scholarly journals Environmental DNA variability in lake sediment cores

2021 ◽  
Vol 4 ◽  
Author(s):  
John Pearman ◽  
Georgia Thomson-Laing ◽  
Jamie Howarth ◽  
Marcus Vandergoes ◽  
Lucy Thompson ◽  
...  
Keyword(s):  
16S Rrna ◽  
General Trend ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Biological Communities ◽  
The Core ◽  
Community Dissimilarity ◽  
Sample Heterogeneity ◽  
Read Abundance ◽  
Natural Archives

Lake sediments are natural archives that accumulate information about biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further studies investigating factors such as sample heterogeneity and DNA degradation are required. Here we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices. Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths (1-cm width) which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Rarefaction curves showed that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Within slice similarity was higher than between slice similarity. No general trend was observed in variability among replicates with depth amongst the lakes. In one core. there was a higher community dissimilarity in older sediment, which may be due to laminae not being horizontal. These results highlight the fact that microbial communities can be differentiated with depth however it is critical to interpret these results in the context of the stratigraphic data of the core.

scholarly journals Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250783
Author(s):  
John K. Pearman ◽  
Georgia Thomson-Laing ◽  
Jamie D. Howarth ◽  
Marcus J. Vandergoes ◽  
Lucy Thompson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sediment Cores ◽  
Microbial Community Composition ◽  
Environmental Dna ◽  
Scaling Analysis ◽  
Biological Communities ◽  
Accumulation Curves ◽  
Community Dissimilarity ◽  
Sample Heterogeneity ◽  
Read Abundance

Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.

Imaging of ribosomal RNA-protein interactions by dark-field STEM

1989 ◽  
Vol 47 ◽  
pp. 250-251
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
S. Tumminia ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
Nucleic Acid ◽  
16S Rrna ◽  
Dark Field ◽  
Radius Of Gyration ◽  
Central Domain ◽  
The Core ◽  
16S Rna ◽  
30S Subunit ◽  
Core Particles

Success in protein-free deposition of native nucleic acid molecules from solutions of selected ionic conditions prompted attempts for high resolution imaging of nucleic acid interactions with proteins, not attainable by conventional EM. Since the nucleic acid molecules can be visualized in the dark-field STEM mode without contrasting by heavy atoms, the established linearity between scattering cross-section and molecular weight can be applied to the determination of their molecular mass (M) linear density (M/L), mass distribution and radius of gyration (RG). Determination of these parameters promotes electron microscopic imaging of biological macromolecules by STEM to a quantitative analytical level. This technique is applied to study the mechanism of 16S rRNA folding during the assembly process of the 30S ribosomal subunit of E. coli. The sequential addition of protein S4 which binds to the 5'end of the 16S rRNA and S8 and S15 which bind to the central domain of the molecule leads to a corresponding increase of mass and increased coiling of the 16S rRNA in the core particles. This increased compactness is evident from the decrease in RG values from 114Å to 91Å (in “ribosomal” buffer consisting of 10 mM Hepes pH 7.6, 60 mM KCl, 2 m Mg(OAc)2, 1 mM DTT). The binding of S20, S17 and S7 which interact with the 5'domain, the central domain and the 3'domain, respectively, continues the trend of mass increase. However, the RG values of the core particles exhibit a reverse trend, an increase to 108Å. In addition, the binding of S7 leads to the formation of a globular mass cluster with a diameter of about 115Å and a mass of ∽300 kDa. The rest of the mass, about 330 kDa, remains loosely coiled giving the particle a “medusa-like” appearance. These results provide direct evidence that 16S RNA undergoes significant structural reorganization during the 30S subunit assembly and show that its interactions with the six primary binding proteins are not sufficient for 16S rRNA coiling into particles resembling the native 30S subunit, contrary to what has been reported in the literature.

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

scholarly journals Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Héctor Argüello ◽  
Jordi Estellé ◽  
Finola C. Leonard ◽  
Fiona Crispie ◽  
Paul D. Cotter ◽  
...  
Keyword(s):  
Public Health ◽  
16S Rrna ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Current Control ◽  
Growing Pigs ◽  
Microbiota Composition ◽  
Core Microbiome ◽  
The Core ◽  
The Impact

ABSTRACT Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.

Retrieval of nearly complete 16S rRNA gene sequences from environmental DNA following 16S rRNA-based community fingerprinting

2005 ◽  
Vol 7 (5) ◽  
pp. 670-675 ◽  
Author(s):  
Manfred G. Hofle ◽  
Sebastien Flavier ◽  
Richard Christen ◽  
Julia Botel ◽  
Matthias Labrenz ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Environmental Dna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Community Fingerprinting

scholarly journals Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan

2009 ◽  
Vol 75 (22) ◽  
pp. 7153-7162 ◽  
Author(s):  
Junichi Miyazaki ◽  
Ryosaku Higa ◽  
Tomohiro Toki ◽  
Juichiro Ashi ◽  
Urumu Tsunogai ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Methane Seep ◽  
Core Sediments ◽  
The Core ◽  
Group 2

ABSTRACT The potential for microbial nitrogen fixation in the anoxic methane seep sediments in a mud volcano, the number 8 Kumano Knoll, was characterized by molecular phylogenetic analyses. A total of 111 of the nifH (a gene coding a nitrogen fixation enzyme, Fe protein) clones were obtained from different depths of the core sediments, and the phylogenetic analysis of the clones indicated the genetic diversity of nifH genes. The predominant group detected (methane seep group 2), representing 74% of clonal abundance, was phylogenetically related to the nifH sequences obtained from the Methanosarcina species but was most closely related to the nifH sequences potentially derived from the anoxic methanotrophic archaea (ANME-2 archaea). The recovery of the nif gene clusters including the nifH sequences of the methane seep group 2 and the subsequent reverse transcription-PCR detection of the nifD and nifH genes strongly suggested that the genetic components of the gene clusters would be operative for the in situ assimilation of molecular nitrogen (N2) by the host microorganisms. DNA-based quantitative PCR of the archaeal 16S rRNA gene, the group-specific mcrA (a gene encoding the methyl-coenzyme M reductase α subunit) gene, and the nifD and nifH genes demonstrated the similar distribution patterns of the archaeal 16S rRNA gene, the mcrA groups c-d and e, and the nifD and nifH genes through the core sediments. These results supported the idea that the anoxic methanotrophic archaea ANME-2c could be the microorganisms hosting the nif gene clusters and could play an important role in not only the in situ carbon (methane) cycle but also the nitrogen cycle in subseafloor sediments.

scholarly journals Glacial-Marine Sedimentation, Canadian Polar Margin, North of Axel Heiberg Island

2007 ◽  
Vol 45 (2) ◽  
pp. 213-227 ◽  
Author(s):  
Frances J. Hein ◽  
Peta J. Mudie
Keyword(s):  
Sediment Cores ◽  
Open Water ◽  
Silty Clay ◽  
Sedimentation Rates ◽  
The Core ◽  
Marine Sedimentation ◽  
Northwestern Shelf ◽  
History Of ◽  
Axel Heiberg Island ◽  
High Sediment

ABSTRACT Sediment cores, taken at depths of 140 to 300 m across the northwestern shelf of Axel Heiberg Island (82° N), record the deposition of sediments under perennial sea ice. Five sedimentary fades are recognized: (A) soft pebbly-sandy-mud with dropstone structures; (B) bioturbated silty muds; (C) wispy-laminated silty clay/clay; (D) laminated sands/silts and mud; (E) firm pebbly-sandy-mud with chaotic pebble fabrics. Other sediments include terrestrial bedrock of Paleogene Eureka Sound Group, and a younger Tertiary deposit, possibly the Beaufort Formation. Ages range from 1530 ± 60 BP (Fades A) to 9950 ± 80 BP (Fades D). Sedimentation rates vary as follows: - 0.8 cm ka-1, Fades B; 4 cm ka"\ Fades A; 90 cm ka-1, Fades C; 134 cm ka~', Fades D. The sedimentation history, as interpreted from the sedimentology, palynology and foraminiferal results, suggests intervals of more continuous ice cover, with a reduced influx of coarse ice-rafted detritus, alternating with more open water conditions, and high sediment input from meltwater and/or floating icebergs. Only marine sediments overlie Neogene bedrock in the cores. The absence of diamictons at the core sites suggests that grounded ice perhaps never occupied this part of the Axel Heiberg Island shelf. The interpreted history of sedimentation generally corresponds to the land-based record from Ellesmere Island, but differs significantly from marine-based studies in more southern latitudes.

scholarly journals Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment

2017 ◽  
Vol 84 (1) ◽  
Author(s):  
Richard Kevorkian ◽  
Jordan T. Bird ◽  
Alexander Shumaker ◽  
Karen G. Lloyd
Keyword(s):  
Population Dynamics ◽  
Microbial Community ◽  
16S Rrna ◽  
Sulfate Reduction ◽  
Relative Quantification ◽  
Turnover Rates ◽  
Content Type ◽  
Sulfate Reducing ◽  
Population Turnover ◽  
Read Abundance

ABSTRACT The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for “fraction of read abundance times cells”), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community. IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for “fraction of read abundance times cells,” which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.

scholarly journals Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.

2018 ◽  
Author(s):  
Hugo R Barajas de la Torre ◽  
Miguel Romero ◽  
Shamayim Martínez-Sánchez ◽  
Luis D Alcaraz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Core Genome ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Phylogeny ◽  
The Core ◽  
Sequence Identity ◽  
Core Proteins ◽  
Genomic Similarity

Background. Comparative genomics between closely related bacterial strains can distinguish important features determining pathogenesis, antibiotic resistance, and phylogenetic structure. The Streptococcus genus is relevant to public health and food safety and it is well-represented (>100 genomes) in databases of publicly available databases. Streptococci are cosmopolitan, with multiple sources of isolation, from humans to dairy products. The Streptococcus genus has been classified by morphology, serotypes, 16S rRNA gene, and Multi Locus Sequence Types (MLST). The Genomic Similarity Score (GSS) is proposed as a tool to quantify genome level relatedness between species of Streptococcus. The Streptococcus core genome can be used to assess strain specific abundances in metagenomic sequences. Methods. A 16S rRNA gene phylogeny was calculated for 108 strains, belonging to 16 Streptococcus species and compared to a dendrogram using GSS pairwise distances for the same genomes. The core and pan-genome were calculated for these 108 genomes. The core genome sequences were analyzed and used as a resource to discriminate homologous fragment reads from closely related strains in metagenomic samples. Results. A total of 404 proteins are shared by all 108 Streptococcus genomes, which is the core genome. The pairwise amino acid identity values of the core proteins for all the compared strains and outgroups are reported. Lower sequence identity variation (90-100%) is predominantly found in core clusters containing ribosomal and translation-related proteins. For 48 core proteins (11.8%) no functional assignment could be made and those proteins have larger sequence identity variations than other core proteins. The sequence identity of the core genome diminishes as GSS score between species decreases. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). Finally, the core genome was used to distinguish between closely related species within human oral metagenomes. Discussion. The Streptococcus genus provides a benchmark dataset for comparative genomic studies due to the breath depth of genomic coverage. Comparing metagenomic shotgun fragment reads to the core genome using rapid alignment tools allows species-specific abundance estimates in metagenomic samples. Understanding of genomic variability and strains relatedness is the goal of tools like GSS, which make use of both pairwise shared core and pan-genomic homologous shared sequences for its calculation.

scholarly journals MAUI-seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction

2019 ◽  
Author(s):  
Bryden Fields ◽  
Sara Moeskjær ◽  
Ville-Petri Friman ◽  
Stig U. Andersen ◽  
J. Peter W. Young
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Error Correction ◽  
High Throughput ◽  
Environmental Dna ◽  
Amplicon Sequencing ◽  
Efficient Elimination

AbstractBackgroundSequencing and PCR errors are a major challenge when characterising genetic diversity using high-throughput amplicon sequencing (HTAS).ResultsWe have developed a multiplexed HTAS method, MAUI-seq, which uses unique molecular identifiers (UMIs) to improve error correction by exploiting variation among sequences associated with a single UMI. We show that two main advantages of this approach are efficient elimination of chimeric and other erroneous reads, outperforming DADA2 and UNOISE3, and the ability to confidently recognise genuine alleles that are present at low abundance or resemble chimeras.ConclusionsThe method provides sensitive and flexible profiling of diversity and is readily adaptable to most HTAS applications, including microbial 16S rRNA profiling and metabarcoding of environmental DNA.

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