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Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands.

https://arctichealth.org/en/permalink/ahliterature299361
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
Christina M Ridley
Gerrit Voordouw
Author Affiliation
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada.
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Alberta
Bacteria, Aerobic - classification - genetics - isolation & purification
Biodegradation, Environmental
Fungi - classification - genetics - isolation & purification
Hydrocarbons - metabolism
Microbiota - genetics
Oil and Gas Fields - microbiology
RNA, Ribosomal, 16S - genetics
Soil Microbiology
Abstract
Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8°C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment.
PubMed ID
29688331 View in PubMed
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Comparing rock-inhabiting microbial communities in different rock types from a high arctic polar desert.

https://arctichealth.org/en/permalink/ahliterature299360
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
06-01-2018
Author
Yong-Hoe Choe
Mincheol Kim
Jusun Woo
Mi Jung Lee
Jong Ik Lee
Eun Ju Lee
Yoo Kyung Lee
Author Affiliation
Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea.
Source
FEMS Microbiol Ecol. 2018 06 01; 94(6):
Date
06-01-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Antarctic Regions
Arctic Regions
Bacteria - classification - genetics - isolation & purification
Fungi - classification - genetics - isolation & purification
Geologic Sediments - microbiology
Microbiota
Norway
RNA, Ribosomal, 16S - genetics
RNA, Ribosomal, 28S - genetics
Soil Microbiology
Svalbard
Abstract
Although rocks are habitable places for microbes in extreme environments, microbial diversity in these lithic environments is still poorly understood. The diversity and abundance of rock-inhabiting microbial communities in different types of rock in Svalbard, Norwegian High Arctic were examined using NGS sequencing of bacterial 16S rRNA genes and fungal 28S rRNA genes. Compositions of both bacterial and fungal communities varied across different rock types: sandstone, limestone, basalt, granite and travertine. Bacterial communities were dominated by Actinobacteria, Proteobacteria, Chloroflexi, Bacteroidetes and Acidobacteria. Fungal communities consisted of Eurotiomycetes, Lecanoromycetes, Dothideomycetes and Leotiomycetes. Both bacterial and fungal community compositions were significantly correlated with the geochemical characteristics of rocks. Bacterial communities were considerably correlated with the rock elements such as Mg and Ca. Fungal communities were considerably correlated with Fe. Interestingly, many dominant bacterial and fungal operational taxonomic units in the investigated rocks from the study area were closely affiliated to those found in other cold regions such as Alpine area, Arctic and Antarctica, suggesting that environmental constraints such as cold temperature may lead to convergence in microbial community composition. These results confirm that rocks in cold environments act as reservoirs of diverse bacteria and fungi, which may improve our understanding of lithic microbial ecology in the cold desert.
PubMed ID
29688499 View in PubMed
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[Comparison of the fungal complexes of the Japanese scallop Mizuhopecten yessoensis (Jay, 1856) from different areas of the Peter the Great Bay, Sea of Japan].

https://arctichealth.org/en/permalink/ahliterature262068
Source
Mikrobiologiia. 2014 Sep-Oct;83(5):599-604
Publication Type
Article
Author
O G Borzykh
L V Zvereva
Source
Mikrobiologiia. 2014 Sep-Oct;83(5):599-604
Language
Russian
Publication Type
Article
Keywords
Animals
Biodiversity
Fungi - classification - genetics - isolation & purification
Oceans and Seas
Pectinidae - microbiology
Phylogeny
Siberia
Abstract
Mycological investigation of the Japanese scallop Mizuhopecten yessoensis (Jay) (Bivalvia) collected in different areas of the Peter the Great Bay, Sea of Japan, was carried out. A total of 72 species of filamentous fungi belonging to 30 genera of ascomycetes, anamorphous fungi, and zygomycetes was isolated from the internal organs of the scallop. The species.diversity of mycelial fungi in the internal organs, especially of members of the generaAspergillus, Penicillium, Cladosporium, and Chaetomium, was found to increase in polluted coastal waters.
PubMed ID
25844471 View in PubMed
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Diversity and significance of mold species in Norwegian drinking water.

https://arctichealth.org/en/permalink/ahliterature167130
Source
Appl Environ Microbiol. 2006 Dec;72(12):7586-93
Publication Type
Article
Date
Dec-2006
Author
Gunhild Hageskal
Ann Kristin Knutsen
Peter Gaustad
G Sybren de Hoog
Ida Skaar
Author Affiliation
National Veterinary Institute, Section for Food and Feed Microbiology, P.O. Box 8156 Dep., 0033 Oslo, Norway.
Source
Appl Environ Microbiol. 2006 Dec;72(12):7586-93
Date
Dec-2006
Language
English
Publication Type
Article
Keywords
Aspergillus - classification - genetics - isolation & purification
Fresh Water - microbiology
Fungi - classification - genetics - isolation & purification
Humans
Molecular Sequence Data
Norway
Penicillium - classification - genetics - isolation & purification
Sequence Analysis, DNA
Species Specificity
Trichoderma - classification - genetics - isolation & purification
Water Pollution - analysis
Water supply
Abstract
In order to determine the occurrence, distribution, and significance of mold species in groundwater- and surface water-derived drinking water in Norway, molds isolated from 273 water samples were identified. Samples of raw water, treated water, and water from private homes and hospital installations were analyzed by incubation of 100-ml membrane-filtered samples on dichloran-18% glycerol agar. The total count (number of CFU per 100 ml) of fungal species and the species diversity within each sample were determined. The identification of mold species was based on morphological and molecular methods. In total, 94 mold species belonging to 30 genera were identified. The mycobiota was dominated by species of Penicillium, Trichoderma, and Aspergillus, with some of them occurring throughout the drinking water system. Several of the same species as isolated from water may have the potential to cause allergic reactions or disease in humans. Other species are common contaminants of food and beverages, and some may cause unwanted changes in the taste or smell of water. The present results indicate that the mycobiota of water should be considered when the microbiological safety and quality of drinking water are assessed. In fact, molds in drinking water should possibly be included in the Norwegian water supply and drinking water regulations.
Notes
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PubMed ID
17028226 View in PubMed
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Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest.

https://arctichealth.org/en/permalink/ahliterature279800
Source
Appl Environ Microbiol. 2016 May;82(9):2632-43
Publication Type
Article
Date
May-2016
Author
Hui Sun
Eeva Terhonen
Andriy Kovalchuk
Hanna Tuovila
Hongxin Chen
Abbot O Oghenekaro
Jussi Heinonsalo
Annegret Kohler
Risto Kasanen
Harri Vasander
Fred O Asiegbu
Source
Appl Environ Microbiol. 2016 May;82(9):2632-43
Date
May-2016
Language
English
Publication Type
Article
Keywords
Biodiversity
Ecosystem
Finland
Forests
Fungi - classification - genetics - isolation & purification - metabolism
Sequence Analysis, DNA
Soil - chemistry
Soil Microbiology
Trees - microbiology
Wood - microbiology
Abstract
Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P
Notes
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PubMed ID
26896139 View in PubMed
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Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization.

https://arctichealth.org/en/permalink/ahliterature123144
Source
Appl Environ Microbiol. 2012 Sep;78(17):6078-86
Publication Type
Article
Date
Sep-2012
Author
Tarah S Sullivan
Neil R Gottel
Nicholas Basta
Philip M Jardine
Christopher W Schadt
Author Affiliation
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Source
Appl Environ Microbiol. 2012 Sep;78(17):6078-86
Date
Sep-2012
Language
English
Publication Type
Article
Keywords
Biodiversity
Carboxylic Acids - metabolism
Cluster analysis
DNA, Fungal - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Fungi - classification - genetics - isolation & purification - metabolism
Genes, rRNA
Humans
Lead - metabolism
Molecular Sequence Data
Phylogeny
RNA, Fungal - genetics
RNA, Ribosomal, 28S - genetics
Sequence Analysis, DNA
Soil Microbiology
Soil Pollutants - metabolism
Tennessee
Abstract
Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.
Notes
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PubMed ID
22729539 View in PubMed
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Fungal and bacterial diversity of Svalbard subglacial ice.

https://arctichealth.org/en/permalink/ahliterature307508
Source
Sci Rep. 2019 12 27; 9(1):20230
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-27-2019
Author
L Perini
C Gostincar
N Gunde-Cimerman
Author Affiliation
Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000, Ljubljana, Slovenia.
Source
Sci Rep. 2019 12 27; 9(1):20230
Date
12-27-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Bacteria - classification - genetics - isolation & purification
Basidiomycota - classification - genetics - isolation & purification
Biodiversity
Ecosystem
Fresh Water - microbiology
Fungi - classification - genetics - isolation & purification
Genetic Variation
Geography
Ice Cover - microbiology
Proteobacteria - classification - genetics - isolation & purification
RNA, Ribosomal, 16S - genetics
Seawater - microbiology
Sequence Analysis, DNA - methods
Species Specificity
Svalbard
Abstract
The composition of fungal and bacterial communities in three polythermal glaciers and associated aquatic environments in Kongsfjorden, Svalbard was analysed using a combination of cultivation and amplicon sequencing. 109 fungal strains belonging to 30 mostly basidiomycetous species were isolated from glacial samples with counts up to 103 CFU/100?ml. Glaciozyma-related taxon and Phenoliferia psychrophenolica were the dominant species. Unexpectedly, amplicon sequencing uncovered sequences of Chytridiomycota in all samples and Rozellomycota in sea water, lake water, and tap water. Sequences of Malassezia restricta and of the extremely halotolerant Hortaea werneckii were also found in subglacial habitats for the first time. Overall, the fungal communities within a glacier and among glaciers were diverse and spatially heterogenous. Contrary to this, there was a large overlap between the bacterial communities of different glaciers, with Flavobacterium sp. being the most frequently isolated. In amplicon sequencing Actinobacteria and Proteobacteria sequences were the most abundant.
PubMed ID
31882659 View in PubMed
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Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs.

https://arctichealth.org/en/permalink/ahliterature288282
Source
ISME J. 2017 09;11(9):1964-1974
Publication Type
Article
Date
09-2017
Author
Raisa Mäkipää
Tiina Rajala
Dmitry Schigel
Katja T Rinne
Taina Pennanen
Nerea Abrego
Otso Ovaskainen
Source
ISME J. 2017 09;11(9):1964-1974
Date
09-2017
Language
English
Publication Type
Article
Keywords
Fungi - classification - genetics - isolation & purification - metabolism
Mycorrhizae - classification - genetics - isolation & purification - metabolism
Norway
Picea - microbiology
Soil - chemistry
Soil Microbiology
Wood - microbiology
Abstract
We investigated the interaction between fungal communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the fungal communities from soil, some fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting fungal communities interact at all decay phases of wood that has important implications in fungal community dynamics and thus nutrient transportation.
Notes
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PubMed ID
28430188 View in PubMed
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Investigation of the microbiota associated with ungerminated and germinated Norwegian barley cultivars with focus on lactic acid bacteria.

https://arctichealth.org/en/permalink/ahliterature311140
Source
Int J Food Microbiol. 2021 Mar 02; 341:109059
Publication Type
Journal Article
Date
Mar-02-2021
Author
Hilde Marit Østlie
Davide Porcellato
Guro Kvam
Trude Wicklund
Author Affiliation
Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway. Electronic address: hilde.ostlie@nmbu.no.
Source
Int J Food Microbiol. 2021 Mar 02; 341:109059
Date
Mar-02-2021
Language
English
Publication Type
Journal Article
Keywords
Carnobacterium - classification - genetics - isolation & purification
Enterococcus - classification - genetics - isolation & purification
Fungi - classification - genetics - isolation & purification
Germination - physiology
Hordeum - microbiology
Lactococcus lactis - classification - genetics - isolation & purification
Leuconostoc - classification - genetics - isolation & purification
Microbiota
Norway
RNA, Ribosomal, 16S - genetics
Abstract
The microbial community of ungerminated and germinated barley grains from three different cultivars grown at four different locations in Norway was investigated by culture dependent and culture independent methods. Lactic acid bacteria (LAB) was focused in this study and was isolated from germinated barley. The number of LAB ranged between 2.8 and 4.6 log cfu/g in ungerminated grains and between 4.9 and 6.3 log cfu/g in germinated grains. In total 66 out of 190 isolates were Gram+, catalase-negative and presumptive LAB. The LAB isolates were by 16S rRNA sequencing identified to be Carnobacterium maltaromaticum (6), Lactococcus lactis (2), Enterococcus sp. (1) and Leuconostoc sp. (57). Germination significantly influenced the bacterial composition. Regarding the different cultivars and growth places no significant difference in bacterial composition was seen. The most abundant bacterial genus was Pantoea (18.5% of the total sequences), followed by Rhizobium (10.1%) and Sphingomonas (9.9%). Fungal composition was significantly influenced by the germination process and the cultivation place, but no significant difference in fungal composition was detected between the 3 cultivars. The most abundant fungal genera were Cryptococcus (43.8% of all the sequences), Cladosporium (8.2%), Pyrenophora (7.4%) and Vagicola (6.3%). This study revealed knowledge of barley grain associated microbes of Norwegian barley that can be useful to control the malt quality. Germination affected both bacterial and fungal microbiota composition. No difference in bacterial microbiota composition was seen regarding cultivars and cultivation place, however, the fungal microbiota composition was significantly influenced by the cultivation place. Differences in fungal community of ungerminated and germinated barley samples of different geographical locations were more pronounced than differences in bacterial communities.
PubMed ID
33508581 View in PubMed
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Microbial diversity along a gradient in peatlands treating mining-affected waters.

https://arctichealth.org/en/permalink/ahliterature302169
Source
FEMS Microbiol Ecol. 2018 10 01; 94(10):
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Date
10-01-2018
Author
Katharina Kujala
Anu Mikkonen
Karita Saravesi
Anna-Kaisa Ronkanen
Marja Tiirola
Author Affiliation
Water Resources and Environmental Engineering Research Unit, University of Oulu, PO Box 4300, FI-90014 Oulu, Finland.
Source
FEMS Microbiol Ecol. 2018 10 01; 94(10):
Date
10-01-2018
Language
English
Publication Type
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Archaea - classification - genetics - isolation & purification - metabolism
Bacteria - classification - genetics - isolation & purification - metabolism
Biodiversity
Finland
Fungi - classification - genetics - isolation & purification - metabolism
Microbiota
Mining
Soil Microbiology
Water Pollutants, Chemical - analysis - metabolism
Water Purification - methods
Abstract
Peatlands are used for the purification of mining-affected waters in Northern Finland. In Northern climate, microorganisms in treatment peatlands (TPs) are affected by long and cold winters, but studies about those microorganisms are scarce. Thus, the bacterial, archaeal and fungal communities along gradients of mine water influence in two TPs were investigated. The TPs receive waters rich in contaminants, including arsenic (As), sulfate (SO42-) and nitrate (NO3-). Microbial diversity was high in both TPs, and microbial community composition differed between the studied TPs. Bacterial communities were dominated by Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria, archaeal communities were dominated by Methanomicrobia and the Candidate phylum Bathyarchaeota, and fungal communities were dominated by Ascomycota (Leotiomycetes, Dothideomycetes, Sordariomycetes). The functional potential of the bacterial and archaeal communities in TPs was predicted using PICRUSt. Sampling points affected by high concentrations of As showed higher relative abundance of predicted functions related to As resistance. Functions potentially involved in nitrogen and SO42- turnover in TPs were predicted for both TPs. The results obtained in this study indicate that (i) diverse microbial communities exist in Northern TPs, (ii) the functional potential of the peatland microorganisms is beneficial for contaminant removal in TPs and (iii) microorganisms in TPs are likely well-adapted to high contaminant concentrations as well as to the Northern climate.
PubMed ID
30137344 View in PubMed
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