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Original Article
| Open AccessSticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling
- Jiro F Mori
- , Nico Ueberschaar
- & Kirsten Küsel
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Original Article |
Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands
- Julia Kyaschenko
- , Karina E Clemmensen
- & Björn D Lindahl
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Original Article |
Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen-limited Chlamydomonas
- Jasmin Krismer
- , Manu Tamminen
- & Anita Narwani
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Original Article |
Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics
- Freya Mosbæk
- , Henrik Kjeldal
- & Jeppe L Nielsen
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Perspective
| Open AccessEngineering microbial consortia for controllable outputs
- Stephen R Lindemann
- , Hans C Bernstein
- & Alexander S Beliaev
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Original Article |
Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children
- Jing Cheng
- , Tamar Ringel-Kulka
- & Reetta Satokari
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Original Article
| Open AccessMassively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers
- Sarah J Spencer
- , Manu V Tamminen
- & Eric J Alm
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Short Communication |
16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies
- Matthew Perisin
- , Madlen Vetter
- & Joy Bergelson
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Original Article |
Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves
- Florian Ryffel
- , Eric JN Helfrich
- & Julia A Vorholt
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Original Article |
Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils
- Hilary T C Leung
- , Kendra R Maas
- & William W Mohn
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Short Communication
| Open AccessIn situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice
- Christiane Uhlig
- , Fabian Kilpert
- & Bánk Beszteri
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Original Article |
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution
- Joran Martijn
- , Frederik Schulz
- & Thijs J G Ettema
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Original Article |
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification
- Marius Vital
- , Benli Chai
- & James M Tiedje
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Original Article |
Water fleas require microbiota for survival, growth and reproduction
- Marilou P Sison-Mangus
- , Alexandra A Mushegian
- & Dieter Ebert
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Original Article
| Open AccessGenome-wide analysis of Sphingomonas wittichii RW1 behaviour during inoculation and growth in contaminated sand
- Silvia K Moreno-Forero
- & Jan Roelof van der Meer
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Original Article |
Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes
- Kevin C-Y Lee
- , Xochitl C Morgan
- & Matthew B Stott
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Original Article |
A microarray for assessing transcription from pelagic marine microbial taxa
- Irina N Shilova
- , Julie C Robidart
- & Jonathan P Zehr
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Original Article |
Ecogenomic sensor reveals controls on N2-fixing microorganisms in the North Pacific Ocean
- Julie C Robidart
- , Matthew J Church
- & Jonathan P Zehr
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Original Article |
Ecological succession among iron-oxidizing bacteria
- Emily J Fleming
- , Ivona Cetinić
- & David Emerson
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Original Article |
In and out: an analysis of epibiotic vs periplasmic bacterial predators
- Z Pasternak
- , M Njagi
- & E Jurkevitch
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Original Article |
Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method
- Yuya Tada
- & Hans-Peter Grossart
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Original Article |
Genome-wide analysis of lysine catabolism in bacteria reveals new connections with osmotic stress resistance
- Izabella AP Neshich
- , Eduardo Kiyota
- & Paulo Arruda
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Original Article |
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
- Yong-Jin Lee
- , Joy D van Nostrand
- & Jizhong Zhou
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Original Article |
Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits
- David Goudenège
- , Yannick Labreuche
- & Frédérique Le Roux
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Original Article |
The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis
- Adam C-N Wong
- , John M Chaston
- & Angela E Douglas
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Original Article |
Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges
- Jason N Woodhouse
- , Lu Fan
- & Brett A Neilan
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Original Article |
Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi
- Otso Ovaskainen
- , Dmitry Schigel
- & Jenni Nordén
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Original Article |
Microbial metabolic exchange in 3D
- Jeramie D Watrous
- , Vanessa V Phelan
- & Pieter C Dorrestein
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Original Article |
Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study
- Charles Bachy
- , John R Dolan
- & David Moreira
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Original Article
| Open AccessTargeted recovery of novel phylogenetic diversity from next-generation sequence data
- Michael D J Lynch
- , Andrea K Bartram
- & Josh D Neufeld
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Original Article |
Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis
- Thomas Danhorn
- , Curtis R Young
- & Edward F DeLong
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Short Communication
| Open AccessUltra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
- J Gregory Caporaso
- , Christian L Lauber
- & Rob Knight
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Original Article |
Reproducibility and quantitation of amplicon sequencing-based detection
- Jizhong Zhou
- , Liyou Wu
- & Yunfeng Yang
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Original Article |
Complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea
- Céline Brochier-Armanet
- , Philippe Deschamps
- & David Moreira
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Original Article |
Capturing diversity of marine heterotrophic protists: one cell at a time
- Jane L Heywood
- , Michael E Sieracki
- & Ramunas Stepanauskas
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Original Article |
Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time
- Edward K Hall
- , Gabriel A Singer
- & Tom J Battin
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Original Article |
Competitive interactions in Escherichia coli populations: the role of bacteriocins
- Hadeel Majeed
- , Osnat Gillor
- & Margaret A Riley
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Short Communication |
Succession of methanotrophs in oxygen–methane counter-gradients of flooded rice paddies
- Sascha Krause
- , Claudia Lüke
- & Peter Frenzel
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Short Communication |
Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations
- Suzan Yilmaz
- , Mohamed F Haroon
- & Philip Hugenholtz
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Original Article |
GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity
- Zhili He
- , Ye Deng
- & Jizhong Zhou
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Original Article |
Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA
- Jon Bråte
- , Ramiro Logares
- & Kamran Shalchian-Tabrizi
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Original Article |
Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing
- Rohit Ghai
- , Ana-Belén Martin-Cuadrado
- & Francisco Rodriguez-Valera
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Commentary |
Further limitations of phylogenetic group-specific probes used for detection of bacteria in environmental samples
- Jeremy J Barr
- , Linda L Blackall
- & Philip Bond
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Original Article |
Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species
- Wai Ling Chow
- , Dan Cheng
- & Jianzhong He
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Original Article |
Bacterial diversity in rhizosphere soil from Antarctic vascular plants of Admiralty Bay, maritime Antarctica
- Lia C R S Teixeira
- , Raquel S Peixoto
- & Alexandre S Rosado
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Original Article |
Bacterial diversity in the oral cavity of 10 healthy individuals
- Elisabeth M Bik
- , Clara Davis Long
- & David A Relman
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Original Article |
PANGEA: pipeline for analysis of next generation amplicons
- Adriana Giongo
- , David B Crabb
- & Eric W Triplett
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Original Article |
Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere
- Claudia Knief
- , Alban Ramette
- & Julia A Vorholt
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