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Plastics and the microbiome: impacts and solutions Stand. Genomic. Sci. Pub Date : 2021-01-20 G. Lear; J. M. Kingsbury; S. Franchini; V. Gambarini; S. D. M. Maday; J. A. Wallbank; L. Weaver; O. Pantos
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 widely reported, particularly on marine vertebrates, impacts on microbial life remain poorly understood. Plastics impact microbiomes directly, exerting toxic effects, providing supplemental carbon
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Microbial diversity of co-occurring heterotrophs in cultures of marine picocyanobacteria Stand. Genomic. Sci. Pub Date : 2021-01-06 Sean M. Kearney; Elaina Thomas; Allison Coe; Sallie W. Chisholm
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-isolated with these picocyanobacteria in seawater enrichment cultures that contain no added organic carbon; heterotrophs grow on organic carbon supplied by the photolithoautotrophs. For examining
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Falling bacterial communities from the atmosphere Stand. Genomic. Sci. Pub Date : 2020-12-10 Cheolwoon Woo; Naomichi Yamamoto
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, including the water cycle. In this study, we aim to investigate the taxonomic compositions and flux densities of bacterial deposition, for which little is known regarding the relative contributions
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The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania Stand. Genomic. Sci. Pub Date : 2020-12-09 Dipti W. Pitta; Nagaraju Indugu; John D. Toth; Joseph S. Bender; Linda D. Baker; Meagan L. Hennessy; Bonnie Vecchiarelli; Helen Aceto; Zhengxia Dou
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 environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG)
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A rather dry subject; investigating the study of arid-associated microbial communities Stand. Genomic. Sci. Pub Date : 2020-12-01 Peter Osborne; Lindsay J. Hall; Noga Kronfeld-Schor; David Thybert; Wilfried Haerty
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 great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and
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Correction to: Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment Stand. Genomic. Sci. Pub Date : 2020-11-30 Antoine Bagnaro; Federico Baltar; Gretchen Brownstein; William G. Lee; Sergio E. Morales; Daniel W. Pritchard; Christopher D. Hepburn
An amendment to this paper has been published and can be accessed via the original article.
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Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond Stand. Genomic. Sci. Pub Date : 2020-10-28 Jessica Chopyk; Daniel J. Nasko; Sarah Allard; Anthony Bui; Mihai Pop; Emmanuel F. Mongodin; Amy R. Sapkota
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 to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial
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Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato Stand. Genomic. Sci. Pub Date : 2020-09-17 Peter Kusstatscher; Wisnu Adi Wicaksono; Alessandro Bergna; Tomislav Cernava; Nick Bergau; Alain Tissier; Bettina Hause; Gabriele Berg
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 metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial
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Reducing the arbitrary: fuzzy detection of microbial ecotones and ecosystems – focus on the pelagic environment Stand. Genomic. Sci. Pub Date : 2020-08-13 Antoine Bagnaro; Federico Baltar; Gretchen Brownstein; William G. Lee; Sergio E. Morales; Daniel W. Pritchard; Christopher D. Hepburn
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 provinces and regions, but the identification of their boundaries remains challenging, hindering our ability to study transition zones (i.e. ecotones) and microbial ecosystem heterogeneity. Fuzzy
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BLAST-QC: automated analysis of BLAST results Stand. Genomic. Sci. Pub Date : 2020-08-12 Behzad Torkian; Spencer Hann; Eva Preisner; R. Sean Norman
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 software, it is well known that analyzing the results of a large BLAST search can be tedious and time-consuming. Furthermore, with the recent discussions over the effects of parameters such as ‘-max_target_seqs’
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Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research Stand. Genomic. Sci. Pub Date : 2020-07-28 Kari Oline Bøifot; Jostein Gohli; Gunnar Skogan; Marius Dybwad
Reliable identification and quantification of bioaerosols is fundamental in aerosol microbiome research, highlighting the importance of using sampling equipment with well-defined performance characteristics. Following advances in sequencing technology, shotgun metagenomic sequencing (SMS) of environmental samples is now possible. However, SMS of air samples is challenging due to low biomass, but with
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Correction to: Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China Stand. Genomic. Sci. Pub Date : 2020-07-15 Xiangming Tang; Guijuan Xie; Keqiang Shao; Yang Hu; Jian Cai; Chengrong Bai; Yi Gong; Guang Gao
An amendment to this paper has been published and can be accessed via the original article.
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Meeting report of the third annual Tri-Service Microbiome Consortium symposium. Stand. Genomic. Sci. Pub Date : 2020-07-13 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,Jason W Soares
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 resource, material and information sharing among consortium members. The 2019 annual symposium was held 22–24 October 2019 at Wright-Patterson Air Force Base in Dayton, OH. Presentations and discussions
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Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences Stand. Genomic. Sci. Pub Date : 2020-05-18 Franziska Wemheuer; Jessica A. Taylor; Rolf Daniel; Emma Johnston; Peter Meinicke; Torsten Thomas; Bernd Wemheuer
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 developed for the prediction of functional profiles from 16S rRNA gene sequencing data, because numerous questions in ecosystem ecology require knowledge of community functions in addition to taxonomic
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Contrast diversity patterns and processes of microbial community assembly in a river-lake continuum across a catchment scale in northwestern China Stand. Genomic. Sci. Pub Date : 2020-04-25 Xiangming Tang; Guijuan Xie; Keqiang Shao; Yang Hu; Jian Cai; Chengrong Bai; Yi Gong; Guang Gao
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 microbial ecology and biogeography. However, the diversity of microorganisms and the forces that control this diversity are poorly understood. This is particularly true within the framework of the river-lake
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Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales Stand. Genomic. Sci. Pub Date : 2020-04-16 Lewis M. Ward; Usha F. Lingappa; John P. Grotzinger; Woodward W. Fischer
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 recognized clades, and has enabled a more accurate determination of the extant distribution of key metabolisms and how they evolved over Earth history. Here, we present metagenome-assembled genomes of
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Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America Stand. Genomic. Sci. Pub Date : 2020-03-19 Renxing Liang; Maggie C. Y. Lau; Evan T. Saitta; Zachary K. Garvin; Tullis C. Onstott
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 been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although
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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 Stand. Genomic. Sci. Pub Date : 2020-03-02 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; Andreas Schlüter
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 thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and
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Unravelling the effects of tropical land use conversion on the soil microbiome Stand. Genomic. Sci. Pub Date : 2020-02-03 Dirk Berkelmann; Dominik Schneider; Anja Meryandini; Rolf Daniel
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 managed systems such as rubber and oil palm plantations have been shown by 16S rRNA gene analysis previously, but functional profile shifts have been rarely addressed. In this study, we analysed the
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Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades Stand. Genomic. Sci. Pub Date : 2020-01-21 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; Jordan A. Rose; Mulan Yin; Ayumi Hyodo; Kathleen Lail; Christopher Daum; Alicia Clum; Alex Copeland;
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 Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well
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Characterization of the microbiome associated with in situ earthen materials Stand. Genomic. Sci. Pub Date : 2020-01-20 Alexis Simons; Alexandra Bertron; Jean-Emmanuel Aubert; Christophe Roux; Christine Roques
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 materials can be responsible for the degradation of indoor air quality that can increase health-risk to occupants. Raw earth materials are still widely used throughout the world and, in some cases, are
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Microbial community dynamics and coexistence in a sulfide-driven phototrophic bloom Stand. Genomic. Sci. Pub Date : 2020-01-17 Srijak Bhatnagar; Elise S. Cowley; Sebastian H. Kopf; Sherlynette Pérez Castro; Sean Kearney; Scott C. Dawson; Kurt Hanselmann; S. Emil Ruff
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 frequently disturbed by weather, tides, and human activities. Here, we investigated a shallow lagoon in New England. The brackish ecosystem releases hydrogen sulfide particularly upon physical disturbance
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Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research Stand. Genomic. Sci. Pub Date : 2020-01-13 Kari Oline Bøifot; Jostein Gohli; Line Victoria Moen; Marius Dybwad
Aerosol microbiome research advances our understanding of bioaerosols, including how airborne microorganisms affect our health and surrounding environment. Traditional microbiological/molecular methods are commonly used to study bioaerosols, but do not allow for generic, unbiased microbiome profiling. Recent studies have adopted shotgun metagenomic sequencing (SMS) to address this issue. However, SMS
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Correction to: Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease Stand. Genomic. Sci. Pub Date : 2019-12-27 Viviane Radl; Jana Barbro Winkler; Susanne Kublik; Luhua Yang; Traud Winkelmann; Gisle Vestergaard; Peter Schröder; Michael Schloter
Following publication of the original article [1], the authors advised that their article had published with an error in the title.
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Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease Stand. Genomic. Sci. Pub Date : 2019-11-07 Viviane Radl; Jana Barbro Winkler; Susanne Kublik; Luhua Yang; Traud Winkelmann; Gisle Vestergaard; Peter Schröder; Michael Schloter
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 in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. As expected, the biomass of plants grown in replant soil was significantly lower compared
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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples Stand. Genomic. Sci. Pub Date : 2019-10-24 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; Nicole Stoesser
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 many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the
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Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils Stand. Genomic. Sci. Pub Date : 2019-09-18 Jana Voříšková; Bo Elberling; Anders Priemé
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 considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore
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Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes Stand. Genomic. Sci. Pub Date : 2019-09-18 Parul Mittal; Vishnu Prasoodanan PK; Darshan B. Dhakan; Sanjiv Kumar; Vineet K. Sharma
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, and increased organic load in the Yamuna directly affects the organisms that thrive inside or around this river. It also makes it an ideal site for studying the impact of pollution on the river
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Genome sequence of Epibacterium ulvae strain DSM 24752T, an indigoidine-producing, macroalga-associated member of the marine Roseobacter group Stand. Genomic. Sci. Pub Date : 2019-08-06 Sven Breider; Shama Sehar; Martine Berger; Torsten Thomas; Thorsten Brinkhoff; Suhelen Egan
Strain U95T (= DSM 24752T = LMG 26464T) 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 U95T was isolated from the macroalga Ulva australis, is Gram-negative, rod-shaped and motile. Here we describe the permanent draft genome sequence and annotation of E. ulvae U95T with a focus on secondary
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The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers Stand. Genomic. Sci. Pub Date : 2019-07-04 Axel Aigle; James I. Prosser; Cécile Gubry-Rangin
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 latter including ammonia monooxygenase subunit A (amoA), a key functional gene for ammonia oxidising bacteria (AOB) and archaea (AOA). The availability of these techniques, in combination with developments
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Welcome to Environmental Microbiome Stand. Genomic. Sci. Pub Date : 2019-04-01 Joy E. M. Watts
I am delighted to serve as Editor-in-Chief for Environmental Microbiome, sister publication to Microbiome and Animal Microbiome. We are kicking off Environmental Microbiome with a research article by Barbara Cania and colleagues: 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
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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 Stand. Genomic. Sci. Pub Date : 2019-03-28 Barbara Cania; Gisle Vestergaard; Maike Krauss; Andreas Fliessbach; Michael Schloter; Stefanie Schulz
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. Soil aggregation can be enhanced by bacteria through their ability to produce exopolysaccharides and lipopolysaccharides. These compounds stabilize soil aggregates by “gluing” soil particles together
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Complete genome of Rhizobium leguminosarum Norway, an ineffective Lotus micro-symbiont Stand. Genomic. Sci. Pub Date : 2018-12-05 Juan Liang; Anne Hoffrichter; Andreas Brachmann; Macarena Marín
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 suboptimal resulting in the formation of ineffective nodules in which little or no atmospheric nitrogen fixation occurs. Norway induces ineffective nodules in a wide range of hosts. To investigate the
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Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains Stand. Genomic. Sci. Pub Date : 2018-11-29 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; Roger Stephan; Angelika Lehner; Ben D. Tall; Gopal R. Gopinath
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, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and
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High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium Mucilaginibacter pedocola TBZ30T Stand. Genomic. Sci. Pub Date : 2018-11-28 Xia Fan; Jingwei Tang; Li Nie; Jing Huang; Gejiao Wang
Mucilaginibacter pedocola TBZ30T (= CCTCC AB 2015301T = KCTC 42833T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn2+ and Cd2+ during cultivation. In addition, strain TBZ30T produces exopolysaccharides (EPS). These features make it a great potential
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Complete genome sequence of Arcticibacterium luteifluviistationis SM1504T, a cytophagaceae bacterium isolated from Arctic surface seawater Stand. Genomic. Sci. Pub Date : 2018-11-26 Yi Li; Xiao-Han Guo; Yan-Ru Dang; Lin-Lin Sun; Xi-Ying Zhang; Xiu-Lan Chen; Qi-Long Qin; Peng Wang
Arcticibacterium luteifluviistationis SM1504T 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 genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839 bp with an average
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The draft genome sequence of “Nitrospira lenta” strain BS10, a nitrite oxidizing bacterium isolated from activated sludge Stand. Genomic. Sci. Pub Date : 2018-11-22 Dimitra Sakoula; Boris Nowka; Eva Spieck; Holger Daims; Sebastian Lücker
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 phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed
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Complete genome sequence of Planococcus sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants Stand. Genomic. Sci. Pub Date : 2018-11-09 Jong-Hyun Jung; Min-Ho Joe; Dong-Ho Kim; Hyun Park; Jong-il Choi; Sangyong Lim
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 sequence information of the genus Planococcus with its annotated sequence, genetic features for bioremediation, and oxidative stress capacity. The Planococcus sp. PAMC21323 possesses chromosomal
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Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito_F321, an endophyte microorganism from Vitis vinifera with biocontrol potential Stand. Genomic. Sci. Pub Date : 2018-11-01 Cátia Pinto; Susana Sousa; Hugo Froufe; Conceição Egas; Christophe Clément; Florence Fontaine; Ana C Gomes
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 phytopathogens of grapevine, including those responsible for the Botryosphaeria dieback, a GTD disease. Herein we report the draft genome sequence of B. amyloliquefaciens subsp. plantarum Fito_F321
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High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T Stand. Genomic. Sci. Pub Date : 2018-10-25 Xian Xia; Jiahong Li; Zijie Zhou; Dan Wang; Jing Huang; Gejiao Wang
Pseudaminobacter manganicus JH-7T (= KCTC 52258T = CCTCC AB 2016107T) is a Gram-staining-negative, aerobic and non-motile strain that was isolated from a manganese mine. The strain JH-7T shows multiple heavy metal resistance and can effectively remove Mn2+ and Cd2+. In addition, it is able to produce exopolysaccharides (EPS), which may contribute to metal remove/adsorption. Thus, strain JH-7T shows
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Complete genome sequence of the nitrogen-fixing bacterium Azospirillum humicireducens type strain SgZ-5T Stand. Genomic. Sci. Pub Date : 2018-10-16 Zhen Yu; Guiqin Yang; Xiaoming Liu; Yueqiang Wang; Li Zhuang; Shungui Zhou
The Azospirillum humicireducens strain SgZ-5T, belonging to the Order Rhodospirillales and the Family Rhodospirillaceae, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has shown that strain SgZ-5T was able to fix atmospheric nitrogen involved in plant growth promotion. Here we present the complete genome of A. humicireducens SgZ-5T, which consists of a circular
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Draft genomes of “Pectobacterium peruviense” strains isolated from fresh water in France Stand. Genomic. Sci. Pub Date : 2018-10-12 Pierre Faye; Claire Bertrand; Jacques Pédron; Marie-Anne Barny
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, gathers strains isolated from potato tubers cultivated in Peru at high altitude. Here we report the draft genome sequence of two strains belonging to “P. peruviense” isolated from river water
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Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay Stand. Genomic. Sci. Pub Date : 2018-10-12 Juan J Fuentes-Valdés; Katia Soto-Liebe; Danilo Pérez-Pantoja; Javier Tamames; Lucy Belmar; Carlos Pedrós-Alió; Daniel Garrido; Mónica Vásquez
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 Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these C. raciborskii strains using the assembly of reads
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Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough Stand. Genomic. Sci. Pub Date : 2018-10-11 Mohamed Seghir Daas; Albert Remus R. Rosana; Jeella Z. Acedo; Malika Douzane; Farida Nateche; Salima Kebbouche-Gana; John C. Vederas
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 diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant
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Draft genome sequences of ‘Candidatus Chloroploca asiatica’ and ‘Candidatus Viridilinea mediisalina’, candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications Stand. Genomic. Sci. Pub Date : 2018-10-11 Denis S. Grouzdev; Maria S. Rysina; Irina A. Bryantseva; Vladimir M. Gorlenko; Vasil A. Gaisin
‘Candidatus Chloroploca asiatica’ B7–9 and ‘Candidatus Viridilinea mediisalina’ Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of ‘Ca. Chloroploca asiatica ’ B7–9 and ‘Ca. Viridilinea mediisalina’ Kir15-3F
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The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil Stand. Genomic. Sci. Pub Date : 2018-10-10 Ruiqi Yang; Guangxiu Liu; Tuo Chen; Wei Zhang; Gaosen Zhang; Sijing Chang
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 sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48
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One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070 Stand. Genomic. Sci. Pub Date : 2018-10-10 Nassima Illikoud; Christophe Klopp; Alain Roulet; Olivier Bouchez; Nathalie Marsaud; Emmanuel Jaffrès; Monique Zagorec
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, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both on strains and on food matrix. Several B. thermosphacta
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First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico Stand. Genomic. Sci. Pub Date : 2018-10-10 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; Vasco A C Azevedo
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. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico
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Functional and taxonomic classification of a greenhouse water drain metagenome Stand. Genomic. Sci. Pub Date : 2018-10-05 Gamaliel López-Leal; Fernanda Cornejo-Granados; Juan Manuel Hurtado-Ramírez; Alfredo Mendoza-Vargas; Adrian Ochoa-Leyva
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 drain. We found that the greenhouse is not a diverse niche, mainly dominated by and Rodobacterales. The analysis of the functions encoded in the metagenome showed enrichment of characteristic features
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Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus Stand. Genomic. Sci. Pub Date : 2018-10-01 Ji-Hyun Yun; Hojun Sung; Hyun Sik Kim; Euon Jung Tak; Woorim Kang; June-Young Lee; Dong-Wook Hyun; Pil Soo Kim; Jin-Woo Bae
Kushneria konosiri X49T 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 X49T reported here provides a genetic basis for its halophilic character. Diverse genes were involved in salt-in and -out strategies enabling adaptation of X49T to hypersaline environments. Due to resistance to high
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Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123 Stand. Genomic. Sci. Pub Date : 2018-09-18 Xinye Wang; Yantao Luo; Dongying Liu; Jiamei Wang; Shi Wei; Liang Zhao
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-negative, non-spore-forming rod strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete genome sequence information and genome annotation. The 7,374,589 bp long genome
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Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Stand. Genomic. Sci. Pub Date : 2018-08-09 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; Nicolas Rodriguez; Falk Schreiber; Lucian Smith; Fengkai Zhang; Eric Bonnet
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: Bio program SEMS, FKZ 031 6194)”.
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A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences Stand. Genomic. Sci. Pub Date : 2018-07-11 Samuel C. Epstein; Louise K. Charkoudian; Marnix H. Medema
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 organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular
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Correction to: Complete genome of a novel virulent phage ST0 lysing Escherichia coli H8 Stand. Genomic. Sci. Pub Date : 2018-07-04 Honghui Liu; Xinchun Liu; Jinqing Li
Table 1 of this original publication contained an error. The updated Table 1 is published in this correction article [1].
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Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno Stand. Genomic. Sci. Pub Date : 2018-05-09 Samuel M. Luedin; Joël F. Pothier; Francesco Danza; Nicola Storelli; Niels-Ulrik Frigaard; Matthias Wittwer; Mauro Tonolla
“Thiodictyon syntrophicum” sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation
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Short genome report of cellulose-producing commensal Escherichia coli 1094 Stand. Genomic. Sci. Pub Date : 2018-05-09 Joaquin Bernal-Bayard; Laura Gomez-Valero; Aimee Wessel; Varun Khanna; Christiane Bouchier; Jean-Marc Ghigo
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 Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and
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High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease Stand. Genomic. Sci. Pub Date : 2018-04-27 David Alvarez-Ponce; Chava L. Weitzman; Richard L. Tillett; Franziska C. Sandmeier; C. Richard Tracy
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 genomes of M. agassizii strains PS6T (ATCC 700616) and 723 (ATCC 700617) isolated from the upper respiratory tract of a Mojave desert tortoise and a gopher tortoise, respectively, both with
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Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01 Stand. Genomic. Sci. Pub Date : 2018-04-19 Rakshak Kumar; Vishal Acharya; Dharam Singh; Sanjay Kumar
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 clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the
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High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment Stand. Genomic. Sci. Pub Date : 2018-04-12 Alejandro Mateos-Rivera; Tajul Islam; Ian P. G. Marshall; Lars Schreiber; Lise Øvreås
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 species genus with a sequenced genome. The other is M. miyakonense HT12, which is the type strain of the species and the type species of the genus Methylovulum. We present the genome of M. psychrotolerants
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High quality draft genome sequence of Mycoplasma testudineum strain BH29T, isolated from the respiratory tract of a desert tortoise Stand. Genomic. Sci. Pub Date : 2018-04-11 Chava L. Weitzman; Richard L. Tillett; Franziska C. Sandmeier; C. Richard Tracy; David Alvarez-Ponce
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 BH29T (ATCC 700618T = MCCM 03231T), isolated from the upper respiratory tract of a Mojave desert tortoise with upper respiratory tract disease. The sequenced draft genome, organized in 25 scaffolds, has a length of 960,895 bp