scholarly journals Metagenomic screening of global microbiomes identifies pathogen-enriched environments

2018 ◽  
Author(s):  
Xiaofang Li
Keyword(s):  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Quantitative Estimate ◽  
Bioinformatic Analysis ◽  
Polluted Water ◽  
Ocean Water ◽  
Human Pathogens ◽  
Precautionary Measures ◽  
Enriched Environments ◽  
Almost All

AbstractBackgroundHuman pathogens are widespread in the environment, and examination of pathogen-enriched environments in a rapid and high-throughput fashion is important for development of pathogen-risk precautionary measures.MethodsIn this study, a Local BLASTP procedure for metagenomic screening of pathogens in the environment was developed using a toxin-centered database. A total of 27 microbiomes derived from ocean water, freshwater, soil, feces, and wastewater were screened using the Local BLASTP procedure. Bioinformatic analysis and Canonical Correspondence Analysis were conducted to examine whether the toxins included in the database were taxonomically associated.ResultsThe specificity of the Local BLASTP method was tested with known and unknown toxin sequences. Bioinformatic analysis indicated that most toxins were phylum-specific but not genus-specific. Canonical Correspondence Analysis implied that almost all of the toxins were associated with the phyla ofProteobacteria,NitrospiraeandFirmicutes. Local BLASTP screening of the global microbiomes showed that pore-forming RTX toxin and adenylate cyclase Cya were most prevalent globally in terms of relative abundance, while polluted water and feces samples were the most pathogen-enriched.ConclusionsA Local BLASTP procedure was established for rapid detection of toxins in environmental samples. Screening of global microbiomes in this study provided a quantitative estimate of the most prevalent toxins and most pathogen-enriched environment.

Relationship between Chrysophyte Assemblages and Environmental Variables in Seventy-Two Sudbury Lakes as Examined by Canonical Correspondence Analysis (CCA)

1989 ◽  
Vol 46 (10) ◽  
pp. 1667-1676 ◽  
Author(s):  
Sushil S. Dixit ◽  
Aruna S. Dixit ◽  
John P. Smol
Keyword(s):  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Surface Sediment ◽  
Important Variable ◽  
Great Promise ◽  
Calibration Model ◽  
Ph Indicator ◽  
History Of ◽  
Inferred Ph ◽  
Almost All

Relationship between surface sediment chrysophyte scales and limnological variables in 72 Sudbury lakes was examined using canonical correspondence analysis (CCA). CCA is a recently developed multivariate direct gradient analysis that has many advantages over indirect gradient analyses. Lakewater pH was identified as the most important variable influencing the distribution of scaled chrysophytes in Sudbury lakes. Almost all common chrysophyte taxa can be assigned a pH indicator value. In addition to pH, many chrysophyte taxa are sensitive to metal concentrations. A calibration model was developed to predict chrysophyte inferred pH using CCA. The model proved to be far superior to traditionally used models derived from multiple regression of pH indicator chyrsophyte assemblages. Applicability of the predictive pH equation was examined by reconstructing the recent pH history of Lohi Lake. The study provides compelling evidence that canonical correspondence analysis offers great promise in surface sediment calibration and pH reconstruction studies.

Environmental factors including management practices as correlates of weed community composition in spring seeded crops

1992 ◽  
Vol 70 (10) ◽  
pp. 1931-1939 ◽  
Author(s):  
M. R. T. Dale ◽  
A. G. Thomas ◽  
E. A. John
Keyword(s):  
Community Composition ◽  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Environmental Variables ◽  
Management Practices ◽  
Geographic Region ◽  
Climatic Conditions ◽  
Weed Species ◽  
Weed Communities ◽  
Seed Crops

The relationship between the weed communities and environmental variables such as soil, crop, and management was investigated in two provinces of Canada. The frequencies of weed species were recorded in cereal and oilseed fields in Saskatchewan (2244 fields over 4 years) and Manitoba (864 fields over 3 years), Canada. Information on some of the physical characteristics of the fields and on the management practices imposed on them was also collected, in part by questionnaire. The two kinds of data were ordinated together using canonical correspondence analysis to assess the relationships between the species and the environmental variables. In the Saskatchewan data, there was a clear and consistent separation of the species into groups along an axis correlated with soil zone and the associated climatic gradient. In the Manitoba data, the same groups of species did not separate as clearly or as consistently, although geographic region was a major determinant of the weed communities. The greater variability may be due to the fact that the gradient of soil types is much more restricted in Manitoba and not as closely correlated with climatic conditions. In both provinces, culture practices were less important as correlates of the weed community composition than soil type or, to a certain extent, the previous crop. Key words: canonical correspondence analysis, cereal crops, oil seed crops.

scholarly journals Desmid algae (Charophyta: Conjugatophyceae) of Ekaterinburg, Middle Urals, Russia

2018 ◽  
Vol 55 ◽  
pp. 7-15
Author(s):  
Andrei S. Shakhmatov ◽  
Evgeniy V. Pavlovskiy ◽  
Alexander G. Paukov
Keyword(s):  
Species Composition ◽  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Habitat Preferences ◽  
Water Bodies ◽  
Middle Urals ◽  
The Middle Urals

Species composition of desmid algae and their habitat preferences in water bodies of Ekaterinburg city were studied during the 2013–2017. Thirty-seven species and subspecific taxa which belong to 12 genera and 2 families were identified, of which 17 species are new for the eastern macroslope of the Middle Urals. Canonical correspondence analysis, which was performed to reveal habitat preferences, demonstrates that the majority of analyzed species prefer quarry lakes, ponds and overgrown lake shores, contrary to fens and rivers.

scholarly journals On the Use of Selected Ordination Techniques to Analyze the Parliamentary Election Results

2016 ◽  
Vol 3 (322) ◽  
Author(s):  
Małgorzata Misztal
Keyword(s):  
Correspondence Analysis ◽  
Canonical Correspondence Analysis ◽  
Redundancy Analysis ◽  
Social Research ◽  
Economic Research ◽  
Parliamentary Election ◽  
Ecological Research ◽  
Parliamentary Elections ◽  
Ordination Techniques ◽  
Election Results

Ordination techniques such as CCA (Canonical Correspondence Analysis) or RDA (Redundancy Analysis) are very popular in ecological research but almost completely unknown in, for example, socio-economic research. The goal of this paper is to concisely organize the concepts and terminology associated with ordination and to present the possibilities of its application in social research with an example of the analysis of the 2015 parliamentary elections results.

scholarly journals Water Quality Assessment of West Tarum Canal for Drinking Water Supply

2021 ◽  
Vol 277 ◽  
pp. 04003
Author(s):  
Ayu Widya Utami ◽  
Dwi Nowo Martono ◽  
Haruki Agustina
Keyword(s):  
Water Quality ◽  
Drinking Water ◽  
Integrated Management ◽  
Water Quality Assessment ◽  
Polluted Water ◽  
Infrastructure Development ◽  
Raw Water ◽  
Agriculture Industry ◽  
The Government ◽  
Almost All

West Tarum Canal (WTC) is a canal that drains raw water from the Jatiluhur Dam. Nearly 81% of the raw water for drinking water used by Jakarta’s people comes from this canal. However, various land uses such as agriculture, industry, settlements, and infrastructure development impact WTC’s water quality. This research aims to assess WTC’s water quality in 2016-2020 based on water quality standards set by the Government and using the STORET method. The results of this research indicate that the concentrations of TDS (142-351 mg/L), Fe (0.1-0.15 mg/L), Mn (0.03-0.1 mg/L) are meet the standards, while DO (3.6-4.9 mg/L), BOD (4-10 mg/L), COD (13-30 mg/L) are not meet the standards. Almost all monitoring points have pH values between 5.75-7.68 that are meet the standards. The STORET score of WTC is from -26 to -38 with an average of -30, which indicates that WTC’s water quality is moderately polluted. Water contamination in WTC will burden the drinking water processing and ultimately affect the community’s ability to pay for drinking water. This research also shows the need for integrated management of WTC from upstream to downstream and the need to increase collaboration between stakeholders in carrying out this management.

Canonical Correspondence Analysis

2006 ◽  
Author(s):  
I. T. Jolliffe ◽  
T. J. Ringrose
Keyword(s):  
Correspondence Analysis ◽  
Canonical Correspondence Analysis
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