Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

Diversity of KaiC-based timing systems in marine Cyanobacteria

(2014) Ilka M. Axmann et al.   Marine Genomics

CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity

(2014) Rodolphe Barrangou et al.   MOLECULAR CELL

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

Microbial Contributions to Phosphorus Cycling in Eutrophic Lakes and Wastewater

(2013) Katherine D. McMahon et al.   Annual Review of Microbiology

Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

(2013) Chih-Ying Lay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

High-precision characterization of individualE. colicell morphology by scanning flow cytometry

(2013) Anastasiya I. Konokhova et al.   CYTOMETRY PART A

Programmed cell death in the marine cyanobacterium Trichodesmium mediates carbon and nitrogen export

(2013) Edo Bar-Zeev et al.   ISME Journal

Microbial biodiversity in glacier-fed streams

(2013) Linda Wilhelm et al.   ISME Journal

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust

(2013) Lara Rajeev et al.   ISME Journal

Dissecting genomic diversity, one cell at a time

(2013) Paul C Blainey et al.   NATURE METHODS

Metabolic potential of lithifying cyanobacteria-dominated thrombolitic mats

(2013) Jennifer M. Mobberley et al.   PHOTOSYNTHESIS RESEARCH

Effect of Temperature on Photosynthesis and Growth in Marine Synechococcus spp.

(2013) K. R. M. Mackey et al.   PLANT PHYSIOLOGY

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus

(2013) P. Flombaum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

(2013) A. Kampa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont

(2013) Jason A. Hilton et al.   Nature Communications

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

(2013) Luke R. Thompson et al.   Ecology and Evolution

Expanding the Marine Virosphere Using Metagenomics

(2013) Carolina Megumi Mizuno et al.   PLoS Genetics

The epsomitic phototrophic microbial mat of Hot Lake, Washington: community structural responses to seasonal cycling

(2013) Stephen R. Lindemann et al.   Frontiers in Microbiology

Synthetic biology of cyanobacteria: unique challenges and opportunities

(2013) Bertram M. Berla et al.   Frontiers in Microbiology

Separation of bacteria with imprinted polymeric films

(2012) Romana Schirhagl et al.   ANALYST

Comparative Metagenomics of Two Microbial Mats at Cuatro Ciénegas Basin II: Community Structure and Composition in Oligotrophic Environments

(2012) Germán Bonilla-Rosso et al.   ASTROBIOLOGY

Dual purpose microalgae–bacteria-based systems that treat wastewater and produce biodiesel and chemical products within a Biorefinery

(2012) Eugenia J. Olguín   BIOTECHNOLOGY ADVANCES

Denoising PCR-amplified metagenome data

(2012) Michael J Rosen et al.   BMC BIOINFORMATICS

Bacterial composition of microbial mats in hot springs in Northern Patagonia: variations with seasons and temperature

(2012) Roy Mackenzie et al.   EXTREMOPHILES

Viral clones from the GOS expedition with an unusual photosystem-I gene cassette organization

(2012) Oded Béjà et al.   ISME Journal

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis

(2012) Rex R Malmstrom et al.   ISME Journal

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics

(2012) Luke C Burow et al.   ISME Journal

Novel Miniature Transposable Elements in Thermophilic Synechococcus Strains and Their Impact on an Environmental Population

(2012) W. C. Nelson et al.   JOURNAL OF BACTERIOLOGY

Ecological and evolutionary genomics of marine photosynthetic organisms

(2012) Susana M. Coelho et al.   MOLECULAR ECOLOGY

Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation

(2012) D. M. Karl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative single-cell characterization of bacterial interactions reveals type VI secretion is a double-edged sword

(2012) M. LeRoux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level

(2012) Stephan Binder et al.   GENOME BIOLOGY

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

Genomic Analysis at the Single-Cell Level

(2011) Tomer Kalisky et al.   Annual Review of Genetics

Metagenomic Analysis of Stress Genes in Microbial Mat Communities from Antarctica and the High Arctic

(2011) Thibault Varin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exopolysaccharide-producing cyanobacteria in heavy metal removal from water: molecular basis and practical applicability of the biosorption process

(2011) Roberto De Philippis et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Cyanobacterial genomics for ecology and biotechnology

(2011) Wolfgang R Hess   CURRENT OPINION IN MICROBIOLOGY

The biosynthesis of cyanobacterial sunscreen scytonemin in intertidal microbial mat communities

(2011) Emily P. Balskus et al.   FEMS MICROBIOLOGY ECOLOGY

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton

(2011) Manuel Martinez-Garcia et al.   ISME Journal

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

(2011) Christian G Klatt et al.   ISME Journal

Unraveling Cyanobacteria Ecology in Wastewater Treatment Plants (WWTP)

(2011) Joana Martins et al.   MICROBIAL ECOLOGY

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage

(2011) Rashel V. Grindberg et al.   PLoS One

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis

(2011) M. S. Donia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering cyanobacteria to generate high-value products

(2011) Daniel C. Ducat et al.   TRENDS IN BIOTECHNOLOGY

Determining cell shape: adaptive regulation of cyanobacterial cellular differentiation and morphology

(2011) Shailendra P. Singh et al.   TRENDS IN MICROBIOLOGY

Bacterial epidemiology and biology - lessons from genome sequencing

(2011) Julian Parkhill et al.   GENOME BIOLOGY

Whole gene amplification and protein separation from a few cells

(2010) Bor-han Chueh et al.   ANALYTICAL BIOCHEMISTRY

Microfluidic Platforms for Single-Cell Analysis

(2010) Richard N. Zare et al.   Annual Review of Biomedical Engineering

Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity amongSynechococcusPopulations in an Alkaline Siliceous Hot Spring Microbial Mat

(2010) Melanie C. Melendrez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Single-cell analysis and isolation for microbiology and biotechnology: methods and applications

(2010) Satoshi Ishii et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Fabrication of microfluidic devices using polydimethylsiloxane

(2010) James Friend et al.   Biomicrofluidics

Recent advances in DNA sequencing methods – general principles of sample preparation

(2010) Sten Linnarsson   EXPERIMENTAL CELL RESEARCH

Biogeography of thermophilic cyanobacteria: insights from the Zerka Ma'in hot springs (Jordan)

(2010) Danny Ionescu et al.   FEMS MICROBIOLOGY ECOLOGY

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

(2010) Maria R Gomez-Garcia et al.   ISME Journal

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

(2010) Yanmei Shi et al.   ISME Journal

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

(2010) M. T. J. van der Meer et al.   JOURNAL OF BACTERIOLOGY

Digital MDA for enumeration of total nucleic acid contamination

(2010) P. C. Blainey et al.   NUCLEIC ACIDS RESEARCH

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

(2010) William P. Inskeep et al.   PLoS One

Improvement of  29 DNA polymerase amplification performance by fusion of DNA binding motifs

(2010) M. de Vega et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering cyanobacteria for fuels and chemicals production

(2010) Jie Zhou et al.   Protein & Cell

Ecological Genomics of Marine Picocyanobacteria

(2009) D. J. Scanlan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Photosystem I gene cassettes are present in marine virus genomes

(2009) Itai Sharon et al.   NATURE

Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes

(2009) John F. Heidelberg et al.   PLoS One

Assembling the Marine Metagenome, One Cell at a Time

(2009) Tanja Woyke et al.   PLoS One

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Characterization of the Interactions of Lysozyme with DNA by Surface Plasmon Resonance and Circular Dichroism Spectroscopy

(2008) Kuo-Chih Lin et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

CandidatusDesulfovibrio trichonymphae, a novel intracellular symbiont of the flagellateTrichonympha agilisin termite gut

(2008) Tomoyuki Sato et al.   ENVIRONMENTAL MICROBIOLOGY

Phosphorus Deprivation Responses and Phosphonate Utilization in a Thermophilic Synechococcus sp. from Microbial Mats

(2008) M. M. Adams et al.   JOURNAL OF BACTERIOLOGY

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments

(2008) Jonathan Kennedy et al.   Microbial Cell Factories

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy

(2008) Bruce E. Rittmann et al.   NATURE REVIEWS MICROBIOLOGY

Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell

(2008) Y. Hongoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA