Articles

Unravelling the effects of tropical land use conversion on the soil microbiome

The consequences of deforestation and agricultural treatments are complex and affect all trophic levels. Changes of microbial community structure and composition associated with rainforest conversion to manage...

Authors: Dirk Berkelmann, Dominik Schneider, Anja Meryandini and Rolf Daniel

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

Currently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everg...

Authors: Briana S. Abraham, Deniz Caglayan, Natalie V. Carrillo, Matthew C. Chapman, Claire T. Hagan, Skye T. Hansen, Ralph O. Jeanty, Alexander A. Klimczak, Marcos J. Klingler, Thomas P. Kutcher, Sydney H. Levy, Angel A. Millard-Bruzos, Thomas B. Moore, David J. Prentice, Matthew E. Prescott, Richard Roehm…

Characterization of the microbiome associated with in situ earthen materials

The current increase in public awareness of environmental risks is giving rise to a growth of interest in the microbiological safety of buildings. In particular, microbial proliferation on construction materia...

Authors: Alexis Simons, Alexandra Bertron, Jean-Emmanuel Aubert, Christophe Roux and Christine Roques

Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom

Lagoons are common along coastlines worldwide and are important for biogeochemical element cycling, coastal biodiversity, coastal erosion protection and blue carbon sequestration. These ecosystems are frequent...

Authors: Srijak Bhatnagar, Elise S. Cowley, Sebastian H. Kopf, Sherlynette Pérez Castro, Sean Kearney, Scott C. Dawson, Kurt Hanselmann and S. Emil Ruff

Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research

Aerosol microbiome research advances our understanding of bioaerosols, including how airborne microorganisms affect our health and surrounding environment. Traditional microbiological/molecular methods are com...

Authors: Kari Oline Bøifot, Jostein Gohli, Line Victoria Moen and Marius Dybwad

Correction to: Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease

Following publication of the original article [1], the authors advised that their article had published with an error in the title.

Authors: Viviane Radl, Jana Barbro Winkler, Susanne Kublik, Luhua Yang, Traud Winkelmann, Gisle Vestergaard, Peter Schröder and Michael Schloter

Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease

Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed...

Authors: Viviane Radl, Jana Barbro Winkler, Susanne Kublik, Luhua Yang, Traud Winkelmann, Gisle Vestergaard, Peter Schröder and Michael Schloter

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are m...

Authors: H. Soon Gweon, Liam P. Shaw, Jeremy Swann, Nicola De Maio, Manal AbuOun, Rene Niehus, Alasdair T. M. Hubbard, Mike J. Bowes, Mark J. Bailey, Tim E. A. Peto, Sarah J. Hoosdally, A. Sarah Walker, Robert P. Sebra, Derrick W. Crook, Muna F. Anjum, Daniel S. Read…

Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are consider...

Authors: Jana Voříšková, Bo Elberling and Anders Priemé

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes

Yamuna, a major tributary of Ganga, which flows through the national capital region of Delhi, is among the major polluted rivers in India. The accumulation of various effluents, toxic chemicals, heavy metals, ...

Authors: Parul Mittal, Vishnu Prasoodanan PK, Darshan B. Dhakan, Sanjiv Kumar and Vineet K. Sharma

Genome sequence of Epibacterium ulvae strain DSM 24752^T, an indigoidine-producing, macroalga-associated member of the marine Roseobacter group

Strain U95^T (= DSM 24752^T = LMG 26464^T) is the type strain of Epibacterium ulvae, which is the type species of the genus Epibacterium. This genus belongs to the marine Roseobacter group. E. ulvae Strain U95^T was ...

Authors: Sven Breider, Shama Sehar, Martine Berger, Torsten Thomas, Thorsten Brinkhoff and Suhelen Egan

The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers

Characterisation of microbial communities increasingly involves use of high throughput sequencing methods (e.g. MiSeq Illumina) that amplify relatively short sequences of 16S rRNA or functional genes, the latt...

Authors: Axel Aigle, James I. Prosser and Cécile Gubry-Rangin

Welcome to Environmental Microbiome

Authors: Joy E. M. Watts

A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides

Stable soil aggregates are essential for optimal crop growth and preventing soil erosion. However, tillage is often used in agriculture to loosen the soil, which disrupts the integrity of these aggregates. Soi...

Authors: Barbara Cania, Gisle Vestergaard, Maike Krauss, Andreas Fliessbach, Michael Schloter and Stefanie Schulz

Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont

Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic interaction with legume plants in which a bidirectional nutrient exchange takes place. Occasionally, this interaction is subopti...

Authors: Juan Liang, Anne Hoffrichter, Andreas Brachmann and Macarena Marín

Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains

Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia,...

Authors: Hyein Jang, Jungha Woo, Youyoung Lee, Flavia Negrete, Samantha Finkelstein, Hannah R. Chase, Nicole Addy, Laura Ewing, Junia Jean Gilles Beaubrun, Isha Patel, Jayanthi Gangiredla, Athmanya Eshwar, Ziad W. Jaradat, Kunho Seo, Srikumar Shabarinath, Séamus Fanning…

High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30^T

Mucilaginibacter pedocola TBZ30^T (= CCTCC AB 2015301^T = KCTC 42833^T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resi...

Authors: Xia Fan, Jingwei Tang, Li Nie, Jing Huang and Gejiao Wang

Complete genome sequence of Arcticibacterium luteifluviistationis SM1504^T, a cytophagaceae bacterium isolated from Arctic surface seawater

Arcticibacterium luteifluviistationis SM1504^T was isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their ge...

Authors: Yi Li, Xiao-Han Guo, Yan-Ru Dang, Lin-Lin Sun, Xi-Ying Zhang, Xiu-Lan Chen, Qi-Long Qin and Peng Wang

The draft genome sequence of “Nitrospira lenta” strain BS10, a nitrite oxidizing bacterium isolated from activated sludge

The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phyloge...

Authors: Dimitra Sakoula, Boris Nowka, Eva Spieck, Holger Daims and Sebastian Lücker

Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants

The Planococcus sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King George Island in Antarctica; it has a broad growth temperature range of 5–40 °C. Herein, we describe the complete genome se...

Authors: Jong-Hyun Jung, Min-Ho Joe, Dong-Ho Kim, Hyun Park, Jong-il Choi and Sangyong Lim

Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential

Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321 is a naturally occurring strain in vineyard, with the ability to colonise grapevine and which unveils a naturally antagonistic potential against phytop...

Authors: Cátia Pinto, Susana Sousa, Hugo Froufe, Conceição Egas, Christophe Clément, Florence Fontaine and Ana C Gomes

High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7^T

Pseudaminobacter manganicus JH-7^T (= KCTC 52258^T = CCTCC AB 2016107^T) is a Gram-staining-negative, aerobic and non-motile strain that was isolated from a manganese mine. The strain JH-7^T shows multiple heavy meta...

Authors: Xian Xia, Jiahong Li, Zijie Zhou, Dan Wang, Jing Huang and Gejiao Wang

Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5^T

The Azospirillum humicireducens strain SgZ-5^T, belonging to the Order Rhodospirillales and the Family Rhodospirillaceae, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has sho...

Authors: Zhen Yu, Guiqin Yang, Xiaoming Liu, Yueqiang Wang, Li Zhuang and Shungui Zhou

Draft genomes of “Pectobacterium peruviense” strains isolated from fresh water in France

Bacteria belonging to the genus Pectobacterium are responsible for soft rot disease on a wide range of cultivated crops. The “Pectobacterium peruviense” specie, recently proposed inside the Pectobacterium genus, ...

Authors: Pierre Faye, Claire Bertrand, Jacques Pédron and Marie-Anne Barny

Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay

Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Urugu...

Authors: Juan J Fuentes-Valdés, Katia Soto-Liebe, Danilo Pérez-Pantoja, Javier Tamames, Lucy Belmar, Carlos Pedrós-Alió, Daniel Garrido and Mónica Vásquez

Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough

Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic...

Authors: Mohamed Seghir Daas, Albert Remus R. Rosana, Jeella Z. Acedo, Malika Douzane, Farida Nateche, Salima Kebbouche-Gana and John C. Vederas

Draft genome sequences of ‘Candidatus Chloroploca asiatica’ and ‘Candidatus Viridilinea mediisalina’, candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications

‘Candidatus Chloroploca asiatica’ B7–9 and ‘Candidatus Viridilinea mediisalina’ Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became availa...

Authors: Denis S. Grouzdev, Maria S. Rysina, Irina A. Bryantseva, Vladimir M. Gorlenko and Vasil A. Gaisin

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil

Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been seq...

Authors: Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang and Sijing Chang

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070

Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, m...

Authors: Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, Emmanuel Jaffrès and Monique Zagorec

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico

Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseud...

Authors: Doglas Parise, Mariana T D Parise, Marcus V C Viana, Adrian V Muñoz-Bucio, Yazmin A Cortés-Pérez, Beatriz Arellano-Reynoso, Efrén Díaz-Aparicio, Fernanda A Dorella, Felipe L Pereira, Alex F Carvalho, Henrique C P Figueiredo, Preetam Ghosh, Debmalya Barh, Anne C P Gomide and Vasco A C Azevedo

Functional and taxonomic classification of a greenhouse water drain metagenome

Microbiome sequencing has become the standard procedure in the study of new ecological and human-constructed niches. To our knowledge, this is the first report of a metagenome from the water of a greenhouse dr...

Authors: Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas and Adrian Ochoa-Leyva

Complete genome sequence of the halophile bacterium Kushneria konosiri X49^T, isolated from salt-fermented Konosirus punctatus

Kushneria konosiri X49^T is a member of the Halomonadaceae family within the order Oceanospirillales and can be isolated from salt-fermented larval gizzard shad. The genome of K. konosiri X49^T reported here provid...

Authors: Ji-Hyun Yun, Hojun Sung, Hyun Sik Kim, Euon Jung Tak, Woorim Kang, June-Young Lee, Dong-Wook Hyun, Pil Soo Kim and Jin-Woo Bae

Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123

Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province, China. M. amorphae CCNWGS0123 is an aerobic, Gram...

Authors: Xinye Wang, Yantao Luo, Dongying Liu, Jiamei Wang, Shi Wei and Liang Zhao

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Following publication of the original article [1], the author requested this addition to the ‘Acknowledgements’ section of the article: “DW is funded by the German Federal Ministry of Education and Research (e...

Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier…

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences

Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of o...

Authors: Samuel C. Epstein, Louise K. Charkoudian and Marnix H. Medema

Correction to: Complete genome of a novel virulent phage ST0 lysing Escherichia coli H8

Table 1 of this original publication contained an error. The updated Table 1 is published in this correction article [1].

Authors: Honghui Liu, Xinchun Liu and Jinqing Li

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16^T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno

“Thiodictyon syntrophicum” sp. nov. strain Cad16^T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16^T was isolated fr...

Authors: Samuel M. Luedin, Joël F. Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer and Mauro Tonolla

Short genome report of cellulose-producing commensal Escherichia coli 1094

Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobac...

Authors: Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier and Jean-Marc Ghigo

High quality draft genome sequences of Mycoplasma agassizii strains PS6^T and 723 isolated from Gopherus tortoises with upper respiratory tract disease

Mycoplasma agassizii is one of the known causative agents of upper respiratory tract disease (URTD) in Mojave desert tortoises (Gopherus agassizii) and in gopher tortoises (Gopherus polyphemus). We sequenced the ...

Authors: David Alvarez-Ponce, Chava L. Weitzman, Richard L. Tillett, Franziska C. Sandmeier and C. Richard Tracy

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01

A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clusteri...

Authors: Rakshak Kumar, Vishal Acharya, Dharam Singh and Sanjay Kumar

High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment

Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph isolated from Hardangervidda national park (Norway). This strain represents the second of the two validly published specie...

Authors: Alejandro Mateos-Rivera, Tajul Islam, Ian P. G. Marshall, Lars Schreiber and Lise Øvreås

High quality draft genome sequence of Mycoplasma testudineum strain BH29^T, isolated from the respiratory tract of a desert tortoise

Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease in desert tortoises, Gopherus agassizii. We sequenced the genome of M. testudineum BH29^T (ATCC 700618^T = MCCM 03231^T),...

Authors: Chava L. Weitzman, Richard L. Tillett, Franziska C. Sandmeier, C. Richard Tracy and David Alvarez-Ponce

Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut

We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy...

Authors: Mamadou Beye, Sofiane Bakour, Sory Ibrahima Traore, Jaishriram Rathored, Noémie Labas, Didier Raoult and Pierre-Edouard Fournier

Genome sequence of Planktotalea frisia type strain (SH6-1^T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom

Planktotalea frisia SH6-1^T Hahnke et al. (Int J Syst Evol Microbiol 62:1619–24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobac...

Authors: Insa Bakenhus, Sonja Voget, Anja Poehlein, Thorsten Brinkhoff, Rolf Daniel and Meinhard Simon

Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey

This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae. Bosea sp. WAO was isolated from p...

Authors: Alexandra B. Walczak, Nathan Yee and Lily Y. Young

The current state and future direction of DoD gut microbiome research: a summary of the first DoD gut microbiome informational meeting

The gut microbiome is increasingly recognized as integral to human health, and is emerging as a mediator of human physical and cognitive performance. This has led to the recognition that US Department of Defen...

Authors: Steven Arcidiacono, Jason W. Soares, J. Philip Karl, Linda Chrisey, C. P. T. Blair C. R. Dancy, Michael Goodson, Fredrick Gregory, Rasha Hammamieh, Nancy Kelley Loughnane, Robert Kokoska, C. A. P. T. Mark Riddle, Keith Whitaker and Kenneth Racicot

Correction to: Neisseria lactamica Y92–1009 complete genome sequence

After publication of the original article [1] it was identified that an incorrect version of the manuscript has been published. This was caused by a technical error which led to a discrepancy between the edito...

Authors: Anish K. Pandey, David W. Cleary, Jay R. Laver, Martin C. J. Maiden, Xavier Didelot, Andrew Gorringe and Robert C. Read

Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants

In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain...

Authors: Jakub Ridl, Jachym Suman, Serena Fraraccio, Miluse Hradilova, Michal Strejcek, Tomas Cajthaml, Andrea Zubrova, Tomas Macek, Hynek Strnad and Ondrej Uhlik

Draft genome sequence of Streptomyces hyaluromycini MB-PO13^T, a hyaluromycin producer

Streptomyces hyaluromycini MB-PO13^T (=NBRC 110483^T = DSM 100105^T) is type strain of the species, which produces a hyaluronidase inhibitor, hyaluromycin. Here, we report the draft genome sequence of this strain to...

Authors: Enjuro Harunari, Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Akane Kimura, Moriyuki Hamada and Yasuhiro Igarashi

Genomic insights into Mycobacterium simiae human colonization

Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung 12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium species found in environmental niches, and recently evid...

Authors: José L. Steffani-Vallejo, Marion E. Brunck, Erika Y. Acosta-Cruz, Rafael Montiel and Francisco Barona-Gómez