Assessment of bacterial community composition in response to uranium levels in sediment samples of sacred Cauvery River

Effects of Detoxifying Substances on Uranium Removal by Bacteria Isolated from Mine Soils: Performance, Mechanisms, and Bacterial Communities

In this study, we investigated the effect of detoxifying substances on U(VI) removal by bacteria isolated from mine soil. The results demonstrated that the highest U(VI) removal efficiency (85.6%) was achieved at pH 6.0 and a temperature of 35 °C, with an initial U(VI) concentration of 10 mg/L. For detoxifying substances, signaling molecules acyl homoserine lactone (AHLs, 0.1 µmol/L), anthraquinone-2, 6-disulfonic acid (AQDS, 1 mmol/L), reduced glutathione (GSH, 0.1 mmol/L), selenium (Se, 1 mg/L), montmorillonite (MT, 1 g/L), and ethylenediaminetetraacetic acid (EDTA, 0.1 mmol/L) substantially enhanced the bacterial U(VI) removal by 34.9%, 37.4%, 54.5%, 35.1%, 32.8%, and 47.8% after 12 h, respectively. This was due to the alleviation of U(VI) toxicity in bacteria through detoxifying substances, as evidenced by lower malondialdehyde (MDA) content and higher superoxide dismutase (SOD) and catalase (CAT) activities for bacteria exposed to U(VI) and detoxifying substances, compared to those exposed to U(VI) alone. FTIR results showed that hydroxyl, carboxyl, phosphorus, and amide groups participated in the U(VI) removal. After exposure to U(VI), the relative abundances of Chryseobacterium and Stenotrophomonas increased by 48.5% and 12.5%, respectively, suggesting their tolerance ability to U(VI). Gene function prediction further demonstrated that the detoxifying substances AHLs alleviate U(VI) toxicity by influencing bacterial metabolism. This study suggests the potential application of detoxifying substances in the U(VI)-containing wastewater treatment through bioremediation.

Deciphering Indigenous Bacterial Diversity of Co-Polluted Sites to Unravel Its Bioremediation Potential: A Metagenomic Approach

Polluted drains across the globe are affected due to reckless disposal of untreated industrial effluents resulting in significant water pollution affecting microbial community structure/dynamics. To elucidate this, polluted samples were collected from Budha Nala (BN) drain, Tung Dhab (TD) drain, and wastewater treatment plant (WWTP) receiving an inflow of organic pollutants as well as heavy metals due to anthropogenic activities. The sample of unpolluted pristine soil (PS) was used as control, as there is no history of usage of organic chemicals at this site. The bacterial diversity of these samples was sequenced using the Illumina MiSeq platform by amplifying the V3/V4 region of 16S rRNA. The majority of operational taxonomic unit (OTUs) at polluted sites belonged to phyla Proteobacteria specifically Gammaproteobacteria class, followed by Actinobacteria, Bacteriodetes, Chloroflexi, Firmicutes, Planctomycetes, WS6, and TM7, whereas unpolluted site revealed the prevalence of Proteobacteria followed by Actinobacteria, Planctomycetes, Firmicutes, Acidobacteria, Chloroflexi, Bacteroidetes, Verrucomicrobia, and Nitrospirae. The data sets decode unclassified species of the phyla Proteobacteria, Bacteriodetes, Chloroflexi, Firmicutes, and WS6, along with some unclassified bacterial species. The study provided a comparative study of changed microbial community structure, their possible functions across diverse geographical locations, and identifying specific bacterial genera as pollution bio-indicators of aged polluted drains.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Assessing the chronic effect of the bioavailable fractions of radionuclides and heavy metals on stream microbial communities: A case study at the Rophin mining site

This study aimed to assess the potential impact of long-term chronic exposure (69 years) to naturally-occurring radionuclides (RNs) and heavy metals on microbial communities in sediment from a stream flowing through a watershed impacted by an ancient mining site (Rophin, France). Four sediment samples were collected along a radioactivity gradient (for 238U368 to 1710 Bq.Kg-1) characterized for the presence of the bioavailable fractions of radionuclides (226Ra, 210Po), and trace metal elements (Th, U, As, Pb, Cu, Zn, Fe). Results revealed that the available fraction of contaminants was significant although it varied considerably from one element to another (0 % for As and Th, 5-59 % for U). Nonetheless, microbial communities appeared significantly affected by such chronic exposure to (radio)toxicities. Several microbial functions carried by bacteria and related with carbon and nitrogen cycling have been impaired. The high values of fungal diversity and richness observed with increasing downstream contamination (H' = 4.4 and Chao1 = 863) suggest that the community had likely shifted toward a more adapted/tolerant one as evidenced, for example, by the presence of the species Thelephora sp. and Tomentella sp. The bacterial composition was also affected by the contaminants with enrichment in Myxococcales, Acidovorax or Nostocales at the most contaminated points. Changes in microbial composition and functional structure were directly related to radionuclide and heavy metal contaminations, but also to organic matter which also significantly affected, directly or indirectly, bacterial and fungal compositions. Although it was not possible to distinguish the specific effects of RNs from heavy metals on microbial communities, it is essential to continue studies considering the available fraction of elements, which is the only one able to interact with microorganisms.

Enhanced indigenous consortia for the remediation of uranium-contaminated groundwater by bioaugmentation: Reducing and phosphate-solubilizing consortia

To investigate the strengthening effects and mechanisms of bioaugmentation on the microbial remediation of uranium-contaminated groundwater via bioreduction coupled to biomineralization, two exogenous microbial consortia with reducing and phosphate-solubilizing functions were screened and added to uranium-contaminated groundwater as the experimental groups (group B, reducing consortium added; group C, phosphate-solubilizing consortium added). β-glycerophosphate (GP) was selected to stimulate the microbial community as the sole electron donor and phosphorus source. The results showed that bioaugmentation accelerated the consumption of GP and the proliferation of key functional microbes in groups B and C. In group B, Dysgonomonas, Clostridium_sensu_stricto_11 and Clostridium_sensu_stricto_13 were the main reducing bacteria, and Paenibacillus was the main phosphate-solubilizing bacteria. In group C, the microorganisms that solubilized phosphate were mainly unclassified_f_Enterobacteriaceae. Additionally, bioaugmentation promoted the formation of unattached precipitates and alleviated the inhibitory effect of cell surface precipitation on microbial metabolism. As a result, the formation rate of U-phosphate precipitates and the removal rates of aqueous U(VI) in both groups B and C were elevated significantly after bioaugmentation. The U(VI) removal rate was poor in the control group (group A, with only an indigenous consortium). Propionispora, Sporomusa and Clostridium_sensu_stricto_11 may have played an important role in the removal of uranium in group A. Furthermore, the addition of a reducing consortium promoted the reduction of U(VI) to U(IV), and immobilized uranium existed in the form of U(IV)-phosphate and U(VI)-phosphate precipitates in group B. In contrast, U was present mainly as U(VI)-phosphate precipitates in groups A and C. Overall, bioaugmentation with an exogenous consortium resulted in the rapid removal of uranium from groundwater and the formation of U-phosphate minerals and served as an effective strategy for improving the treatment of uranium-contaminated groundwater in situ.

Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities

Little is still known about the low dose effects of radiation on the microbial communities in the environment. Mineral springs are ecosystems than can be affected by natural radioactivity. These extreme environments are, therefore, observatories for studying the influence of chronic radioactivity on the natural biota. In these ecosystems we find diatoms, unicellular microalgae, playing an essential role in the food chain. The present study aimed to investigate, using DNA metabarcoding, the effect of natural radioactivity in two environmental compartments (i.e. spring sediments and water) on the genetic richness, diversity and structure of diatom communities in 16 mineral springs in the Massif Central, France. Diatom biofilms were collected during October 2019, and a 312 bp region of the chloroplast gene rbcL (coding for the Ribulose Bisphosphate Carboxylase) used as a barcode for taxonomic assignation. A total of 565 amplicon sequence variants (ASV) were found. The dominant ASV were associated with Navicula sanctamargaritae, Gedaniella sp., Planothidium frequentissimum, Navicula veneta, Diploneis vacillans, Amphora copulata, Pinnularia brebissonii, Halamphora coffeaeformis, Gomphonema saprophilum, and Nitzschia vitrea, but some of the ASVs could not be assigned at the species level. Pearson correlation failed to show a correlation between ASV' richness and radioactivity parameters. Non-parametric MANOVA analysis based on ASVs occurrence or abundances revealed that geographical location was the main factor influencing ASVs distribution. Interestingly, ²³⁸U was the second factor that explained diatom ASV structure. Among the ASVs in the mineral springs monitored, ASV associated with one of the genetic variants of Planothidium frequentissimum was well represented in the springs and with higher levels of ²³⁸U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium.

Impact of microbial processes on the safety of deep geological repositories for radioactive waste

To date, the increasing production of radioactive waste due to the extensive use of nuclear power is becoming a global environmental concern for society. For this reason, many countries have been considering the use of deep geological repositories (DGRs) for the safe disposal of this waste in the near future. Several DGR designs have been chemically, physically, and geologically well characterized. However, less is known about the influence of microbial processes for the safety of these disposal systems. The existence of microorganisms in many materials selected for their use as barriers for DGRs, including clay, cementitious materials, or crystalline rocks (e.g., granites), has previously been reported. The role that microbial processes could play in the metal corrosion of canisters containing radioactive waste, the transformation of clay minerals, gas production, and the mobility of the radionuclides characteristic of such residues is well known. Among the radionuclides present in radioactive waste, selenium (Se), uranium (U), and curium (Cm) are of great interest. Se and Cm are common components of the spent nuclear fuel residues, mainly as 79Se isotope (half-life 3.27 × 105 years), 247Cm (half-life: 1.6 × 107 years) and 248Cm (half-life: 3.5 × 106 years) isotopes, respectively. This review presents an up-to-date overview about how microbes occurring in the surroundings of a DGR may influence their safety, with a particular focus on the radionuclide-microbial interactions. Consequently, this paper will provide an exhaustive understanding about the influence of microorganisms in the safety of planned radioactive waste repositories, which in turn might improve their implementation and efficiency.

Response of soil microbial communities to natural radionuclides along specific-activity gradients

Understanding the response of soil microbial community to abnormal natural radionuclides is important to maintain soil ecological function, but the underlying mechanism of tolerance and survival of microbes is poorly studied. The effects of natural radionuclides on the topsoil microbial communities in anomalous natural radiation area were investigated in this work, and it was found that microbial community composition was significantly influenced by the specific-activities of natural radionuclides. The results revealed that relative abundances of 10 major microbial phyla and genera displayed different patterns along specific-activity gradients, including decreasing, increasing, hump-shaped, U-shaped, and similar sinusoidal or cosine wave trends, which indicated that the natural radionuclides were the predominant driver for change of microbial community structure. At the phylum and genus level, microbial communities were divided into two special groups according to the tolerance to natural radionuclides, such as ²³⁸U and ²³²Th, including tolerant and sensitive groups. Taken together, our findings suggest that the high specific-activities of natural radionuclides can obviously drive changes in microbial communities, providing a possibility for future studies on the microbial tolerance genes and bioremediation strains.

Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar

Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.

Assessment, characterization, and quantification of microplastics from river sediments

Microplastic (MP), as a pollutant, is currently posing a biological hazard to the aquatic environment. The study aims to isolate, quantify, and characterize the MP pollutants in sediment samples from 14 study sites at Kaveri River, Killa Chinthamani, Tiruchirappalli, South India. With Sediment-MP Isolation (SMI) unit, density separation was done with a hydrogen peroxide solution. Four forms of MPs namely, fragments, films, foams, and fibers with orange, white, green, and saffron red were observed. The plenitude and distribution of four forms of MPs and natural substrates were geometrically independent, with large amounts of microfragments within the research region accounting for 79.72% variation by Principal Component Analysis. FT-IR analyses of MPs showed the presence of polyamide, polyethylene, polyethylene glycol, polyethylene terephthalate, polypropylene, and polystyrene. Additionally, the scanning electron microscopic analysis revealed that the MPs have differential surface morphology with rough surfaces, porous structures, fissures, and severe damage. Most MPs comprised Si, Mg, Cu, and Al, according to energy dispersive X-ray analyses. The combined SMI, instrumental analyses and evaluation (heat map) of MPs in river sediments help assess contamination levels and types of MPs. The findings might provide an insight into the status of MPs in Kavery River sediments that could help in formulating regulations for MPs reduction and contamination in rivers eventually to protect the environment.

Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39-47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO₂²⁺ and Fe³⁺. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.

Optimization of Environmental Conditions for Microbial Stabilization of Uranium Tailings, and the Microbial Community Response

Uranium pollution in tailings and its decay products is a global environmental problem. It is of great significance to use economical and efficient technologies to remediate uranium-contaminated soil. In this study, the effects of pH, temperature, and inoculation volume on stabilization efficiency and microbial community response of uranium tailings were investigated by a single-factor batch experiment in the remediation process by mixed sulfate-reducing bacteria (SRB) and phosphate-solubilizing bacteria (PSB, Pantoea sp. grinm-12). The results showed that the optimal parameters of microbial stabilization by mixed SRB-PSB were pH of 5.0, temperature of 25°C, and inoculation volume of 10%. Under the optimal conditions, the uranium in uranium tailings presented a tendency to transform from the acid-soluble state to residual state. In addition, the introduction of exogenous SRB-PSB can significantly increase the richness and diversity of endogenous microorganisms, effectively maintain the reductive environment for the microbial stabilization system, and promote the growth of functional microorganisms, such as sulfate-reducing bacteria (Desulfosporosinus and Desulfovibrio) and iron-reducing bacteria (Geobacter and Sedimentibacter). Finally, PCoA and CCA analyses showed that temperature and inoculation volume had significant effects on microbial community structure, and the influence order of the three environmental factors is as follows: inoculation volume > temperature > pH. The outcomes of this study provide theoretical support for the control of uranium in uranium-contaminated sites.

Biological Removal of Se and Cd from Acidic Selenite- and Cadmium-containing Wastewater with Limited Carbon Availability

This study presents a successful treatment of biological acidic Se(IV)- and Cd(II)-containing wastewater via the SBR with limited carbon source (100 mg/L COD). Scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDS), high solution transmission electron microscopy (HRTEM) and X-ray photoelectron spectrometer (XPS) results verified the formation of elemental Se and CdSe nanoparticles in the sludge. The abundance of genera in the microbial community gradually changed over the treatment phases depending on the Se(IV) and Cd(II) exposure with different influent COD concentrations. The taxa of Proteiniclasticum, Clostridium_sensu_stricto_12, Longilinea and Mycobacterium were dominant. Redundancy analysis (RDA) indicates that COD concentrations had the greatest impact on Zoogloea and Pseudomonas by promoting an increased abundance and decreased abundance, respectively. Overall, the results extended our understanding of the mechanisms and microbial community responding for the Se(IV) and Cd(II) removal under limited carbon availability in acidic wastewater.

A new era of radiation resistance bacteria in bioremediation and production of bioactive compounds with therapeutic potential and other aspects: An in-perspective review

Microorganisms that survive in extreme environmental conditions are known as 'extremophiles'. Recently, extremophiles draw an impression in biotechnology/pharmaceutical researches/industries because of their novel molecules, known as 'extremolytes'. The intriguing phenomenon of microbial radiation resistance probably arose independently throughout their evolution of selective pressures (e.g. UV, X-ray, Gamma radiation etc.). Radiation produces multiple types of damage/oxidation to nucleic acids, proteins and other crucial cellular components. Most of the literature on microbial radiation resistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures isolation and their application on bioremediation/therapeutic field. There is much less information other than bioremediation and therapeutic application of such promising microbes we called as 'new era'. Here we discus origin and diversity of radiation resistance bacteria as well as selective mechanisms by which microorganisms can sustain in radiation rich environment. Potential uses of these radiations resistant microbes in the field of bioremediation, bioactive compounds and therapeutic industry. Last but not the least, which is the new aspect of radiation resistance microbes. Our review suggest that resistance to chronic radiation is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap molecular mechanisms of resistance to radiation and other stressors. These stress tolerance potential make them potential for radionuclides remediation, their extremolytes can be useful as anti-oxidant and anti-proliferative agents. In current scenario they can be useful in various fields from natural dye synthesis to nanoparticles production and anti-cancer treatment.

Response and Dynamic Change of Microbial Community during Bioremediation of Uranium Tailings by Bacillus sp

Bacillus sp. is widely used in the remediation of uranium-contaminated sites. However, little is known about the competitive process of microbial community in the environment during bioremediation. The bioremediation of uranium tailings using Bacillus sp. was explored, and the bacterial community was analyzed by high-throughput sequencing at different stages of remediation. Bacillus sp. reduced the leaching of uranium from uranium tailings. The lowest uranium concentration was 17.25 μg/L. Alpha diversity revealed that the abundance and diversity of microorganisms increased with the extension of the culture time. The microbial abundance and diversity were higher in the treatment group than in the control group. The dominant species at the phyla level were Firmicutes and Proteobacteria in the uranium tailings environment, whereas the phylum of Proteobacteria was significantly increased in the treatment group. Based on the genus level, the proportions of Arthrobacter, Rhodococcus and Paenarthrobacter decreased significantly, whereas those of Clostridium sp., Bacillus and Pseudomonas increased dramatically. Hence, the remediation of uranium contamination in the environment was due to the functional microorganisms, which gradually became the dominant strain in the treatment, such as Desulfotomaculum, Desulfosporporosinus, Anaerocolumna, Ruminiclostridium and Burkholderia. These findings provided a promising outlook of the potential for remediation strategies of soil contaminated by uranium. The dynamic characteristics of the microbial community are likely to provide a foundation for the bioremediation process in practice.

Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics

Microbial communities are considered as vital members to reflect the health of a riverine system. Among them, pathogenic and fecal indicators imply health risks involved with potability of river water. The present study explores the diverse microbial communities, distribution pattern of potential pathogens, and fecal indicators between the geographically distinct Himalayan and Peninsular river systems of India. It also inquires into the environmental factors associated with community variance and distribution pattern of microbial indicators. The application of high-throughput amplicon sequencing approach unveiled significant demarcation (p < 0.004, Anosim R = 0.62) of samples suggesting unique microbial diversities in these two river sediments. Random forest analysis revealed Desulfobulbulus, PSB_M_3, and Opitutus in Himalayan, while DA101, Bacillus, and Streptomyces in the Peninsular as significant contributors to develop overall dissimilarity between the river systems. Permutational multivariate analysis of variance and co-occurrence network analysis were used to study the relationships between microbial taxa and environmental factors. Amongst the various studied environmental parameters, pH, K, Ca, Mg, Ba, and Al in the Himalayan and salinity, Na, temperature, and Th in the Peninsular significantly influenced shaping of distinct microbial communities. Furthermore, the potential pathogenic genera, including Flavobacterium, Clostridium, Arcobacter, Pseudomonas, and Bacillus were highly prevalent in both the river systems. Arcobacter, Clostridium, Acinetobacter, Bacteroides, and Caloramator were the prominent fecal indicators in these river systems. Our findings provide salient information about the crucial role and interplay between various environmental factors and anthropogenic influences in framing the microbiome of the distinct river systems in India. Moreover, assessing potential pathogenic and fecal indicators suggest the public health risk associated with untreated sewage discharge into these water sources. The detection of various F/S indicators and potentially pathogenic bacteria in Himalayan and Peninsular river systems emphasize the urgent need for future monitoring and management of major riverine systems in India.

Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications

Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.

River contamination shapes the microbiome and antibiotic resistance in sharpbelly (Hemiculter leucisculus)

Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10^-1/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.

Microbial characteristic and bacterial community assessment of sediment sludge upon uranium exposure

The microbial characteristics and bacterial communities of sediment sludge upon different concentrations of exposure to uranium were investigated by high solution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and high-throughput sequencing. After exposure to initial uranium concentrations of 10-50 μM for 24 h in synthetic wastewater, the removal efficiencies of uranium reached 80.7%-96.5%. The spherical and short rod bacteria were dominant in the sludge exposed to uranium. HRTEM-EDS and XPS analyses indicated that reduction and adsorption were the main mechanisms for uranium removal. Short-term exposure to low concentrations of uranium resulted in a decrease in bacterial richness but an increase in diversity. A dramatic change in the composition and abundances of the bacterial community were present in the sediment sludge exposed to uranium. The highest removal efficiency was identified in the sediment sludge exposed to 30 μM uranium, and the dominant bacteria included Acinetobacter (44.9%), Klebsiella (20.0%), Proteiniclasticum (6.7%), Enterobacteriaceae (6.6%), Desulfovibrio (4.4%), Porphyromonadaceae (4.1%), Comamonas (2.4%) and Sedimentibacter (2.3%). By comparison to the inoculum sediment sludge, exposure to uranium caused a substantial difference in the majority of bacterial abundance.

Roles of extracellular polymeric substances in uranium immobilization by anaerobic sludge

The specific roles of extracellular polymeric substances (EPS) and how factors influenced EPS’s roles during U(VI) immobilization are still unclear. In this study, high content of U with the main form of nanoparticles was detected in EPS, accounting for 10–42% of total U(VI) removal. EPS might be utilized as energy source or even as electron donors when external carbon source was unavailable. The influencing degree of each experimental parameter to uranium (U) removal process was elucidated. The influential priority to U(IV)/U(VI) ratios in sludge was as follows: acetate, U(VI), and nitrate. The influential priority to total EPS contents was as follows: U(VI), nitrate and acetate. The complex interaction mechanism between U(VI) and EPS in the U immobilization process was proposed, which might involve three ways including biosorption, bioreduction and bioprecipitation. These results indicate important and various roles of EPS in U(VI) immobilization.

Antibiotic Resistome Biomarkers associated to the Pelagic Sediments of the Gulfs of Kathiawar Peninsula and Arabian Sea

Antibiotic resistance has been one of the most persistent global issue. Specifically, marine microbiomes have served as complex reservoirs of antibiotic resistant genes. Molecular advancements have enabled exploration of the uncultured microbial portion from hitherto difficult to sample niches such as deeper oceans. The Gulfs of Kathiawar Peninsula have been known for their unique properties like extreme tidal variations, different sediment textures and physicochemical variations. Pelagic sediment cores across four coordinates each of the Gulf of Kutch, Gulf of Khambhat and an open Arabian Sea were collected, processed for metagenomic sequencing and assessed for antibiotic and metal resistome. The dominant genes were mostly resistant to macrolides, glycopeptides and tetracycline drugs. Studied samples divided into three clusters based on their resistome with carA, macB, bcrA, taeA, srmB, tetA, oleC and sav1866 among the abundant genes. Samples from creek of Gulf of Kutch and mouth of Gulf of Khambhat were most diverse in resistance gene profile. Biomarkers observed include gyrA mutation conferring resistance gene in the Arabian Sea; Proteobacteria species in Gulf of Kutch and Arabian sea; while Aquificae, Acidobacteria and Firmicutes species in the Gulf of Khambhat. Region-wise differentially abundant 23 genes and 3 taxonomic biomarkers were proposed for antibiotic resistance monitoring.

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City

Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO₃⁻) and ammonia (NH₄⁺) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5–84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH₄⁺ was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH₄⁺ on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.

Antibiotic resistance genes are abundant and diverse in raw sewage used for urban agriculture in Africa and associated with urban population density

A comparative study was conducted to (1) assess the potential of raw sewage used for urban agriculture to disseminate bacterial resistance in two cities of different size in Cameroon (Central Africa) and (2) compare the outcome with data obtained in Burkina Faso (West Africa). In each city, raw sewage samples were sampled from open-air canals in three neighbourhoods. After DNA extraction, the microbial population structure and function, presence of pathogens, antibiotic resistance genes and Enterobacteriaceae plasmids replicons were analysed using whole genome shotgun sequencing and bioinformatics. Forty-three pathogen-specific virulenc e factor genes were detected in the sewage. Eighteen different incompatibility groups of Enterobacteriaceae plasmid replicon types (ColE, A/C, B/O/K/Z, FIA, FIB, FIC, FII, H, I, N, P, Q, R, T, U, W, X, and Y) implicated in the spread of drug-resistance genes were present in the sewage samples. One hundred thirty-six antibiotic resistance genes commonly associated with MDR plasmid carriage were identified in both cities. Enterobacteriaceae plasmid replicons and ARGs found in Burkina Faso wastewaters were also present in Cameroon waters. The abundance of Enterobacteriaceae, plasmid replicons and antibiotic resistance genes was greater in Yaounde, the city with the greater population. In conclusion, the clinically relevant environmental resistome found in raw sewage used for urban agriculture is common in West and Central Africa. The size of the city impacts on the abundance of drug-resistant genes in the raw sewage while ESBL gene abundance is related to the prevalence of Enterobacteriaceae along with plasmid Enterobacteriaceae abundance associated to faecal pollution.

Analysis of uranium removal capacity of anaerobic granular sludge bacterial communities under different initial pH conditions

The bacterial community of an anaerobic granular sludge associated with uranium depletion was investigated following its exposure to uranium under different initial pH conditions (pH 4.5, 5.5, and 6.5). The highest uranium removal efficiency (98.1%) was obtained for the sample with an initial pH of 6.5, which also supported the highest bacterial community richness and diversity. Venn diagrams visualized the decrease in the number of genera present in both the inoculum and the uranium-exposed biomass as the initial pH decreased from 6.5 to 4.5. Compared with the inoculum, a significant increase in the abundances of the phyla Chloroflexi and Proteobacteria was observed following uranium exposure. At initial pH conditions of 6.5 to 4.5, the proportions of the taxa Anaerolineaceae, Chryseobacterium, Acinetobacter, Pseudomonas, and Sulfurovum increased significantly, likely contributing to the observed uranium removal. Uranium exposure induced a greater level of dynamic diversification of bacterial abundances than did the initial pH difference.

Wastewater used for urban agriculture in West Africa as a reservoir for antibacterial resistance dissemination

State of art metagenomics were used to investigate the microbial population, antibiotic resistance genes and plasmids of medical interest in wastewater used for urban agriculture in Ouagadougou (Burkina Faso). Wastewater samples were collected from three canals near agricultural fields in three neighbourhoods. Assessment of microbial population diversity revealed different microbial patterns among the different samples. Sequencing reads from the wastewaters revealed different functional specializations of microbial communities, with the predominance of carbohydrates and proteins metabolism functions. Eleven pathogen-specific and 56 orthologous virulence factor genes were detected in the wastewater samples. These virulence factors are usually found in human pathogens that cause gastroenteritis and/or diarrhoea. A wide range of antibiotic resistance genes was identified; 81 are transmissible by mobile genetic elements. These included seven different extended spectrum β-lactamase genes encoding synthesis of four enzyme families, including two metallo-β-lactamases (bla_AIM-1 and bla_GES-21). Ten different incompatibility groups of Enterobacteriaceae plasmid replicons (ColE, FIB, FIC, FII, P, Q, R, U, Y, and A/C), and 30 plasmid replicon types from Gram-positive bacteria. All are implicated in the wide distribution of antibiotic resistance genes. We conclude that wastewater used for urban agriculture in the city represents a high risk for spreading bacteria and antimicrobial resistance among humans and animals.

Assessment of Bacterial Community Composition of Anaerobic Granular Sludge in Response to Short-Term Uranium Exposure

The effect of 10-50 μM uranium (U(VI)) on the bacterial community of anaerobic granular sludge was investigated by 24-h exposure tests, after which the bacterial community was analyzed by high-throughput sequencing. The specific U(VI) reducing activity of the anaerobic granular sludge ranged between 3.1 to 19.7 μM U(VI) g^-1(VSS) h^-1, independently of the initial U(VI) concentration. Alpha diversity revealed that microbial richness and diversity was the highest for anaerobic granular sludge upon 10 μM uranium exposure. Compared with the original biomass, the phylum of Euryarchaeota was significantly affected, whereas the Bacteroidetes, Firmicutes, and Synergistetes phyla were only slightly affected. However, the abundance of Chloroflexi and Proteobacteria phyla clearly increased after 24 h uranium exposure. Based on the genus level analysis, significant differences appeared in the bacterial abundance after uranium exposure. The proportions of Pseudomonas, Acinetobacter, Parabacteroides, Brevundimonas, Sulfurovum, and Trichococcus increased significantly, while the abundance of Paludibacter and Erysipelotrichaceae incertae sedis decreased dramatically. This study shows a dynamic diversification of the bacterial composition as a response to a short time (24 h) U(VI) exposure (10-50 μM).

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.

High-throughput profiling and analysis of antibiotic resistance genes in East Tiaoxi River, China

The rapid human activities and urbanization exacerbate the human health risks induced by antibiotic resistance genes (ARGs). In this study, the profiling of ARGs was investigated using high-throughput qPCR from water samples of 13 catchment areas in East Tiaoxi River, China. High prevalence of ARGs indicated significant antibiotic resistance pollution in the research area (absolute abundance: 6.1 × 10⁸-2.1 × 10¹⁰ copies/L; relative abundance: 0.033-0.158 copies/cell). Conventional water qualities (COD, TN, TP, NH₃-N), bacterial communities and mobile gene elements (MGEs) were detected and analyzed as factors of ARGs shift. Nutrient and MGEs showed positive correlation with most ARGs (P < 0.05) and bacteria community was identified as the key contributing factor driving ARGs alteration. With the land-use study and field investigation, country area, especially arable, was expected as a high spot for ARGs shift and pathogen breeding. Comparing to environmental background, promotion of ARGs and marked shift of bacterial community were observed in country and urban city areas, indicating that human activities may lead to the spread of ARGs. Analysis of factors affecting ARGs in this study may shed new light on the mechanism of the maintenance and propagation of ARGs in urban rivers.