Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System

Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

(2019) Zhi‐Feng Zhang et al.   JOURNAL OF BIOGEOGRAPHY

High‐quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep‐branching lineages of the phylum Actinobacteria

(2019) Rita Severino et al.   MicrobiologyOpen

Subterranean karst environments as a global sink for atmospheric methane

(2018) Kevin D. Webster et al.   EARTH AND PLANETARY SCIENCE LETTERS

Aerobiological behavior of Paleolithic decorated caves: a comparative study of five caves in the Gard department (France)

(2018) Johann Leplat et al.   AEROBIOLOGIA

Rock substrate rather than black stain alterations drives microbial community structure in the passage of Lascaux Cave

(2018) Lise Alonso et al.   Microbiome

Resource limitation of soil microbes in karst ecosystems

(2018) Hao Chen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

(2017) Eric D. Becraft et al.   Frontiers in Microbiology

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation

(2017) Shubin He et al.   Scientific Reports

Bacterial Diversity and Composition in Oylat Cave (Turkey) with Combined Sanger/Pyrosequencing Approach 

(2016) Yasemin Gulecal-Pektas   Polish Journal of Microbiology

Bacterial communities in oil contaminated soils: Biogeography and co-occurrence patterns

(2016) Shuo Jiao et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Relationship between pH and Bacterial Communities in a Single Karst Ecosystem and Its Implication for Soil Acidification

(2016) Yuan Yun et al.   Frontiers in Microbiology

Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

(2016) Denis V. Axenov-Gibanov et al.   PLoS One

Five-Year Monitoring of Bacterial Communities in Dripping Water from the Heshang Cave in Central China: Implication for Paleoclimate Reconstruction and Ecological Functions

(2015) Yuan Yun et al.   GEOMICROBIOLOGY JOURNAL

Microbial Diversity in Caves

(2015) Karolina Tomczyk-Żak et al.   GEOMICROBIOLOGY JOURNAL

Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability

(2015) Kathleen Brannen-Donnelly et al.   Frontiers in Microbiology

Profiling bacterial diversity in a limestone cave of the western Loess Plateau of China

(2015) Yucheng Wu et al.   Frontiers in Microbiology

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

(2015) Cristina Riquelme et al.   Frontiers in Microbiology

Metagenomic Evidence for Sulfide Oxidation in Extremely Acidic Cave Biofilms

(2014) Daniel S. Jones et al.   GEOMICROBIOLOGY JOURNAL

The Transport of Nonindigenous Microorganisms Into Caves by Human Visitation: A Case Study at Carlsbad Caverns National Park

(2014) Dale W. Griffin et al.   GEOMICROBIOLOGY JOURNAL

High Phylogenetic Diversity of Bacteria in the Area of Prehistoric Paintings in Magura Cave, Bulgaria

(2014) Violina Ivanova et al.   JOURNAL OF CAVE AND KARST STUDIES

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Microbial community responses to anthropogenically induced environmental change: towards a systems approach

(2013) Andrew Bissett et al.   ECOLOGY LETTERS

Mass effects meet species sorting: transformations of microbial assemblages in epiphreatic subsurface karst water pools

(2013) Tanja Shabarova et al.   ENVIRONMENTAL MICROBIOLOGY

Mn(II)-oxidizing Bacteria are Abundant and Environmentally Relevant Members of Ferromanganese Deposits in Caves of the Upper Tennessee River Basin

(2013) Mary J. Carmichael et al.   GEOMICROBIOLOGY JOURNAL

Comparative microbial community composition from secondary carbonate (moonmilk) deposits: implications for the Cansiliella servadeii cave hygropetric food web

(2013) Annette Summers Engel et al.   INTERNATIONAL JOURNAL OF SPELEOLOGY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The Actinobacterial Colonization of Etruscan Paintings

(2013) Marta Diaz-Herraiz et al.   Scientific Reports

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Comparative analysis of yellow microbial communities growing on the walls of geographically distinct caves indicates a common core of microorganisms involved in their formation

(2012) Estefania Porca et al.   FEMS MICROBIOLOGY ECOLOGY

Bacterial community survey of sediments at Naracoorte Caves, Australia

(2012) Eric Adetutu et al.   INTERNATIONAL JOURNAL OF SPELEOLOGY

Human urine in Lechuguilla Cave: the microbiological impact and potential for bioremediation

(2012) Michael Johnston et al.   JOURNAL OF CAVE AND KARST STUDIES

Bacteria isolated from dripping water in the oligotrophic Heshang cave in Central China

(2012) Qianying Liu et al.   Journal of Earth Science

Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

(2012) Marianyoly Ortiz et al.   MICROBIAL ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

Using species combinations in indicator value analyses

(2012) Miquel De Cáceres et al.   Methods in Ecology and Evolution

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Bacterial and Archaeal Community Structure of Two Adjacent Calcite Speleothems in Kartchner Caverns, Arizona, USA

(2011) Antje Legatzki et al.   GEOMICROBIOLOGY JOURNAL

Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm

(2011) Daniel S Jones et al.   ISME Journal

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

(2011) Albert Barberán et al.   ISME Journal

Coherent dynamics and association networks among lake bacterioplankton taxa

(2011) Alexander Eiler et al.   ISME Journal

A framework for estimating niche metrics using the resemblance between qualitative resources

(2011) Miquel De Cáceres et al.   OIKOS

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy

(2010) D. S. Jones et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Karst pools in subsurface environments: collectors of microbial diversity or temporary residence between habitat types

(2010) Tanja Shabarova et al.   ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Improving indicator species analysis by combining groups of sites

(2010) Miquel De Cáceres et al.   OIKOS

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Assessment of Bacterial and Fungal Growth on Natural Substrates: Consequences for Preserving Caves with Prehistoric Paintings

(2009) Francesca Stomeo et al.   CURRENT MICROBIOLOGY

Centrality measures and the importance of generalist species in pollination networks

(2009) Ana M. Martín González et al.   Ecological Complexity

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia

(2009) Lejla PaÅ¡ić et al.   FEMS MICROBIOLOGY ECOLOGY

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

A unified approach to false discovery rate estimation

(2008) Korbinian Strimmer   BMC BIOINFORMATICS

Pseudonocardia in white colonizations in two caves with Paleolithic paintings

(2008) F. Stomeo et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION