Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

Lifestyle adaptations ofRhizobiumfrom rhizosphere to symbiosis

(2020) Rachel M. Wheatley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Sparse Compositional Technique Reveals Microbial Perturbations

(2019) Cameron Martino et al.   mSystems

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Rhizobia: from saprophytes to endosymbionts

(2018) Philip Poole et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

(2018) Petra Pjevac et al.   Frontiers in Microbiology

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Regulation of benthic oxygen fluxes in permeable sediments of the coastal ocean

(2017) Soeren Ahmerkamp et al.   LIMNOLOGY AND OCEANOGRAPHY

Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria

(2017) Hongwei Liu et al.   Frontiers in Microbiology

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Plant growth-promoting bacterial endophytes

(2016) Gustavo Santoyo et al.   MICROBIOLOGICAL RESEARCH

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

High rates of microbial dinitrogen fixation and sulfate reduction associated with the Mediterranean seagrass Posidonia oceanica

(2016) Nadine Lehnen et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Methane Seep in Shallow-Water Permeable Sediment Harbors High Diversity of Anaerobic Methanotrophic Communities, Elba, Italy

(2016) S. Emil Ruff et al.   Frontiers in Microbiology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

(2016) Jillian M. Petersen et al.   Nature Microbiology

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

(2015) Danilo J. P. Rocha et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Microbiomes of Streptophyte Algae and Bryophytes Suggest That a Functional Suite of Microbiota Fostered Plant Colonization of Land

(2015) J. J. Knack et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria

(2015) Sebastiàn Lòpez-Fernàndez et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

The Contamination of Commercial 15N2 Gas Stocks with 15N–Labeled Nitrate and Ammonium and Consequences for Nitrogen Fixation Measurements

(2014) Richard Dabundo et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The effect of FISH and CARD-FISH on the isotopic composition of 13C- and 15N-labeled Pseudomonas putida cells measured by nanoSIMS

(2014) Niculina Musat et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Biological nitrogen fixation in non-legume plants

(2013) Carole Santi et al.   ANNALS OF BOTANY

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Terminator still moving forward: expanding roles for Rho factor

(2013) Marc Boudvillain et al.   CURRENT OPINION IN MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Out with the old and in with the new: rapid specimen preparation procedures for electron microscopy of sectioned biological material

(2013) Kent L. McDonald   PROTOPLASMA

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Effects of transient bottom water currents and oxygen concentrations on benthic exchange rates as assessed by eddy correlation measurements

(2013) Moritz Holtappels et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Look@NanoSIMS - a tool for the analysis of nanoSIMS data in environmental microbiology

(2012) Lubos Polerecky et al.   ENVIRONMENTAL MICROBIOLOGY

Seagrass ecosystems as a globally significant carbon stock

(2012) James W. Fourqurean et al.   Nature Geoscience

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Unicellular Cyanobacterium Symbiotic with a Single-Celled Eukaryotic Alga

(2012) A. W. Thompson et al.   SCIENCE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

A blueprint for blue carbon: toward an improved understanding of the role of vegetated coastal habitats in sequestering CO2

(2011) Elizabeth Mcleod et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization

(2010) Devon Metcalf et al.   ANAEROBE

The value of estuarine and coastal ecosystem services

(2010) Edward B. Barbier et al.   ECOLOGICAL MONOGRAPHS

Seagrass community metabolism: Assessing the carbon sink capacity of seagrass meadows

(2010) Carlos M. Duarte et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Celerinatantimonas diazotrophica gen. nov., sp. nov., a nitrogen-fixing bacterium representing a new family in the Gammaproteobacteria, Celerinatantimonadaceae fam. nov.

(2010) M. J. Cramer et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Application of Oxygen Eddy Correlation in Aquatic Systems

(2010) Claudia Lorrai et al.   JOURNAL OF ATMOSPHERIC AND OCEANIC TECHNOLOGY

Double Labeling of Oligonucleotide Probes for Fluorescence In Situ Hybridization (DOPE-FISH) Improves Signal Intensity and Increases rRNA Accessibility

(2009) K. Stoecker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pathway of  -Aminobutyrate Metabolism in Rhizobium leguminosarum 3841 and Its Role in Symbiosis

(2009) J. Prell et al.   JOURNAL OF BACTERIOLOGY

Accelerating loss of seagrasses across the globe threatens coastal ecosystems

(2009) M. Waycott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Pectin structure and biosynthesis

(2008) D MOHNEN   CURRENT OPINION IN PLANT BIOLOGY

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)

(2008) M. Martens et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Properties of bacterial endophytes and their proposed role in plant growth

(2008) Pablo R. Hardoim et al.   TRENDS IN MICROBIOLOGY