Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation

[1]  D. Daffonchio,et al.  The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature‐based solutions for mangroves , 2023, Microbial biotechnology.

[2]  D. Daffonchio,et al.  Morphological characteristics and abundance of prokaryotes associated with gills in mangrove brachyuran crabs living along a tidal gradient , 2022, PloS one.

[3]  M. Medema,et al.  Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure , 2021, bioRxiv.

[4]  D. Daffonchio,et al.  Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees , 2021, NPJ biofilms and microbiomes.

[5]  D. Daffonchio,et al.  Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline , 2021, The ISME Journal.

[6]  P. Wilmes,et al.  Homogeneous selection promotes microdiversity in the glacier-fed stream microbiome , 2020, bioRxiv.

[7]  R. Irizarry ggplot2 , 2019, Introduction to Data Science.

[8]  D. Daffonchio,et al.  Developmental stages and gut microenvironments influence gut microbiota dynamics in the invasive beetle Popillia japonica Newman (Coleoptera: Scarabaeidae). , 2019, Environmental microbiology.

[9]  D. Daffonchio,et al.  The role of fungi in heterogeneous sediment microbial networks , 2019, Scientific Reports.

[10]  James T. Morton,et al.  Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales of ecological data , 2019, Ecological Monographs.

[11]  D. Daffonchio,et al.  Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions , 2019, Scientific Reports.

[12]  J. B. Vicente,et al.  Hydrogen Sulfide Oxidation: Adaptive Changes in Mitochondria of SW480 Colorectal Cancer Cells upon Exposure to Hypoxia , 2019, Oxidative medicine and cellular longevity.

[13]  Shen Jean Lim,et al.  Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species , 2018, The ISME Journal.

[14]  R. Jeewon,et al.  Metatranscriptomics analysis of mangroves habitats around Mauritius , 2018, World journal of microbiology & biotechnology.

[15]  N. Dubilier,et al.  Metaorganisms in extreme environments: do microbes play a role in organismal adaptation? , 2018, Zoology.

[16]  C. Duarte,et al.  Carbon Dioxide and Methane Emissions from Red Sea Mangrove Sediments , 2018 .

[17]  D. Daffonchio,et al.  The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence , 2018, The ISME Journal.

[18]  U. Stingl,et al.  Genomic diversification of giant enteric symbionts reflects host dietary lifestyles , 2017, Proceedings of the National Academy of Sciences.

[19]  R. Naderloo Atlas of Crabs of the Persian Gulf , 2017 .

[20]  B. Bergman,et al.  High abundance and expression of transposases in bacteria from the Baltic Sea , 2017, The ISME Journal.

[21]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[22]  G. Flik,et al.  Branchial nitrogen cycle symbionts can remove ammonia in fish gills. , 2016, Environmental microbiology reports.

[23]  E. Li,et al.  Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water , 2016, PloS one.

[24]  B. Bohannan,et al.  Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development , 2015, The ISME Journal.

[25]  D. Daffonchio,et al.  Thermal specialization across large geographical scales predicts the resilience of mangrove crab populations to global warming , 2015 .

[26]  M. Georgieff,et al.  Sulfide-inhibition of mitochondrial respiration at very low oxygen concentrations. , 2014, Nitric oxide : biology and chemistry.

[27]  H. Pörtner,et al.  Improved heat tolerance in air drives the recurrent evolution of air-breathing , 2014, Proceedings of the Royal Society B: Biological Sciences.

[28]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[29]  B. Jørgensen,et al.  Succession of cable bacteria and electric currents in marine sediment , 2014, The ISME Journal.

[30]  Vladimir B. Bajic,et al.  INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles , 2013, PloS one.

[31]  Susumu Goto,et al.  Data, information, knowledge and principle: back to metabolism in KEGG , 2013, Nucleic Acids Res..

[32]  A. Tanguy,et al.  Endosymbiotic bacteria in the bivalve Loripes lacteus: Localization, characterization and aspects of symbiont regulation , 2013 .

[33]  S. Ōmura,et al.  Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand. , 2013, International journal of systematic and evolutionary microbiology.

[34]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[35]  H. Horikawa,et al.  Complete genome sequence of Ilumatobacter coccineum YM16-304T , 2013, Standards in genomic sciences.

[36]  Manesh Shah,et al.  Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts , 2013, mBio.

[37]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[38]  Anke Schmitz,et al.  Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky. , 2013, Comprehensive Physiology.

[39]  M. L. Negreiros-Fransozo,et al.  Morphological diversity of setae on the second maxilliped of fiddler crabs (Decapoda: Ocypodidae) from the southwestern Atlantic coast , 2013 .

[40]  B. Vanhoorne,et al.  World Register of Marine Species , 2013 .

[41]  C. A. Soares,et al.  Boronated tartrolon antibiotic produced by symbiotic cellulose-degrading bacteria in shipworm gills , 2013, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[43]  H. Onken,et al.  Multiple functions of the crustacean gill: osmotic/ionic regulation, acid-base balance, ammonia excretion, and bioaccumulation of toxic metals , 2012, Front. Physio..

[44]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[45]  H. Olff,et al.  A Three-Stage Symbiosis Forms the Foundation of Seagrass Ecosystems , 2012, Science.

[46]  J. Adams,et al.  The effects of environmental variables on mortality and growth of mangroves at Mngazana Estuary, Eastern Cape, South Africa , 2012, Wetlands Ecology and Management.

[47]  J. Adams,et al.  The effects of environmental variables on mortality and growth of mangroves at Mngazana Estuary, Eastern Cape, South Africa , 2012, Wetlands Ecology and Management.

[48]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[49]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[50]  M. Grube,et al.  Age, sun and substrate: triggers of bacterial communities in lichens. , 2012, Environmental microbiology reports.

[51]  D. Warton,et al.  Distance‐based multivariate analyses confound location and dispersion effects , 2012 .

[52]  M. McFall-Ngai,et al.  Metaorganisms as the new frontier. , 2011, Zoology.

[53]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[54]  Campbell O. Webb,et al.  Picante: R tools for integrating phylogenies and ecology , 2010, Bioinform..

[55]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[56]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[57]  Robert A. Edwards,et al.  Transposases are the most abundant, most ubiquitous genes in nature , 2010, Nucleic acids research.

[58]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[59]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[60]  R. Manasrah,et al.  Spatial and seasonal variations of sea level in the Red Sea, 1958–2001 , 2009 .

[61]  W. Verstraete,et al.  Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. , 2009, FEMS microbiology reviews.

[62]  M. Grube,et al.  Species-specific structural and functional diversity of bacterial communities in lichen symbioses , 2009, The ISME Journal.

[63]  Warren W. Burggren,et al.  Biology of the Land Crabs , 2009 .

[64]  M. Mulvey,et al.  Bacterial landlines: contact-dependent signaling in bacterial populations. , 2009, Current opinion in microbiology.

[65]  Mathieu Bastian,et al.  Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.

[66]  E. Cabré,et al.  Adalimumab-induced lupus erythematosus in Crohn's disease patients previously treated with infliximab. , 2008, Gut.

[67]  Sébastien Lê,et al.  FactoMineR: An R Package for Multivariate Analysis , 2008 .

[68]  Eduardo P C Rocha,et al.  Causes of insertion sequences abundance in prokaryotic genomes. , 2007, Molecular biology and evolution.

[69]  D. Alongi,et al.  Control by fiddler crabs (Uca vocans) and plant roots (Avicennia marina) on carbon, iron, and sulfur biogeochemistry in mangrove sediment , 2006 .

[70]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[71]  Laura S. Frost,et al.  Mobile genetic elements: the agents of open source evolution , 2005, Nature Reviews Microbiology.

[72]  D. Towle,et al.  Ammonia excretion in aquatic and terrestrial crabs , 2004, Journal of Experimental Biology.

[73]  N. Lo,et al.  A symbiont of the tick Ixodes ricinus invades and consumes mitochondria in a mode similar to that of the parasitic bacterium Bdellovibrio bacteriovorus. , 2004, Tissue & cell.

[74]  J. Maina,et al.  Structure, function and evolution of the gas exchangers: comparative perspectives , 2002, Journal of anatomy.

[75]  D. Towle,et al.  Active ammonia excretion across the gills of the green shore crab Carcinus maenas: participation of Na(+)/K(+)-ATPase, V-type H(+)-ATPase and functional microtubules. , 2002, The Journal of experimental biology.

[76]  N. Koedam,et al.  Mangrove species zonation and soil redox state, sulphide concentration and salinity in Gazi Bay (Kenya), a preliminary study , 1999 .

[77]  Peter Saenger,et al.  Redox stratification and heavy metal partitioning in Avicennia-dominated mangrove sediments: a geochemical model , 1998 .

[78]  J. Levinton,et al.  Molecular phylogeny analysis of fiddler crabs: test of the hypothesis of increasing behavioral complexity in evolution. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[79]  J. Kitheka,et al.  Water circulation dynamics, water column nutrients and plankton productivity in a well-flushed tropical bay in Kenya , 1996 .

[80]  P. Wright Nitrogen excretion: three end products, many physiological roles. , 1995, The Journal of experimental biology.

[81]  D. A. Hudson,et al.  Parasites and symbionts of wild mud crabs Scylla serrata (Forskal) of potential significance in aquaculture , 1994 .

[82]  R. Amann,et al.  Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations , 1990, Applied and environmental microbiology.

[83]  Ronald D. Jones,et al.  Cycling of methane, carbon monoxide, nitrous oxide, and hydroxylamine in a meromictic, coastal lagoon , 1988 .

[84]  C. Farrelly,et al.  The morphology and vasculature of the lungs and gills of the soldier crab, Mictyris longicarpus , 1987, Journal of morphology.

[85]  D. Maitland Crabs that breathe air with their legs-Scopimera and Dotilla , 1986, Nature.

[86]  J. Christy,et al.  ECOLOGY AND EVOLUTION OF MATING SYSTEMS OF FIDDLER CRABS (GENUS UCA) , 1984 .

[87]  C. Little The Colonisation of Land: Origins and Adaptations of Terrestrial Animals , 1984 .

[88]  A. Farrell,et al.  The Evolution of Air Breathing in Vertebrates , 1981 .

[89]  L. Powers,et al.  Temperature variation in fiddler crab microhabitats , 1976 .

[90]  A. Lugo,et al.  The Ecology of Mangroves , 1974 .

[91]  Peter H. A. Sneath,et al.  Numerical Taxonomy: The Principles and Practice of Numerical Classification , 1973 .

[92]  R. P. Forster,et al.  Urea biosynthesis in the South American lungfish, Lepidosiren paradoxa: relation to its ecology. , 1972, Comparative biochemistry and physiology. A, Comparative physiology.

[93]  D. Bliss,et al.  Adaptations of Crustaceans to Land: A Summary and Analysis of New Findings , 1968 .

[94]  Akshay Chandra Dey,et al.  Worms , 1919, The Indian medical gazette.

[95]  Pringl Miller,et al.  Red Sea. , 2019, Journal of palliative medicine.

[96]  I. F. Stewart,et al.  The Red Sea: The Formation, Morphology, Oceanography and Environment of a Young Ocean Basin , 2015 .

[97]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[98]  H. Shih,et al.  SYSTEMATICS OF THE INDO-WEST PACIFIC BROAD-FRONTED FIDDLER CRABS (CRUSTACEA: OCYPODIDAE: GENUS UCA) , 2013 .

[99]  Robert C. Edgar,et al.  Search and clustering orders of magnitude faster than BLAST , 2010 .

[100]  Andy Liaw,et al.  Classification and Regression by randomForest , 2007 .

[101]  He Fuchu,et al.  Integrated nr Database in Protein Annotation System and Its Localization , 2006 .

[102]  K. Choe,et al.  The multifunctional fish gill: dominant site of gas exchange, osmoregulation, acid-base regulation, and excretion of nitrogenous waste. , 2005, Physiological reviews.

[103]  R. Hill,et al.  Novel actinobacteria from marine sponges , 2004, Antonie van Leeuwenhoek.

[104]  T. Naruse,et al.  A FIRST FOSSIL RECORD OF THE TERRESTRIAL CRAB, GEOTHELPHUSA TENUIMANUS (MIYAKE & MINEI, 1965) (DECAPODA, BRACHYURA, POTAMIDAE) FROM OKINAWA ISLAND, CENTRAL RYUKYUS, JAPAN , 2003 .

[105]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[106]  C. Thurman Evaporative water loss, corporal temperature and the distribution of sympatric fiddler crabs (Uca) from south Texas. , 1998, Comparative biochemistry and physiology. Part A, Molecular & integrative physiology.

[107]  R. Amann,et al.  Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. , 1993, Cytometry.

[108]  C. Little The Terrestrial Invasion: An Ecophysiological Approach to the Origins of Land Animals , 1990 .

[109]  P. Sneath,et al.  Numerical Taxonomy , 1962, Nature.

[110]  Ying Gao,et al.  Bioinformatics Applications Note Sequence Analysis Cd-hit Suite: a Web Server for Clustering and Comparing Biological Sequences , 2022 .