Articles

Archaeal and bacterial communities assembly and co-occurrence networks in subtropical mangrove sediments under Spartina alterniflora invasion

Mangrove ecosystems are vulnerable due to the exotic Spartina alterniflora (S. alterniflora) invasion in China. However, little is known about mangrove sediment microbial community assembly processes and interact...

Authors: Weidong Chen and Donghui Wen

Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community ...

Authors: Wenjun Li and Xiaofang Li

Genome-wide gene expression changes of Pseudomonas veronii 1YdBTEX2 during bioaugmentation in polluted soils

Bioaugmentation aims to use the capacities of specific bacterial strains inoculated into sites to enhance pollutant biodegradation. Bioaugmentation results have been mixed, which has been attributed to poor in...

Authors: Marian Morales, Vladimir Sentchilo, Noushin Hadadi and Jan Roelof van der Meer

Coupled microbiome analyses highlights relative functional roles of bacteria in a bivalve hatchery

Microbial communities are ubiquitous throughout ecosystems and are commensal with hosts across taxonomic boundaries. Environmental and species-specific microbiomes are instrumental in maintaining ecosystem and...

Authors: Emma Timmins-Schiffman, Samuel J. White, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline, Brook L. Nunn and Steven B. Roberts

Deep learning approaches for natural product discovery from plant endophytic microbiomes

Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants ap...

Authors: Shiva Abdollahi Aghdam and Amanda May Vivian Brown

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salin...

Authors: Pedro J. Cabello-Yeves, Cristiana Callieri, Antonio Picazo, Maliheh Mehrshad, Jose M. Haro-Moreno, Juan J. Roda-Garcia, Nina Dzhembekova, Violeta Slabakova, Nataliya Slabakova, Snejana Moncheva and Francisco Rodriguez-Valera

Facilitation in the soil microbiome does not necessarily lead to niche expansion

The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in...

Authors: Xue Zhou, Márcio F. A. Leite, Zhenqing Zhang, Lei Tian, Jingjing Chang, Lina Ma, Xiujun Li, Johannes A. van Veen, Chunjie Tian and Eiko E. Kuramae

Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol

Bacillus subtilis strains have been widely studied for their numerous benefits in agriculture, including viticulture. Providing several assets, B. subtilis spp. are described as promising plant-protectors against...

Authors: Catarina Leal, Florence Fontaine, Aziz Aziz, Conceiçao Egas, Christophe Clément and Patricia Trotel-Aziz

Plastics and the microbiome: impacts and solutions

Global plastic production has increased exponentially since manufacturing commenced in the 1950’s, including polymer types infused with diverse additives and fillers. While the negative impacts of plastics are...

Authors: G. Lear, J. M. Kingsbury, S. Franchini, V. Gambarini, S. D. M. Maday, J. A. Wallbank, L. Weaver and O. Pantos

Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria

The cyanobacteria Prochlorococcus and Synechococcus are responsible for around 10% of global net primary productivity, serving as part of the foundation of marine food webs. Heterotrophic bacteria are often co-is...

Authors: Sean M. Kearney, Elaina Thomas, Allison Coe and Sallie W. Chisholm

Falling bacterial communities from the atmosphere

Bacteria emitted into the atmosphere eventually settle to the pedosphere via sedimentation (dry deposition) or precipitation (wet deposition), constituting a part of the global cycling of substances on Earth, ...

Authors: Cheolwoon Woo and Naomichi Yamamoto

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environ...

Authors: Dipti W. Pitta, Nagaraju Indugu, John D. Toth, Joseph S. Bender, Linda D. Baker, Meagan L. Hennessy, Bonnie Vecchiarelli, Helen Aceto and Zhengxia Dou

A rather dry subject; investigating the study of arid-associated microbial communities

Almost one third of Earth’s land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a ...

Authors: Peter Osborne, Lindsay J. Hall, Noga Kronfeld-Schor, David Thybert and Wilfried Haerty

Correction to: Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment

An amendment to this paper has been published and can be accessed via the original article.

Authors: Antoine Bagnaro, Federico Baltar, Gretchen Brownstein, William G. Lee, Sergio E. Morales, Daniel W. Pritchard and Christopher D. Hepburn

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard...

Authors: Jessica Chopyk, Daniel J. Nasko, Sarah Allard, Anthony Bui, Mihai Pop, Emmanuel F. Mongodin and Amy R. Sapkota

Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato

The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolite...

Authors: Peter Kusstatscher, Wisnu Adi Wicaksono, Alessandro Bergna, Tomislav Cernava, Nick Bergau, Alain Tissier, Bettina Hause and Gabriele Berg

Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment

One of the central objectives of microbial ecology is to study the distribution of microbial communities and their association with their environments. Biogeographical studies have partitioned the oceans into ...

Authors: Antoine Bagnaro, Federico Baltar, Gretchen Brownstein, William G. Lee, Sergio E. Morales, Daniel W. Pritchard and Christopher D. Hepburn

BLAST-QC: automated analysis of BLAST results

The Basic Local Alignment Search Tool (BLAST) from NCBI is the preferred utility for sequence alignment and identification for bioinformatics and genomics research. Among researchers using NCBI’s BLAST softwar...

Authors: Behzad Torkian, Spencer Hann, Eva Preisner and R. Sean Norman

Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research

Reliable identification and quantification of bioaerosols is fundamental in aerosol microbiome research, highlighting the importance of using sampling equipment with well-defined performance characteristics. F...

Authors: Kari Oline Bøifot, Jostein Gohli, Gunnar Skogan and Marius Dybwad

Correction to: Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China

An amendment to this paper has been published and can be accessed via the original article.

Authors: Xiangming Tang, Guijuan Xie, Keqiang Shao, Yang Hu, Jian Cai, Chengrong Bai, Yi Gong and Guang Gao

Meeting report of the third annual Tri-Service Microbiome Consortium symposium

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among U.S. Department of Defense (DoD) organizations and to facilitate ...

Authors: J. Philip Karl, Robyn A. Barbato, Laurel A. Doherty, Aarti Gautam, Sarah M. Glaven, Robert J. Kokoska, Dagmar Leary, Rebecca L. Mickol, Matthew A. Perisin, Andrew J. Hoisington, Edward J. Van Opstal, Vanessa Varaljay, Nancy Kelley-Loughnane, Camilla A. Mauzy, Michael S. Goodson and Jason W. Soares

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

Sequencing of 16S rRNA genes has become a powerful technique to study microbial communities and their responses towards changing environmental conditions in various ecosystems. Several tools have been develope...

Authors: Franziska Wemheuer, Jessica A. Taylor, Rolf Daniel, Emma Johnston, Peter Meinicke, Torsten Thomas and Bernd Wemheuer

Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China

Microorganisms in rivers and lakes are essential for nutrient recycling in aquatic ecosystems. Understanding the ecological processes shaping microbial communities is of crucial importance for aquatic microbia...

Authors: Xiangming Tang, Guijuan Xie, Keqiang Shao, Yang Hu, Jian Cai, Chengrong Bai, Yi Gong and Guang Gao

Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales

Genome-resolved metagenomic sequencing approaches have led to a substantial increase in the recognized diversity of microorganisms; this included the discovery of novel metabolic pathways in previously recogni...

Authors: Lewis M. Ward, Usha F. Lingappa, John P. Grotzinger and Woodward W. Fischer

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has...

Authors: Renxing Liang, Maggie C. Y. Lau, Evan T. Saitta, Zachary K. Garvin and Tullis C. Onstott

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermo...

Authors: Irena Maus, Michael Klocke, Jaqueline Derenkó, Yvonne Stolze, Michael Beckstette, Carsten Jost, Daniel Wibberg, Jochen Blom, Christian Henke, Katharina Willenbücher, Madis Rumming, Antje Rademacher, Alfred Pühler, Alexander Sczyrba and Andreas Schlüter

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