Spatial heterogeneity in sediment-associated bacterial and eukaryotic communities in a landfill leachate-contaminated aquifer

Eukaryotic community composition and dynamics during solid waste decomposition

Consortia of microbial community are involved in organic waste decomposition in municipal solid waste (MSW) landfill via competition, syntropy, and predation. Bacterial and archaeal community structure and function have been extensively studied in this process, whereas the eukaryotic community structure and function are largely unidentified. This gap stands for one of the fundamental researches of microbial ecology, that is, "what is the importance of variation in eukaryotic community structure and function to solid waste decomposition? The main idea of this work is to characterize changes in eukaryotic community composition and the associated driver during solid waste decomposition. Using high throughput sequencing targeting 18S rRNA genes, community composition and dynamics of eukaryotic during solid wasted decomposition were studied, as well as the differences with solid waste and leachate physiochemical parameters. Concomitant to the expected changes in physiochemical factors, eukaryotic community composition and diversity changed along solid waste decomposition indicated by aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) and the structure was shaped by the nutrients (BOD₅, total phosphorus, and nitrate) in leachate. Ascomycota, the predominant eukaryote, showed significant (p < 0.05) different structure among AP, ACP, and MP in phylum, genera, and species levels. Abundant Freshwater Opisthokonta was present in MP, suggesting a methane carbon cycling via grazing methane oxidation microorganism. Amoebozoa, Alveolata, Rhizaria, and Stramenopiles showed successional pattern during solid waste decomposition, indicating a short food chain establishment. Characterization on eukaryotic community composition and dynamics during solid waste decomposition are crucial for understanding of microbial consortia ecological function on solid waste decomposition and are also helpful for MSW management.Key points• Abundant Ascomycota significantly differed at AP, ACP, and MP.• Eukaryotic succession indicated a short food chain establishment.• Entire eukaryotic community structure was associated to nutrients in leachate.

Application of Nanodiamonds in Modelled Bioremediation of Phenol Pollution in River Sediments

The pollution of aquatic ecosystems is a big problem that has its impact on river sediments. In recent decades, an effective solution to this problem has been the application of bioremediation technologies. Nanoremediation is an innovative part of these technologies. We still know little about the efficiency of nanoparticles, especially nanodiamonds, in modelled conditions. The aim of the present study is to investigate the effect of nanodiamonds on the key parameters of modelled bioremediation of river sediments that are polluted with phenol, as well their effect on the structures and functions of microbial communities. An important indicative mechanism that was used is the application of fluorescent in situ hybridization for sediment microbial communities. The results of this study revealed the positive role of nanodiamonds that is associated with their intoxication with high concentrations of phenol. Readaptation was also found, in which the xenobiotic biodegradation potential evolved by increasing the relative proportions of non-culturable bacteria, namely Acinetobacter (at the 144th hour) and Pseudomonas (at the 214th hour). The results can help to find an effective solution to the question of how information from such precise molecular methods and the application of nanodiamonds can be translated into the accessible language of management and bioremediation technologies.

Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream

Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg²⁺) and sulfate (SO₄^2-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO₄^2-, Mg²⁺ and Na⁺. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.

Leachate microbiome profile reveals bacteria, archaea and eukaryote dynamics and methanogenic function during solid waste decomposition

Bacterial, archaeal, and eukaryotic community composition and dynamics in leachate during solid waste decomposition were investigated using Illumina MiSeq sequencing. The functional enzyme-encoding genes of methanogenic pathways were also predicted via PICRUSt. Succession of bacterial, archaeal, and eukaryotic community composition in aerobic phase (AP), anaerobic acid phase (ACP), and methanogenic phase (MP) was observed. The main representatives of microbial phyla, genera, and species significantly (p < 0.05) differed at least two phases. Protist Ciliophora occurred at ACP and was prevalent in MP, suggesting a short food chain establishment in the methanogenesis. Bacterial, archaeal, fungi and eukaryotic community structure were all pH and biochemical oxygen demand (BOD₅) dependent patter. Acetoclastic and hydrogenotrophic methanogenesis pathways with associated functional genes differed during solid waste decomposition and were inhibited in ACP.

Anaerobic/aerobic conditions determine antibiotic resistance genes removal patterns from leachate by affecting bacteria taxa-genes co-occurrence modules

Landfill treatment of municipal solid waste treatment produces a large amount of leachate, which has been an important hotspot of ARGs. This study aimed to investigate the ARGs removal potential, kinetics and mechanism from leachate in aerobic and anaerobic conditions. Simulated landfill reactors showed the efficacy in reducing ARGs, and the removal efficiencies depended on ARGs types and aerobic/anaerobic conditions. The ARGs tetQ and bla_CTX-M were more likely to attenuate with the log-removal efficiencies of 1.50-3 order of magnitude. The ARGs removal kinetic was well fitted by modified Collins-Selleck model, and aerobic condition showed better removal capacities and kinetics than anaerobic condition. Among the ARGs with great removal performance, sul2, aadA1and bla_CTX-M were eliminated from leachate and refuse simultaneously, but tetM, ermB, and mefA were removed from leachate but enriched in refuse. Aerobic/anaerobic states might drive the bacterial community shift of leachate and refuse, and topology property comparison of co-occurrence networks suggested that refuse had a closer non-random host relationship between ARGs and microbial taxa than leachate. Further module analyses revealed that ARGs removal efficiencies depended on the taxonomy of host bacteria in leachate, while the refuse taxa-ARGs correlation determined ARGs removal patterns. By selecting distinct bacteria cluster in different conditions, aerobic treatment benefited ARGs reduction in leachate and refuse, while anaerobic treatment enhanced the enrichment of ARGs in refuse. These findings can potentially foster the understanding of ARGs removal mechanism in biological treatment processes.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River

Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump and the adjoining Duhaney River near Kingston City, Jamaica. We identified no overlap between the microbial communities inhabiting the Riverton City dump leachate and the Duhaney River. Both communities are predicted to degrade aromatic compounds, which are ubiquitous environmental pollutants. Adversely, microbes in both environments are predicted to withstand widely used antibiotics, antiseptics, and metal contamination. The absence of evidence for microbial transfer from the leachate to the river is encouraging; however, the Duhaney River contained several organisms with predicted pathogenic lifestyles, indicating that the river represents a human health risk regardless of impact from the dump.

The Riverton City dump is Jamaica’s largest solid waste disposal site, but it lacks engineered protection for leachate containment and treatment. Shotgun metagenomics was used to survey the microbial communities in the Riverton City dump leachate and in surface waters of the Duhaney River, an urban waterway abutting the dump. The community within the leachate pond was taxonomically distinct from that found in the surface waters of the Duhaney River. Higher microbial diversity was observed within the dump leachate, with members of the Bacteroidetes, Firmicutes, Gammaproteobacteria, Deltaproteobacteria, and Tenericutes being the most abundant, while the river community was dominated by Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The microbial communities exhibit similar functional potential profiles, including chemoorganoheterotrophy as the dominant metabolism, and the potential to degrade aromatic compounds. From reconstruction of metagenome-assembled genomes (MAGs), organisms within both environments are predicted to survive in the presence of multiple antibiotics, antiseptics, biocides, and metals. Strong virulence potential coincided with the most diverse multiple resistance profiles in 1 of 5 leachate MAGs and 5 of 33 river MAGs. Unexpectedly, the microbial resistance profiles were more varied and widespread in the river populations, where we had expected the chemical composition of the leachate to select and enrich for resistance characteristics. This study provides valuable insights into the total functional potential of a landfill leachate microbial community and identifies possible human health hazards within the Duhaney River and Riverton City dump, urban environments with the potential to impact human populations.

IMPORTANCE Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump and the adjoining Duhaney River near Kingston City, Jamaica. We identified no overlap between the microbial communities inhabiting the Riverton City dump leachate and the Duhaney River. Both communities are predicted to degrade aromatic compounds, which are ubiquitous environmental pollutants. Adversely, microbes in both environments are predicted to withstand widely used antibiotics, antiseptics, and metal contamination. The absence of evidence for microbial transfer from the leachate to the river is encouraging; however, the Duhaney River contained several organisms with predicted pathogenic lifestyles, indicating that the river represents a human health risk regardless of impact from the dump.

Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions

Micro scale processes are expected to have a fundamental role in shaping groundwater ecosystems and yet they remain poorly understood and under-researched. In part, this is due to the fact that sampling is rarely carried out at the scale at which microorganisms, and their grazers and predators, function and thus we lack essential information. While set within a larger scale framework in terms of geochemical features, supply with energy and nutrients, and exchange intensity and dynamics, the micro scale adds variability, by providing heterogeneous zones at the micro scale which enable a wider range of redox reactions. Here we outline how understanding micro scale processes better may lead to improved appreciation of the range of ecosystems functions taking place at all scales. Such processes are relied upon in bioremediation and we demonstrate that ecosystem modelling as well as engineering measures have to take into account, and use, understanding at the micro scale. We discuss the importance of integrating faunal processes and computational appraisals in research, in order to continue to secure sustainable water resources from groundwater.

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.

The fungal microbiota of de-novo paediatric inflammatory bowel disease

Inflammatory bowel disease (IBD) is characterised by an inappropriate chronic immune response against resident gut microbes. This may be on account of distinct changes in the gut microbiota termed as dysbiosis. The role of fungi in this altered luminal environment has been scarcely reported. We studied the fungal microbiome in de-novo paediatric IBD patients utilising next generation sequencing and compared with adult disease and normal controls. We report a distinct difference in fungal species with Ascomycota predominating in control subjects compared to Basidiomycota dominance in children with IBD, which could be as a result of altered tolerance in these patients.

Assessment of anaerobic toluene biodegradation activity by bssA transcript/gene ratios

Benzylsuccinate synthase (bssA) genes associated with toluene degradation were profiled across a groundwater contaminant plume under nitrate-reducing conditions and were detected in significant numbers throughout the plume. However, differences between groundwater and core sediment samples suggested that microbial transport, rather than local activity, was the underlying cause of the high copy numbers within the downgradient plume. Both gene transcript and reactant concentrations were consistent with this hypothesis. Expression of bssA genes from denitrifying toluene degraders was induced by toluene but only in the presence of nitrate, and transcript abundance dropped rapidly following the removal of either toluene or nitrate. The drop in bssA transcripts following the removal of toluene could be described by an exponential decay function with a half-life on the order of 1 h. Interestingly, bssA transcripts never disappeared completely but were always detected at some level if either inducer was present. Therefore, the detection of transcripts alone may not be sufficient evidence for contaminant degradation. To avoid mistakenly associating basal-level gene expression with actively degrading microbial populations, an integrated approach using the ratio of functional gene transcripts to gene copies is recommended. This approach minimizes the impact of microbial transport on activity assessment and allows reliable assessments of microbial activity to be obtained from water samples.

Spatial heterogeneity of bacterial communities in sediments from an infiltration basin receiving highway runoff

The bacterial community diversity of highway runoff-contaminated sediment that had undergone 19 years of acetate-based de-icing agents addition followed by three years of acetate-free de-icing agents was investigated. Analysis of 26 sediment samples from two drilled soil cores by means of 16S rDNA PCR generated 3,402 clones, indicating an overall high bacterial diversity, with no prominent members within the communities. Sequence analyses provided evidences that each sediment sample displayed a specific structure bacterial community. Proteobacteria-affiliated clones (58% and 43% for the two boreholes) predominated in all samples, followed by Actinobacteria (12% and 16%), Firmicutes (7% and 12%) and Chloroflexi (7% and 11%). The subsurface geochemistry complemented the molecular methods to further distinguish ambient and contaminant plume zones. Principal component analysis revealed that the levels of Fe(II) and dissolved oxygen were strongly correlated with bacterial communities. At elevated Fe(II) levels, sequences associated with anaerobic bacteria were detected in high levels. As iron levels declined and oxygen levels increased below the plume bottom, there was a gradual shift in the community structure toward the increase of aerobic bacteria.

Fluorescence in situ hybridization (CARD-FISH) of microorganisms in hydrocarbon contaminated aquifer sediment samples

Groundwater ecosystems are the most important sources of drinking water worldwide but they are threatened by contamination and overexploitation. Petroleum spills account for the most common source of contamination and the high carbon load results in anoxia and steep geochemical gradients. Microbes play a major role in the transformation of petroleum hydrocarbons into less toxic substances. To investigate microbial populations at the single cell level, fluorescence in situ hybridization (FISH) is now a well-established technique. Recently, however, catalyzed reporter deposition (CARD)-FISH has been introduced for the detection of microbes from oligotrophic environments. Nevertheless, petroleum contaminated aquifers present a worst case scenario for FISH techniques due to the combination of high background fluorescence of hydrocarbons and the presence of small microbial cells caused by the low turnover rates characteristic of groundwater ecosystems. It is therefore not surprising that studies of microorganisms from such sites are mostly based on cultivation techniques, fingerprinting, and amplicon sequencing. However, to reveal the population dynamics and interspecies relationships of the key participants of contaminant degradation, FISH is an indispensable tool. In this study, a protocol for FISH was developed in combination with cell quantification using an automated counting microscope. The protocol includes the separation and purification of microbial cells from sediment particles, cell permeabilization and, finally, CARD-FISH in a microwave oven. As a proof of principle, the distribution of Archaea and Bacteria was shown in 60 sediment samples taken across the contaminant plume of an aquifer (Leuna, Germany), which has been heavily contaminated with several ten-thousand tonnes of petroleum hydrocarbons since World War II.

Effect of pumping on the spatio-temporal distribution of microbial communities in a water well field

A water well field adjacent to the North Saskatchewan River (City of North Battleford, Saskatchewan, Canada) with a history of rapid deterioration of both well water quality and yield was selected to study the spatial and temporal distribution of subsurface microbial communities and their response to water pumping. A range of conventional cultural, microscopic and molecular techniques, including confocal laser scanning microscopy (CLSM), Biolog, qPCR and Denaturing Gradient Gel Electrophoresis (DGGE), was used during this study. Redox data and water and sediment chemistry showed that the aquifer was anoxic and harbored substantial amounts of Fe and Mn. CLSM analyses of incubated coupons indicated extensive biofilm growth in the zone immediately surrounding the well and was coincident with reduced water well yield. PCR screening and qPCR analyses showed that the potential for iron- and sulfate-reducing activity increased with proximity to the well. Bacterial communities inhabiting the zone closest to the well showed the greatest changes and differences in metabolic activities and composition as revealed by PCA (Principal Components Analysis) of the Biolog and DGGE data. The sequence analysis of all the samples revealed that Sulfuricurvum spp., Methylobacter spp., Geobacter spp. and Rhodobacter spp. were most commonly detected in this aquifer. Overall the findings demonstrated that the microbial numbers, metabolic activities and the community composition changed in response to water pumping but effects did not extend beyond 1-2m zone from the well.