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https://www.readbyqxmd.com/read/29453617/site-suitability-evaluation-of-an-old-operating-landfill-using-ahp-and-gis-techniques-and-integrated-hydrogeological-and-geophysical-surveys
#1
Masoud Saatsaz, Iman Monsef, Mostafa Rahmani, Abdolreza Ghods
Because of the outdated methods of common landfill selection, it is imperative to reevaluate the usage suitability. To assess the suitability of the existing waste landfill in Zanjan, Iran, we have used a combination of the analytical hierarchy process (AHP) and GIS techniques, along with fieldwork surveys. Four major criteria and 12 subcriteria were considered, and the AHP was applied to assign the relative importance weights of criteria and subcriteria to each other. Finally, a landfill suitability map was generated and ranked based on the final suitability scores...
February 16, 2018: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29453260/a-new-cell-extraction-method-reveals-hemolymph-microbiome-of-three-aquatic-invertebrates
#2
Xinxu Zhang, Zaiqiao Sun, Xusheng Zhang, Ming Zhang, Shengkang Li
Symbiotic microorganisms have been found in the hemolymph (blood) of many aquatic invertebrates, such as crabs, shrimps and oysters. Hemolymph is a critical site in host immune response. Currently, studies on hemolymph microorganisms are mostly performed with culture-dependent strategies using selective media (e.g., TCBS, 2216E, and LB) for enumerating and isolating microbial cells. However, doubts remain about the "true" representation of the microbial abundance and diversity of symbiotic microorganisms in hemolymph, particularly for uncultivable microorganisms which are believed to be more abundant than the cultured...
February 16, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29446455/uncultivated-stromal-vascular-fraction-is-equivalent-to-adipose-derived-stem-and-stromal-cells-on-porous-polyurethrane-scaffolds-forming-adipose-tissue-in-vivo
#3
Michael Griessl, Anna-Maria Buchberger, Sybille Regn, Kilian Kreutzer, Katharina Storck
OBJECTIVES/HYPOTHESIS: To find an alternative approach to contemporary techniques in tissue augmentation and reconstruction, tissue engineering strategies aim to involve adipose-derived stem and stromal cells (ASCs) harboring a strong differentiation potential into various tissue types such as bone, cartilage, and fat. STUDY DESIGN: Animal research. METHODS: The stromal vascular fraction (SVF) was used directly as a cell source to provide a potential alternative to contemporary ASC-based adipose tissue engineering...
February 15, 2018: Laryngoscope
https://www.readbyqxmd.com/read/29423768/diversity-patterns-and-isolation-of-planctomycetes-associated-with-metalliferous-deposits-from-hydrothermal-vent-fields-along-the-valu-fa-ridge-sw-pacific
#4
Julia Endresen Storesund, Anders Lanzèn, Antonio García-Moyano, Anna-Louise Reysenbach, Lise Øvreås
The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes...
February 8, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29420776/cladogenesis-and-genomic-streamlining-in-extracellular-endosymbionts-of-tropical-stink-bugs
#5
Alejandro Otero-Bravo, Shana Goffredi, Zakee L Sabree
Phytophagous stink bugs are globally-distributed and many harbor vertically-inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont's genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts of distantly-related stink bugs has precluded inferring patterns of extracellular symbiont genome evolution. To address this knowledge gap, we completely sequenced the genomes of the uncultivable bacterial symbionts of four neotropical stink bugs of the Edessa genus...
February 6, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29396619/untapped-bacterial-diversity-and-metabolic-potential-within-unkeshwar-hot-springs-india
#6
Gajanan Mehetre, Manan Shah, Syed G Dastager, Mahesh S Dharne
Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India...
February 2, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29385846/unraveling-uncultivable-pesticide-degraders-via-stable-isotope-probing-sip
#7
Bo Jiang, Naifu Jin, Yi Xing, Yuping Su, Dayi Zhang
Uncultivable microorganisms account for over 99% of all species on earth, playing essential roles in ecological processes such as carbon/nitrogen cycle and chemical mineralization. Their functions remain unclear in ecosystems and natural habitats, requiring cutting-edge biotechnologies for a deeper understanding. Stable isotope probing (SIP) incorporates isotope-labeled elements, e.g. 13 C, 18 O or 15 N, into the cellular components of active microorganisms, serving as a powerful tool to link phylogenetic identities to their ecological functions in situ...
February 1, 2018: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29379208/differential-depth-distribution-of-microbial-function-and-putative-symbionts-through-sediment-hosted-aquifers-in-the-deep-terrestrial-subsurface
#8
Alexander J Probst, Bethany Ladd, Jessica K Jarett, David E Geller-McGrath, Christian M K Sieber, Joanne B Emerson, Karthik Anantharaman, Brian C Thomas, Rex R Malmstrom, Michaela Stieglmeier, Andreas Klingl, Tanja Woyke, M Cathryn Ryan, Jillian F Banfield
An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths...
January 29, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29365170/origin-of-pest-lineages-of-the-colorado-potato-beetle-coleoptera-chrysomelidae
#9
Victor M Izzo, Yolanda H Chen, Sean D Schoville, Cong Wang, David J Hawthorne
Colorado potato beetle (Leptinotarsa decemlineata Say [Coleoptera: Chrysomelidae]) is a pest of potato throughout the Northern Hemisphere, but little is known about the beetle's origins as a pest. We sampled the beetle from uncultivated Solanum host plants in Mexico, and from pest and non-pest populations in the United States and used mitochondrial DNA and nuclear loci to examine three hypotheses on the origin of the pest lineages: 1) the pest beetles originated from Mexican populations, 2) they descended from hybridization between previously divergent populations, or 3) they descended from populations that are native to the Plains states in the United States...
January 21, 2018: Journal of Economic Entomology
https://www.readbyqxmd.com/read/29364908/landscapes-with-different-biodiversity-influence-distribution-of-small-mammals-and-their-ectoparasitic-chigger-mites-a-comparative-study-from-southwest-china
#10
Pei-Ying Peng, Xian-Guo Guo, Dao-Chao Jin, Wen-Ge Dong, Ti-Jun Qian, Feng Qin, Zhi-Hua Yang, Rong Fan
From a previous field investigation in Yunnan, southwest China between 2001 and 2015, we selected two types of landscapes to make a retrospectively comparative study on the distribution of small mammals and their ectoparasitic chigger mites. One landscape is "mountainous uncultivated land (MUL)" with higher biodiversity, which is located in a famous "World Nature Heritage Site", the Three-Parallel-Rivers Region in the northwest of Yunnan. The other is "cultivated flatland landscape (CFL)" with lower biodiversity, which is located in the south of Yunnan...
2018: PloS One
https://www.readbyqxmd.com/read/29363425/eztree-an-automated-pipeline-for-identifying-phylogenetic-marker-genes-and-inferring-evolutionary-relationships-among-uncultivated-prokaryotic-draft-genomes
#11
Yu-Wei Wu
BACKGROUND: Inferring phylogenetic trees for newly recovered genomes from metagenomic samples is very useful in determining the identities of uncultivated microorganisms. Even though 16S ribosomal RNA small subunit genes have been established as "gold standard" markers for inferring phylogenetic trees, they usually cannot be assembled very well in metagenomes due to shared regions among 16S genes. Using single-copy marker genes to build genome trees has become increasingly popular for uncultivated species...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29345036/application-of-molecular-tools-to-elucidate-the-microbiota-of-seafood
#12
Paloma de Almeida Rodrigues, Rafaela Gomes Ferrari, Carlos Adam Conte Junior
The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages, and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result...
January 18, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29335639/reply-to-the-commentary-uncultivated-microbes-in-need-of-their-own-nomenclature
#13
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
No abstract text is available yet for this article.
January 15, 2018: ISME Journal
https://www.readbyqxmd.com/read/29322618/genome-enabled-metabolic-reconstruction-of-dominant-chemosynthetic-colonizers-in-deep-sea-massive-sulfide-deposits
#14
Shingo Kato, Takazo Shibuya, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Katsuhiko Suzuki
Deep-sea massive sulfide deposits remaining after ceasing of hydrothermal activity potentially provide energy for a chemosynthetic ecosystem in the dark, cold marine environments. Although yet-uncultivated bacteria in the phylum Nitrospirae and the class Deltaproteobacteria are known to dominate the microbial communities of sulfide deposits at and below the seafloor, their metabolic capabilities remain largely elusive. Here, we reveal the metabolic potential of these yet-uncultivated bacteria in hydrothermally inactive sulfide deposits collected at the Southern Mariana Trough by seafloor drilling...
January 10, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29314604/unravelling-the-identity-metabolic-potential-and-global-biogeography-of-the-atmospheric-methane-oxidising-upland-soil-cluster-%C3%AE
#15
Jennifer Pratscher, John Vollmers, Sandra Wiegand, Marc G Dumont, Anne-Kristin Kaster
Understanding of global methane sources and sinks is a prerequisite for the design of strategies to counteract global warming. Microbial methane oxidation in soils represents the largest biological sink for atmospheric methane. However, still very little is known about the identity, metabolic properties, and distribution of the microbial group proposed to be responsible for most of this uptake, the uncultivated upland soil cluster α (USCα). Here, we reconstructed a draft genome of USCα from a combination of targeted cell sorting and metagenomes from forest soil, providing the first insights into its metabolic potential and environmental adaptation strategies...
January 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29310749/culture-independent-approaches-to-chlamydial-genomics
#16
Alyce Taylor-Brown, Danielle Madden, Adam Polkinghorne
The expanding field of bacterial genomics has revolutionized our understanding of microbial diversity, biology and phylogeny. For most species, DNA extracted from culture material is used as the template for genome sequencing; however, the majority of microbes are actually uncultivable, and others, such as obligate intracellular bacteria, require laborious tissue culture to yield sufficient genomic material for sequencing. Chlamydiae are one such group of obligate intracellular microbes whose characterization has been hampered by this requirement...
January 3, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29297295/comet-a-workflow-using-contig-coverage-and-composition-for-binning-a-metagenomic-sample-with-high-precision
#17
Damayanthi Herath, Sen-Lin Tang, Kshitij Tandon, David Ackland, Saman Kumara Halgamuge
BACKGROUND: In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as well as the recovery of individual genomes from a sample of uncultivable microbial organisms. Both supervised and unsupervised learning methods have been employed in binning; however, characterizing a metagenomic sample containing multiple strains remains a significant challenge...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29291350/accessing-chemical-diversity-from-the-uncultivated-symbionts-of-small-marine-animals
#18
Thomas E Smith, Christopher D Pond, Elizabeth Pierce, Zachary P Harmer, Jason Kwan, Malcolm M Zachariah, Mary Kay Harper, Thomas P Wyche, Teatulohi K Matainaho, Tim S Bugni, Louis R Barrows, Chris M Ireland, Eric W Schmidt
Chemistry drives many biological interactions between the microbiota and host animals, yet it is often challenging to identify the chemicals involved. This poses a problem, as such small molecules are excellent sources of potential pharmaceuticals, pretested by nature for animal compatibility. We discovered anti-HIV compounds from small, marine tunicates from the Eastern Fields of Papua New Guinea. Tunicates are a reservoir for new bioactive chemicals, yet their small size often impedes identification or even detection of the chemicals within...
January 1, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29274958/mining-metagenomic-and-metatranscriptomic-data-for-clues-about-microbial-metabolic-functions-in-ruminants
#19
Fuyong Li, Andre L A Neves, Bibaswan Ghoshal, Le Luo Guan
Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption...
December 20, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29274798/adapting-the-caesium-137-technique-to-document-soil-redistribution-rates-associated-with-traditional-cultivation-practices-in-haiti
#20
H Velasco, R Torres Astorga, D Joseph, J S Antoine, L Mabit, A Toloza, G Dercon, Des E Walling
Large-scale deforestation, intensive land use and unfavourable rainfall conditions are responsible for significant continuous degradation of the Haitian uplands. To develop soil conservation strategies, simple and cost-effective methods are needed to assess rates of soil loss from farmland in Haiti. The fallout radionuclide caesium-137 (137Cs) provides one such means of documenting medium-term soil redistribution rates. In this contribution, the authors report the first use in Haiti of 137Cs measurements to document soil redistribution rates and the associated pattern of erosion/sedimentation rates along typical hillslopes within a traditional upland Haitian farming area...
December 21, 2017: Journal of Environmental Radioactivity
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