Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Bacterial succession during 500 years of soil development under agricultural use

(2012) Jun Cui et al.   ECOLOGICAL RESEARCH

Cultivation of a highly enriched ammonia-oxidizing archaeon of thaumarchaeotal group I.1b from an agricultural soil

(2012) Jong-Geol Kim et al.   ENVIRONMENTAL MICROBIOLOGY

Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae

(2012) O. A. Podosokorskaya et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Effect of Genetically Modified Poplars on Soil Microbial Communities during the Phytoremediation of Waste Mine Tailings

(2011) Moonsuk Hur et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils

(2011) Huaiying Yao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

(2011) Andrea Bannert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Effect of long-term fertilization on bacterial composition in rice paddy soil

(2011) Minna Wu et al.   BIOLOGY AND FERTILITY OF SOILS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

Spotlight on the Thaumarchaeota

(2011) C Brochier-Armanet et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Differentiated Response of Denitrifying Communities to Fertilization Regime in Paddy Soil

(2011) Zhe Chen et al.   MICROBIAL ECOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in Northeast China

(2010) Ju-Pei Shen et al.   APPLIED SOIL ECOLOGY

Community level functional diversity and enzyme activities in paddy soils under different long-term fertilizer management practices

(2010) Md. Rashedul Islam et al.   BIOLOGY AND FERTILITY OF SOILS

The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer

(2010) Jongsik Chun et al.   BMC MICROBIOLOGY

Archaea rather than bacteria control nitrification in two agricultural acidic soils

(2010) Cécile Gubry-Rangin et al.   FEMS MICROBIOLOGY ECOLOGY

Biogeochemistry of paddy soils

(2010) Ingrid Kögel-Knabner et al.   GEODERMA

Methanocella arvoryzae sp. nov., a hydrogenotrophic methanogen isolated from rice field soil

(2010) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

Temporal Dynamics of Bacterial and Fungal Communities in a Genetically Modified (GM) Rice Ecosystem

(2010) Seung-Hoon Lee et al.   MICROBIAL ECOLOGY

Vertical changes in bacterial and archaeal communities with soil depth in Japanese paddy fields

(2010) Takeshi WATANABE et al.   SOIL SCIENCE AND PLANT NUTRITION

Methanogenic archaeal communities in paddy field soils in north-east China as evaluated by PCR-DGGE, sequencing and real-time PCR analyses

(2010) Guanghua WANG et al.   SOIL SCIENCE AND PLANT NUTRITION

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional and structural response of the methanogenic microbial community in rice field soil to temperature change

(2009) Ralf Conrad et al.   ENVIRONMENTAL MICROBIOLOGY

Microcalorimetric assessment of microbial activity in long-term fertilization experimental soils of Southern China

(2009) Bocar Ahamadou et al.   FEMS MICROBIOLOGY ECOLOGY

Acidiplasma aeolicum gen. nov., sp. nov., a euryarchaeon of the family Ferroplasmaceae isolated from a hydrothermal pool, and transfer of Ferroplasma cupricumulans to Acidiplasma cupricumulans comb. nov.

(2009) O. V. Golyshina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling

(2008) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria

(2008) Graeme W. Nicol et al.   ENVIRONMENTAL MICROBIOLOGY

Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy

(2008) Jørn Einen et al.   FEMS MICROBIOLOGY LETTERS

Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.

(2008) S. Sakai et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota

(2008) Céline Brochier-Armanet et al.   NATURE REVIEWS MICROBIOLOGY

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization

(2008) Yanan Wang et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Comparison of bacterial community structures at main habitats in paddy field ecosystem based on DGGE analysis

(2007) Susumu Asakawa et al.   SOIL BIOLOGY & BIOCHEMISTRY