global scales. To reveal the changes of diversity and community structure of protists along the salinity gradients, community compositions of active protistan assemblages were characterized along a transect from the lower Pearl River estuary to the open waters of the South China Sea (SCS), using high-throughput sequencing of the hyper-variable V9 regions of 18S rRNA. This study showed that the alpha diversity of protists, both in the freshwater and in the coastal SCS stations was higher than that in the estuary...
January 31, 2018: European Journal of Protistology
Eva C M Nowack, Andreas P M Weber
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles...
February 28, 2018: Annual Review of Plant Biology
Yuehui Tian, Shiqiang Gao, Shang Yang, Georg Nagel
It is since many years textbook knowledge that the concentration of the second messenger cGMP is regulated in animal rod and cone cells by type-II rhodopsins via a G protein signaling cascade. Microbial rhodopsins with enzymatic activity for regulation of cGMP concentration were only recently discovered: in 2014 light-activated guanylyl cyclase opsins in fungi and in 2017 a novel rhodopsin phosphodiesterase in the protist Salpingoeca rosetta ( Sr RhoPDE). The light-regulation of Sr RhoPDE however, seemed very weak or absent...
February 26, 2018: Biochemical Journal
Daniela Sparvoli, Elisabeth Richardson, Hiroko Osakada, Xun Lan, Masaaki Iwamoto, Grant R Bowman, Cassandra Kontur, William A Bourland, Denis H Lynn, Jonathan K Pritchard, Tokuko Haraguchi, Joel B Dacks, Aaron P Turkewitz
In the endocytic pathway of animals, two related complexes, called CORVET (class C core vacuole/endosome transport) and HOPS (homotypic fusion and protein sorting), act as both tethers and fusion factors for early and late endosomes, respectively. Mutations in CORVET or HOPS lead to trafficking defects and contribute to human disease, including immune dysfunction. HOPS and CORVET are conserved throughout eukaryotes, but remarkably, in the ciliate Tetrahymena thermophila, the HOPS-specific subunits are absent, while CORVET-specific subunits have proliferated...
February 21, 2018: Current Biology: CB
Yusuke Kinoshita, Motoki Kayama, Yuichiro Kashiyama, Hitoshi Tamiaki
Divinyl-132 ,173 -cyclopheophorbide-a enol was in vivo produced as a metabolite of divinyl-chlorophyll-a by protists and in vitro prepared by the intramolecular cyclization of methyl divinyl-pyropheophorbide-a, one of the divinyl-chlorophyll-a derivatives. The1 H NMR spectra in CDCl3 showed that the obtained product took exclusively its enol form in the solution. The intramolecular cyclization of chlorin π-system at the C132 and C173 positions affected the optical properties of such chlorophyll derivatives including the non-fluorescent emission of the enol...
February 9, 2018: Bioorganic & Medicinal Chemistry Letters
Akshari Gupta, Daiju Kitagawa
Several decades of centriole research have revealed the beautiful symmetry present in these microtubule-based organelles, which are required to form centrosomes, cilia, and flagella in many eukaryotes. Centriole architecture is largely conserved across most organisms, however, individual centriolar features such as the central cartwheel or microtubule walls exhibit considerable variability when examined with finer resolution. Here, we review the ultrastructural characteristics of centrioles in commonly studied organisms, highlighting the subtle and not-so-subtle differences between specific structural components of these centrioles...
February 16, 2018: Journal of Biochemistry
Noor Akbar, Ruqaiyyah Siddiqui, Mazhar Iqbal, K Sagathevan, Naveed Ahmed Khan
Here, we hypothesized that the microbial gut flora of animals/pests living in polluted environments, produce substances to thwart bacterial infections. The overall aim of this study was to source microbes inhabiting unusual environmental niches for potential antimicrobial activity. Two cockroach species, Gromphadorhina portentosa (Madagascar) and Blaptica dubia (Dubia) were selected. The gut bacteria from these species were isolated and grown in RPMI 1640 and conditioned media were prepared. Conditioned media were tested against a panel of Gram-positive (Methicillin resistant Staphylococcus aureus, Streptococcus pyogenes, Bacillus cereus) and Gram-negative (Escherichia coli K1, Salmonella enterica, Serratia marcescens, Pseudomonas aeruginosa, Klebsiella pneumoniae) bacteria, as well as the protist pathogen, Acanthamoeba castellanii...
February 19, 2018: Letters in Applied Microbiology
Petra Bukovská, Michael Bonkowski, Tereza Konvalinková, Olena Beskid, Martina Hujslová, David Püschel, Veronika Řezáčová, María Semiramis Gutiérrez-Núñez, Milan Gryndler, Jan Jansa
Arbuscular mycorrhizal (AM) fungi can significantly contribute to plant nitrogen (N) uptake from complex organic sources, most likely in concert with activity of soil saprotrophs and other microbes releasing and transforming the N bound in organic forms. Here, we tested whether AM fungus (Rhizophagus irregularis) extraradical hyphal networks showed any preferences towards certain forms of organic N (chitin of fungal or crustacean origin, DNA, clover biomass, or albumin) administered in spatially discrete patches, and how the presence of AM fungal hyphae affected other microbes...
February 17, 2018: Mycorrhiza
Stefan Geisen, Edward A D Mitchell, Sina Adl, Michael Bonkowski, Micah Dunthorn, Flemming Ekelund, Leonardo D Fernández, Alexandre Jousset, Valentyna Krashevska, David Singer, Frederick W Spiegel, Julia Walochnik, Enrique Lara
Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests...
February 13, 2018: FEMS Microbiology Reviews
Canan Karakoç, Viktoriia Radchuk, Hauke Harms, Antonis Chatzinotas
Ecological disturbances are important drivers of biodiversity patterns. Many biodiversity studies rely on endpoint measurements instead of following the dynamics that lead to those outcomes and testing ecological drivers individually, often considering only a single trophic level. Manipulating multiple factors (biotic and abiotic) in controlled settings and measuring multiple descriptors of multi-trophic communities could enlighten our understanding of the context dependency of ecological disturbances. Using model microbial communities, we experimentally tested the effects of imposed disturbances (i...
February 14, 2018: Scientific Reports
Fatma Gomaa, Maxim Gersh, Colleen Cavanaugh
Diverse species of Legionella and Legionella-like amoebal pathogens (LLAPs) have been identified as intracellular bacteria in many amoeboid protists. There are, however, other amoeboid groups such as testate amoeba for which we know little about their potential to host such bacteria. In this study we assessed the occurrence and diversity of Legionella spp. in cultures and environmental isolates of freshwater arcellinid testate amoebae species, Arcella hemispherica, Arcella intermedia, and Arcella vulgaris, via 16S rRNA gene sequence analyses and fluorescent in situ hybridization (FISH)...
February 14, 2018: Journal of Eukaryotic Microbiology
Seyyed Hamidreza Hashemipetroudi, Ghorbanali Nematzadeh, Gholamreza Ahmadian, Ahad Yamchi, Markus Kuhlmann
One method extensively used for the quantification of gene expression changes and transcript abundances is reverse-transcription quantitative real-time PCR (RT-qPCR). It provides accurate, sensitive, reliable, and reproducible results. Several factors can affect the sensitivity and specificity of RT-qPCR. Residual genomic DNA (gDNA) contaminating RNA samples is one of them. In gene expression analysis, non-specific amplification due to gDNA contamination will overestimate the abundance of transcript levels and can affect the RT-qPCR results...
January 22, 2018: Journal of Visualized Experiments: JoVE
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