scholarly journals Entirely Off-Grid and Solar-Powered DNA Sequencing of Microbial Communities during an Ice Cap Traverse Expedition

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 902 ◽  
Author(s):  
Glen-Oliver. F. Gowers ◽  
Oliver Vince ◽  
John-Henry Charles ◽  
Ingeborg Klarenberg ◽  
Tom Ellis ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Hot Spring ◽  
Sample Collection ◽  
Human Power ◽  
Remote Locations ◽  
Ice Cap ◽  
Metagenomic Study ◽  
Northern Edge ◽  
Solar Powered

Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth’s surface. The principal reason for this is the inaccessibility of most of these areas due to their extreme isolation and challenging environmental conditions. While remote research stations have significantly lowered the barrier to studying the microbial communities on icecaps, their use has led to a bias for data collection in the near vicinity of these institutions. Here, miniaturisation of a DNA sequencing lab suitable for off-grid metagenomic studies is demonstrated. Using human power alone, this lab was transported across Europe’s largest ice cap (Vatnajökull, Iceland) by ski and sledge. After 11 days of unsupported polar-style travel, a metagenomic study of a geothermal hot spring gorge was conducted on the remote northern edge of the ice cap. This tent-based metagenomic study resulted in over 24 h of Nanopore sequencing, powered by solar power alone. This study demonstrates the ability to conduct DNA sequencing in remote locations, far from civilised resources (mechanised transport, external power supply, internet connection, etc.), whilst greatly reducing the time from sample collection to data acquisition.

scholarly journals A metagenomic study of the microbial communities in four parallel biogas reactors

2014 ◽  
Vol 7 (1) ◽  
Author(s):  
Linn Solli ◽  
Othilde Elise Håvelsrud ◽  
Svein Jarle Horn ◽  
Anne Gunn Rike
Keyword(s):  
Microbial Communities ◽  
Biogas Reactors ◽  
Metagenomic Study

scholarly journals Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques

2020 ◽  
Author(s):  
Kevin R. Theis ◽  
Roberto Romero ◽  
Andrew D. Winters ◽  
Alan H. Jobe ◽  
Nardhy Gomez-Lopez
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Rhesus Macaques ◽  
Uterine Wall ◽  
Bacterial Burden ◽  
Multiple Modes ◽  
Fetal Tissues ◽  
Microbial Invasion ◽  
Cutibacterium Acnes

ABSTRACTThe prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.

Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

2021 ◽  
Author(s):  
Sakcham Bairoliya ◽  
Jonas Koh Zhi Xiang ◽  
Bin Cao
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Environmental Samples ◽  
Environmental Dna ◽  
Extracellular Dna ◽  
Biodiversity Assessment ◽  
Microbial Biodiversity ◽  
Technical Details ◽  
The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

Research Tools and Methods for the Analysis of Microbiota in Dairy Products

2018 ◽  
pp. 23-53 ◽  
Author(s):  
Sylvia Klaubauf ◽  
Frank J. J. Segers
Keyword(s):  
Dna Sequencing ◽  
Production Process ◽  
Microbial Communities ◽  
Dairy Products ◽  
Starter Cultures ◽  
Direct Pcr ◽  
Culture Independent ◽  
Profiling Techniques ◽  
Tools And Methods ◽  
Culture Dependent

Microorganisms play important roles in dairy products. They can be a source of spoilage, or they promote health or cause diseases. In dairy fermentations, microorganisms are of great importance due to their function as starter cultures and during the production process of dairy products. In order to better understand and improve the process, it is essential to identify the species that are involved and to monitor the development of microbial communities. There are several different approaches for the detection and analysis of the microbiota. The methods can be culture dependent and, for example, make use of morphological and physiological characters or DNA sequencing. Culture-independent methods include direct PCR and qPCR, but also electrophoresis-based profiling techniques as well as metagenomics. Descriptions of relevant methods are provided and their applications are discussed in this chapter.

scholarly journals Aspects of the Glaciology of Meighen Island, Northwest Territories, Canada

1965 ◽  
Vol 5 (40) ◽  
pp. 399-410 ◽  
Author(s):  
K. C. Arnold
Keyword(s):  
Snow Accumulation ◽  
The Arctic ◽  
North Coast ◽  
Ice Cap ◽  
The North ◽  
Four Seasons ◽  
Northern Half ◽  
Northern Edge ◽  
Summer Temperatures ◽  
Made In

Abstract Meighen Island lies in the centre of the north coast of the Queen Elizabeth Islands and fronts on the Arctic Ocean. An ice cap of about 76 km.2 covers about one-tenth of the island. Its greatest thickness of 150 m. occurs under the summit, near the south end, which was 268 m. above sea-level in 1960. The northern half of the ice cap is less than 30 m. thick; and the total volume is of the order of 2,000 × 106 m.3. Precipitation is low in the northern Queen Elizabeth Islands, and Meighen Island lies in an area where summer temperatures are lowest. In the winters of 1959–60, 1960–61 and 1961–62, the snow accumulation was 12.6, 18.2 and 14.1 cm. of water equivalent. Some snowfall remained on the higher part of the ice cap in the cold summer of 1961; but the ice cap diminished in volume in each year; by 36 × 106, 72 × 106, 22 × 106 and 91 × 106 m.3 in the 1959, 1960, 1961 and 1962 ablation seasons. If the conditions of these four seasons were maintained the ice cap would disappear in about 100 yr. However, a radio-carbon dating of a saxifrage exposed by the retreat of the ice from a small nunatak near the northern edge gave a date of less than 100 yr., and it appears that the existence of the ice cap might be sensitively related to recent climatic change. Careful surveys were made in 1959, 1960 and 1961 in an attempt to detect movement in the ice cap. Unequivocal evidence is not available from these surveys; but the stake network has been maintained and another survey has recently been completed.

scholarly journals Assessment of a portable clinical blood analyzer during space flight

1997 ◽  
Vol 43 (6) ◽  
pp. 1056-1065 ◽  
Author(s):  
Scott M Smith ◽  
Janis E Davis-Street ◽  
Tina B Fontenot ◽  
Helen W Lane
Keyword(s):  
Space Shuttle ◽  
Medical Data ◽  
Ionized Calcium ◽  
Sample Collection ◽  
Laboratory Methods ◽  
Remote Locations ◽  
Fluid Redistribution ◽  
Reliable Instrument ◽  
Orbiting Spacecraft ◽  
Control Samples

Abstract This study was designed to validate the utility of a commercial portable clinical blood analyzer (PCBA) in ground-based studies and on the space shuttle. Ionized calcium, pH, electrolytes, glucose, and hematocrit were determined. Results agreed well with those from traditional laboratory methods, and the PCBA demonstrated good between-day precision for all analytes. In-flight analysis of control samples revealed differences in one analyte (sodium). There were few changes in crew members’ results during flight, and these were expected. Potassium increased in flight compared with before flight, and potassium, pH, and hematocrit decreased after flight. Ionized calcium was decreased in flight and on landing day. Changes during flight were likely related to sample collection technique. Postflight changes likely reflected the fluid redistribution that occurs after exposure to weightlessness. These data confirm that the PCBA is a reliable instrument for most analytes, and can provide important medical data in remote locations, such as orbiting spacecraft.

‘Candidatus Oscillochloris kuznetsovii’ a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments

2020 ◽  
Vol 367 (19) ◽  
Author(s):  
Vasil A Gaisin ◽  
Denis S Grouzdev ◽  
Maria S Krutkina ◽  
Aleksandr A Ashikhmin ◽  
Maria A Sinetova ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Performance ◽  
Hot Spring ◽  
Calvin Cycle ◽  
Phylogenomic Analysis ◽  
Coastal Environments ◽  
Anoxygenic Phototrophs ◽  
Thermal Environments ◽  
Genes Encoding ◽  
Kandalaksha Gulf

ABSTRACT Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named ‘Candidatus Oscillochloris kuznetsovii’. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.

scholarly journals Metagenomics in ophthalmology: current findings and future prospectives

2019 ◽  
Vol 4 (1) ◽  
pp. e000248 ◽  
Author(s):  
Davide Borroni ◽  
Vito Romano ◽  
Stephen B Kaye ◽  
Tobi Somerville ◽  
Luca Napoli ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
High Throughput ◽  
Ocular Surface ◽  
Future Research ◽  
Ocular Infection ◽  
Ocular Diseases ◽  
Ocular Surface Diseases ◽  
High Throughput Dna Sequencing ◽  
Functional Profiles

Less than 1% of all microorganisms of the available environmental microbiota can be cultured with the currently available techniques. Metagenomics is a new methodology of high-throughput DNA sequencing, able to provide taxonomic and functional profiles of microbial communities without the necessity to culture microbes in the laboratory. Metagenomics opens to a ‘hypothesis-free’ approach, giving important details for future research and treatment of ocular diseases in ophthalmology, such as ocular infection and ocular surface diseases.

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