scholarly journals Simultaneous preservation of the DNA quality, the community composition and the density of freshwater oligochaetes for the development of genetically based biological indices

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6050 ◽  
Author(s):  
Régis Vivien ◽  
Inge Werner ◽  
Benoit J.D. Ferrari
Keyword(s):  
Community Composition ◽  
Sediment Quality ◽  
Low Ph ◽  
Coi Gene ◽  
Absolute Ethanol ◽  
Sediment Samples ◽  
Biological Indices ◽  
Dna Quality ◽  
Freshwater Oligochaetes ◽  
Formalin Fixed

IntroductionOligochaetes are recognized as valuable bioindicators of sediment quality in streams and lakes. The development of an oligochaete index based on the identification of specimens using DNA barcodes requires a method for simultaneously preserving the DNA quality and information on the specimen density and oligochaete community composition. Absolute ethanol optimally preserves DNA but fixation of freshwater oligochaetes with this medium can cause disintegration and fragmentation of specimens. Here, we investigated the possibility to preserve oligochaete specimens in low-pH formalin and in neutral buffered formalin for up to four weeks before genetic analyses and tested if the addition of absolute ethanol to formalin-fixed oligochaetes resulted in a loss of specimens and/or species.MethodsWe performed guanidine extraction and polymerase chain reaction (PCR) amplification/sequencing of a fragment of the cytochrome c oxidase I (COI) gene on tissue fragments preserved in low-pH formalin for up to 3 weeks and in neutral buffered formalin for up to 4 weeks. In addition, we compared the density and taxonomic composition of formalin-fixed oligochaetes of several sieved sediment samples before and after the addition of absolute ethanol.ResultsThe COI fragment of all oligochaete specimens preserved in neutral buffered formalin for up to 28 days was successfully amplified by PCR and obtained sequences were complete and of high quality. The amplification success rate for low-pH formalin fixed specimens declined after 7 days of storage. The addition of absolute ethanol to formalin-fixed oligochaete communities did not alter density or diversity estimates.DiscussionOur results indicate that sediment samples can be stored in neutral buffered formalin for up to 4 weeks and the sieved material can then be transferred to absolute ethanol, without affecting DNA quality, density and community composition of oligochaetes. Based on these results, a protocol for preserving freshwater oligochaetes, describing all the steps from collection of sediments to preservation of the biological material in absolute ethanol, is proposed. This method of fixation/preservation is of relevance for establishing DNA barcode reference databases, inventories of genetic diversity and developing genetically based biological indices.

Potential Oxygen Consumption and Community Composition of Sediment Bacteria in a Seasonally Hypoxic Enclosed Bay

2021 ◽  
Author(s):  
Fumiaki Mori ◽  
Yu Umezawa ◽  
Ruji Kondo ◽  
Gregory N. Nishihara ◽  
Minoru Wada
Keyword(s):  
Oxygen Consumption ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sediment Surface ◽  
Tetrazolium Chloride ◽  
Sediment Samples ◽  
Potential Oxygen

Abstract The dynamics of potential oxygen consumption at the sediment surface in a seasonally hypoxic bay were monitored monthly by applying a tetrazolium dye (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride [INT]) reduction assay to intact sediment core samples for two consecutive years (2012–2013). Based on the empirically determined correlation between INT reduction (INT-formazan formation) and actual oxygen consumption of sediment samples, we inferred the relative contribution of biological and non-biological (chemical) processes to the potential whole oxygen consumption in the collected sediment samples. It was demonstrated that both potentials consistently increased and reached a maximum during summer hypoxia in each year. For samples collected in 2012, amplicon sequence variants (ASVs) of the bacterial 16S rRNA genes derived from the sediment surface revealed a notable shift in the bacterial community composition before and after the INT assay incubation. Within the bacterial community that was predominated by the ASVs closely related to Woeseia (Woeseiaceae, Gammaproteobacteria), the relative abundance of ASVs affiliated with Arcobacter (Arcobacteraceae, Campylobacteria), a putative sulfur-oxidizing bacterial genus, increased markedly in the summer samples. These findings have implications not only for the group of bacteria that are consistently responsible for the consumption of dissolved oxygen (DO) year-round in the sediment, but also for those that might grow rapidly in response to episodic DO supply on the sediment surface during midst of seasonal hypoxia.

scholarly journals Occurrence and Distribution of Polycyclic Aromatic Hydrocarbons in Water and Sediment Collected along the Harbour Line, Mumbai, India

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
V. Dhananjayan ◽  
S. Muralidharan ◽  
Vinny R. Peter
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Sediment Quality ◽  
Quality Criteria ◽  
Marine Organisms ◽  
High Concentration ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Polycyclic Aromatic ◽  
Water And Sediment Samples

This study investigated the occurrence of polycyclic aromatic hydrocarbons (PAHs) in water and sediment samples collected along the harbour line, Mumbai, India. The ∑PAHs quantified in water and sediment samples were ranged from 8.66 ng/L to 46.74 ng/L and from 2608 ng/g to 134134 ng/g dry wt., respectively. Significantly high concentration of ∑PAHs was found in water samples of Sewri and sediment samples of Mahul (P<0.05). PAH concentrations detected in the present study were several folds higher than the existing sediment quality criteria suggested by various statutory agencies. The PAH composition patterns in water and sediments suggest the dominance of high molecular weight compounds and indicate important pyrolytic and petrogenic sources. The occurrence of PAHs in the marine environment has attracted the attention of the scientific community as these compounds are frequently detected in seawater and sediments at increasing levels and can have adverse health effects on marine organisms and humans. PAH concentrations detected at Sewri-Mahul site were sufficiently high to pose a risk to marine organisms if they are exposed continuously to this concentration. Hence, continuous monitoring of the ecosystem is highly warranted.

scholarly journals Deterministic Assessment of the Risk of Phthalate Esters in Sediments of U-Tapao Canal, Southern Thailand

Toxics ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 93
Author(s):  
Okpara Kingsley ◽  
Banchong Witthayawirasak
Keyword(s):  
Ecological Risk ◽  
Total Concentration ◽  
Phthalate Esters ◽  
Sediment Quality ◽  
Potential Ecological Risk ◽  
Concentration Addition ◽  
Sediment Samples ◽  
Mixture Effects ◽  
Quality Guidelines ◽  
Southern Thailand

This baseline study evaluated the ecological risk associated with the concentration of six common Phthalate esters (PAEs) in sediment samples collected from the U-Tapao canal in Southern Thailand. Deterministic approaches consisting of standard sediment quality guidelines (SQGs) and Risk quotient (RQ) were used to evaluate the potential ecological risk of individuals and a mixture of Phthalate esters (PAEs) detected in sediment samples. Of the 6 PAEs measured, only three, including di-n-butyl phthalate (DBP), di-2-ethyl hexyl phthalate (DEHP) and di-isononyl phthalate (DiNP), were identified and quantified. The total concentration of the 3 PAEs congeners found in the sediment samples ranged from 190 to 2010 ng/g dw. The results from the SQGs and RQ were not consistent with each other. The SQGs results for individual PAEs showed that DEHP and DBP found in sediment was estimated to cause moderate risk on benthic organisms, DiNP was not estimated due to lack of SQGs data. However, the RQ method indicated a low risk of DEHP and DBP on algae, crustacean and fish, whereas DiNP poses no risk on crustacean. Furthermore, based on the result obtained in this study, the consensus SQGs for mixture effects prove to be a more protective tool than the RQ concentration addition approach in predicting mixture effects. Despite inevitable uncertainties, the integration of several screening approaches of ecological risk assessment (ERA) can help get a more inclusive and credible result of the first tier of individuals and a mixture of these pollutants.

scholarly journals Trace Metal Content of Sediments Close to Mine Sites in the Andean Region

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Cristina Yacoub ◽  
Agustí Pérez-Foguet ◽  
Nuria Miralles
Keyword(s):  
Trace Metal ◽  
Ecological Risk ◽  
Metal Content ◽  
Sediment Quality ◽  
Pollution Sources ◽  
Quality Analysis ◽  
Mine Site ◽  
Sediment Samples ◽  
Trace Metal Content ◽  
Mine Sites

This study is a preliminary examination of heavy metal pollution in sediments close to two mine sites in the upper part of the Jequetepeque River Basin, Peru. Sediment concentrations of Al, As, Cd, Cu, Cr, Fe, Hg, Ni, Pb, Sb, Sn, and Zn were analyzed. A comparative study of the trace metal content of sediments shows that the highest concentrations are found at the closest points to the mine sites in both cases. The sediment quality analysis was performed using the threshold effect level of the Canadian guidelines (TEL). The sediment samples analyzed show that potential ecological risk is caused frequently at both sites by As, Cd, Cu, Hg, Pb, and Zn. The long-term influence of sediment metals in the environment is also assessed by sequential extraction scheme analysis (SES). The availability of metals in sediments is assessed, and it is considered a significant threat to the environment for As, Cd, and Sb close to one mine site and Cr and Hg close to the other mine site. Statistical analysis of sediment samples provides a characterization of both subbasins, showing low concentrations of a specific set of metals and identifies the main characteristics of the different pollution sources. A tentative relationship between pollution sources and possible ecological risk is established.

scholarly journals The Effect of Nitrogen Content on Archaeal Diversity in an Arctic Lake Region

2019 ◽  
Vol 7 (11) ◽  
pp. 543 ◽  
Author(s):  
Lv ◽  
Liu ◽  
Han ◽  
Wang ◽  
Zhu ◽  
...  
Keyword(s):  
Nitrogen Content ◽  
Community Composition ◽  
Archaeal Community ◽  
Soil Samples ◽  
The Arctic ◽  
Rrna Genes ◽  
Lake Area ◽  
Sediment Samples ◽  
Arctic Lake ◽  
Geochemical Properties

The function of Arctic soil ecosystems is crucially important for the global climate, and nitrogen (N) is the major limiting nutrient in these environments. This study assessed the effects of changes in nitrogen content on archaeal community diversity and composition in the Arctic lake area (London Island, Svalbard). A total of 16S rRNA genes were sequenced to investigate archaeal community composition. First, the soil samples and sediment samples were significantly different for the geochemical properties and archaeal community composition. Thaumarchaeota was an abundant phylum in the nine soil samples. Moreover, Euryarchaeota, Woesearchaeota, and Bathyarchaeota were significantly abundant phyla in the three sediment samples. Second, it was found that the surface runoff caused by the thawing of frozen soil and snow changed the geochemical properties of soils. Then, changes in geochemical properties affected the archaeal community composition in the soils. Moreover, a distance-based redundancy analysis revealed that NH4+–N (p < 0.05) and water content were the most significant factors that correlated with the archaeal community composition. Our study suggests that nitrogen content plays an important role in soil archaeal communities. Moreover, archaea play an important role in the carbon and nitrogen cycle in the Arctic lake area.

scholarly journals Shift from Acetoclastic to H2-Dependent Methanogenesis in a West Siberian Peat Bog at Low pH Values and Isolation of an Acidophilic Methanobacterium Strain

2007 ◽  
Vol 73 (7) ◽  
pp. 2344-2348 ◽  
Author(s):  
O. R. Kotsyurbenko ◽  
M. W. Friedrich ◽  
M. V. Simankova ◽  
A. N. Nozhevnikova ◽  
P. N. Golyshin ◽  
...  
Keyword(s):  
Community Composition ◽  
Methane Production ◽  
Archaeal Community ◽  
Low Ph ◽  
Peat Bog ◽  
Ph Values ◽  
Different Temperatures

ABSTRACT Methane production and archaeal community composition were studied in samples from an acidic peat bog incubated at different temperatures and pH values. H2-dependent methanogenesis increased strongly at the lowest pH, 3.8, and Methanobacteriaceae became important except for Methanomicrobiaceae and Methanosarcinaceae. An acidophilic and psychrotolerant Methanobacterium sp. was isolated using H2-plus-CO2-supplemented medium at pH 4.5.

scholarly journals Evaluation of water and sediment quality of urban streams in Santa Cruz do Sul County, RS, Brasil, using ecotoxicological assays

2014 ◽  
Vol 26 (1) ◽  
pp. 18-25 ◽  
Author(s):  
Luã de Vargas ◽  
Camila Athanásio ◽  
Adriana Düpont ◽  
Adilson Ben da Costa ◽  
Eduardo Aléxis Lobo
Keyword(s):  
Local Population ◽  
Sediment Quality ◽  
Test Organism ◽  
Ceriodaphnia Dubia ◽  
Urban Streams ◽  
Santa Cruz ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Water And Sediment Quality

AIM: This study aimed to assess the quality of water and sediment of urban streams (Lajeado, Preto, Pedras and Lewis-Pedroso) located in Santa Cruz do Sul County, RS, Brazil, using the microcrustacean Ceriodaphnia dubia as test-organism. METHODS: Quarterly scientific excursions to the streams were held on August and November 2011, February and May of 2012 in order to collect water and sediment samples, in the upper reaches (P1, P3, P5, P7) and lower reaches (P2, P4, P6, P8), totalizing 8 points. To evaluate the toxicity (acute and chronic), the microcrustacean C. dubia was used. RESULTS AND CONCLUSION: The results indicated high toxicity levels detected in samples P2, P6 and P8 (lower reaches), as they caused the mortality of 100% of organisms in the water samples (P6 and P8) and sediment samples (P2 and P8), denoting acute effect. Yet, all upstream sites showed chronic effects in sediment samples, at least for one collection period, with the highest significant toxicity level among all samples (55.2%), which indicates the presence of contamination even in upper areas. These results indicated a strong degradation of the water and sediment quality of urban streams coming from the wastewater and industrial discharges of the urban area, which can cause damage to the biota as well as the public health, due to the multiples uses of water that the local population does, highlighting many of them as inappropriate to the water quality detected, such as the primary contact recreation (balneability).

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