Enhanced mutualistic symbiosis between soil phages and bacteria with elevated chromium-induced environmental stress

Lysogenic reproductive strategies of viral communities vary with soil depth and are correlated with bacterial diversity

(2020) Xiaolong Liang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial and Viral Communities and Their Antibiotic Resistance Genes Throughout a Hospital Wastewater Treatment System

(2020) Morgan L. Petrovich et al.   Frontiers in Microbiology

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

(2020) Lucas P. P. Braga et al.   Microbiome

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

(2020) Kira Moon et al.   Microbiome

Depth-related variability in viral communities in highly stratified sulfidic mine tailings

(2020) Shao-Ming Gao et al.   Microbiome

Host-hijacking and planktonic piracy: how phages command the microbial high seas

(2019) Joanna Warwick-Dugdale et al.   Virology Journal

Bacteriophages as Environmental Reservoirs of Antibiotic Resistance

(2019) William Calero-Cáceres et al.   TRENDS IN MICROBIOLOGY

Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome

(2019) Andrey N. Shkoporov et al.   Cell Host & Microbe

Remediation of heavy metal contaminated soil by asymmetrical alternating current electrochemistry

(2019) Jinwei Xu et al.   Nature Communications

Cr(VI) reductase activity locates in the cytoplasm of Aeribacillus pallidus BK1, a novel Cr(VI)-reducing thermophile isolated from Tengchong geothermal region, China

(2019) Yan Ma et al.   CHEMICAL ENGINEERING JOURNAL

Heavy metal pollution of soils from coal mines in China

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The concurrent decline of soil lead and children’s blood lead in New Orleans

(2019) Howard W. Mielke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences

(2019) Ramith R. Nair et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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(2018)   BIOINFORMATICS

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China

(2018) Dan-Ting Yu et al.   JOURNAL OF SOILS AND SEDIMENTS

The forest communities of Shebenik-Jabllanicë National Park (Central Albania)

(2018) Michele De Sanctis et al.   PHYTOCOENOLOGIA

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

Phage puppet masters of the marine microbial realm

(2018) Mya Breitbart et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

High-Resolution Temporal and Spatial Patterns of Virome in Wastewater Treatment Systems

(2018) Yulin Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing

(2018) Gareth Trubl et al.   mSystems

Suppression of Enteric Bacteria by Bacteriophages: Importance of Phage Polyvalence in the Presence of Soil Bacteria

(2017) Pingfeng Yu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Lysogeny in nature: mechanisms, impact and ecology of temperate phages

(2017) Cristina Howard-Varona et al.   ISME Journal

The Human Gut Phage Community and Its Implications for Health and Disease

(2017) Pilar Manrique et al.   Viruses-Basel

Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses

(2017) Amir Mohaghegh Motlagh et al.   Frontiers in Microbiology

Control of Antibiotic-Resistant Bacteria in Activated Sludge Using Polyvalent Phages in Conjunction with a Production Host

(2017) Pingfeng Yu et al.   Environmental Science & Technology Letters

Environmental drivers of viral community composition in Antarctic soils identified by viromics

(2017) Evelien M. Adriaenssens et al.   Microbiome

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

(2017) Dae-Wook Kang et al.   Microbiome

Environmental Remediation and Application of Nanoscale Zero-Valent Iron and Its Composites for the Removal of Heavy Metal Ions: A Review

(2016) Yidong Zou et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

(2015) Pingfeng Yu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Competitive adsorption of heavy metals by extracellular polymeric substances extracted from Klebsiella sp. J1

(2015) Jixian Yang et al.   BIORESOURCE TECHNOLOGY

Bacteriophage therapy for membrane biofouling in membrane bioreactors and antibiotic-resistant bacterial biofilms

(2015) Ananda Shankar Bhattacharjee et al.   BIOTECHNOLOGY AND BIOENGINEERING

Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

(2015) Pauline D. Scanlan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A new perspective on lysogeny: prophages as active regulatory switches of bacteria

(2015) Ron Feiner et al.   NATURE REVIEWS MICROBIOLOGY

Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater

(2015) Yu Miao et al.   WATER RESEARCH

Well-temperate phage: optimal bet-hedging against local environmental collapses

(2015) Sergei Maslov et al.   Scientific Reports

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Correlation between viral production and carbon mineralization under nitrate-reducing conditions in aquifer sediment

(2014) Donald Pan et al.   ISME Journal

Unveiling viral–host interactions within the ‘microbial dark matter’

(2014) Manuel Martínez-García et al.   Nature Communications

Chemical and microbial remediation of hexavalent chromium from contaminated soil and mining/metallurgical solid waste: A review

(2013) B. Dhal et al.   JOURNAL OF HAZARDOUS MATERIALS

The virocell concept and environmental microbiology

(2012) Patrick Forterre   ISME Journal

Chromium(VI) Bioremoval byPseudomonasBacteria: Role of Microbial Exudates for Natural Attenuation and Biotreatment of Cr(VI) Contamination

(2011) Nazime Mercan Dogan et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The good viruses: viral mutualistic symbioses

(2011) Marilyn J. Roossinck   NATURE REVIEWS MICROBIOLOGY

The Pfam protein families database

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Viral and microbial community dynamics in four aquatic environments

(2010) Beltran Rodriguez-Brito et al.   ISME Journal

Simultaneous chromate reduction and azo dye decolourization by Brevibacterium casei: Azo dye as electron donor for chromate reduction

(2010) Tsz Wai Ng et al.   JOURNAL OF HAZARDOUS MATERIALS

Biocontrol of biomass bulking caused by Haliscomenobacter hydrossis using a newly isolated lytic bacteriophage

(2010) Shireen M. Kotay et al.   WATER RESEARCH

Organogenesis relies on SoxC transcription factors for the survival of neural and mesenchymal progenitors

(2010) Pallavi Bhattaram et al.   Nature Communications

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Contribution of mobile genetic elements toDesulfovibrio vulgarisgenome plasticity

(2009) Christopher B. Walker et al.   ENVIRONMENTAL MICROBIOLOGY

Bacteriophage predation regulates microbial abundance and diversity in a full-scale bioreactor treating industrial wastewater

(2009) Orr H Shapiro et al.   ISME Journal

A critical review on the bio-removal of hazardous heavy metals from contaminated soils: Issues, progress, eco-environmental concerns and opportunities

(2009) Gang Wu et al.   JOURNAL OF HAZARDOUS MATERIALS

Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism

(2009) K. M. Oliver et al.   SCIENCE

Response surface methodology approach for optimization of biosorption process for removal of Cr (VI), Ni (II) and Zn (II) ions by immobilized bacterial biomass sp. Bacillus brevis

(2008) Rajender Kumar et al.   CHEMICAL ENGINEERING JOURNAL

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

Removal of Cr(VI) and Ni(II) from aqueous solution by fused yeast: Study of cations release and biosorption mechanism

(2008) Hua Yin et al.   JOURNAL OF HAZARDOUS MATERIALS