High-throughput metagenomic assessment of Cango Cave microbiome-A South African limestone cave

Microorganisms inhabiting caves exhibit medical or biotechnological promise, most of which have been attributed to factors such as antimicrobial activity or the induction of mineral precipitation. This dataset explored the shotgun metagenomic sequencing of the Cango cave microbial community in Oudtshoorn, South Africa. The aimed to elucidate both the structure and function of the microbial community linked to the cave. DNA sequencing was conducted using the Illumina NovaSeq platform, a next-generation sequencing. The data comprises 4,738,604 sequences, with a cumulative size of 1,180,744,252 base pairs and a GC content of 52%. Data derived from the metagenome sequences can be accessed through the bioproject number PRJNA982691 on NCBI. Using an online metagenome server, MG-RAST, the subsystem database revealed that bacteria displayed the highest taxonomical representation, constituting about 98.66%. Archaea accounted for 0.05%, Eukaryotes at 1.20%, viruses were 0.07%, while unclassified sequences had a representation of 0.02%. The most abundant phyla were Proteobacteria (81.74%), Bacteroidetes (10.57%), Actinobacteria (4.16%), Firmicutes (SK‒1.03%), Acidobacteria (0.20), and Planctomycetes (SK‒0.16%). Functional annotation using subsystem analysis revealed that clustering based on subsystems had 13.44%, while amino acids and derivatives comprised 11.41%. Carbohydrates sequences constituted 9.55%, along with other advantageous functional traits essential for growth promotion and plant management.

A quantitative comparison of macro-plastic debris between undisturbed and populous coastal ecosystems of West Bengal, India

Unmanaged plastic debris from both terrestrial and aquatic sources is causing havoc on Indian coastlines. Tajpur Beach and Haliday Island were selected as two distinct coastal ecosystems in West Bengal for inventorying sighted macro-plastics, aiming to assess their distribution and compare pollution levels. This study employs a comprehensive methodological approach, integrating field-based observations along with lab-based measurements, and information derived from geospatial analysis. Total 34 random points across two study sites were considered for the physical, chemical, and biological characterization of macro-plastics to assess their relative abundance. Areas with higher human footfalls exhibited greater accumulation of plastic debris, with polypropylene, either alone or in combination with polyurethane and polystyrene, identified as highly toxic. Fragmented plastic debris was prevalent at both test sites, yet undisturbed Haliday Island exhibited an abundance of less fragmented materials. Emphasis was also given on implementing appropriate management regimes to achieve plastic-free diverse coastal landscapes.

Dataset of amplicon metagenomic assessment of barley rhizosphere bacteria under different fertilization regimes

The metagenomic dataset profiled in this research is built on bacterial 16S rRNA gene amplicon of DNA mined from barley rhizosphere under chemical (CB) and organic (OB) fertilization. Amplicon-based sequencing was prepared by the Illumina platform, and the raw sequence dataset was examined using Metagenomic Rast Server (MG-RAST). The metagenome comprised sixteen samples that include CB1 (494,583 bp), CB2 (586,532 bp), CB3 (706,685 bp), CB4 (574,606 bp), CB5 (395,460 bp), CB6 (520,822 bp), CB7 (511,729 bp), CB8 (548,074 bp), OB1 (642,794 bp), OB2 (513,767 bp), OB3 (461,293 bp), OB4 (498,241 bp), OB5 (689,497 bp), OB6 (423,436 bp), OB7 (478,657 bp) and OB8 (279,186 bp). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA827679 (CB1), PRJNA827686 (CB2), PRJNA827693 (CB3), PRJNA827699 (CB4), PRJNA827706 (CB5), PRJNA827761 (CB6), PRJNA827780 (CB7), PRJNA827786 (CB8), PRJNA826806 (OB1), PRJNA826824 (OB2), PRJNA826834 (OB3), PRJNA826841 (OB4), PRJNA826853 (OB5), PRJNA827254 (OB6), PRJNA827256 (OB7), and PRJNA827257 (OB8) at NCBI. Actinobacteria dominated the soil samples at the phylum level.

Spatial-temporal pattern and urban-rural gradient of comprehensive ecological security in urban agglomeration in South China from 2000 to 2020

The ecological security (ES) of urban agglomeration and surrounding environmental system is related to the sustainable development of cities, which is a hot spot that we must pay attention to. In this study, four subsystems composed of natural base, landscape structure, ecosystem stability, and anthropogenic interference were used to evaluate the comprehensive ecological security (CES) of Guangdong-Hong Kong-Macao Greater Bay Area (GHMGBA) in 2000, 2010 and 2020. The results show that CES of the region was generally well. The central urban region of GHMGBA was unsafety with an area proportion of about 24.5%, the periphery was safety with an area proportion of about 43.5%, and the others are transitional zone. From 2000 to 2020, the CES change first slightly decreases and then relatively stable, and the transfer of different safety levels mainly occurs in the transitional zone. In 2010-2020 the transfer of different levels of CES is more frequent than in 2000-2010, indicating that the spatial-temporal pattern of CES fluctuated sharply during 2010-2020. The urban-rural gradient showed that with the increase of distance, CES fluctuations increase, but decreases at about 20-40km, 60-80km and 120-140km away from the city center, which may be sub-urban regions. The overall CES change range gradually decreases with increasing distance from urban centers. This study helps to understand the temporal and spatial distribution of ecological environment and urban-rural gradient in typical urban regions, and provides a reference for the collaborative planning of urban agglomeration.

Assessment of water quality and ecosystem health of a canal system during the lockdown period

The impacts of the lockdown period on water quality and ecosystem health in an artificial canal water system were investigated from the rapidly growing Kozhikode City in India. The ecosystem health is measured in terms of water quality indicators such as pH, electrical conductivity (EC), dissolved oxygen (DO), biological oxygen demand (BOD) and Escherichia coli (E. coli) during the pre-lockdown and lockdown period. The study reveals the massive improvement of the ecosystem health of the canal in terms of DO, BOD, and E. coli during the lockdown period. DO values were improved from anoxic (0 mg/L) to oxic (> 5 mg/L), BOD reduced from 31 to 0.7 mg/L as well as E. coli at major urban stretches were 800 MPN/100 mL, which was observed to be absent during the lockdown period. Urban stretches of the canal implicitly proved that the lockdown period was not sufficient to recover the natural ecosystem condition of the canal system. Principal component analysis revealed that the ecosystem health of the canal majorly governs two factors, such as the weathering process and anthropogenic waste sources. The study advocates the policy makers that temporary pollution source control in a timely interval may heal the environment and is useful to the regulatory bodies for suggesting the pollution source control mechanism.

Ecological risks associated to trace metals of contaminated sediments from a densely urbanized tropical eutrophic estuary

The sediment contamination by trace metals in coastal aquatic ecosystems is a worldwide environmental problem, since metals can be toxic, persistent, and bioaccumulated. In case of natural events, such as storms, or anthropogenic activities, like dredging, the sediment resuspension to the water column occurs and can solubilize metals, probably increasing their bioavailability and consequently the risk to aquatic life. This study evaluated the bioavailability on reactive trace metals (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) in estuarine sediments from Iguaçu and Meriti Rivers, both in the drainage basin of Guanabara Bay (Rio de Janeiro, Brazil). Additionally, a discussion about the anthropogenic interference throughout time of six short sediments cores, calculating three different indexes (contamination factors, CF; potential ecological risk index for a single heavy metal, Eⁱf for short; potential ecological risk, PERI) was performed. It was considered as reactive phase, the metal concentrations obtained using a weak acid extraction (in HCl 1 mol L^-1 solution). Zn presented high concentrations after resuspension, being above effect range medium (ERM) (52.81 to 1337.4 mg kg^-1). The CF indicated very high contamination degree for Cu (14.62 to 17.96) and Zn (27.80 to 35.85) for both rivers. The Eⁱf for short presented higher risk to Cu and Zn for Iguaçu and Meriti rivers. PERI index classified Meriti River samples as severely contaminated (238.10 to 351.62).

High-throughput sequencing data of soil bacterial communities from Tweefontein indigenous and commercial forests, South Africa

In this report, the high-throughput sequencing data of soil bacterial communities from indigenous and commercial forests in Tweefontein, South Africa are presented. These data were collected to study the influence of land-use change on soil bacterial diversity and community structure in forests. Illumina Miseq sequencing of 16S rRNA gene amplicon was carried out on soils sampled from Tweefontein commercial (TC) and indigenous (TI) forests in South Africa. The metagenome contained 101,938 sequences with 46,709,377 bp size and 57% G + C content in TI and 91,160 sequences with 41,707,827 bp size and 57% G + C content in TC. Metagenome sequence information are available at NCBI under the Sequence Read Archive (SRA) database with accession numbers SRR8134476 (TI) and SRR8135323 (TC). Taxonomic hits distribution from Metagenomic Rast Server (MG-RAST) analysis of the TI sample revealed the dominance of the phyla Acidobacteria (21.61%), Actinobacteria (18.23%) and Verrucomicrobia (16.78%). Predominant genera were Candidatus Koribacter (12.82%), Candidatus Solibacter (11.74%) and Chthoniobacter (9.36%). MG-RAST assisted analysis of TC sample also detected the dominance of Actinobacteria (23.62%) along with Verrucomicrobia (21.92%) and Acidobacteria (20.74%). Predominant genera were Chthoniobacter (24.94%), Candidatus Solibacter (16.74%) and Candidatus Koribacter (9.39%) which play vital ecological functions in forest ecosystems.