scholarly journals Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

2021 ◽  
Vol 12 ◽  
Author(s):  
Eduard Fadeev ◽  
Magda G. Cardozo-Mino ◽  
Josephine Z. Rapp ◽  
Christina Bienhold ◽  
Ian Salter ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
Arctic Ocean ◽  
The Arctic ◽  
Rrna Gene ◽  
Marine Habitats ◽  
The Arctic Ocean ◽  
Primer Sets ◽  
Extreme Seasonality

Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3–V4 and V4–V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3–V4, and the phylum Planctomycetes by V4–V5). However, the V4–V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10–20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4–V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment.

scholarly journals Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean

2011 ◽  
Vol 61 (4) ◽  
pp. 850-853 ◽  
Author(s):  
Yong Yu ◽  
Hui-Rong Li ◽  
Yin-Xin Zeng
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Arctic Ocean ◽  
Chukchi Sea ◽  
Sequence Similarity ◽  
The Arctic ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
The Arctic Ocean

A novel psychrotolerant bacterial strain, BCw111T, was isolated from seawater samples from the Chukchi Sea in the Arctic Ocean. Cells of strain BCw111T were Gram-negative, motile, facultatively anaerobic, curved rods and were able to grow at 0–30 °C (optimum 23–25 °C). Strain BCw111T had Q-8 as the major respiratory quinone and contained iso-C15 : 0 2-OH and/or C16 : 1ω7c (28.13 %), C16 : 0 (13.28 %) and C17 : 1 (12.90 %) as the major cellular fatty acids. The genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BCw11T formed a distinct lineage within the genus Colwellia and exhibited the highest 16S rRNA gene sequence similarity with Colwellia polaris 537T (97.8 %) and Colwellia aestuarii SMK-10T (97.1 %). Based on phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Colwellia chukchiensis sp. nov., is proposed. The type strain is BCw111T ( = CGMCC 1.9127T  = LMG 25329T  = DSM 22576T).

scholarly journals An 18S V4 rDNA metabarcoding dataset of protist diversity in the Atlantic inflow to the Arctic Ocean, through the year and down to 1000 m depth

2021 ◽  
Author(s):  
Elianne Egge ◽  
Stephanie Elferink ◽  
Daniel Vaulot ◽  
Uwe John ◽  
Gunnar Bratbak ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
High Throughput Sequencing ◽  
Sea Water ◽  
Size Fraction ◽  
The Arctic ◽  
Reference Database ◽  
Rrna Gene ◽  
Svalbard Archipelago ◽  
The Arctic Ocean ◽  
Epipelagic Zone

AbstractArctic marine protist communities have been understudied due to challenging sampling conditions, in particular during winter and in deep waters. The aim of this study was to improve our knowledge on Arctic protist diversity through the year, both in the epipelagic (< 200 m depth) and mesopelagic zones (200-1000 m depth). Sampling campaigns were performed in 2014, during five different months, to capture the various phases of the Arctic primary production: January (winter), March (pre-bloom), May (spring bloom), August (post-bloom) and November (early winter). The cruises were undertaken west and north of the Svalbard archipelago, where warmer Atlantic waters from the West Spitsbergen Current meets cold Arctic waters from the Arctic Ocean. From each cruise, station, and depth, 50 L of sea water were collected and the plankton was size-fractionated by serial filtration into four size fractions between 0.45-200 µm, representing the picoplankton, nanoplankton and microplankton. In addition vertical net hauls were taken from 50 m depth to the surface at selected stations. From the plankton samples DNA was extracted, the V4 region of the 18S rRNA-gene was amplified by PCR with universal eukaryote primers and the amplicons were sequenced by Illumina high-throughput sequencing. Sequences were clustered into Amplicon Sequence Variants (ASVs), representing protist genotypes, with the dada2 pipeline. Taxonomic classification was made against the curated Protist Ribosomal Reference database (PR2). Altogether 6,536 protist ASVs were obtained (including 54 fungal ASVs). Both ASV richness and taxonomic composition were strongly dependent on size-fraction, season, and depth. ASV richness was generally higher in the smaller fractions, and higher in winter and the mesopelagic samples than in samples from the well-lit epipelagic zone during summer. During spring and summer, the phytoplankton groups diatoms, chlorophytes and haptophytes dominated in the epipelagic zone. Parasitic and heterotrophic groups such as Syndiniales and certain dinoflagel-lates dominated in the mesopelagic zone all year, as well as in the epipelagic zone during the winter. The dataset is available at https://doi.org/10.17882/79823, (Egge et al., 2014).

scholarly journals Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

2019 ◽  
Vol 85 (7) ◽  
Author(s):  
Alexander Burkert ◽  
Thomas A. Douglas ◽  
Mark P. Waldrop ◽  
Rachel Mackelprang
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Community Composition ◽  
Environmental Conditions ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Subzero Temperatures ◽  
Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

scholarly journals Advantage of Using Inosine at the 3′ Termini of 16S rRNA Gene Universal Primers for the Study of Microbial Diversity

2006 ◽  
Vol 72 (11) ◽  
pp. 6902-6906 ◽  
Author(s):  
Eitan Ben-Dov ◽  
Orr H. Shapiro ◽  
Nachshon Siboni ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Environmental Samples ◽  
Annealing Temperature ◽  
Universal Primers ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Primer Sets

ABSTRACT To overcome the shortcomings of universal 16S rRNA gene primers 8F and 907R when studying the diversity of complex microbial communities, the 3′ termini of both primers were replaced with inosine. A comparison of the clone libraries derived using both primer sets showed seven bacterial phyla amplified by the altered primer set (8F-I/907R-I) whereas the original set amplified sequences belonging almost exclusively to Proteobacteria (95.8%). Sequences belonging to Firmicutes (42.6%) and Thermotogae (9.3%) were more abundant in a library obtained by using 8F-I/907R-I at a PCR annealing temperature of 54°C, while Proteobacteria sequences were more frequent (62.7%) in a library obtained at 50°C, somewhat resembling the result obtained using the original primer set. The increased diversity revealed by using primers 8F-I/907R-I confirms the usefulness of primers with inosine at the 3′ termini in studying the microbial diversity of environmental samples.

Freshwater microbial community diversity in a rapidly changing High Arctic watershed

2019 ◽  
Vol 95 (11) ◽  
Author(s):  
Maria Antonia Cavaco ◽  
Vincent Lawrence St. Louis ◽  
Katja Engel ◽  
Kyra Alexandra St. Pierre ◽  
Sherry Lin Schiff ◽  
...  
Keyword(s):  
Ecosystem Services ◽  
Microbial Community ◽  
Microbial Communities ◽  
Active Layer ◽  
Hydrological Cycle ◽  
High Arctic ◽  
The Arctic ◽  
Future Climate Change ◽  
Freshwater Ecosystem ◽  
Rrna Gene

ABSTRACT Current models predict increases in High Arctic temperatures and precipitation that will have profound impacts on the Arctic hydrological cycle, including enhanced glacial melt and thawing of active layer soils. However, it remains uncertain how these changes will impact the structure of downstream resident freshwater microbial communities and ensuing microbially driven freshwater ecosystem services. Using the Lake Hazen watershed (Nunavut, Canada; 82°N, 71°W) as a sentinel system, we related microbial community composition (16S rRNA gene sequencing) to physicochemical parameters (e.g. dissolved oxygen and nutrients) over an annual hydrological cycle in three freshwater compartments within the watershed: (i) glacial rivers; (ii) active layer thaw-fed streams and waterbodies and (iii) Lake Hazen, into which (i) and (ii) drain. Microbial communities throughout these freshwater compartments were strongly interconnected, hydrologically, and often correlated with the presence of melt-sourced chemicals (e.g. dissolved inorganic carbon) as the melt season progressed. Within Lake Hazen itself, water column microbial communities were generally stable over spring and summer, despite fluctuating lake physicochemistry, indicating that these communities and the potential ecosystem services they provide therein may be resilient to environmental change. This work helps to establish a baseline understanding of how microbial communities and the ecosystem services they provide in Arctic watersheds might respond to future climate change.

scholarly journals Distribution of Acetothermia-dominated microbial communities in alkaline hot springs of Baikal Rift Zone.

2017 ◽  
Author(s):  
Svetlana V. Zaitseva ◽  
Elena V. Lavrentieva ◽  
Aryuna A. Radnagurueva ◽  
Olga A. Baturina ◽  
Marsel R. Kabilov ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Hot Springs ◽  
Rift Zone ◽  
Hot Spring ◽  
Baikal Rift Zone ◽  
Rrna Gene ◽  
Acetyl Coa Pathway

Alkaline hot springs are unique extreme habitats resemble the early Earth and present a valuable resource for the discovery of procaryotic community diversity and isolation of the novel thermophilic Bacteria and Archaea. One of the model for the possible origin of biochemistry in alkaline hot springs revealed the acetyl-CoA pathway of CO2 fixation might be the most ancient form of carbon metabolism. Recent phylogenetic studies have suggested that the phylum Acetothermia is one of the deep branches of the Bacteria domain. Firstly Acetothermia (Candidate division OP1) was characterized in a culture independent molecular phylogenetic survey based on the 16S rRNA gene of the sulfide-rich hot spring, Obsidian Pool, a 75 to 95oC hot spring. Two nearly complete genomes of Acetothermia were established based on genome-resolved metagenomic analysis and its capability of implementing acetogenesis through the ancient reductive acetyl-CoA pathway by utilizing CO2 and H2 was revealed. Although genomic, proteomic and metagenomic approaches investigate basic metabolism and potentional energy conservation of uncultivated candidate phyla but ecological roles of these bacteria and general patterns of diversity and community structure stay unclear. General hydrochemical and geological characterization of alkaline thermal springs of the Baikal Rift zone with high silica concentrations and a nitrogen dominated gas phase is provided. Previous microbiogical studies based on culture-dependent methods recovered a large number of bacterial strains from thermal springs located in Baikal Rift zone. We combined microbial communities analysis by using high-throughput 16S rRNA gene sequencing, biogeochemical measurements, sediment mineralogy and physicochemical characteristics to investigate ecosystems of alkaline hot springs located in the Baikal Rift zone. Uncultivated bacteria belonging to the phylum Acetothermia, along with members of the phyla Firmicutes and Proteobacteria, were identified as the dominant group in hydrothermal sediments communities in the alkaline hot springs of Baikal Rift zone. In bottom sediments of the Alla hot spring, about 57% of all classified sequences represent this phylum. Geochemistry of fluids and sample type were strongly correlated with microbial community composition. The Acetothermia exhibited the highest relative abundance in sediment microbial community associated with alkaline thermal fluids enriched in Fe, Zn, Ni, Al and Cr.

scholarly journals Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community

2018 ◽  
Author(s):  
Alexandra Perras ◽  
Kaisa Koskinen ◽  
Maximilian Mora ◽  
Michael Beck ◽  
Lisa Wink ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Human Health ◽  
Gene Targeting ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
Stool Samples ◽  
Human Stool

AbstractThe gut microbiome is strongly interwoven with human health. Conventional gut microbiome analysis generally involves 16S rRNA gene targeting next generation sequencing (NGS) of stool microbial communities, and correlation of results with clinical parameters. However, some microorganisms may not be alive at the time of sampling, and thus their impact on the human health is potentially less significant. As conventional NGS methods do not differentiate between viable and dead microbial components, retrieved results provide only limited information.Propidium monoazide (PMA) is frequently used in food safety monitoring and other disciplines to discriminate living from dead cells. PMA binds to free DNA and masks it for subsequent procedures. In this article we show the impact of PMA on the results of 16S rRNA gene-targeting NGS from human stool samples and validate the optimal applicable concentration to achieve a reliable detection of the living microbial communities.Fresh stool samples were treated with a concentration series of zero to 300 μM PMA, and were subsequently subjected to amplicon-based NGS. The results indicate that a substantial proportion of the human microbial community is not intact at the time of sampling. PMA treatment significantly reduced the diversity and richness of the sample depending on the concentration and impacted the relative abundance of certain important microorganisms (e.g. Akkermansia, Bacteroides). Overall, we found that a concentration of 100 μM PMA was sufficient to quench signals from disrupted microbial cells.The optimized protocol proposed here can be easily implemented in classical microbiome analyses, and helps to retrieve an improved and less blurry picture of the microbial community composition by excluding signals from background DNA.

The response of microbial communities to diverse organic matter sources in the Arctic Ocean

2009 ◽  
Vol 56 (17) ◽  
pp. 1249-1263 ◽  
Author(s):  
Rachael Y. Dyda ◽  
Marcelino T. Suzuki ◽  
Marcos Y. Yoshinaga ◽  
H. Rodger Harvey
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Arctic Ocean ◽  
The Arctic ◽  
Organic Matter Sources ◽  
The Arctic Ocean

scholarly journals Distribution of PAHs and the PAH-degrading bacteria in the deep-sea sediments of the high-latitude Arctic Ocean

2014 ◽  
Vol 11 (9) ◽  
pp. 13985-14021 ◽  
Author(s):  
C. Dong ◽  
X. Bai ◽  
H. Sheng ◽  
L. Jiao ◽  
H. Zhou ◽  
...  
Keyword(s):  
Arctic Ocean ◽  
Deep Sea ◽  
High Throughput Sequencing ◽  
The Arctic ◽  
Rrna Gene ◽  
Long Distance ◽  
Degrading Bacteria ◽  
The Arctic Ocean ◽  
Deep Sea Sediments

Abstract. Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants, which can be transferred to a long distance and tend to accumulation in marine sediment. However, PAHs distribution and natural bioattenuation is less known in open sea, especially in the Arctic Ocean. In this report, sediment samples were collected at four sites from the Chukchi Plateau to Makarov Basin in the summer of 2010. PAH composition and total concentrations were examined with GC-MS, we found that the concentrations of 16 EPA-priority PAHs varied from 2.0 to 41.6 ng g−1 dry weight in total and decreased with sediment depths and as well as from the southern to northern sites. Among the targeted PAHs, phenanthrene was relatively abundant in all sediments. To learn the diversity of bacteria involved in PAHs degradation in situ, the 16S rRNA gene of the total environmental DNA was analyzed with Illumina high throughput sequencing (IHTS). In all the sediments, occurred the potential degraders including Cycloclasticus, Pseudomonas, Halomonas, Pseudoalteromonas, Marinomonas, Bacillus, Dietzia, Colwellia, Acinetobacter, Alcanivorax, Salinisphaera and Shewanella, with Dietzia as the most abundant. Meanwhile on board, enrichment with PAHs was initiated and repeated transfer in laboratory to obtain the degrading consortia. Most above mentioned bacteria in addition to Hahella, Oleispira, Oceanobacter and Hyphomonas, occurred alternately as a predominant member in enrichment cultures from different sediments, as revealed with IHTS and PCR-DGGE. To reconfirm their role in PAH degradation, 40 different bacteria were isolated and characterized, among which Cycloclasticus and Pseudomonas showed the best degradation capability under low temperature. Taken together, PAHs and PAH-degrading bacteria were widespread in the deep-sea sediments of the Arctic Ocean. We propose that bacteria of Cycloclasticus, Pseudomonas, Pseudoalteromonas, Halomonas, Marinomonas and Dietzia may play the most important role in PAHs mineralization in situ.

scholarly journals Intersection of historical museum collections and modern systematics: a relict population of the Arctic nudibranch Dendronotus velifer G.O. Sars, 1878 in a Swedish fjord

2017 ◽  
Vol 86 (4) ◽  
pp. 303-318 ◽  
Author(s):  
Kennet Lundin ◽  
Tatyana Korshunova ◽  
Klas Malmberg ◽  
Alexander Martynov
Keyword(s):  
Arctic Ocean ◽  
Molecular Data ◽  
Genetic Distances ◽  
The Arctic ◽  
Integrative Approach ◽  
Marine Habitats ◽  
Relict Population ◽  
Nearest Point ◽  
The Arctic Ocean ◽  
Shallow Water Species

Based on morphological, bathymetric and molecular data comparing recently collected Arctic and North Atlantic specimens with morphological and bathymetrical data on historical museum specimens, a unique relict population of the deep-water mollusc Dendronotus velifer G.O. Sars, 1878 (Gastropoda: Nudibranchia) is shown to have existed in the deepest section of the Swedish Gullmar Fjord (the only true silled fjord in Sweden) at least until the middle of the 20th century. This population is more than 1500 km away from the nearest point in the species’ distributional range in the Arctic Ocean today. Using an integrative approach incorporating the data mentioned above, including genetic distances, from recently collected specimens taken from the Arctic Ocean, D. velifer is validated and its species status is restored, for the first time in more than a century after being regarded as a junior synonym of D. robustus. The bathymetric data for historical and recently collected specimens of D. velifer demonstrate significant differences compared to the shallow-water species D. robustus. The findings support the necessity of a stronger protection for the unique marine habitats of the Gullmar Fjord.

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