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Pauline Bernardo, Tristan Charles-Dominique, Mohamed Barakat, Philippe Ortet, Emmanuel Fernandez, Denis Filloux, Penelope Hartnady, Tony A Rebelo, Stephen R Cousins, François Mesleard, Damien Cohez, Nicole Yavercovski, Arvind Varsani, Gordon W Harkins, Michel Peterschmitt, Carolyn M Malmstrom, Darren P Martin, Philippe Roumagnac
Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plant-associated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France)...
October 20, 2017: ISME Journal
Aharon Oren, George M Garrity
No abstract text is available yet for this article.
October 20, 2017: ISME Journal
Peter Morrison-Whittle, Matthew R Goddard
Humans have been making wine for thousands of years and microorganisms play an integral part in this process as they not only drive fermentation, but also significantly influence the flavour, aroma, and quality of finished wines. Since fruits are ephemeral, they cannot comprise a permanent microbial habitat; thus, an age-old unanswered question concerns the origin of fruit and ferment associated microbes. Here we use next-generation sequencing approaches to examine and quantify the roles of native forests, vineyard soil, bark, and fruit habitats as sources of fungal diversity in ferments...
October 20, 2017: Environmental Microbiology
Marina Solis, Carlos Bonetto, Natalia Marrochi, Ariel Paracampo, Hernán Mugni
Agriculture intensification in Argentina has increased agrochemicals consumption in the last decades and might represent an environmental risk for adjacent water bodies. The objective of the present work was to assess the effect of land use on water quality and invertebrate assemblages in the Argentine Pampas streams. Eight streams were sampled on 4 occasions during the 2013/14 growing season. Three streams are located within a biosphere reserve, two drain basins with extensive livestock fields, and three run through intensively cultivated plots; one of them contained a 30m wide uncultivated grass-covered strip between the crop and the stream...
October 10, 2017: Ecotoxicology and Environmental Safety
Elizabeth Hutchison, Nicholas A Yager, May N Taw, Matthew Taylor, Francine Arroyo, David R Sannino, Esther R Angert
Few studies have described chromosomal dynamics in bacterial cells with more than two complete chromosome copies or described changes with respect to development in polyploid cells. We examined the arrangement of chromosomal loci in the very large, highly polyploid, uncultivated intestinal symbiont Epulopiscium sp. type B using fluorescent in situ hybridization (FISH). We found that in new offspring, chromosome replication origins (oriCs) are arranged in a three-dimensional array throughout the cytoplasm. As development progresses, most oriCs become peripherally located...
October 10, 2017: Molecular Microbiology
Simon Roux, Leong-Keat Chan, Rob Egan, Rex R Malmstrom, Katherine D McMahon, Matthew B Sullivan
Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera...
October 11, 2017: Nature Communications
Anna Beltrame, Patrizia Danesi, Claudio Farina, Pierantonio Orza, Francesca Perandin, Claudia Zanardello, Paola Rodari, Silvia Staffolani, Zeno Bisoffi
Lobomycosis is a chronic skin mycosis endemic in Amazon regions characterized by chronic nodular or keloidal lesions caused by Lacazia loboi, an uncultivable fungus. Imported cases in nonendemic countries are rare and diagnosed after years. We describe a case of lobomycosis in a healthy 55-year-old Italian traveler who had acquired the infection during 5-day-honeymoon in the Amazon region of Venezuela in 1999. Several weeks after return, he recalled pruritus and papular skin lesions on the left lower limb, subsequently evolving to a plaque-like lesion...
September 25, 2017: American Journal of Tropical Medicine and Hygiene
K Holý, M Mullerová, V Palušová, M Bulko
Various approaches of determining CO2 fluxes from the soil based on 222Rn calibrated method were tested. It was shown that the exponential fits of CO2 and 222Rn depth profiles led to uncertainties up to 50% if the depth profiles of CO2 and 222Rn concentration were not measured at sufficient depths. However, CO2 fluxes determined from linear fits of CO2 and 222Rn concentrations in the surface layer of the soil are lower than the fluxes determined from exponential fits, and have lower uncertainties. The comparison of CO2 fluxes derived from 222Rn calibrated methods with directly measured CO2 fluxes showed that the latter are usually on the order of tens of percent higher than the former...
September 18, 2017: Radiation Protection Dosimetry
Fangyuan Bian, Zheke Zhong, Xiaoping Zhang, Chuanbao Yang
This study was conducted to investigate the capability of moso bamboo grown alone and in combination with Sedum plumbizincicola to remediate heavy metals. Monoculture of moso bamboo (MM), intercropping of moso bamboo × S. plumbizincicola (IMS), and control (uncultivated, CK) were established in Cu-, Zn-, and Cd-contaminated soil. Soil properties and heavy metal removal capacity were assessed. Results showed that the available and total heavy metal contents in soil (0-20 and 20-40 cm soil layers) were ranked IMS < MM < CK...
September 30, 2017: Environmental Science and Pollution Research International
Juan de Dios Caballero, Rafael Vida, Marta Cobo, Luis Máiz, Lucrecia Suárez, Javier Galeano, Fernando Baquero, Rafael Cantón, Rosa Del Campo
Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities...
September 26, 2017: MBio
Simon Roux, Joanne B Emerson, Emiley A Eloe-Fadrosh, Matthew B Sullivan
BACKGROUND: Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates...
2017: PeerJ
Vijaya Gupta, Naveen Gupta, Neena Capalash, Prince Sharma
Bacterial diversity of hot springs of northern Himalayan region of India was studied and explored for laccases, the multicopper enzymes applicable in a large number of industries due to their ability to utilize a wide range of substrates. 220 operational taxonomic units (OTUs) out of 5551 sequence reads for bacterial diversity and 3 OTUs out of 19 sequence reads for Laccase like multicopper oxidases (LMCOs) diversity were generated. Bacteroidetes (74.28%) was the most abundant phylum including genus Paludibacter (66...
September 2017: Indian Journal of Microbiology
J Cameron Thrash, Kiley W Seitz, Brett J Baker, Ben Temperton, Lauren E Gillies, Nancy N Rabalais, Bernard Henrissat, Olivia U Mason
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called "dead zones," are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown...
September 12, 2017: MBio
Masaru Konishi Nobu, Takashi Narihiro, Miaomiao Liu, Kyohei Kuroda, Ran Mei, Wen-Tso Liu
Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility...
September 11, 2017: Environmental Microbiology
Rani Anupama, Amitava Mukherjee, Subramanian Babu
Metagenomic analysis of biofilm forming bacteria in environmental samples remains challenging due to the non-availability of gene sequences of most of the uncultivable bacteria. Sequences of Pseudomonas aeruginosa PAO1-UW genes involved either directly or indirectly in biofilm formation were analyzed using BLASTn to obtain matching sequences from different strain, species and genus. Conserved regions in the functional domain of the amino acid sequences were used to design common primers for direct PCR analysis of freshwater metagenomes...
September 4, 2017: Genomics
Alyce Taylor-Brown, Labolina Spang, Nicole Borel, Adam Polkinghorne
Advances in culture-independent methods have meant that we can more readily detect and diagnose emerging infectious disease threats in humans and animals. Metagenomics is fast becoming a popular tool for detection and characterisation of novel bacterial pathogens in their environment, and is particularly useful for obligate intracellular bacteria such as Chlamydiae that require labour-intensive culturing. We have used this tool to investigate the microbial metagenomes of Chlamydia-positive cloaca and choana samples from snakes...
September 6, 2017: Scientific Reports
Joshua J Hamilton, Sarahi L Garcia, Brittany S Brown, Ben O Oyserman, Francisco Moya-Flores, Stefan Bertilsson, Rex R Malmstrom, Katrina T Forest, Katherine D McMahon
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E...
July 2017: MSystems
Shihomi Uzuhashi, Rikiya Endoh, Ri-Ichiroh Manabe, Moriya Ohkuma
Pilasporangium apinafurcum, formerly classified as Pythium apinafurcum, is a unique oomycete that infects plants asymptomatically. Here, we present the draft genome sequences of two variants of P. apinafurcum, JCM 30513 and JCM 30514, isolated from uncultivated field soil in Wakayama Prefecture, Japan.
August 31, 2017: Genome Announcements
Mahnaz Rashidi, Richard G Novy, Christopher M Wallis, Arash Rashed
'Candidatus Liberibacter solanacearum' (Lso), an uncultivable phloem-limited phytopathogenic bacteria, is known to be associated with Zebra Chip disease (ZC), which represents a major threat to potato production in the US and elsewhere. This pathogen is transmitted by the phloem-feeding potato psyllid, Bactericera cockerelli Sulc (Hem. Triozidae). Currently, there are no reports of resistance to ZC in cultivated potatoes. This greenhouse study was conducted to evaluate Lso transmission success and the susceptibility of 11 potato breeding clones, representing diverge genetic background, to ZC, in relation to a susceptible commercial cultivar, Russet Burbank...
2017: PloS One
Aravind Madhavan, Raveendran Sindhu, Binod Parameswaran, Rajeev K Sukumaran, Ashok Pandey
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities...
August 16, 2017: Applied Biochemistry and Biotechnology
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