Organic Amendments in a Long-term Field Trial—Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics

(2017) Francis Cheng-Hsuan Weng et al.   Frontiers in Microbiology

Nitrogen fertilizer rate affects root exudation, the rhizosphere microbiome and nitrogen-use-efficiency of maize

(2016) Shusheng Zhu et al.   APPLIED SOIL ECOLOGY

Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system

(2016) Jun Zhao et al.   APPLIED SOIL ECOLOGY

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

(2016) Ning Ling et al.   SOIL BIOLOGY & BIOCHEMISTRY

Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil

(2016) Samiran Banerjee et al.   SOIL BIOLOGY & BIOCHEMISTRY

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

(2016) Cynthia M. Kallenbach et al.   Nature Communications

Comparing the effect of digestate and chemical fertiliser on soil bacteria

(2015) Melanie Sapp et al.   APPLIED SOIL ECOLOGY

Soil microbial community structure and function are significantly affected by long-term organic and mineral fertilization regimes in the North China Plain

(2015) Juan Li et al.   APPLIED SOIL ECOLOGY

Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle

(2015) Ruibo Sun et al.   APPLIED SOIL ECOLOGY

Effect of Nitrogen Management on Soil Microbial Community and Enzymatic Activities inJatropha curcasL. Plantation

(2015) Doongar Ram Chaudhary et al.   CLEAN-Soil Air Water

Changes in the abundance and structure of bacterial communities under long-term fertilization treatments in a peanut monocropping system

(2015) Wuxing Liu et al.   PLANT AND SOIL

Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw

(2015) Ruibo Sun et al.   SOIL BIOLOGY & BIOCHEMISTRY

Transplanting Soil Microbiomes Leads to Lasting Effects on Willow Growth, but not on the Rhizosphere Microbiome

(2015) Etienne Yergeau et al.   Frontiers in Microbiology

Restoring Soil Quality to Mitigate Soil Degradation

(2015) Rattan Lal   Sustainability

BioMiCo: a supervised Bayesian model for inference of microbial community structure

(2015) Mahdi Shafiei et al.   Microbiome

Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

(2015) Elizaveta Pershina et al.   PLoS One

Improved appreciation of the functioning and importance of biological soil crusts in Europe: the Soil Crust International Project (SCIN)

(2014) Burkhard Büdel et al.   BIODIVERSITY AND CONSERVATION

Organic amendments as ecosystem engineers: Microbial, biochemical and genomic evidence of soil health improvement in a tropical arid zone field site

(2014) K. Aparna et al.   ECOLOGICAL ENGINEERING

Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil

(2014) Yao Pan et al.   FEMS MICROBIOLOGY ECOLOGY

Distinct soil microbial diversity under long-term organic and conventional farming

(2014) Martin Hartmann et al.   ISME Journal

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas

(2014) Belén Carbonetto et al.   PLoS One

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

(2014) Zhen Zhen et al.   PLoS One

Long-term effects of mineral fertilizers on soil microorganisms – A review

(2014) Daniel Geisseler et al.   SOIL BIOLOGY & BIOCHEMISTRY

Omics-based interpretation of synergism in a soil-derived cellulose-degrading microbial community

(2014) Yizhuang Zhou et al.   Scientific Reports

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

(2013) Joseph D. Coolon et al.   PLoS One

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

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

Changes in Soil Microbial Community Structure Influenced by Agricultural Management Practices in a Mediterranean Agro-Ecosystem

(2013) Fuensanta García-Orenes et al.   PLoS One

Associating microbiome composition with environmental covariates using generalized UniFrac distances

(2012) Jun Chen et al.   BIOINFORMATICS

Pyrosequencing of 16S rRNA genes in fecal samples reveals high diversity of hindgut microflora in horses and potential links to chronic laminitis

(2012) Samantha M Steelman et al.   BMC Veterinary Research

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

(2012) Michele C. Pereira e Silva et al.   PLoS One

Carbon sequestration and soil carbon pools in a rice?wheat cropping system: Effect of long-term use of inorganic fertilizers and organic manure

(2012) B.S. Brar et al.   SOIL & TILLAGE RESEARCH

Cellulolytic bacteria from soils in harsh environments

(2012) Fábio Lino Soares et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Effect of mineral and organic fertilization on crop yield, nitrogen uptake, carbon and nitrogen balances, as well as soil organic carbon content and dynamics: results from 20 European long-term field experiments of the twenty-first century

(2012) Martin Körschens et al.   Archives of Agronomy and Soil Science

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

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

Antibiotic resistance gene spread due to manure application on agricultural fields

(2011) Holger Heuer et al.   CURRENT OPINION IN MICROBIOLOGY

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons

(2011) Megan L. Shepherd et al.   FEMS MICROBIOLOGY LETTERS

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Gaiella occulta gen. nov., sp. nov., a novel representative of a deep branching phylogenetic lineage within the class Actinobacteria and proposal of Gaiellaceae fam. nov. and Gaiellales ord. nov.

(2011) Luciana Albuquerque et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Characterization of a Defined Cellulolytic and Xylanolytic Bacterial Consortium for Bioprocessing of Cellulose and Hemicelluloses

(2010) Benedict C. Okeke et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Archaea rather than bacteria control nitrification in two agricultural acidic soils

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

Molecular identification and pectate lyase production by Bacillus strains involved in cocoa fermentation

(2010) Honoré G. Ouattara et al.   FOOD MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Long-term effects of organic amendments on soil fertility. A review

(2009) Mariangela Diacono et al.   Agronomy for Sustainable Development

Phenotypic and genotypic bacterial antimicrobial resistance in liquid pig manure is variously associated with contents of tetracyclines and sulfonamides

(2009) C.S. Hölzel et al.   JOURNAL OF APPLIED MICROBIOLOGY

A high prevalence of antimicrobial resistantEscherichia coliisolated from pigs and a low prevalence of antimicrobial resistantE. colifrom cattle and sheep in Great Britain at slaughter

(2008) Virve I. Enne et al.   FEMS MICROBIOLOGY LETTERS