scholarly journals Metagenomics data of microbial communities in bacterial mats and bottom sediments in water bodies within the Kurai Mercury Province (Gorny Altai, Russia)

Data in Brief ◽  
2021 ◽  
pp. 107099
Author(s):  
Alexei S. Rozanov ◽  
Irina N. Myagkaya ◽  
Anton V. Korzhuk ◽  
Nikita I. Ershov ◽  
Ivan S. Kirichenko ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bottom Sediments ◽  
Water Bodies ◽  
Bacterial Mats ◽  
Gorny Altai ◽  
Metagenomics Data

Oxygen Regime of the Water Bodies as Main Factor of Different Metals Forms Migration within the System “Bottom Sediments - Water”

2009 ◽  
Vol 45 (2) ◽  
pp. 85-105 ◽  
Author(s):  
P. N. Linnik ◽  
O. V. Timchenko ◽  
A. V. Zubko ◽  
I. B. Zubenko ◽  
L. A. Malinovskaya
Keyword(s):  
Bottom Sediments ◽  
Water Bodies ◽  
Oxygen Regime ◽  
Main Factor

scholarly journals Collection of a Bacterial Community Reconstructed from Marine Metagenomes Derived from Jinhae Bay, South Korea

Data ◽  
2021 ◽  
Vol 6 (5) ◽  
pp. 44
Author(s):  
Jae-Hyun Lim ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Sampling Site ◽  
Community Change ◽  
Rrna Gene ◽  
Water Column Stratification ◽  
Metagenomics Data ◽  
Jinhae Bay

Marine bacteria are known to play significant roles in marine biogeochemical cycles regarding the decomposition of organic matter. Despite the increasing attention paid to the study of marine bacteria, research has been too limited to fully elucidate the complex interaction between marine bacterial communities and environmental variables. Jinhae Bay, the study area in this work, is the most anthropogenically eutrophied coastal bay in South Korea, and while its physical and biogeochemical characteristics are well described, less is known about the associated changes in microbial communities. In the present study, we reconstructed a metagenomics data based on the 16S rRNA gene to investigate temporal and vertical changes in microbial communities at three depths (surface, middle, and bottom) during a seven-month period from June to December 2016 at one sampling site (J1) in Jinhae Bay. Of all the bacterial data, Proteobacteria, Bacteroidetes, and Cyanobacteria were predominant from June to November, whereas Firmicutes were predominant in December, especially at the middle and bottom depths. These results show that the composition of the microbial community is strongly associated with temporal changes. Furthermore, the community compositions were markedly different between the surface, middle, and bottom depths in summer, when water column stratification and bottom water hypoxia (low dissolved oxygen level) were strongly developed. Metagenomics data contribute to improving our understanding of important relationships between environmental characteristics and microbial community change in eutrophication-induced and deoxygenated coastal areas.

scholarly journals The study of the suitability for use in agriculture of sludge and hydrochemical indicators of water in the reservoirs of the fish farm LLC “Albashi”

2020 ◽  
Vol 175 ◽  
pp. 02001
Author(s):  
Natalya Yurina ◽  
Denis Yurin ◽  
Irina Astakhova ◽  
Tatyana Shcherbatova ◽  
Igor Shcherbatov
Keyword(s):  
Bottom Sediment ◽  
Fresh Water ◽  
Bottom Sediments ◽  
Suspended Matter ◽  
Agricultural Production ◽  
Water Bodies ◽  
Hydrochemical Regime ◽  
Bottom Deposits ◽  
Environmentally Safe ◽  
Reservoir Type

The study of suitability for the use in agriculture of sludge deposits and hydrochemical indices of water bodies of fish-growing enterprise of LLC “Albashi” were carried out. It is an enterprise engaged in breeding and growing pond fish and sturgeon in pools and gardens, crayfish, growing aquapon greens. Fresh water bodies of reservoir type LLC “Albashi” contain a large number of bottom deposits. The layer of sludge deposits on the bottom in places reaches the power of 2-5 meters, and the underground power is difficult. Bottom sediments were taken from a depth of 1.0-1.2 m from the surface. The hydrochemical regime of the studied water bodies fully corresponds to the cultivation of aquaculture objects and hydroponic plants. Sufficient suspended matter in water (8.2 mg/dm3). The complete absence of dichlorodiphenyl trichloroethane, its metabolites and pesticides characterizes the products produced as environmentally safe. Consequently, bottom sediment site under study can be considered suitable for agricultural production.

scholarly journals PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data

2020 ◽  
Vol 36 (10) ◽  
pp. 3043-3048 ◽  
Author(s):  
Michael A Peabody ◽  
Wing Yin Venus Lau ◽  
Gemma R Hoad ◽  
Baofeng Jia ◽  
Finlay Maguire ◽  
...  
Keyword(s):  
Water Quality ◽  
Subcellular Localization ◽  
Microbial Communities ◽  
Cell Envelope ◽  
Supplementary Information ◽  
Protein Subcellular Localization ◽  
Metagenomic Sequence ◽  
Archaeal Protein ◽  
Wide Range ◽  
Metagenomics Data

Abstract Motivation Many methods for microbial protein subcellular localization (SCL) prediction exist; however, none is readily available for analysis of metagenomic sequence data, despite growing interest from researchers studying microbial communities in humans, agri-food relevant organisms and in other environments (e.g. for identification of cell-surface biomarkers for rapid protein-based diagnostic tests). We wished to also identify new markers of water quality from freshwater samples collected from pristine versus pollution-impacted watersheds. Results We report PSORTm, the first bioinformatics tool designed for prediction of diverse bacterial and archaeal protein SCL from metagenomics data. PSORTm incorporates components of PSORTb, one of the most precise and widely used protein SCL predictors, with an automated classification by cell envelope. An evaluation using 5-fold cross-validation with in silico-fragmented sequences with known localization showed that PSORTm maintains PSORTb’s high precision, while sensitivity increases proportionately with metagenomic sequence fragment length. PSORTm’s read-based analysis was similar to PSORTb-based analysis of metagenome-assembled genomes (MAGs); however, the latter requires non-trivial manual classification of each MAG by cell envelope, and cannot make use of unassembled sequences. Analysis of the watershed samples revealed the importance of normalization and identified potential biomarkers of water quality. This method should be useful for examining a wide range of microbial communities, including human microbiomes, and other microbiomes of medical, environmental or industrial importance. Availability and implementation Documentation, source code and docker containers are available for running PSORTm locally at https://www.psort.org/psortm/ (freely available, open-source software under GNU General Public License Version 3). Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Metagenomic Sequences of Three Drinking Water and Two Shower Hose Biofilm Samples Treated with or without Copper-Silver Ionization

2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Anke Stüken ◽  
Thomas H. A. Haverkamp
Keyword(s):  
Drinking Water ◽  
Microbial Communities ◽  
Tap Water ◽  
Data Sets ◽  
Sequence Analyses ◽  
Illumina Hiseq ◽  
Shotgun Metagenomics ◽  
Premise Plumbing ◽  
Plumbing Systems ◽  
Metagenomics Data

We announce five shotgun metagenomics data sets from two Norwegian premise plumbing systems. The samples were shotgun sequenced on two lanes of an Illumina HiSeq 3000 instrument (THRUplex chemistry, 151 bp, paired-end reads), providing an extensive resource for sequence analyses of tap water and biofilm microbial communities.

scholarly journals Habitat conditions of astatic pools and differentiation of vegetation connected with them

2014 ◽  
Vol 54 (2) ◽  
pp. 131-145 ◽  
Author(s):  
Małgorzata Nieckuła ◽  
Wiesław Podyma
Keyword(s):  
Bottom Sediments ◽  
Specific Conductivity ◽  
Organic Matter Content ◽  
Chemical Properties ◽  
Water Hardness ◽  
Chloride Content ◽  
Matter Content ◽  
Water Bodies ◽  
Habitat Conditions ◽  
Physico Chemical

In 12 astatic pools, each of which was characterised by the dominance of phytocenoses of one of three plant associations, investigations were performed on the physico-chemical properties of the water and bottom sediments, in order to establish the relations between the habitat conditions and vegetation. The criterion of the degree of saltiness of the bottom sediments and the specific conductivity of water in these water bodies allows to order them according to their decreasing fertility as follows: 1) water bodies with dominant phytocenoses of the association <em>Equisetetum limosi</em>, 2) with <em>Caricetum elatae</em>, 3) with <em>Typhetum latifoliae</em>. The type of vegetation indicates also connections with other properties of the water (hardness, oxidability, pH, chloride content) and of the bottom sediment (organic matter content, chlorides, magnesium and various forms of nitrogen). Correlation between the chemical composition of the water and depostis has only been demonstrated in the case of chlorides.

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