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"Microbial ecology"

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https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#1
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28639032/case-study-microbial-ecology-and-forensics-of-chinese-drywall-elemental-sulfur-disproportionation-as-primary-generator-of-hydrogen-sulfide
#2
Francisco A Tomei Torres
Drywall manufactured in China released foul odors attributed to volatile sulfur compounds. These included hydrogen sulfide, methyl mercaptan, and sulfur dioxide. Given that calcium sulfate is the main component of drywall, one would suspect bacterial reduction of sulfate to sulfide as the primary culprit. However, when the forensics, i.e., the microbial and chemical signatures left in the drywall, are studied, the evidence suggests that, rather than dissimilatory sulfate reduction, disproportionation of elemental sulfur to hydrogen sulfide and sulfate was actually the primary cause of the malodors...
June 21, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#3
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28625991/different-amplicon-targets-for-sequencing-based-studies-of-fungal-diversity
#4
Francesca De Filippis, Manolo Laiola, Giuseppe Blaiotta, Danilo Ercolini
Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes with the 16S rRNA being the gold standard for bacteria. As for Fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28621836/-dietary-advanced-glycation-end-products-modify-gut-microbial-composition-and-partially-increase-colon-permeability-in-rats
#5
Wanting Qu, Xiaojin Yuan, Jinsong Zhao, Yingxiao Zhang, Jing Hu, Jiawei Wang, Juxiu Li
SCOPE: The adverse impacts of dietary advanced glycation end products (AGEs) on health are currently of interest. These compounds are inevitably formed during thermal food processing and make foods less digestible because of protein cross-linking. This study examined not only whether dietary AGEs alter cecal microbiota and their metabolites but also their effects on colon permeability. METHODS AND RESULTS: Sprague-Dawley rats were exposed to a high-AGEs diet (AGEs content was increased by heating food at 125°C/3 h) for 6, 12, or 18 weeks...
June 16, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28614743/impacts-of-biostimulation-and-bioaugmentation-on-the-performance-and-microbial-ecology-in-methanogenic-reactors-treating-purified-terephthalic-acid-wastewater
#6
Miaomiao Liu, Shanquan Wang, Masaru Konishi Nobu, Benjamin T W Bocher, Scott A Kaley, Wen-Tso Liu
Up-flow anaerobic sludge blanket (UASB) processes treating purified terephthalic acid (PTA) wastewater often face challenges associated with biomass loss. As excessive biomass loss could lead to deterioration of PTA removal, biostimulation and bioaugmentation were often practiced without understanding the microbial impact in UASB. Three laboratory-scale UASB reactors were operated with synthetic PTA wastewater as the feed, with two added with co-substrate (glucose or molasses) on Day 170 for 90 days, and one with external granules on Day 118...
June 4, 2017: Water Research
https://www.readbyqxmd.com/read/28611749/sustaining-rare-marine-microorganisms-macroorganisms-as-repositories-and-dispersal-agents-of-microbial-diversity
#7
Marc Troussellier, Arthur Escalas, Thierry Bouvier, David Mouillot
Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28609134/relationships-among-microbial-communities-maternal-cells-oligosaccharides-and-macronutrients-in-human-milk
#8
Janet E Williams, William J Price, Bahman Shafii, Katherine M Yahvah, Lars Bode, Mark A McGuire, Michelle K McGuire
BACKGROUND: Human milk provides all essential nutrients necessary for early life and is rich in nonnutrients, maternally derived (host) cells, and bacteria, but almost nothing is known about the interplay among these components. Research aim: The primary objective of this research was to characterize relationships among macronutrients, maternal cells, and bacteria in milk. METHODS: Milk samples were collected from 16 women and analyzed for protein, lipid, fatty acid, lactose, and human milk oligosaccharide concentrations...
June 1, 2017: Journal of Human Lactation: Official Journal of International Lactation Consultant Association
https://www.readbyqxmd.com/read/28607347/living-microorganisms-change-the-information-shannon-content-of-a-geophysical-system
#9
Fiona H M Tang, Federico Maggi
The detection of microbial colonization in geophysical systems is becoming of interest in various disciplines of Earth and planetary sciences, including microbial ecology, biogeochemistry, geomicrobiology, and astrobiology. Microorganisms are often observed to colonize mineral surfaces, modify the reactivity of minerals either through the attachment of their own biomass or the glueing of mineral particles with their mucilaginous metabolites, and alter both the physical and chemical components of a geophysical system...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28600313/novel-microbial-assemblages-dominate-weathered-sulfide-bearing-rock-from-copper-nickel-deposits-in-the-duluth-complex-minnesota-usa
#10
Daniel S Jones, Kim A Lapakko, Zachary J Wenz, Michael C Olson, Elizabeth W Roepke, Michael J Sadowsky, Paige J Novak, Jake V Bailey
The Duluth Complex in northeastern Minnesota hosts economically-significant deposits of copper, nickel, and platinum group elements (PGEs). The primary sulfide mineralogy of these deposits includes the minerals pyrrhotite, chalcopyrite, pentlandite, and cubanite, and weathering experiments show that most sulfide-bearing rock from the Duluth Complex generates moderately acidic leachate (pH 4-6). Microorganisms are important catalysts for metal sulfide oxidation and could influence water quality from mines in the Duluth Complex...
June 9, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28588144/effect-of-water-flow-and-chemical-environment-on-microbiota-growth-and-composition-in-the-human-colon
#11
Jonas Cremer, Markus Arnoldini, Terence Hwa
The human gut harbors a dynamic microbial community whose composition bears great importance for the health of the host. Here, we investigate how colonic physiology impacts bacterial growth, which ultimately dictates microbiota composition. Combining measurements of bacterial physiology with analysis of published data on human physiology into a quantitative, comprehensive modeling framework, we show how water flow in the colon, in concert with other physiological factors, determine the abundances of the major bacterial phyla...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28586691/marine-protists-are-not-just-big-bacteria
#12
REVIEW
Patrick J Keeling, Javier Del Campo
The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern...
June 5, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28576374/molecular-investigation-of-bacterial-communities-during-the-manufacturing-and-ripening-of-semi-hard-iranian-liqvan-cheese
#13
M Ramezani, S M Hosseini, I Ferrocino, M A Amoozegar, L Cocolin
Liqvan (or Lighvan) is a traditional Iranian cheese from the East Azerbaijan province of Iran, which is made of raw ewe's milk without the addition of a starter. The grazing pastures, environmental conditions and the ancient regional production methods allocate a distinctive microbial ecology to this type of cheese, and these factors are consequently associated with the quality of the product. In this study, the microbiota of the milk, curd and cheese has been investigated using culture independent approaches...
September 2017: Food Microbiology
https://www.readbyqxmd.com/read/28574490/capturing-the-genetic-makeup-of-the-active-microbiome-in-situ
#14
Esther Singer, Michael Wagner, Tanja Woyke
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates...
June 2, 2017: ISME Journal
https://www.readbyqxmd.com/read/28572798/phylogenetic-diversity-of-t4-type-phages-in-sediments-from-the-subtropical-pearl-river-estuary
#15
Maoqiu He, Lanlan Cai, Chuanlun Zhang, Nianzhi Jiao, Rui Zhang
Viruses are an abundant and active component of marine sediments and play a significant role in microbial ecology and biogeochemical cycling at local and global scales. To obtain a better understanding of the ecological characteristics of the viriobenthos, the abundance and morphology of viruses and the diversity and community structure of T4-type phages were systematically investigated in the surface sediments of the subtropical Pearl River Estuary (PRE). Viral abundances ranged from 4.49 × 10(8) to 11.7 × 10(8) viruses/g and prokaryotic abundances ranged from 2...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28559161/dna-metabarcoding-to-assess-indoor-fungal-communities-electrostatic-dust-collectors-and-illumina-sequencing
#16
Steffi Rocchi, Benoit Valot, Gabriel Reboux, Laurence Millon
DNA metabarcoding is increasingly being used to characterize the microbiological composition of both the indoor and outdoor environments of dwellings. Our study aimed to evaluate metabarcoding and bioinformatic analysis resulting from calibrated samples and samples collected by an electrostatic dust collector (EDC) in dwellings with no moisture problems. Thus, the fungal communities of 14 dwellings (eastern France, Franche-Comté region) were analyzed by Illumina MiSeq technology after amplification of the ITS2 region...
May 27, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28558432/bioaerosol-sampling-and-detection-methods-based-on-molecular-approaches-no-pain-no-gain
#17
Hamza Mbareche, Evelyne Brisebois, Marc Veillette, Caroline Duchaine
Bioaerosols are among the less studied particles in the environment. The lack of standardization in sampling procedures, difficulties related to the effect of sampling processes on the integrity of microorganisms, and challenges associated with the application of environmental microbiology analyses and molecular and culture methods frighten many young scientists. Every microorganism has its own particularities and acts differently when aerosolized in various conditions. Because the air is an extremely biologically diluted environment, it is necessary to concentrate its content before any analysis is performed...
December 1, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28553266/the-grapevine-and-wine-microbiome-insights-from-high-throughput-amplicon-sequencing
#18
REVIEW
Horatio H Morgan, Maret du Toit, Mathabatha E Setati
From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#19
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28523076/metaproteomics-guided-selection-of-targeted-enzymes-for-bioprospecting-of-mixed-microbial-communities
#20
Jutta Speda, Bengt-Harald Jonsson, Uno Carlsson, Martin Karlsson
BACKGROUND: Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state...
2017: Biotechnology for Biofuels
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