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Molecular ecology

Masatoshi Matsunami, Daiji Endo, Naruya Saitou, Hitoshi Suzuki, Manabu Onuma
The wood mouse (genus Apodemus ) is one of the most common rodents in broad-leaf forests in the temperate zone of the Palaearctic region. Molecular studies of wood mice have critically enhanced the understanding of their evolution and ancestral biogeographic events. However, their molecular data are currently only limited to partial mitochondrial sequences and a few genes. Therefore, we sequenced the wood mouse genome to facilitate the acquisition of useful resources for inferring their molecular evolution...
February 2018: Data in Brief
Atsumi Hirose, Takuya Kasai, Motohide Aoki, Tomonari Umemura, Kazuya Watanabe, Atsushi Kouzuma
Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-dependent pathway to achieve high growth yield. We also show that an Arc regulatory system is involved in sensing electrode potentials and regulating the expression of catabolic genes, including those for NADH dehydrogenase...
March 14, 2018: Nature Communications
Abdullah M S Al-Hatmi, Sarah A Ahmed, Anne D van Diepeningen, Miranda Drogari-Apiranthitou, Paul E Verweij, Jacques F Meis, G Sybren de Hoog
The Fusarium solani species complex (FSSC) is the most common group of fusaria associated with superficial and life-threatening infections in humans. Here we formally introduce Fusarium metavorans sp. nov., widely known as FSSC6 (Fusarium solani species complex lineage 6), one of the most frequent agents of human opportunistic infections. The species is described with multilocus molecular data including sequences of internal transcribed spacer region (ITS), portions of the translation elongation factor 1-a gene (TEF1), and the partial RNA polymerase II gene (rPB2)...
April 1, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Tomas Strucko, Katharina Zirngibl, Filipa Pereira, Eleni Kafkia, Elsayed T Mohamed, Mandy Rettel, Frank Stein, Adam M Feist, Paula Jouhten, Kiran Raosaheb Patil, Jochen Forster
Most microbial species, including model eukaryote Saccharomyces cerevisiae, possess genetic capability to utilize many alternative nutrient sources. Yet, it remains an open question whether these manifest into assimilatory phenotypes. Despite possessing all necessary pathways, S. cerevisiae grows poorly or not at all when glycerol is the sole carbon source. Here we discover, through multiple evolved lineages, genetic determinants underlying glycerol catabolism and the associated fitness trade-offs. Most evolved lineages adapted through mutations in the HOG pathway, but showed hampered osmotolerance...
March 10, 2018: Metabolic Engineering
Andrew J Page, Alexander Wailan, Yan Shao, Kim Judge, Gordon Dougan, Elizabeth J Klemm, Nicholas R Thomson, Jacqueline A Keane
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data...
March 12, 2018: Microbial Genomics
Sathvik X Palakurty, John R Stinchcombe, Michelle E Afkhami
A mechanistic understanding of community ecology requires tackling the nonadditive effects of multispecies interactions, a challenge that necessitates integration of ecological and molecular complexity- namely moving beyond pairwise ecological interaction studies and the 'gene at a time' approach to mechanism. Here, we investigate the consequences of multispecies mutualisms for the structure and function of genome-wide differential coexpression networks for the first time, using the tractable and ecologically-important interaction between legume Medicago truncatula, rhizobia, and mycorrhizal fungi...
March 13, 2018: Molecular Ecology
Chathurika K H Hettiarachchige, Richard M Huggins
Accurate estimation of the size of animal populations is an important task in ecological science. Recent advances in the field of molecular genetics researches allow the use of genetic data to estimate the size of a population from a single capture occasion rather than repeated occasions as in the usual capture-recapture experiments. Estimating the population size using genetic data also has sometimes led to estimates that differ markedly from each other and also from classical capture-recapture estimates. Here, we develop a closed form estimator that uses genetic information to estimate the size of a population consisting of mothers and daughters, focusing on estimating the number of mothers, using data from a single sample...
March 13, 2018: Biometrical Journal. Biometrische Zeitschrift
Wilawan Thongda, Honggang Zhao, Dongdong Zhang, Lauren N Jescovitch, Ming Liu, Ximing Guo, Meagan Schrandt, Sean P Powers, Eric Peatman
Culture of the eastern oyster (Crassostrea virginica) is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. Here, we describe the development and validation of two panels of 58 single nucleotide polymorphism markers (SNPs) for the species. Population analyses revealed three distinct populations, based on FST values and STRUCTURE, among wild oysters sampled from Delaware Bay (1), northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses...
March 13, 2018: Marine Biotechnology
Michael E Alfaro, Brant C Faircloth, Richard C Harrington, Laurie Sorenson, Matt Friedman, Christine E Thacker, Carl H Oliveros, David Černý, Thomas J Near
The Cretaceous-Palaeogene (K-Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K-Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic...
March 12, 2018: Nature Ecology & Evolution
Simonetta Mattiucci, Paolo Cipriani, Arne Levsen, Michela Paoletti, Giuseppe Nascetti
This review addresses the biodiversity, biology, distribution, ecology, epidemiology, and consumer health significance of the so far known species of Anisakis, both in their natural hosts and in human accidental host populations, worldwide. These key aspects of the Anisakis species' biology are highlighted, since we consider them as main driving forces behind which most of the research in this field has been carried out over the past decade. From a public health perspective, the human disease caused by Anisakis species (anisakiasis) appears to be considerably underreported and underestimated in many countries or regions around the globe...
2018: Advances in Parasitology
Federico Sabbadin, Giovanna Pesante, Luisa Elias, Katrin Besser, Yi Li, Clare Steele-King, Meg Stark, Deborah A Rathbone, Adam A Dowle, Rachel Bates, J Reuben Shipway, Simon M Cragg, Neil C Bruce, Simon J McQueen-Mason
Lignocellulose forms the structural framework of woody plant biomass and represents the most abundant carbon source in the biosphere. Turnover of woody biomass is a critical component of the global carbon cycle, and the enzymes involved are of increasing industrial importance as industry moves away from fossil fuels to renewable carbon resources. Shipworms are marine bivalve molluscs that digest wood and play a key role in global carbon cycling by processing plant biomass in the oceans. Previous studies suggest that wood digestion in shipworms is dominated by enzymes produced by endosymbiotic bacteria found in the animal's gills, while little is known about the identity and function of endogenous enzymes produced by shipworms...
2018: Biotechnology for Biofuels
Anusree Mahanta, Piyali Ganguli, Pankaj Barah, Ram Rup Sarkar, Neelanjana Sarmah, Saurav Phukan, Mayuri Bora, Shashi Baruah
Diseases by protozoan pathogens pose a significant public health concern, particularly in tropical and subtropical countries, where these are responsible for significant morbidity and mortality. Protozoan pathogens tend to establish chronic infections underscoring their competence at subversion of host immune processes, an important component of disease pathogenesis and of their virulence. Modulation of cytokine and chemokine levels, their crosstalks and downstream signaling pathways, and thereby influencing recruitment and activation of immune cells is crucial to immune evasion and subversion...
2018: Frontiers in Immunology
John S S Denton
The mesopelagic (midwater) and deep-sea environments together comprise over 90% of the volume of the world ocean [1] and provide services that are only recently becoming recognized [2]. One of the most significant of these services relates to midwater fish biomass, recently estimated to be two orders of magnitude larger than the current worldwide fisheries catch [3, 4]. Calls to exploit midwater fish biomass have increased despite warnings about the unknown recovery potential of such organisms [2] and despite existing data suggesting that deep-sea fishes could be classified as endangered [5]...
March 3, 2018: Current Biology: CB
John S Berriman, Ryan A Ellingson, Jaymes D Awbrey, Diane M Rico, Ángel A Valdés, Nerida G Wilson, Andres Aguilar, David G Herbert, Yayoi M Hirano, Cynthia D Trowbridge, Patrick J Krug
Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates...
March 7, 2018: Molecular Phylogenetics and Evolution
Zohre Kurt, Marco Minoia, Jim C Spain
Resveratrol is among the best-known secondary plant metabolites because of its antioxidant, anti-inflammatory and anticancer properties. It also is an important allelopathic chemical widely credited with protection of plants from pathogens. The ecological role of resveratrol in natural habitats is difficult to establish rigorously because it does not seem to accumulate outside of plant tissue. It is likely that bacterial degradation plays a key role in determining the persistence, and thus the ecological role, of resveratrol in soil...
March 9, 2018: Applied and Environmental Microbiology
Sori Teshale, Dirk Geysen, Gobena Ameni, Pierre Dorny, Dirk Berkvens
BACKGROUND: As evidence of the infection of domestic animals by Anaplasma phagocytophilum and Anaplasma sp. 'Omatjenne' is presently becoming available, understanding the epidemiological and ecological significance of infection is important to quantify the clinical and socio-economic impact of the diseases they cause. METHODS: The first aim of this study was to analyse the occurrence of A. phagocytophilum and Anaplasma sp. 'Omatjenne' in cattle samples collected from selected African countries using a polymerase chain reaction and restriction enzyme fragment length polymorphism...
March 9, 2018: Parasites & Vectors
Hui Wang, Shuangfei Zhang, Amit Pratush, Xueying Ye, Jinli Xie, Huan Wei, Chongran Sun, Zhong Hu
The phylogenetic diversity of bacterial communities in response to environmental disturbances such as organic pollution has been well studied, but little is known about the way in which organic contaminants influence the acclimation of functional bacteria. In the present study, tolerance assays for bacterial communities from the sediment in the Pearl River Estuary were conducted with the isolation of functional bacteria using pyrene and different estrogens as environmental stressors. Molecular ecological networks and phylogenetic trees were constructed using both 16S rRNA gene sequences of cultured bacterial strains and 16S rRNA gene-based pyrosequencing data to illustrate the successions of bacterial communities and their acclimations to the different organic compounds...
2018: Frontiers in Microbiology
Carson Holt, Michael Campbell, David A Keays, Nathaniel Edelman, Aurélie Kapusta, Emily Maclary, Eric Domyan, Alexander Suh, Wesley C Warren, Mark Yandell, M Thomas P Gilbert, Michael D Shapiro
The domestic rock pigeon ( Columba livia ) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general...
March 8, 2018: G3: Genes—Genomes—Genetics
Aud H Halbritter, Simone Fior, Irene Keller, Regula Billeter, Peter Edwards, Rolf Holderegger, Sophie Karrenberg, Andrea R Pluess, Alex Widmer, Jake M Alexander
Studies of genetic adaptation in plant populations along elevation gradients in mountains have a long history, but there has until now been neither a synthesis of how frequently plant populations exhibit adaptation to elevation nor an evaluation of how consistent underlying trait differences across species are. We reviewed studies of adaptation along elevation gradients (i) from a meta-analysis of phenotypic differentiation of three traits (height, biomass and phenology) from plants growing in 70 common garden experiments; (ii) by testing elevation adaptation using three fitness proxies (survival, reproductive output and biomass) from 14 reciprocal transplant experiments; (iii) by qualitatively assessing information at the molecular level, from ten genome-wide surveys and candidate gene approaches...
March 8, 2018: Journal of Evolutionary Biology
Wenfang Dai, Weina Yu, Lixia Xuan, Zhen Tao, Jinbo Xiong
It is now recognized that some gut diseases attribute to polymicrobial pathogens infections. Thus, traditional isolation of single pathogen from disease subjects could bias the identification of causal agents. To fill this gap, using Illumina sequencing of the bacterial 16S rRNA gene, we explored the dynamics of gut bacterial communities over a shrimp disease progression. The results showed significant differences in the gut bacterial communities between healthy and diseased shrimp. Potential pathogens were inferred by a local pathogens database, of which two OTUs (affiliated with Vibrio tubiashii and Vibrio harveyi) exhibited significantly higher abundances in diseased shrimp as compared to healthy subjects...
March 7, 2018: Applied Microbiology and Biotechnology
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