Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments

Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination

Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem

Freshwater network ecosystems consist of interconnected lotic and lentic environments within the same catchment area. Using Plitvice Lakes as an example, we studied the changes in environmental conditions and microbial communities (bacteria and fungi) that occur with downstream flow. Water samples from tributaries, interlake streams, connections of the cascading lakes, and the Korana River, the main outflow of the system, were characterized using amplicon sequencing of bacterial 16S rRNA and fungal ITS2 genes. Our results show that different environmental conditions and bacterial and fungal communities prevail among the three stream types within the freshwater network ecosystem during multiple sampling seasons. Microbial community differences were also confirmed along the longitudinal gradient between the most distant sampling sites. The higher impact of "mass effect" was evident during spring and winter, while "species sorting" and "environmental selection" was more pronounced during summer. Prokaryotic community assembly was majorly influenced by deterministic processes, while fungal community assembly was highly dominated by stochastic processes, more precisely by the undominated fraction, which is not dominated by any process. Despite the differences between stream types, the microbial community of Plitvice Lakes is shown to be very stable by the core microbiome that makes up the majority of stream communities. Our results suggest microbial community succession along the river-lake continuum of microbial communities in small freshwater network ecosystems with developed tufa barriers. IMPORTANCE Plitvice Lakes represent a rare freshwater ecosystem consisting of a complex network of lakes and waterfalls connecting them, as well as rivers and streams supplying water to the lake basin. The unique geomorphological, hydrological, biogeochemical, and biological phenomenon of Plitvice Lakes lies in the biodynamic process of forming tufa barriers. In addition to microbial communities, abiotic water factors also have a major influence on the formation of tufa. Therefore, it is important to understand how changes in environmental conditions and microbial community assembly affect the functioning of the ecosystem of a freshwater network with developed tufa barriers.

The impact of environmental factors on the transport and survival of pathogens in agricultural soils from karst areas of Yunnan province, China: Laboratory column simulated leaching experiments

Introduction

Groundwater is considered the best candidate for drinking water supply in the karst area. The groundwater water resources, however, are vulnerable to pathogenic microorganism contamination because of the typically thin soil layers overlying aquifers and the high permeability of the aquifer host rock, resulting in short residence times and low natural attenuation capacities. Until now, little attention has been paid to the critical environmental factors affecting the pathogenic microorganism contamination in soil-groundwater systems in the karst area.

Methods

In the study, orthogonality column experiments with controlling ambient temperatures, pH values of inlet water, and soil porosities were carried out to investigate the transport and lifespan of pathogenic microorganisms in the leachate of agricultural soils in the karst area of Yunnan province, China. The pathogenic indicators, i.e., total bacteria count (TBC) and total coliforms count (TCC), and hydrochemical parameters, i.e., pH and permanganate index (CODMn) in the leaching water, were systematically monitored.

Results and Discussion

The results showed that bacteria including coliforms can survive for prolonged periods of time in karst soils. The soils overlying the karst rocks were unable to impede the bacteria from seeping into the groundwater. The soils, in turn, likely served as both reservoirs and incubators for pathogenic bacteria. The ambient temperature was the most predominant influential factor affecting both TBC and TCC. The bacteria concentrations were proportional to the temperature in the leachate. Therefore, more attention should be paid to temperature variations in protecting the water supply, particularly in the high-temperature period, such as during the summer months.

Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O₂ (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O₂ and NO₃^- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

Seasonal fluctuation of water quality and ecogenomic phylogeny of novel potential microbial pollution indicators of Veshaw River Kashmir-Western Himalaya

Nearly a billion people, especially in underdeveloped nations, need safe drinking water. Indian studies suggest that most drinking water sources have high coliform levels, and quality assurance is required. This study was conducted in rural parts of South Kashmir in the Western Himalaya from February 2019 to January 2020. Standard river water sampling was done from upstream to downstream of the river. This study examined the detection, molecular identification, and chemical water quality of coliform-contaminated drinking water, which sums up river water pollution. Water quality varied significantly, indicating downstream contamination. Sangam (downstream) had the highest coliform count, showing 72.2600 cfu per litre in summer, while Kongwaton (upstream), near the Veshaw River, had no coliform count in winter. In summer, Sangam (downstream) had the highest water quality metrics (pH 6.847, Electrical conductivity (EC) 71.620 dS/m, Biological oxygen demand (BOD) 1.120 mg/L, and Chemical oxygen demand (COD) 24.637 mg/L) in all seasons. The lowest winter water quality metrics in Kongwaton were pH 8.947, EC 253.680 dS/m, BOD 4.963 mg/L, and COD 51.440 mg/L. Coliforms in water suggest faecal contamination. This study examines the water quality attributes of drinking water and associated factors to determine river pollution. Total DNA was collected and sequenced for 16 S rDNA and metagenomics. Universal primers were used to amplify the bacterial 16 S rRNA. Using BLAST, the amplified 16 S rRNA gene sequence was matched to the NCBI database. A metagenomic study revealed 27 species with different relative abundance. These species include Escherichia coli, E. fergusonii, E. albertii, Klebsiella grimontii, and Shigella dysenteriae. This study is thought to be the first to discriminate against E. fergusonii, E. albertii, K. grimontii, and S. dysenteriae from E. coli and to report on E. fergusonii and E. albertii, K. grimontii, and S. dysenteriae in the river Veshaw water sources in Kulgam, Western Himalaya.

Evaluation of Shallow Groundwater Quality at Regional Scales Using Adaptive Water Quality Indices

Groundwater, which is the main source of water for human consumption in many rural areas, has its quality determined by the complex interaction of environmental factors and anthropogenic activities. The present study evaluated the quality of shallow groundwater (1 to 25 m depth) in the rural area of the Târgovişte Plain, a densely populated area (200 inhabitants/km²) using 80 water samples collected from public wells. In order to explain the spatial distribution of the concentrations of the 19 physicochemical parameters considered (including heavy metals), the evaluation of groundwater quality for human consumption and potential impact on human health was conducted using the Water Quality Index (WQI), Integrated Weight Water Quality Index (IwWQI), Total Hazard Index (THI), and cumulative carcinogenic risk (CCR). For the WQI/IwWQI the comparative analysis of the two indices showed that for the WQI, it is important to select an optimal set of parameters, because use of a large number of physicochemical parameters can eclipse the values that exceed WHO guideline limits. In contrast, the use of entropy in the calculation of the IwWQI did not lead to eclipsing of exceedance, no matter the number of parameters used. Areas with poor and very poor groundwater quality according to the WQI/IwWQI overlapped, with a moderate risk to human health (THI > 1) for noncarcinogenic contaminants and also a risk of developing cancer according to the CCR average value (1.15 × 10^-2). The health of 43% of the rural population in the Târgovişte Plain can be affected if they drink contaminated groundwater, and it is estimated that about 600 people can develop cancer during their lifetime. If the risk of developing cancer is reduced only in the rural population that does not have access to a water source from a centralized and verified network, the results suggest that 385 people (1.15%) can develop cancer as a result of consuming groundwater contaminated with heavy metals based on the average value of CCR. This value is lower than the general mortality rate in areas with high CCR and below the average number of cancer patients in Romania (2.65%). The quality of groundwater and the risk of developing diseases and cancer due to water consumption is directly proportional to the intensity of agricultural land use and inversely proportional to the depth of the groundwater layer, the distance from the main hydrographic network and the reservoirs, and the distance from the main city, Târgovişte. The complex and integrated analysis of groundwater quality using quality indices and indicators of health risk for the population, validated by hot-spot analysis and compared to the mortality rate, is an approach with practical applicability. This integrated approach allows public authorities, policymakers, and health services to implement an efficient monitoring program and optimize anthropogenic activities in order to prevent groundwater contamination and finally improve the quality of life for the residents in the area of this study.

Metal Contents and Pollution Indices Assessment of Surface Water, Soil, and Sediment from the Arieș River Basin Mining Area, Romania

The current study was conducted to assess the level and spatial distribution of metal pollution in surface water, soil, and sediment samples from the Arieș River basin, located in central Romania, an area impacted by various mining and industrial operations. Several pollution indices, spatial distributions, cluster analyses, principal component analyses, and heat maps were applied for evaluating the contamination level with Ni, Cu, Zn, Cd, Pb, Mn, As, and Hg in the area. Based on the results of the Heavy-Metal Pollution Index and of the Heavy-Metal Evaluation Index of the surface-water samples, the middle part of the Arieș River basin, near and downstream of the gold mine impoundment, was characterized by high pollution levels. The metal concentration was higher near the tailing impoundment, with increased levels of Cu, Ni, Zn, and Pb in the soil samples and As, Cd, Pb, Na, K, Ca, Mn, and Al in the sediment samples. Ca (23.7–219 mg/L), Mg (2.55–18.30 mg/L), K (0.64–14.70 mg/L), Al (0.06–22.80 mg/L), and Mn (0.03–22.40 mg/L) had the most remarkable spatial variation among the surface-water samples, while various metal contents fluctuated strongly among the sampling locations. Al varied from 743 to 19.8 mg/kg, Fe from 529 to 11.4 mg/kg, Ca from 2316 to 11.8 mg/kg, and Mg from 967 to 2547 mg/kg in the soil samples, and Al varied from 3106 to 8022 mg/kg, Fe from 314 to 5982 mg/kg, Ca from 1367 to 8308 mg/kg, and Mg from 412 to 1913 mg/kg in the sediment samples. The Potential Ecological Risk Index values for soil and sediments were in the orders Cu > Ni > Pb > Hg > Cr > As > Mn > Zn > Cd and As > Cu > Cr > Cd > Pb > Ni > Hg > Mn > Zn, respectively, and the highest values were found around the gold mine impoundment.