scholarly journals Microbiological indicators for assessing the ecological status of freshwater lakes in Buryatia

2021 ◽  
Vol 885 (1) ◽  
pp. 012067
Author(s):  
S V Zaitseva ◽  
O P Dagurova ◽  
L P Kozyreva
Keyword(s):  
Microbial Communities ◽  
Anthropogenic Impact ◽  
High Throughput Sequencing ◽  
Ecological Status ◽  
Structural Features ◽  
Freshwater Lakes ◽  
Environmental Status ◽  
Freshwater Bodies ◽  
Using Data ◽  
Microbiological Indicators

Abstract Possible complex approaches for assessing the condition of freshwater lakes using data on microbial diversity, obtained by high-throughput sequencing, were considered. The structural features of microbial communities, associated with increased anthropogenic impact, have been revealed. We identified some microbial taxa, which can be considered as indicators of the environmental status of freshwater bodies.

scholarly journals Freshwater microbial taxa as indicators of anthropogenic impact on the freshwater lakes of Buryatia

2021 ◽  
Vol 908 (1) ◽  
pp. 012003
Author(s):  
S V Zaitseva ◽  
O P Dagurova
Keyword(s):  
Water Quality ◽  
Anthropogenic Impact ◽  
Baikal Region ◽  
Environmental Gradients ◽  
Structural Features ◽  
Anthropogenic Pressure ◽  
Nutrient Loads ◽  
Freshwater Lakes ◽  
High Productivity ◽  
Water Quality Deterioration

Abstract Three large freshwater lakes located in the Baikal region (Gusinoye, Shchuchye, and Kotokel) with high touristic significance were studied. Increased anthropogenic pressure is one of the most important causes of water quality deterioration (in particular, high solute and nutrient loads, high productivity). The structural features of microbial communities associated with an increased anthropogenic load have been revealed in different environmental gradients. It was shown that the genera Rhodobacter, Polynucleobacter, and Luteolibacter preferred environments with a higher trophic level and are indicators of possible anthropogenic impact.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

2019 ◽  
Vol 3 ◽  
Author(s):  
Vasselon Valentin ◽  
Rimet Frédéric ◽  
Domaizon Isabelle ◽  
Monnier Olivier ◽  
Reyjol Yorick ◽  
...  
Keyword(s):  
Water Framework Directive ◽  
High Throughput Sequencing ◽  
Ecological Status ◽  
Aquatic Environments ◽  
Morphological Identification ◽  
The Past ◽  
Sequencing Technologies ◽  
Dna Metabarcoding ◽  
Morphological Approach ◽  
Status Assessment

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

scholarly journals Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

scholarly journals The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Sara Atienza Casas ◽  
Markus Majaneva ◽  
Thomas Jensen ◽  
Marie Davey ◽  
Frode Fossøy ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ecological Status ◽  
Ecological Condition ◽  
Molecular Techniques ◽  
Taxonomic Resolution ◽  
Potential Cost ◽  
Running Water ◽  
National Monitoring ◽  
Monitoring Programs ◽  
Dna Metabarcoding

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles. In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway. The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be: - Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes. - Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD. - Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level. - Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD. - Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.

scholarly journals Cladocera remains and vegetation types to assess the state of oxbows

2018 ◽  
Vol 29 ◽  
pp. 27-39
Author(s):  
István Gyulai ◽  
Csilla Lakatos ◽  
János Tamás Kundrát ◽  
Zsuzsanna Balogh ◽  
Edina Simon ◽  
...  
Keyword(s):  
Surface Sediment ◽  
Ecological Status ◽  
Open Water ◽  
Vegetation Types ◽  
Freshwater Lakes ◽  
Chemical Parameters ◽  
Habitat Types ◽  
Cladocera Remains ◽  
Significant Difference ◽  
Physical And Chemical

We assessed the usefulness of Cladocera remains for establishing the ecological status of oxbows and also tested the association of Cladocera species with various vegetation types. Cladocera remains were collected from the surface sediment of four habitat types (tangled vegetation, open water, reeds and tunnels) and 15 physical and chemical parameters of surface water were studied. In the surface sediment samples, we identified 32 Cladocera taxa. There was a significant difference in the number of species amongst habitat types as per ANOVA. The benthic and plant associated Cladocera communities of reeds, tangled vegetation, open water and tunnels were clearly separated from each other by NMDS ordination. CCA showed that habitat types had characteristic Cladocera species: Pleuroxus species were frequent in the tangled vegetation habitat, while Chydorus species were frequent in the open water. Remarkably, in reeds, Bosmina species were frequent, although these species are usually common in open water. Specimens of the Alona genus were found everywhere. Our findings suggest that the remains of Cladocera species may be useful indicators to assess and monitor the structure of freshwater lakes.

scholarly journals Patent-information support for assessing the environmental status of the soil

2015 ◽  
Vol 16 (1-2) ◽  
pp. 36-51 ◽  
Author(s):  
V. L. Samokhvalova ◽  
O. V. Mangryka ◽  
A. I. Fateev ◽  
V. M. Gorjakina
Keyword(s):  
Soil Quality ◽  
Contaminated Soils ◽  
Ecological Status ◽  
Legal Protection ◽  
Water Soluble ◽  
Information Support ◽  
Maximum Efficiency ◽  
Anthropogenic Pressure ◽  
Patent Information ◽  
Environmental Status

Innovative (patent information research, elaboration of new methods and their implementation) and environmental management, the using of human-contaminated soils, soil protection against pollution and its prevention are the basic directions of the strategic management of soil resources. In conditions of intensive anthropogenic pressure the assessment of the ecological status of soils is an important factor, which reduces the risks of soil degradation and to propose ways to restore their productive and ecological functions on the further development of functional - ecological approach in soil science (Dobrovolsky, Nikitin, 1986, 1996). Therefore, urgent and important in theoretical and practical aspect is the elaboration of new technical decisions (methods) of soil quality assessment to create conditions to improve and to prevent the reduction of the level of productivity of soils and plants, the deterioration of their quality. The purpose of the investigations – the analysis of information sources existing patent information base of Ukraine and Russia on the issue of the environmental assessment of soils and perform patent research. Tasks perform patent research: the technical level of the object; analysis of scientific and technical activities leading developers; studying trends existing way to do that; techno-economic analysis of technical solutions/inventions that meet the objectives of the development; the study of the newness and novelty of the developed object and its constituent parts; investigated of the feasibility of its legal protection. It was considered the features of assessment of the soils environmental status in the investigation of the current patent-information database in Ukraine and Russia, components of which are developed new technical decisions. It was reviewed the providing patent information to assess the ecological status of both contaminated and uncontaminated soils. By analysis it was found that the patent-information support of Ukraine and Russia relative to existing methods of soils ecological status assessment is presented by the following ways: the ways of assessing of the soils research background concentrations, mobile, gross or water-soluble forms of trace elements and heavy metals; estimates based on bioassay and bioindication in combination with chemical analytical measurement indicators; comprehensive and expert evaluation of the properties of soils and its contamination; assessment of soil quality, considering the physical, physic-chemical and others properties; assessment of soil pollution using GIS technology, etc. The technical result of the developed methods is to improve the objectivity of assessment of changing soil quality and accuracy of the expert-analytical assessments of functional suitability of soils certain territory to growing different crops on a permanent or constant impact factor of pollution; for zoning for maximum efficiency use of different methods, methods of remediation of contaminated soils or soil improvers of different nature and micronutrients using to optimize the trace element status of soil and plants, soil quality; to evaluate the effectiveness of the testing results of the elaborated technical decisions in different soil-climatic zones.

scholarly journals An environmental database for the status of freshwater in Greece

2013 ◽  
Vol 4 (1) ◽  
pp. 1-14
Keyword(s):  
National Level ◽  
Reference Conditions ◽  
Ecological Status ◽  
Anthropogenic Pressures ◽  
Environmental Pressures ◽  
Physico Chemical ◽  
Other Information ◽  
The Status ◽  
Freshwater Bodies ◽  
Status Data

An environmental database has been created, recording water bodies at a national level and assembling relevant data collected by various public services and institutions in charge of water resources management and research in Greece. Data consists of physico-chemical parameters, geomorphological descriptions, inventories of fauna and flora species, environmental pressures, vulnerability evaluation and other information useful for the assessment of current and future ecological status. Data gathering has proven to be a challenging task, due to the large number and the generally small size of the surface freshwater bodies as well as the numerous competent services and institutions and the multiple and sometimes conflicting responsibilities that therefore result. The latter is also partly the cause of lack of continuity of data, gaps or sometimes questionable reliability. Performing a global data overview, we note that (a) ecological status can be characterized as good for the majority of the sites, especially for small mountain streams, and (b) the general trend in most cases is degradation of current conditions, related either to anthropogenic pressures or to human activity combined with natural factors. This database, in a more completed and enriched form, could assist in the implementation of 2000/60/EC Directive in Greece and the establishment of reference conditions of surface freshwater systems.

scholarly journals Composition and predictive functional analysis of bacterial communities in the surface seawater of the Changjiang Estuary

2017 ◽  
Author(s):  
Dong-Mei Wu ◽  
Jian-Xin Wang ◽  
Xiao-Hui Liu ◽  
Ying-Ping Fan ◽  
Ran Jiang ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Carbon Fixation ◽  
Oxygen Demand ◽  
Environmental Parameters ◽  
Changjiang Estuary ◽  
Surface Seawater ◽  
The Changjiang Estuary

The objective of this study was to characterize the structure and function of microbial communities in surface seawater from the Changjiang Estuary and adjacent areas, China. Sample water was collected at 12 sites and environmental parameters were measured. Community structure was analyzed using high-throughput sequencing of 16S rDNA genes. Predictive metagenomic approach was used to predict the function of bacterial communities. Result showed that sample site A0102 had the highest bacterial abundance and diversity. The heatmap indicated that different samples could be clustered into six groups. Phylogenetic analysis showed that Proteobacteria was the predominant phylum in all samples, followed by Bacteroidetes and Actinobacteria. Alphaproteobacteria and Gammaproteobacteria were the dominant classes. The analysis of predictive metagenomic showed carbon fixation pathways in prokaryotes, nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis and polycyclic aromatic hydrocarbon degradation were enriched in all samples. Redundancy analysis (RDA) identified that dissolved oxygen (DO) and PO43– concentration had positive correlations with the bacterial communities while chemical oxygen demand (COD), dissolved oxygen (DO) and PO43– concentration were significantly associated with microbial functional diversity. This study adds to our knowledge of functional and taxonomic composition of microbial communities.

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