Ecology and exploration of the rare biosphere (Q35570082)

8 August 2017

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title

Ecology and exploration of the rare biosphere (English)

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8 August 2017

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Michael D J Lynch

1

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8 August 2017

Josh D Neufeld

series ordinal

2

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8 August 2017

language of work or name

English

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publication date

2 March 2015

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Nature Reviews Microbiology

8 August 2017

published in

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8 August 2017

volume

13

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8 August 2017

issue

4

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8 August 2017

page(s)

217-229

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maintained by WikiProject

8 August 2017

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Phylogenetic structure of the prokaryotic domain: The primary kingdoms

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Genetic diversity in Sargasso Sea bacterioplankton

31 March 2020

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16S rRNA sequences reveal numerous uncultured microorganisms in a natural community

31 March 2020

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A molecular view of microbial diversity and the biosphere

31 March 2020

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Counting the uncountable: statistical approaches to estimating microbial diversity

31 March 2020

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Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities.

31 March 2020

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Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities

31 March 2020

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Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags

31 March 2020

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Microbial diversity in the deep sea and the underexplored "rare biosphere"

31 March 2020

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'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say?

31 March 2020

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Novelty and uniqueness patterns of rare members of the soil biosphere

31 March 2020

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Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads

31 March 2020

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Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

31 March 2020

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Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products

31 March 2020

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The Rare Bacterial Biosphere

31 March 2020

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Ecology of the rare microbial biosphere of the Arctic Ocean

31 March 2020

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A human gut microbial gene catalogue established by metagenomic sequencing

31 March 2020

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Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

31 March 2020

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Robust estimation of microbial diversity in theory and in practice.

31 March 2020

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Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

31 March 2020

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UniFrac: an effective distance metric for microbial community comparison

31 March 2020

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Moving pictures of the human microbiome

31 March 2020

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Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life.

31 March 2020

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Estimating prokaryotic diversity and its limits

31 March 2020

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Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology

31 March 2020

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What is the extent of prokaryotic diversity?

31 March 2020

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Modeling taxa-abundance distributions in microbial communities using environmental sequence data

31 March 2020

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The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

31 March 2020

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Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

31 March 2020

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Ironing out the wrinkles in the rare biosphere through improved OTU clustering

31 March 2020

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The microbial contribution to macroecology

31 March 2020

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The generation and maintenance of diversity in microbial communities

31 March 2020

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Ecology. Dipping into the rare biosphere.

31 March 2020

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Shifts in the microbial community composition of Gulf Coast beaches following beach oiling

31 March 2020

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Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys

31 March 2020

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Diversity and dynamics of rare and of resident bacterial populations in coastal sands

31 March 2020

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Salt marsh sediment bacteria: their distribution and response to external nutrient inputs

31 March 2020

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Patterns of rare and abundant marine microbial eukaryotes

31 March 2020

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Novel High-Rank Phylogenetic Lineages within a Sulfur Spring (Zodletone Spring, Oklahoma), Revealed Using a Combined Pyrosequencing-Sanger Approach

31 March 2020

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Targeted recovery of novel phylogenetic diversity from next-generation sequence data

31 March 2020

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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

31 March 2020

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The human microbiome project

31 March 2020

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The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

31 March 2020

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Activity of abundant and rare bacteria in a coastal ocean

31 March 2020

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Dormancy contributes to the maintenance of microbial diversity

31 March 2020

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Unraveling assembly of stream biofilm communities

31 March 2020

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Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams

31 March 2020

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Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited.

31 March 2020

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The Paradox of the Plankton

31 March 2020

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Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria

31 March 2020

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Predation on prokaryotes in the water column and its ecological implications

31 March 2020

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Herbivores and the Number of Tree Species in Tropical Forests

31 March 2020

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The impact of phages on interspecific competition in experimental populations of bacteria

31 March 2020

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The contribution of species richness and composition to bacterial services

31 March 2020

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Microbial seed banks: the ecological and evolutionary implications of dormancy

31 March 2020

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The frequency and characteristics of highly thermophilic bacteria in cool soil environments

31 March 2020

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A constant flux of diverse thermophilic bacteria into the cold Arctic seabed

31 March 2020

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Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years

31 March 2020

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Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

31 March 2020

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The seasonal structure of microbial communities in the Western English Channel

31 March 2020

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Defining seasonal marine microbial community dynamics

31 March 2020

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The Western English Channel contains a persistent microbial seed bank

31 March 2020

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Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys

31 March 2020

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Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance

31 March 2020

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Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management

31 March 2020

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Evidence for a persistent microbial seed bank throughout the global ocean

31 March 2020

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'Sponge-specific' bacteria are widespread (but rare) in diverse marine environments

31 March 2020

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Amphibian skin may select for rare environmental microbes

31 March 2020

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Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

31 March 2020

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The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

31 March 2020

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Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters.

31 March 2020

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Fundamentals of microbial community resistance and resilience

31 March 2020

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Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis

31 March 2020

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Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

31 March 2020

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Ecological linkages between aboveground and belowground biota

31 March 2020

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Functional diversity of microbial decomposers facilitates plant coexistence in a plant–microbe–soil feedback model

31 March 2020

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High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean

31 March 2020

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Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.

31 March 2020

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

31 March 2020

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Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

31 March 2020

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The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss

31 March 2020

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Molecular diversity and ecology of microbial plankton

31 March 2020

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Microbial community assembly, theory and rare functions.

31 March 2020

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Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

31 March 2020

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A 'rare biosphere' microorganism contributes to sulfate reduction in a peatland

31 March 2020

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Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism

31 March 2020

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31 March 2020

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Dense populations of a giant sulfur bacterium in Namibian shelf sediments.

31 March 2020

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Reduction of rare soil microbes modifies plant-herbivore interactions.

31 March 2020

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Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression

31 March 2020

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The 'rare biosphere': a reality check

31 March 2020

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Truffles: much more than a prized and local fungal delicacy

31 March 2020

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Insights into the phylogeny and coding potential of microbial dark matter

31 March 2020

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Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees

31 March 2020

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Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities

31 March 2020

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Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

31 March 2020

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Cultivating the uncultured

31 March 2020

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Laboratory cultivation of widespread and previously uncultured soil bacteria

31 March 2020

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Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory

31 March 2020

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Cultivation gives context to the microbial ecologist

31 March 2020

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Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10.

31 March 2020

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Scratching the surface of the rare biosphere with ribosomal sequence tag primers

31 March 2020

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Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms

31 March 2020

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An early-branching microbialite cyanobacterium forms intracellular carbonates

31 March 2020

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The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

31 March 2020

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Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

31 March 2020

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Evaluating bias of illumina-based bacterial 16S rRNA gene profiles

31 March 2020

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PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

31 March 2020

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Structure, function and diversity of the healthy human microbiome

31 March 2020

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Finding the needles in the metagenome haystack

31 March 2020

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Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

31 March 2020

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Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data

31 March 2020

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Computational improvements reveal great bacterial diversity and high metal toxicity in soil

31 March 2020

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Toward a census of bacteria in soil

31 March 2020

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Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

31 March 2020

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Targeted access to the genomes of low-abundance organisms in complex microbial communities.

31 March 2020

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rRNA probe-based cell fishing of bacteria

31 March 2020

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Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

31 March 2020

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DNA stable-isotope probing

31 March 2020

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Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

31 March 2020

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Suicide polymerase endonuclease restriction, a novel technique for enhancing PCR amplification of minor DNA templates.

31 March 2020

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

31 March 2020

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The future is now: single-cell genomics of bacteria and archaea

31 March 2020

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Culturing captures members of the soil rare biosphere

31 March 2020

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Evolution and Measurement of Species Diversity

31 March 2020

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Vegetation of the Siskiyou Mountains, Oregon and California

31 March 2020

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Neutral assembly of bacterial communities

31 March 2020

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Combined niche and neutral effects in a microbial wastewater treatment community.

31 March 2020

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Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

31 March 2020

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Macroecology of unicellular organisms - patterns and processes

31 March 2020

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Spatial scaling of microbial biodiversity

31 March 2020

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Commonness and rarity in the marine biosphere

31 March 2020

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Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

31 March 2020

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A quantitative map of nucleotide substitution rates in bacterial rRNA.

31 March 2020

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Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

31 March 2020

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A framework for human microbiome research

31 March 2020

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Cycling of extracellular DNA in the soil environment

31 March 2020

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Ethidium Monoazide for DNA-Based Differentiation of Viable and Dead Bacteria by 5′-Nuclease PCR

31 March 2020

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Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples

31 March 2020

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Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells

31 March 2020

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Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells

31 March 2020

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Soil microbial abundance and diversity along a low precipitation gradient.

31 March 2020

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Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide

31 March 2020

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Insufficient differentiation of live and dead Campylobacter jejuni and Listeria monocytogenes cells by ethidium monoazide (EMA) compromises EMA/real-time PCR.

31 March 2020

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Unsuitable distinction between viable and dead Staphylococcus aureus and Staphylococcus epidermidis by ethidium bromide monoazide.

31 March 2020

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Molecular methods for the assessment of bacterial viability

31 March 2020

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Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses.

31 March 2020

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Conducting a microbiome study

31 March 2020

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Effects of OTU clustering and PCR artifacts on microbial diversity estimates

31 March 2020

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Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

31 March 2020

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Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing

31 March 2020

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UCHIME improves sensitivity and speed of chimera detection

31 March 2020

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Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

31 March 2020

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Removing noise from pyrosequenced amplicons

31 March 2020

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Accurate determination of microbial diversity from 454 pyrosequencing data

31 March 2020

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Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

31 March 2020

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A filtering method to generate high quality short reads using illumina paired-end technology

31 March 2020

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Secondary structure improves OTU assignments of 16S rRNA gene sequences

31 March 2020

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Infernal 1.0: inference of RNA alignments

31 March 2020

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

31 March 2020

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Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach

31 March 2020

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Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production

31 March 2020

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Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

31 March 2020

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12 December 2020

Dominant marine bacterioplankton species found among colony-forming bacteria

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12 December 2020

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

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12 December 2020

Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity.

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12 December 2020

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

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12 December 2020

Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 degrees N)

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12 December 2020

Identifiers

DOI

10.1038/NRMICRO3400

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8 August 2017

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