scholarly journals Using the predictive functional profiling of microbial communities to assess the ecological quality of reclaimed waters

2021 ◽  
Vol 4 ◽  
Author(s):  
Carlos Rochera ◽  
Maria Peña ◽  
Antonio Picazo ◽  
Javier Miralles-Lorenzo ◽  
Daniel Morant ◽  
...  
Keyword(s):  
Microbial Community ◽  
Marker Genes ◽  
Freshwater Ecosystem ◽  
Natural Environments ◽  
Ecological Quality ◽  
Redox Potentials ◽  
Natural Ecosystems ◽  
Ancillary Benefits ◽  
Plant Materials

The use of proxies for ecosystem function in biomonitoring is desirable to move towards more holistic strategies. Next-generation sequencing of environmental DNA can clearly contribute to these advances. This research is part of a project aimed to use constructed wetlands (CWs), managed by the company Global Omnium (https://www.globalomnium.com/Group/Home/) and having the University of Valencia in charge of the scientific research, in order to improve the ecological quality of already treated wastewaters before being poured into natural environments. The rationale is that, although wastewaters treated by classical methods can meet the standards required by law, transitional constructed ecosystems, as the CWs, can promote ancillary benefits that contribute to the maintenance of the ecological health of receiving natural ecosystems. We propose that some functional traits of the microbial community can be used to outline the process of water renaturation. To assess this, the prokaryotic communities of different types of CWs were profiled by the MiSeq sequencing of the V4 region of the 16S rRNA. Using the sequences obtained, a prediction of the functional capabilities of these communities was made with the bioinformatic package PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; https://github.com/picrust/picrust2), assuming that phylogeny and function are effectively related attributes. Predictions on the occurrence of functional marker genes, particularly those involved in the biogeochemical cycling of main nutrients (C, N, S, P), were then made. The PICRUSt2 predictions were based in the annotated genes catalog of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (https://www.genome.jp/kegg/). In general, results indicated a decline in the CWs effluents of microbial functions typical from wastewater in favor of those more suited for the receiving environment. An enhancement of aerobic metabolism was predicted to occur based on the increase of the gene encoding the cytochrome-c oxidase compared to fermentation pathways. Accordingly, both the denitrification and the dissimilatory reduction of sulfate, that are predominant in the anaerobic environments, also decreased in the effluents of the CWs to lower levels more similar to those observed in natural environments, showing a shift towards reactions at higher redox potentials. On the other hand, a development of metabolic skills for degrading plant materials (e.g., xylose, vanillin, syringate, protocatechuate) was also predicted, which was likely related to a parallel transformation of the organic matter pool in the CWs (more unreactive and natural). Additionally, increases observed in pathways for the synthesis of some cell structural compounds (e.g., mycolic acids) and coenzymes (e.g., F420 cofactor, NAD+) can be related with an enhancement of colonization and competitive potentials of the natural microbial community, as well as with changes in the actual availability of nutrients in the environment. Based on these findings, we raise the possibility of considering these functional surveys made on marker genes as a complementary strategy on the biomonitoring procedures, not only for CWs, but for the general study of freshwater ecosystem potentially affected by wastewater pollution.

scholarly journals Detecting Redox Potentials Using Porous Boron Nitride/ATP-DNA Aptamer/Methylene Blue Biosensor to Monitor Microbial Activities

Micromachines ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 83
Author(s):  
Kai Guo ◽  
Zirui Song ◽  
Gaoxing Wang ◽  
Chengchun Tang
Keyword(s):  
Methylene Blue ◽  
Microbial Community ◽  
Boron Nitride ◽  
Redox Potential ◽  
Microbial Activity ◽  
Potential Change ◽  
Dna Aptamer ◽  
Redox Potentials ◽  
Microplate Reader

Microbial activity has gained attention because of its impact on the environment and the quality of people’s lives. Most of today’s methods, which include genome sequencing and electrochemistry, are costly and difficult to manage. Our group proposed a method using the redox potential change to detect microbial activity, which is rooted in the concept that metabolic activity can change the redox potential of a microbial community. The redox potential change was captured by a biosensor consisting of porous boron nitride, ATP-DNA aptamer, and methylene blue as the fluorophore. This assembly can switch on or off when there is a redox potential change, and this change leads to a fluorescence change that can be examined using a multipurpose microplate reader. The results show that this biosensor can detect microbial community changes when its composition is changed or toxic metals are ingested.

scholarly journals Current Development Status of Forest Therapy in China

Healthcare ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 61
Author(s):  
Zhiyong Zhang ◽  
Peng Wang ◽  
Yue Gao ◽  
Bing Ye
Keyword(s):  
Rural Areas ◽  
Alternative Therapy ◽  
Basic Research ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Rapid Urbanization ◽  
Large Cities ◽  
Healthy Environment ◽  
Health And Wellbeing

As a result of rapid urbanization and urban sprawl, natural ecosystems are shrinking or are fragmented, affecting people’s health and quality of life. Modern people prefer to live in large cities rather than rural areas because of greater convenience and more comfortable living conditions. As a consequence, people are suffering from many psycho-physiological health problems and have a longing for natural environments to escape the concrete jungle. Forest therapy has emerged as a preventive and alternative therapy to cope with stress and enhance people’s health and wellbeing as a result of spending time in a green and healthy environment. Here, we review the activities related to forest therapy in China and discuss the commonalities and differences between the forest therapy types. Furthermore, we summarize the current achievements of forest therapy in basic research and the development of the forest therapy industry. We also describe the challenges that forest therapy has been facing. Finally, we provide suggestions for further development in research and industry.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Comparative analysis of the microbial community and nutritional quality of sufu

2021 ◽  
Author(s):  
Xingjiang Li ◽  
Ying He ◽  
Wei Yang ◽  
Dongdong Mu ◽  
Min Zhang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Microbial Community ◽  
Nutritional Quality

scholarly journals Perceptual uncertainty and action consequences independently affect hand movements in a virtual environment

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Martin Giesel ◽  
Anna Nowakowska ◽  
Julie M. Harris ◽  
Constanze Hesse
Keyword(s):  
Virtual Environments ◽  
Virtual Environment ◽  
Motor Skills ◽  
Hand Movements ◽  
Perceptual Information ◽  
Avoidance Task ◽  
Natural Environments ◽  
Motor Behaviour ◽  
Virtual And Augmented Reality

AbstractWhen we use virtual and augmented reality (VR/AR) environments to investigate behaviour or train motor skills, we expect that the insights or skills acquired in VR/AR transfer to real-world settings. Motor behaviour is strongly influenced by perceptual uncertainty and the expected consequences of actions. VR/AR differ in both of these aspects from natural environments. Perceptual information in VR/AR is less reliable than in natural environments, and the knowledge of acting in a virtual environment might modulate our expectations of action consequences. Using mirror reflections to create a virtual environment free of perceptual artefacts, we show that hand movements in an obstacle avoidance task systematically differed between real and virtual obstacles and that these behavioural differences occurred independent of the quality of the available perceptual information. This suggests that even when perceptual correspondence between natural and virtual environments is achieved, action correspondence does not necessarily follow due to the disparity in the expected consequences of actions in the two environments.

An ecosystem-based approach to evaluate the ecological quality of Mediterranean undersea caves

2015 ◽  
Vol 54 ◽  
pp. 137-152 ◽  
Author(s):  
Pierre-Alexandre Rastorgueff ◽  
Denise Bellan-Santini ◽  
Carlo Nike Bianchi ◽  
Simona Bussotti ◽  
Pierre Chevaldonné ◽  
...  
Keyword(s):  
Ecological Quality

Inhibitory Effect of Commercial Green Tea and Rosemary Leaf Powders on the Growth of Foodborne Pathogens in Laboratory Media and Oriental-Style Rice Cakes

2009 ◽  
Vol 72 (5) ◽  
pp. 1107-1111 ◽  
Author(s):  
SUN-YOUNG LEE ◽  
SO-YOUNG GWON ◽  
SEUNG-JU KIM ◽  
BO KYUNG MOON
Keyword(s):  
Green Tea ◽  
Foodborne Pathogens ◽  
Antimicrobial Activities ◽  
Inhibitory Effect ◽  
Enterobacter Sakazakii ◽  
Inhibitory Effects ◽  
Plant Materials ◽  
Rice Cake ◽  
Rice Cakes

The antimicrobial effects of green tea and rosemary added to foods as antagonists to foodborne pathogens were determined in laboratory media and oriental-style rice cakes. The growth of each pathogen (Bacillus cereus, Salmonella, Typhimurium, Enterobacter sakazakii, Escherichia coli O157:H7, Staphylococcus aureus, and Listeria monocytogenes) in tryptic soy broth or rice cake with or without addition of green tea or rosemary leaf powders before autoclaving or cooking, respectively, was investigated after inoculation. The addition of 1% green tea or rosemary produced similar results for inhibiting the growth of pathogens in tryptic soy broth. However, green tea was more effective than rosemary for inhibiting the growth of L. monocytogenes. Both botanicals had inhibitory effects against all pathogens tested in this study. Green tea was particularly effective against B. cereus, S. aureus, and L. monocytogenes, and rosemary was strongly inhibitory against B. cereus and S. aureus. The addition of 1 or 3% green tea or rosemary to rice cakes did not significantly reduce total aerobic counts; however, levels of B. cereus and S. aureus were significantly reduced in rice cakes stored for 3 days at room temperature (22°C). The order of antimicrobial activities against B. cereus in rice cake was 1% rosemary < 1% green tea < 3% rosemary = 3% green tea. These results indicate that the use of natural plant materials such as green tea and rosemary could improve the microbial quality of foods in addition to their functional properties.

scholarly journals Using virtual reality to estimate aesthetic values of coral reefs

2018 ◽  
Vol 5 (4) ◽  
pp. 172226 ◽  
Author(s):  
Julie Vercelloni ◽  
Sam Clifford ◽  
M. Julian Caley ◽  
Alan R. Pearse ◽  
Ross Brown ◽  
...  
Keyword(s):  
Coral Reef ◽  
Coral Reefs ◽  
Structural Complexity ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Aesthetic Value ◽  
Natural Systems ◽  
Holistic Conservation ◽  
Past Experiences ◽  
Aesthetic Values

Aesthetic value, or beauty, is important to the relationship between humans and natural environments and is, therefore, a fundamental socio-economic attribute of conservation alongside other ecosystem services. However, beauty is difficult to quantify and is not estimated well using traditional approaches to monitoring coral-reef aesthetics. To improve the estimation of ecosystem aesthetic values, we developed and implemented a novel framework used to quantify features of coral-reef aesthetics based on people's perceptions of beauty. Three observer groups with different experience to reef environments (Marine Scientist, Experienced Diver and Citizen) were virtually immersed in Australian's Great Barrier Reef (GBR) using 360° images. Perceptions of beauty and observations were used to assess the importance of eight potential attributes of reef-aesthetic value. Among these, heterogeneity, defined by structural complexity and colour diversity, was positively associated with coral-reef-aesthetic values. There were no group-level differences in the way the observer groups perceived reef aesthetics suggesting that past experiences with coral reefs do not necessarily influence the perception of beauty by the observer. The framework developed here provides a generic tool to help identify indicators of aesthetic value applicable to a wide variety of natural systems. The ability to estimate aesthetic values robustly adds an important dimension to the holistic conservation of the GBR, coral reefs worldwide and other natural ecosystems.

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