Voices of Young Climate Activists of India

1-8Climate change is one of the most pressing issues in the present times. It is affecting weather across the world in extremes such as heat waves, intense droughts, floods, and tropical cyclones

On the inadequacy of environment impact assessments for projects in Bhagwan Mahavir Wildlife Sanctuary and National Park of Goa, India : a peer review

The Environment Impact Assessment (EIA) is a regulatory framework adopted since 1994 in India to evaluate the impact and mitigation measures of projects, however, even after 25 years of adoption, EIAs continue to be of inferior quality with respect to biodiversity documentation and assessment of impacts and their mitigation measures. This questions the credibility of the exercise, as deficient EIAs are habitually used as a basis for project clearances in ecologically sensitive and irreplaceable regions. The authors reiterate this point by analysing impact assessment documents for three projects: the doubling of the National Highway-4A, doubling of the railway-line from Castlerock to Kulem, and laying of a 400-kV transmission line through the Bhagwan Mahavir Wildlife Sanctuary and National Park in the state of Goa. Two of these projects were recently granted ‘Wildlife Clearance’ during a virtual meeting of the Standing Committee of the National Board of Wildlife (NBWL) without a thorough assessment of the project impacts. Assessment reports for the road and railway expansion were found to be deficient on multiple fronts regarding biodiversity assessment and projected impacts, whereas no impact assessment report was available in the public domain for the 400-kV transmission line project. This paper highlights the biodiversity significance of this protected area complex in the Western Ghats, and highlights the lacunae in biodiversity documentation and inadequacy of mitigation measures in assessment documents for all three diversion projects. The EIA process needs to improve substantially if India is to protect its natural resources and adhere to environmental protection policies and regulations nationally and globally

Detection of Salmonella Typhi bacteriophages in surface waters as a scalable approach to environmental surveillance.

BACKGROUND: Environmental surveillance, using detection of Salmonella Typhi DNA, has emerged as a potentially useful tool to identify typhoid-endemic settings; however, it is relatively costly and requires molecular diagnostic capacity. We sought to determine whether S. Typhi bacteriophages are abundant in water sources in a typhoid-endemic setting, using low-cost assays. METHODOLOGY: We collected drinking and surface water samples from urban, peri-urban and rural areas in 4 regions of Nepal. We performed a double agar overlay with S. Typhi to assess the presence of bacteriophages. We isolated and tested phages against multiple strains to assess their host range. We performed whole genome sequencing of isolated phages, and generated phylogenies using conserved genes. FINDINGS: S. Typhi-specific bacteriophages were detected in 54.9% (198/361) of river and 6.3% (1/16) drinking water samples from the Kathmandu Valley and Kavrepalanchok. Water samples collected within or downstream of population-dense areas were more likely to be positive (72.6%, 193/266) than those collected upstream from population centers (5.3%, 5/95) (p=0.005). In urban Biratnagar and rural Dolakha, where typhoid incidence is low, only 6.7% (1/15, Biratnagar) and 0% (0/16, Dolakha) river water samples contained phages. All S. Typhi phages were unable to infect other Salmonella and non-Salmonella strains, nor a Vi-knockout S. Typhi strain. Representative strains from S. Typhi lineages were variably susceptible to the isolated phages. Phylogenetic analysis showed that S. Typhi phages belonged to the class Caudoviricetes and clustered in three distinct groups. CONCLUSIONS: S. Typhi bacteriophages were highly abundant in surface waters of typhoid-endemic communities but rarely detected in low typhoid burden communities. Bacteriophages recovered were specific for S. Typhi and required Vi polysaccharide for infection. Screening small volumes of water with simple, low-cost (~$2) plaque assays enables detection of S. Typhi phages and should be further evaluated as a scalable tool for typhoid environmental surveillance

Detection of Salmonella Typhi bacteriophages in surface waters as a scalable approach to environmental surveillance.

BackgroundEnvironmental surveillance, using detection of Salmonella Typhi DNA, has emerged as a potentially useful tool to identify typhoid-endemic settings; however, it is relatively costly and requires molecular diagnostic capacity. We sought to determine whether S. Typhi bacteriophages are abundant in water sources in a typhoid-endemic setting, using low-cost assays.MethodologyWe collected drinking and surface water samples from urban, peri-urban and rural areas in 4 regions of Nepal. We performed a double agar overlay with S. Typhi to assess the presence of bacteriophages. We isolated and tested phages against multiple strains to assess their host range. We performed whole genome sequencing of isolated phages, and generated phylogenies using conserved genes.FindingsS. Typhi-specific bacteriophages were detected in 54.9% (198/361) of river and 6.3% (1/16) drinking water samples from the Kathmandu Valley and Kavrepalanchok. Water samples collected within or downstream of population-dense areas were more likely to be positive (72.6%, 193/266) than those collected upstream from population centers (5.3%, 5/95) (p=0.005). In urban Biratnagar and rural Dolakha, where typhoid incidence is low, only 6.7% (1/15, Biratnagar) and 0% (0/16, Dolakha) river water samples contained phages. All S. Typhi phages were unable to infect other Salmonella and non-Salmonella strains, nor a Vi-knockout S. Typhi strain. Representative strains from S. Typhi lineages were variably susceptible to the isolated phages. Phylogenetic analysis showed that S. Typhi phages belonged to the class Caudoviricetes and clustered in three distinct groups.ConclusionsS. Typhi bacteriophages were highly abundant in surface waters of typhoid-endemic communities but rarely detected in low typhoid burden communities. Bacteriophages recovered were specific for S. Typhi and required Vi polysaccharide for infection. Screening small volumes of water with simple, low-cost (~$2) plaque assays enables detection of S. Typhi phages and should be further evaluated as a scalable tool for typhoid environmental surveillance

<i>S</i>. Typhi phage isolation from environmental samples collected in Nepal.

S. Typhi phage isolation from environmental samples collected in Nepal.</p

Host range activity of 10 <i>S</i>. Typhi phages isolated in our study.

S. Typhi phages (y-axis) were spotted on S. Typhi isolates (x-axis) belonging to different genotypes. Colored circles represent lytic activity, white circles represent no lytic activity.</p

Phylogenetic tree of 27 S. Typhi phages isolated from Nepal and other 27 phages based on two gene sequences (tail fiber and terminase).

Tail fiber and terminase large subunit sequences of related phages were downloaded from NCBI. Phages isolated in our study are annotated with a black circle. Pickard et al., 2010 [15]* represents a S. Typhi Vi phage collection obtained from Cambridge University, Cambridge, United Kingdom, and originally isolated between the 1930 and 1955. These historical phages are annotated with white circles.</p

Nucleotide-based intergenomic similarities of <i>S</i>. Typhi isolated from Nepal, using VIRIDIC.

A heatmap of hierarchical clustering of the intergenomic similarity values was generated and given as percentage values (right half, blue-green heatmap). Each genome pair is represented by three values (left half), where the top and bottom represent the aligned genome fraction for the genome in the row and column, respectively. The middle value represents the genome length ratio for each genome pair. (TIF)</p

Summary of phage genomics and protein clusters statistics generated by Virclust.

Summary of phage genomics and protein clusters statistics generated by Virclust.</p

VirClust hierarchical clustering of the <i>S</i>. Typhi isolated from Nepal, based on intergenomic distances calculated using the protein cluster content.

The genome clustering was performed based on PCs. The resulting tree was split into VGCs using a 0.9 intergenomic distance threshold. The visual components are described further. 1. Hierarchical tree calculated using PC-based intergenomic distances. 2. Silhouette width, color-coded in a range from −1 (red) to 1 (green). 3. VGC ID. 4. Heatmap representation of the PC distribution in the viral genomes. Rows are represented by individual viral genomes. Columns are represented by individual PCs. The ID of each PC can be read at the bottom of the heatmap. Colors encode the number of each PC per genome, with white signifying the PC absence, and the other colors signifying various degrees of replication. 5. Viral genome-specific statistics: genome length, the proportion of PC shared (dark grey) with any other genomes in the dataset, reported to the total PCs in the genome (light grey bar), the proportion of PC shared in its own VGC, the proportion of PCs shared only in its own VGC, the proportion of PCs shared also outside its own VGC, and the proportion of PC shared only outside own VGC. 6. S. Typhi phage name. (TIF)</p