Environmental Bacterial Communities Research Articles

Coal mining activities driving the changes in bacterial community

The mechanism of the difference in bacterial community composition caused by environmental factors in the underground coal mine is unclear. In order to reveal the influence of coal mining activities on the characteristics of bacterial community structure in coal seam, 16S rRNA gene amplicon sequencing technology was used to determine the species abundance, biodiversity, and gene abundance of bacterial community in a coal mine in Shanxi Province, and the environmental factors such as metal elements, non-metal elements, pH value, and gas concentration of coal samples were determined. The results showed that environmental factors and bacterial communities had obvious regional characteristics. Mining activities greatly affected the α diversity of bacterial communities, mining working face > main airway > roadway roof > unexposed coal seam > tunneling roadway. The bacterial community composition of each sample point is also very different. The main airway, roadway roof, and unexposed coal seam are dominated by Actinobacteria while the mining working face and tunneling roadway are dominated by Proteobacteria. Among the gene abundances of metabolic pathways in each site, Citrate cycle had the greatest difference, followed by glycine, serine and threonine metabolism, and oxidative phosphorylation and methane metabolism had little difference. RDA analysis showed that the environmental factors affecting the bacterial community were mainly cadmium, oxygen, hydrogen, and gas content. CCA analysis divided the bacterial community into three categories. Degradation functional bacteria are located in mining working face, bacteria that tolerate poor environments are located in main airway and tunneling roadway, and human pathogens are mostly located in roadway roof and unexposed coal seam. The research results would provide support for realizing green and safe mining in coal mines.

Machine learning models reveal how polycyclic aromatic hydrocarbons influence environmental bacterial communities

Polycyclic aromatic hydrocarbons (PAHs) are harmful and widespread pollutants in the environment, posing an ecological threat. However, exploring the influence of PAHs on environmental bacterial communities in different habitats (soil, water, and sediment) remains a major challenge. We collected and reanalyzed 1924 16S rRNA sequencing samples to determine the effects of PAHs on bacterial communities in different habitats and used machine learning to predict potential degrading bacteria. It was found that PAHs had substantial effects on the bacterial community, and that the bacterial community structure changed differently in different habitats. PAH contamination decreased the relative abundance of Proteobacteria in the soil (16.3 %) and sediment (10.1 %), whereas the abundance of Proteobacteria in water increased by 20.2 %. Among the tested models, the random forest model best identified the effects of PAHs on bacterial groups, with an accuracy of 99.51 % for soil, 97.72 % for sediment, and 100 % for water at the genus level. Using the random forest model, we identified 70 biomarkers that respond to PAHs, including potentially degrading microorganisms such as A4b, Bacillus, Flavobacterium and Polynucleobacter. Furthermore, PAH contamination did not significantly alter the functions of bacterial communities in the environment. This study provides a candidate strain set for future screening of PAH-degrading bacteria and contributes to the study of the adaptability of engineered PAH-degrading bacteria to the environment.

Combined ozonation-biological activated carbon process for antibiotic resistance control in treated effluent from wastewater treatment plant

Biological activated carbon (BAC) treatment plays a crucial role in wastewater treatment plants due to its economic and effective promotion of organic matter degradation or mineralization. However, whether the changes in antibiotic resistance (AR) resulting from BAC or O3-BAC treatment are related to environmental factors remains unclear, as previous studies have primarily focused on isolated aspects, or have combined these aspects without systematically comparing the BAC and O3-BAC treatment processes or analyzing their interrelationships. In this study, to gain a clearer understanding of the factors related to AR during the BAC treatment, the treatment process of BAC and O3-BAC were comprehensively compared, including antibiotics removal, wastewater matrix changes, antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and bacterial community characteristics. The roles of O3 pretreatment and the bed depth of BAC were also clarified. ARGs were found to be not as sensitive to ozone as ARB. In addition, further strengthening of control measures should be needed for trimethoprim and tetracycline, due to their low removal efficiencies by ozone pretreatment, and their close relationship with the increased AR. Besides, 2 mg/L ozonation pretreatment could significantly influence the microbial community composition of wastewater and biofilm samples, while 1 mg/L ozonation could not. Finally, the correlation of environmental factors, bacterial communities, and ARGs revealed that to reduce the AR risks of O3-BAC treatment, antibiotics in wastewater should be strictly controlled, since they were positively correlated with the accumulation of ARGs and Pseudomonadota, Actinomycetota, and Bacteroidota, which were responsible for carrying and disseminating ARGs. The results showed that higher dose ozonation pre-treatment and longer bed depth of BAC process could help control the AR of BAC.

PH Nonlinearly Dominates Soil Bacterial Community Assembly along an Altitudinal Gradient in Oak-Dominant Forests.

Soil bacteria, the predominant microbiota in soil, are subject to the law of minimum and the law of tolerance, but the assembly patterns of soil bacteria in response to environmental factors remain far from clear. Here, we took advantage of an altitudinal gradient (1020-1770 asl) in oak-dominant forests and assessed whether soil bacteria linearly or nonlinearly respond to environmental properties through the changes in the community diversity and composition. We found that soil bacteria decreased with increasing altitude in terms of the species richness and phylogenetic structure, while they were unchanged with increasing altitude in terms of community composition. The species richness was nonlinearly affected by the soil pH (19.9%), C:N ratio (14.3%), SOC (11.4%), and silt + clay content (9.9%). Specifically, the species richness peaked at a pH of 5.5-6.5, and an SOC of 25-50 g kg-1, and it showed abrupt decreases and increases at a C:N ratio of 14.5 and a silt + clay content of 70%. The community composition was significantly affected by the soil pH (28.2%), then by the SOC (3.6%), available phosphorus (1.0%), and silt + clay content (0.5%), and it showed less turnovers at a pH of 6.0, SOC of 50 g kg-1, and available phosphorus > 3.0 g kg-1. These findings imply that environmental filtering processes nonlinearly shape bacterial communities.

Flooding promotes the coalescence of microbial community in estuarine habitats

Microbial community coalescence describes the mixing of microbial communities and their integration with the surrounding environment, which is common in natural ecosystems and has potential impacts on ecological processes. However, few studies have focused on microbial community coalescence between different habitats in estuarine regions. In this study, we comprehensively investigated the environmental characteristics and bacterial community changes of different habitats (water body (Water), subtidal sediments (SS) and intertidal salt marsh sediments (SM)) in Luanhe estuary during flood and normal flow periods. The results showed that flood event significantly reduced the salinity of the estuarine habitats, changed the nutrient structure and intensified the eutrophication of estuarine water. By calculating the proportion of overlapping groups and applying the ‘FEAST’ algorithm, we revealed that flood event facilitated the migration of bacterial communities along alternative pathways across habitats, markedly enhanced the cross-habitat mobility of bacterial communities, which underscores the pivotal role of flood event in driving bacterial community coalescence. Flood-induced community coalescence not only increased the α-diversity of bacterial communities within habitats, but also increased the proportion of overlapped species between habitats, ultimately leading to homogenization between habitats. Canonical correlation analysis combined co-occurrence network analysis revealed that flood event attenuated the role of environmental filtration in microbial assembly, while increased the impact of dispersal processes and intensified interspecific competition among microorganisms, led to the change of keystone species and reduced the complexity and stability of bacterial communities. In conclusion, this study demonstrates the complex effects of flood events on estuarine microbial communities from the perspective of multi-habitat interactions in the estuary, and emphasizes the key role of river hydrodynamic conditions in facilitating the coalescence of estuarine microbial communities. We look forward to further attention and research on estuarine microbial coalescence, which will provide new insights into assessing the stability and resilience of estuarine ecosystems under flood challenges and the sustainable management of estuarine wetlands.

From local bacterial communities to energy: application of microbial fuel cells in laboratory experimentation.

It is well known that bacterial communities are an essential component to maintain the balance of terrestrial ecosystems due to the functions and services performed by microorganisms in the environment. The research seeking on alternative energy sources has shown that bacterial communities can bioconvert the chemical energy of an organic substrate into electrical energy, within devices known as microbial fuel cells. For this reason, this class project allows students of Biotechnology, Environmental Science, and Microbiology to apply the appropriate methodology to develop a class project throughout an environmental bacterial community capable of generating electrical energy.

The impact of host development and density stress on the diversity of microbial communities in the gut and its surrounding environment of the Chinese alligator

AbstractThe Chinese alligator (Alligator sinensis) is currently an endangered species due to a combination of factors, including climate change, anthropogenic activities, and habitat fragmentation. Captivity plays a crucial role in mitigating the decline of the Chinese alligator population. Currently, there is a lack of clarity regarding the influence of host development and captive conditions on the gut microbiota of Chinese alligators. The aim of the study was to investigate the gut bacterial communities of Chinese alligators and their surrounding environmental bacterial communities using 16S rRNA sequencing. The primary gut flora of Chinese alligators consists of Proteobacteria, Bacteroidetes, and Firmicutes. Proteobacteria is the most abundant and efficient settler in the gut, water, and sediment. PCoA and Adonis test revealed significant differences in bacterial communities across these habitats. Venn analysis revealed overlap in OTUs among the gut, water, and sediment, varying with growth stage and density stress. Different growth stages of Chinese alligator guts harbor distinct pathogenic bacteria, requiring attention. Density stress leads to an increase in pathogenic bacteria, a decrease in gut absorption efficiency. PICRUst2 predicts more abundant metabolic pathways related to gut function during high‐density stress, possibly linked to Roseburia. SourceTracker Analysis indicated that water bacteria have a greater impact on Chinese alligator gut bacteria than sediment, and density stress significantly affects the contribution of environmental microorganisms to the gut microbes of Chinese alligator. BugBase analysis identified water body microbes as the main source of “potentially pathogenic” phenotypes in the gut microbiota. RDA analysis found dissolved oxygen (DO) in water to be the most significant factor influencing water microorganisms, positively correlated with certain pathogenic strains. These findings enhance our understanding of the significance of microbial communities in the gut and surrounding aquatic environment of the Chinese alligator. Furthermore, they provide theoretical support for environmental regulation, disease control, and healthy breeding.

Effect of rainfall in shaping microbial community during Microcystis bloom in Nakdong River, Korea

Various environmental factors play a role in the formation and collapse of Microcystis blooms. This study investigates the impact of heavy rainfall on cyanobacterial abundance, microbial community composition, and functional dynamics in the Nakdong River, South Korea, during typical and exceptionally rainy years. The results reveal distinct responses to rainfall variations, particularly in cyanobacterial dominance and physicochemical characteristics. In 2020, characterized by unprecedented rainfall from mid-July to August, Microcystis blooms were interrupted significantly, exhibiting lower cell densities and decreased water temperature, compared to normal bloom patterns in 2019. Moreover, microbial community composition varied, with increases in Gammaproteobacteria and notably in genera of Limnohabitans and Fluviicola. These alterations in environmental conditions and bacterial community were similar to those of the post-bloom period in late September 2019. It shows that heavy rainfall during summer leads to changes in environmental factors, consequently causing shifts in bacterial communities akin to those observed during the autumn-specific post-bloom period in typical years. These changes also accompany shifts in bacterial functions, primarily involved in the degradation of organic matter such as amino acids, fatty acids, and terpenoids, which are assumed to have been released due to the significant collapse of cyanobacteria. Our results demonstrate that heavy rainfall in early summer induces changes in the environmental factors and subsequently microbial communities and their functions, similar to those of the post-bloom period in autumn, leading to the earlier breakdown of Microcystis blooms.

Biochar reduces gaseous emissions during poultry manure composting: Evidence from the evolution of associated functional genes

Biochar has demonstrated the potential in mitigating pollutant gaseous emission during composting. However, little is known about the difference among biochars derived from different plant feedstocks on the critical genes' expression and microbial communities’ succession for gaseous emissions. In this study, the effects of biochar (from wood chips, cornstalks, and rice husks) on gaseous emissions during chicken manure composting were investigated. Environmental factors, bacterial communities, and functional genes related to CH4, N2O, NH3, and H2S emissions were analyzed to reveal the reduction pathways of different biochar amendments during composting. Results showed that all biochar treatments improved the seed germination index of the compost from unmature (55.74%) to mature (70.28–75.23%). The CH4, N2O, NH3, and H2S emissions from all biochar-treated composts were reduced by 18.93–27.47%, 35.74–52.82%, 1.26–36.38%, and 8.57–24.14%, respectively, and the cornstalk biochar had the highest emission reduction performance. Temperature, pH, and NH4+ were the major environmental factors that affected Lactobacillus and Bacillus activities, which critically influenced the CH4, N2O, NH3, and H2S emissions during composting. Furthermore, cornstalk biochar mainly improved pmoA for CH4 reduction, whereas wood chip biochar increased amoA for NH3 oxidation. Rice husk biochar mostly decreased nirS and nirK and increased norB, narG, and nosZ during N2O reduction. Cornstalk biochar also increased dsrB and decreased aprA during H2S reduction. Overall, cornstalk biochar was determined to be an optimal additive for simultaneously improving compost maturity and reducing gaseous pollutant emissions during chicken manure composting. This study verified the mechanisms of three plant derived biochars in pollutant gas control in composting, and thus provided evidence for facilitating the sustainable development of composting technologies.

Identifying environmental factors affecting the microbial community composition on outdoor structural timber

Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors.Key points• Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage• Fungal community composition on timber is affected by its surrounding environment• Bacterial community composition on structural timber is affected by soil contact

Branched GDGT source shift identification allows improved reconstruction of an 8,000-year warming trend on Sumatra

Branched Glycerol Dialkyl Glycerol Tetraethers (brGDGTs) in sedimentary archives are increasingly used for paleotemperature reconstructions due to their strong correlation with mean annual air temperature. However, environmental factors can influence the brGDGT producing bacterial community, potentially affecting the brGDGT-temperature relationship and introducing fundamental errors in reconstructions. Here we assess the reliability of the methylation index of brGDGTs (MBT′5ME) in sediments as a paleotemperature proxy by tracking provenance differences based on brGDGT fractional abundances in a short lake core, two peat cores and surface soils on Sumatra (n = 333 in total). Then, we attempt to reconstruct the Holocene paleotemperatures on Sumatra using the two peat cores. Our results indicate distinct brGDGT and H-shaped brGDGT (H-GDGT) compositions in soil, lake and peat environments, suggesting production by different bacterial communities. We introduce a new index, the isomerization of H-GDGTs (IRH) that can distinguish between these environments. In an 11,000-year long peat core from Diatas, we find that brGDGT composition changes are dominated by bacterial community shifts rather than temperature changes. In contrast, a core from the nearby Padang peatland can be robustly used for a brGDGT-based paleotemperature reconstruction since there are no signs of past environmental or brGDGT source shifts. The results from Padang indicate a gradual warming trend over the past 8,000 years, consistent with climate model simulations and nearby sea surface temperature reconstructions. However, current MBT′5ME calibrations yield larger warming trends compared to simulations and other proxy studies, suggesting the need for tropical and/or peat-specific brGDGT temperature calibrations. Our findings demonstrate the importance of assessing environmental shifts and bacterial source community changes when employing brGDGT paleothermometry. The methodological framework outlined in this study can be used in future research for reliable down-core brGDGT temperature reconstructions. Our proxy reconstruction over the past 8,000 years offers novel insights into the Holocene temperature evolution from a region with low climate seasonality.

Deciphering antibiotic resistome variations during nitrogen removal process transition under mixed antibiotics stress: Assembly process and driving factors

Antibiotic resistome, which encompasses all types of antibiotic resistance genes (ARGs) in a given environment, has received increasing attention in research on different wastewater treatment processes. However, the variation in antibiotic resistome during the transition from the full nitrification–denitrification to the shortcut nitrification–denitrification process remains unclear. In this study, a total of 269 targeted gene subtypes were identified, along with 108 genes were consistently present in all samples. The introduction of mixed antibioticsrapidly increased the abundance of corresponding and non-corresponding ARGs, as well as that of mobile genetic elements.The variations in of the antibiotic resistome were primarily driven by dissolved oxygen and nitrite accumulation rate. Moreover, 34 bacterial genera were identified as potential ARG hosts, with most denitrifiers considered as potential antibiotic-resistant bacteria, including Branchymonas, Rhodobacter, and Thauera. This study provides a method for controlling antibiotic resistance by regulating the changes in environmental variables and bacterial communities.

Effect of the lignocellulolytic Psychrotroph Lelliottia sp. on bacterial community succession in corn straw compost.

This study aimed to explore the effect of an inoculation, Lelliottia sp., on the corn straw compost's physico-chemical properties, composition, and the succession of bacterial community structure. The compost community composition and succession changed after Lelliottia sp. inoculation. Inoculation increased the bacterial community diversity and abundance in the compost to promote composting. The inoculated group entered the thermophilic stage on the first day, lasting 8 days. Judging the pile maturity based on the carbon:nitrogen ratio and germination index values, the inoculated group reached the maturity standard, which was 6 days faster than the control group. The relationship between environmental factors and bacterial communities was comprehensively analyzed using redundancy analysis. Temperature and carbon:nitrogen ratio were the main environmental factors driving the succession of bacterial communities, to provide basic information on the changes of physicochemical indexes and bacterial community succession in Lelliottia sp. inoculated maize straw composting, providing assistance for practical composting applications of this strain.

Surfaces of gymnastic equipment as reservoirs of microbial pathogens with potential for transmission of bacterial infection and antimicrobial resistance.

Gymnastic equipment surfaces are shared by many people, and could mediate the transfer of bacterial pathogens. To better understand this detrimental potential, investigations on the reservoirs of bacterial pathogens and antimicrobial resistance on the surfaces of gymnastic equipment were performed by analyzing the bacterial community structures, prevalence of viable bacteria, and presence of antimicrobial resistance on both indoor and outdoor gymnastic facilities. The results of high-throughput 16S rDNA amplicon sequencing showed that Gram-positive bacteria on the surfaces of indoor gymnastic equipment significantly enriched, including the opportunistic pathogen Staphylococcus strains, while Enterobacteriaceae significantly enriched on surfaces of outdoor gymnastic equipment. The analysis of α-diversities showed a higher richness and diversity for bacterial communities on the surfaces of gymnastic equipment than the environment. Analysis of β-diversities showed that the bacterial communities on the surfaces of gymnastic equipment differ significantly from environmental bacterial communities, while the bacterial communities on indoor and outdoor equipment are also significantly different. Thirty-four bacterial isolates were obtained from the surfaces of gymnastic equipment, including three multidrug Staphylococcus and one multidrug resistant Pantoea. In particular, Staphylococcus hemolyticus 5-6, isolated from the dumbbell surface, is a multidrug resistant, hemolytic, high- risk pathogen. The results of quantitative PCR targeting antibiotic resistance related genes (intI1, sul1 and bla TEM) showed that the abundances of sul1 and bla TEM genes on the surfaces of gymnastic equipment are higher than the environment, while the abundances of sul1 gene on indoor equipment are higher than outdoor equipment. These results lead to the conclusion that the surfaces of gymnastic equipment are potential dissemination pathways for highly dangerous pathogens as well as antimicrobial resistance, and the risks of indoor equipment are higher than outdoor equipment.

Polyethylene Microplastic Particles Alter the Nature, Bacterial Community and Metabolite Profile of Reed Rhizosphere Soils

With the wide use of polyethylene film, the influence of polyethylene microplastic particles produced by its weathering on the rhizosphere soil microenvironment has attracted more and more attention from scientific research circles. In this study, the effects of low (0.2% w/w), medium (1% w/w), and high (2% w/w) doses of polyethylene particles and the combined reed biomass (2% w/w) on soil environmental factors and bacterial communities and metabolites in the reed rhizosphere were evaluated by a 90-day pot microscopic simulation system. The shape and surface microstructure of polyethylene particles in each treatment group changed obviously. A high (2% w/w) dose of microplastics significantly increased the TKN, TOC, and TP in reed root soil. The addition of the biomass significantly improved the activities of urease and sucrase in the soil. The α diversity of bacteria was not significantly affected by the addition of LDPE microplastics and biomass, but the β diversity of the bacterial community and the relative abundance of the Candidatus_Roku Bacteria, Chloroflexi, Unclassified_Blastocatella_Genus were significantly changed by the addition of middle (1% w/w) and high (2% w/w) doses of microplastics. In addition, the spectrum analysis of the soil metabolites showed that the abundance of soil metabolites was changed in each treatment group, and the differential metabolites were significantly up-regulated or down-regulated. Our findings provide a scientific reference to elucidate the impact of LDPE microplastic particles on the inter-rooted soil microenvironment and improve our understanding of the potential risks of microplastics in soil ecosystems.

Climate Warming Does Not Override Eutrophication, but Facilitates Nutrient Release from Sediment and Motivates Eutrophic Process.

The climate is changing. The average temperature in Wuhan, China, is forecast to increase by at least 4.5 °C over the next century. Shallow lakes are important components of the biosphere, but they are sensitive to climate change and nutrient pollution. We hypothesized that nutrient concentration is the key determinant of nutrient fluxes at the water-sediment interface, and that increased temperature increases nutrient movement to the water column because warming stimulates shifts in microbial composition and function. Here, twenty-four mesocosms, mimicking shallow lake ecosystems, were used to study the effects of warming by 4.5 °C above ambient temperature at two levels of nutrients relevant to current degrees of lake eutrophication levels. This study lasted for 7 months (April-October) under conditions of near-natural light. Intact sediments from two different trophic lakes (hypertrophic and mesotrophic) were used, separately. Environmental factors and bacterial community compositions of overlying water and sediment were measured at monthly intervals (including nutrient fluxes, chlorophyll a [chl a], water conductivity, pH, sediment characteristics, and sediment-water et al.). In low nutrient treatment, warming significantly increased chl a in the overlying waters and bottom water conductivity, it also drives a shift in microbial functional composition towards more conducive sediment carbon and nitrogen emissions. In addition, summer warming significantly accelerates the release of inorganic nutrients from the sediment, to which microorganisms make an important contribution. In high nutrient treatment, by contrast, the chl a was significantly decreased by warming, and the nutrient fluxes of sediment were significantly enhanced, warming had considerably smaller effects on benthic nutrient fluxes. Our results suggest that the process of eutrophication could be significantly accelerated in current projections of global warming, especially in shallow unstratified clear-water lakes dominated by macrophytes.

Insights into remediation effects and bacterial diversity of different remediation measures in rare earth mine soil with SO4 2- and heavy metals.

The increased demand for rare earth resources has led to an increase in the development of rare earth mines (REMs). However, the production of high-concentration leaching agents (SO4 2-) and heavy metals as a result of rare earth mining has increased, necessitating the removal of contaminants. Here, a series of experiments with different remediation measures, including control (CK), sulfate-reducing bacteria (SRB) alone (M), chemicals (Ca(OH)2, 1.5 g/kg) plus SRB (CM-L), chemicals (Ca(OH)2, 3.0 g/kg) plus SRB (CM-M), and chemicals (Ca(OH)2, 4.5 g/kg) plus SRB (CM-H), were conducted to investigate the removal effect of SO4 2-, Pb, Zn, and Mn from the REM soil. Then, a high-throughput sequencing technology was applied to explore the response of bacterial community diversity and functions with different remediation measures. The results indicated that CM-M treatment had a more efficient removal effect for SO4 2-, Pb, Zn, and Mn than the others, up to 94.6, 88.3, 98.7, and 91%, respectively. Soil bacterial abundance and diversity were significantly affected by treatments with the inoculation of SRB in comparison with CK. The relative abundance of Desulfobacterota with the ability to transform SO4 2- into S2- increased significantly in all treatments, except for CK. There was a strong correlation between environmental factors (pH, Eh, SO4 2-, Pb, and Zn) and bacterial community structure. Furthermore, functional prediction analysis revealed that the SRB inoculation treatments significantly increased the abundance of sulfate respiration, sulfite respiration, and nitrogen fixation, while decreasing the abundance of manganese oxidation, dark hydrogen oxidation, and denitrification. This provides good evidence for us to understand the difference in removal efficiency, bacterial community structure, and function by different remediation measures that help select a more efficient and sustainable method to remediate contaminants in the REM soil.

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology.

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

Using a batch test to derive sorption data of fluoroquinolone antibiotics in humic acids

Fluoroquinolone antibiotics (FQs) are of concern due to their disrupting effects on environmental bacterial communities. Evaluating FQ sorption by soil components is important to understand their interaction with soils and to address their environmental (bio)availability. However, data in soil organic components, especially humic acids, are scarce. Batch experiments following OECD guidelines are suitable for testing the sorption of pollutants in solid matrices. Here, we applied this methodology, with specific changes in the experimental setup, to derive sorption data and to identify the factors affecting sorption of four common FQs in seven humic acids with contrasting properties. The effect of shaking time, pH, calcium concentration in solution and dissolved organic carbon (DOC) content on the quantification of the solid-liquid distribution coefficient (Kd) of norfloxacin in three reference humic acids was evaluated. Sorption reversibility and sorption analogy of four FQs were additionally assessed in these three reference materials, whereas the effect of initial norfloxacin concentration was evaluated in the overall set of seven humic acids. Sorption was fast, strong, non-linear, irreversible and affected by changes in the pH and calcium levels in solution. The bell-shaped sorption trend at varying pH values confirmed the key role of FQ speciation in sorption and the high Kd values indicated a positive effect of soil organic matter components on FQ sorption in bulk soils at environmentally relevant pH values.•Relevant factors affecting sorption of pollutants in environmental matrices must be considered to derive Kd values with low variability and high representativeness.•In this article we modify the experimental conditions of standard batch tests to identify the factors that affect the sorption of FQs in humic acids.•The methodological approach followed can be extrapolated to the evaluation of other combinations of pollutant and environmental matrix.

Determination of antibiotic resistance profile of bacterial community from environmental water using antibiotic-resistant bacterial contamination detection (ABCD) kit

Quick and easy monitoring approaches are needed to assess sources, clinical relevance, and incidences of antibiotic resistance in environmental bacterial communities. In the present work, antibiotic-resistant bacterial contamination detection (ABCD) kits were developed for the same. The method was standardized with strains of Escherichia coli TS7, Staphylococcus arlettae HWI8, Enterococcus faecalis HWI19, and Aerococcus viridans HWII16 with known antibiogram using six clinically important antibiotics. The method was verified with different water sources having different physicochemical parameters successfully. Only 1 ml of sample water is required to be mixed with an optimized concentration of the antibiotic solution and incubated for 6h; subsequently, a color change to pink may be observed within a specified amount of time upon the addition of the bacterial detection PVDF membrane to monitor the presence of resistant bacteria. There is no color change in the case of antibiotic-susceptible bacterial communities or the absence of a resistant community. Moreover, the time taken for color change is inversely related to the magnitude of the antibiotic-resistant communities in terms of enumeration. Up to our understanding, this is the 1st report which can determine an antibiotic-resistance profile of any water source by observing only color change within a maximum of 7 h (6 h for co-culture of bacteria and antibiotics + 1 h for color change detection) time without the aid of any microbiology laboratory or skilled manpower.