High-Level Diversity of Basal Fungal Lineages and the Control of Fungal Community Assembly by Stochastic Processes in Mangrove Sediments

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments

(2021) Zhi-Feng Zhang et al.   mSystems

Diverse Asgard archaea including the novel phylum Gerdarchaeota participate in organic matter degradation

(2020) Mingwei Cai et al.   Science China-Life Sciences

Depth-dependent mycoplankton glycoside hydrolase gene activity in the open ocean—evidence from the Tara Oceans eukaryote metatranscriptomes

(2020) Nathan Chrismas et al.   ISME Journal

Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6

(2019) Jie Pan et al.   MICROBIAL ECOLOGY

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

(2019) Samiran Banerjee et al.   ISME Journal

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

(2019) Patricia Luis et al.   ENVIRONMENTAL MICROBIOLOGY

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

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Strengthening Insights in Microbial Ecological Networks from Theory to Applications

(2019) Xiaofei Lv et al.   mSystems

The role of fungi in heterogeneous sediment microbial networks

(2019) Jenny Marie Booth et al.   Scientific Reports

Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

(2019) Cui-Jing Zhang et al.   mSystems

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

(2019) Weidong Chen et al.   Microbiome

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process

(2019) Huajun Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Decomposition as a regulator of carbon accretion in mangroves: a review

(2018) Shantelle D. Friesen et al.   ECOLOGICAL ENGINEERING

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

(2018) Yuanyuan Mo et al.   ISME Journal

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

(2018) Yang Liu et al.   ISME Journal

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

(2018) Xiaobo Liu et al.   Microbiome

Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

(2018) Felix Heeger et al.   Molecular Ecology Resources

Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments

(2018) Man Kit Cheung et al.   Scientific Reports

Mycobiome diversity: high-throughput sequencing and identification of fungi

(2018) R. Henrik Nilsson et al.   NATURE REVIEWS MICROBIOLOGY

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation

(2017) Wenjing Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Distinct seasonality of chytrid-dominated benthic fungal communities in the neritic oceans (Bohai Sea and North Yellow Sea)

(2017) Yaping Wang et al.   Fungal Ecology

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Fungal community assemblage of different soil compartments in mangrove ecosystem

(2017) Dinesh Sanka Loganathachetti et al.   Scientific Reports

Novel soil-inhabiting clades fill gaps in the fungal tree of life

(2017) Leho Tedersoo et al.   Microbiome

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary

(2016) Guangshan Wei et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi

(2016) Hans-Peter Grossart et al.   Fungal Ecology

Effects of dispersal and selection on stochastic assembly in microbial communities

(2016) Sarah Evans et al.   ISME Journal

Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality

(2016) Jenny Fabian et al.   ISME Journal

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

(2015) Mohammad Bahram et al.   ISME Journal

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

(2015) Lemian Liu et al.   ISME Journal

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Cross-biome comparison of microbial association networks

(2015) Karoline Faust et al.   Frontiers in Microbiology

Soil and Rhizosphere Associated Fungi in Gray Mangroves (Avicennia marina) from the Red Sea — A Metagenomic Approach

(2015) Marta Filipa Simões et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

(2015) Guoqin Yu et al.   PLoS One

Carbon Cycling and Storage in Mangrove Forests

(2014) Daniel M. Alongi   Annual Review of Marine Science

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Is dispersal neutral?

(2014) Winsor H. Lowe et al.   TRENDS IN ECOLOGY & EVOLUTION

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

(2014) C. L. Schoch et al.   Database-The Journal of Biological Databases and Curation

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Relating microbial community structure and environmental variables in mangrove sediments inside Rhizophora mangle L. habitats

(2013) Geórgia Barguil Colares et al.   APPLIED SOIL ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

Effect of salinity on enzymatic activities in a submerged fixed bed biofilm reactor for municipal sewage treatment

(2012) C. Cortés-Lorenzo et al.   BIORESOURCE TECHNOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments

(2011) Takahiko Nagahama et al.   ENVIRONMENTAL MICROBIOLOGY

Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa

(2011) Yonathan Arfi et al.   FEMS MICROBIOLOGY ECOLOGY

Fungal diversity in anoxic-sulfidic sediments in a mangrove soil

(2011) Yonathan Arfi et al.   Fungal Ecology

Discovery of novel intermediate forms redefines the fungal tree of life

(2011) Meredith D. M. Jones et al.   NATURE

Mangroves among the most carbon-rich forests in the tropics

(2011) Daniel C. Donato et al.   Nature Geoscience

Disentangling the importance of ecological niches from stochastic processes across scales

(2011) J. M. Chase et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Validation and justification of the phylum name Cryptomycota phyl. nov.

(2011) Meredith D.M. Jones et al.   IMA Fungus

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Optimization of alkaline cellulase production by the marine-derived fungus Chaetomium sp. using agricultural and industrial wastes as substrates

(2010) Chinnarjan Ravindran et al.   BOTANICA MARINA

Status and distribution of mangrove forests of the world using earth observation satellite data

(2010) C. Giri et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

The Loss of Species: Mangrove Extinction Risk and Geographic Areas of Global Concern

(2010) Beth A. Polidoro et al.   PLoS One

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

Fungal Diversity in Deep-Sea Hydrothermal Ecosystems

(2009) T. Le Calvez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Could nested PCR be applicable for the study of microbial diversity?

(2009) Zhen-Yu Fan et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Threats to mangroves from climate change and adaptation options: A review

(2008) Eric L. Gilman et al.   AQUATIC BOTANY

A general framework for the distance-decay of similarity in ecological communities

(2008) Hélène Morlon et al.   ECOLOGY LETTERS