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Molecular ecology

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https://www.readbyqxmd.com/read/28087942/the-mutualistic-interaction-between-plants-and-arbuscular-mycorrhizal-fungi
#1
Luisa Lanfranco, Paola Bonfante, Andrea Genre
Mycorrhizal fungi belong to several taxa and develop mutualistic symbiotic associations with over 90% of all plant species, from liverworts to angiosperms. While descriptive approaches have dominated the initial studies of these fascinating symbioses, the advent of molecular biology, live cell imaging, and "omics" techniques have provided new and powerful tools to decipher the cellular and molecular mechanisms that rule mutualistic plant-fungus interactions. In this article we focus on the most common mycorrhizal association, arbuscular mycorrhiza (AM), which is formed by a group of soil fungi belonging to Glomeromycota...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28074845/local-coexistence-and-genetic-isolation-of-three-pollinator-species-on-the-same-fig-tree-species
#2
T L Sutton, J L DeGabriel, M Riegler, J M Cook
Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries...
January 11, 2017: Heredity
https://www.readbyqxmd.com/read/28073604/morphometric-and-genetic-analysis-of-arcella-intermedia-and-arcella-intermedia-laevis-amoebozoa-arcellinida-illuminate-phenotypic-plasticity-in-microbial-eukaryotes
#3
Alfredo L Porfírio-Sousa, Giulia M Ribeiro, Daniel J G Lahr
Testate amoebae are eukaryotic microorganisms characterized by the presence of an external shell (test). The shell morphology is used as a diagnostic character, but discordance between morphological and molecular data has been demonstrated in groups of arcellinids (Amoebozoa), one of the principal groups of testate amoebae. Morphology of the test is supposed to differentiate genera and species and it is applied in ecological, monitoring and paleontological studies. However, if phenotype does not reflect genotype, conclusions in these types of studies become severely impaired...
November 25, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28073555/molecular-and-phylogenetic-characterization-of-ostreopsis-dinophyceae-and-the-description-of-a-new-species-ostreopsis-rhodesae-sp-nov-from-a-subtropical-australian-lagoon
#4
Arjun Verma, Mona Hoppenrath, Juan José Dorantes-Aranda, D Tim Harwood, Shauna A Murray
Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described...
December 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073480/a-review-of-the-global-ecology-genomics-and-biogeography-of-the-toxic-cyanobacterium-microcystis-spp
#5
REVIEW
Matthew J Harke, Morgan M Steffen, Christopher J Gobler, Timothy G Otten, Steven W Wilhelm, Susanna A Wood, Hans W Paerl
This review summarizes the present state of knowledge regarding the toxic, bloom-forming cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins, genomics, phylogeny, and ecology. A global analysis found documentation suggesting geographic expansion of Microcystis, with recorded blooms in at least 108 countries, 79 of which have also reported the hepatatoxin microcystin. The production of microcystins (originally "Fast-Death Factor") by Microcystis and factors that control synthesis of this toxin are reviewed, as well as the putative ecophysiological roles of this metabolite...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073454/molecular-tools-to-detect-anatoxin-a-genes-in-aquatic-ecosystems-toward-a-new-nested-pcr-based-method
#6
Benjamin Legrand, Jerome Lesobre, Jonathan Colombet, Delphine Latour, Marion Sabart
Over the last few decades, cyanobacterial mass occurrence has become a recurrent feature of aquatic ecosystems. This has led to ecosystem exposure and health hazards associated with cyanotoxin production. The neurotoxin anatoxin-a and its homologs can be synthesized by benthic cyanobacterial species in lotic systems, but also by planktonic lacustrine species such as Dolichospermum (also known as Anabaena). However, only a few studies have focused on anatoxin-a occurrence and its biosynthesis genes in freshwater lakes...
September 2016: Harmful Algae
https://www.readbyqxmd.com/read/28072853/terrestrial-macrofungal-diversity-from-the-tropical-dry-evergreen-biome-of-southern-india-and-its-potential-role-in-aerobiology
#7
Hema Priyamvada, M Akila, Raj Kamal Singh, R Ravikrishna, R S Verma, Ligy Philip, R R Marathe, L K Sahu, K P Sudheer, S S Gunthe
Macrofungi have long been investigated for various scientific purposes including their food and medicinal characteristics. Their role in aerobiology as a fraction of the primary biological aerosol particles (PBAPs), however, has been poorly studied. In this study, we present a source of macrofungi with two different but interdependent objectives: (i) to characterize the macrofungi from a tropical dry evergreen biome in southern India using advanced molecular techniques to enrich the database from this region, and (ii) to assess whether identified species of macrofungi are a potential source of atmospheric PBAPs...
2017: PloS One
https://www.readbyqxmd.com/read/28072390/a-molecular-portrait-of-maternal-sepsis-from-byzantine-troy
#8
Alison M Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob M Enk, G Brian Golding, John Southon, Melanie Kuch, Ana T Duggan, William Aylward, Shea N Gardner, Jonathan E Allen, Andrew M King, Gerard Wright, Makoto Kuroda, Kengo Kato, Derek Eg Briggs, Gino Fornaciari, Edward C Holmes, Hendrik N Poinar, Caitlin S Pepperell
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman's remains. Scanning electron microscopy of the tissue revealed 'ghost cells', resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses...
January 10, 2017: ELife
https://www.readbyqxmd.com/read/28071972/genetic-identification-for-prey-birds-of-the-endangered-peregrine-falcon-falco-peregrinus
#9
Sang-Hyun Han, Hong-Shik Oh
To reveal the dietary ecology of the peregrine falcon (Falco peregrinus), we conducted a molecular analysis for mitochondrial genes (COI and CYTB) to identify the prey species collected from a feeding place found on Sasu Island, South Korea. The results from noninvasive genetic analysis showed that the sequences obtained came from nine species of birds (Cuculus canorus, Eurystomus orientalis, Limosa limosa, Microscelis amaurotis, Oriolus chinensis, Phasianus colchicus, Sterna hirundo, Streptopelia orientalis, and Turdus pallidus)...
January 10, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28066713/sequencing-and-de-novo-transcriptome-assembly-of-anthopleura-dowii-verrill-1869-from-mexico
#10
Jorge-Tonatiuh Ayala-Sumuano, Alexei Licea-Navarro, Enrique Rudiño-Piñera, Estefanía Rodríguez, Claudia Rodríguez-Almazán
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28065866/multilocus-molecular-phylogeny-of-the-ornamental-wood-eating-catfishes-siluriformes-loricariidae-panaqolus-and-panaque-reveals-undescribed-diversity-and-parapatric-clades
#11
Nathan K Lujan, Christian A Cramer, Raphael Covain, Sonia Fisch-Muller, Hernán López-Fernández
Approximately two-dozen species in three genera of the Neotropical suckermouth armored catfish family Loricariidae are the only described fishes known to specialize on diets consisting largely of wood. We conducted a molecular phylogenetic analysis of 10 described species and 14 undescribed species or morphotypes assigned to the wood-eating catfish genus Panaqolus, and four described species and three undescribed species or morphotypes assigned to the distantly related wood-eating catfish genus Panaque. Our analyses included individuals and species from both genera that are broadly distributed throughout tropical South America east of the Andes Mountains and 13 additional genera hypothesized to have also descended from the most recent common ancestor of Panaqolus and Panaque...
January 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28065710/ecoimmunology-and-microbial-ecology-contributions-to-avian-behavior-physiology-and-life-history
#12
REVIEW
Jessica K Evans, Katherine L Buchanan, Simon C Griffith, Kirk C Klasing, BriAnne Addison
Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories...
January 5, 2017: Hormones and Behavior
https://www.readbyqxmd.com/read/28063202/dna-metabarcoding-reveals-that-200-%C3%AE-m-size-fractionated-filtering-is-unable-to-discriminate-between-planktonic-microbial-and-large-eukaryotes
#13
Lemian Liu, Min Liu, David M Wilkinson, Huihuang Chen, Xiaoqing Yu, Yang Jun
Microeukaryotic plankton (0.2-200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear if we can accurately, effectively, and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analyzed the eukaryotic plankton communities both with, and without, pre-filtering with a 200 μm pore-size sieve - by using SSU rDNA-based high-throughput sequencing on 16 samples with 3 replicates in each sample from two subtropical reservoirs sampled from January to October in 2013...
January 7, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28061879/the-complete-mitochondrial-genomes-of-two-freshwater-snails-provide-new-protein-coding-gene-rearrangement-models-and-phylogenetic-implications
#14
Xidong Mu, Yexin Yang, Yi Liu, Du Luo, Meng Xu, Hui Wei, Dangen Gu, Hongmei Song, Yinchang Hu
BACKGROUND: Mitochondrial (mt) genome sequences are widely used for species identification and to study the phylogenetic relationships among Gastropoda. However, to date, limited data are available as taxon sampling is narrow. In this study we sequenced the complete mt genomes of the freshwater gastropods Radix swinhoei (Lymnaeidae) and Planorbarius corneus (Planorbidae). Based on these sequences, we investigated the gene rearrangement in these two species and the relationships with respect to the ancestral gene order and assessed their phylogenetic relationships...
January 6, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28058113/transmission-bottlenecks-and-rnai-collectively-influence-tick-borne-flavivirus-evolution
#15
Nathan D Grubaugh, Claudia Rückert, Philip M Armstrong, Angela Bransfield, John F Anderson, Gregory D Ebel, Doug E Brackney
Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus) populations in and between both the vertebrate host and arthropod vector...
July 2016: Virus Evolution
https://www.readbyqxmd.com/read/28057824/the-ecology-and-evolution-of-social-behavior-in-microbes
#16
REVIEW
Corina E Tarnita
Cooperation has been studied extensively across the tree of life, from eusociality in insects to social behavior in humans, but it is only recently that a social dimension has been recognized and extensively explored for microbes. Research into microbial cooperation has accelerated dramatically and microbes have become a favorite system because of their fast evolution, their convenience as lab study systems and the opportunity for molecular investigations. However, the study of microbes also poses significant challenges, such as a lack of knowledge and an inaccessibility of the ecological context (used here to include both the abiotic and the biotic environment) under which the trait deemed cooperative has evolved and is maintained...
January 1, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28053872/genetic-identification-of-marine-eels-through-dna-barcoding-from-parangipettai-coastal-waters
#17
Samuel Peninal, Janakiraman Subramanian, Alaganatham Elavarasi, Murugaiyan Kalaiselvam
Anguilliformes, also known as "true eels", are an ecologically diverse group of predominantly marine origin whose members were easily recognized by their extremely elongated bodies with reduced cross-sectional areas and universal lack of pelvic fins. The Marine Eels were collected from landing centres of Parangipettai coastal waters and identified based on their morphometric and meristic characters. The newly recorded species were used for the barcoding analysis. Information on molecular taxonomy of marine eels was very meagre and hence, the present study was aimed to study the barcoding of marine eels which were present along the southeast coast of India...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#18
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28051568/influenza-a-virus-surveillance-in-underrepresented-avian-species-in-ohio-in-2015
#19
Hannah E Urig, Jacqueline M Nolting, Dimitria A Mathys, Blake A Mathys, Andrew S Bowman
We surveyed passerines and other terrestrial avian species for influenza A virus, resulting in molecular detection of virus from 1.5% of the 615 birds. However, no viral isolates were recovered. Little is known about the role that these undersurveilled avian species play in the ecology of influenza A virus.
January 4, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28049420/horizontal-gene-transfer-drives-the-evolution-of-rh50-permeases-in-prokaryotes
#20
Giorgio Matassi
BACKGROUND: Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4(+) across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in eukaryotes but absent in land plants and fungi, and remarkably rare in prokaryotes. The evolutionary history of RH50 genes in prokaryotes is just beginning to be unveiled...
January 3, 2017: BMC Evolutionary Biology
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