Microbial Community Shifts in Response to Acid Mine Drainage Pollution Within a Natural Wetland Ecosystem

Water monitoring with an automated smart sensor supported with solar power for real-time and long range detection of ferrous iron

Low-power and smart sensing systems for iron detection are necessary for in situ monitoring of water quality. Here, a potentiometric Fe2+-selective electrode (ISE) was fabricated based on cyanomethyl N-methyl-N-phenyl dithiocarbamate for the first time as an ionophore. Under optimal conditions, the ISE showed a Nernstian slope of 29.76 ± 0.6 mV per decade for Fe2+ ions over a wide concentration range from 1.0 × 10-1 to 1.0 × 10-5 M with a lower detection limit (LOD) of 1.0 × 10-6 M. The ISE interference of various cations on the potentiometric response was also investigated. The ISE had a response time less than 3 s and the lifetime was two months. Also, an automated, long-range (LoRa), wireless enabled sampling microfluidic device powered with a solar panel as an autonomous power source was developed for a continuous sampling and sensing process. The sensing platform was employed in the determination of Fe2+ in acid mine drainage and spiked water samples with an average recovery of 100.7%. This simple, inexpensive (below $350), portable sensing platform will allow for rapid real-time monitoring of ground-, drinking-, and industrial waters contaminated with iron.

Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture

In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO42-), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO42- levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.

Continuous co-treatment of mine drainage with municipal wastewater

Acid mine drainage (AMD) and municipal wastewater (MWW) are commonly co-occurring waste streams in mining regions. Co-treating AMD at existing wastewater facilities represents an innovative solution for simultaneous AMD reclamation and improved MWW treatment. However, unknowns related to biological processes and continuous treatment performance block full-scale use. The overarching goal of this work was to address questions related to efficacy and performance of continuous processing of AMD in a biological MWW treatment system. Synthetic AMD was co-treated with synthetic MWW in a continuously-operating bench-scale sequencing batch reactor (SBR). SBRs treated MWW with two strengths of AMD (91 and 720 mg/L as CaCO3 Acidity) to capture the variations of coal AMD chemistry and strength observed in the field. Each co-treatment phases lasted 40+ days, during which clarified effluent and settled sludge quality was routinely monitored to determine impacts of co-treatment relative to conventional MWW treatment performance. Co-treatment produced effluent that met key standards for secondary treatment including biochemical oxygen demand (BOD) < 5 mg/L, total suspended solids (TSS) < 20 mg/L, and pH ∼7.0. Addition of AMD also improved treatment performance, increasing Phosphate (PO4) removal by >60% and pathogen removal by an order of magnitude. Furthermore, AMD co-treatment did not exhibit any major impacts on the overall diversity of the wastewater microbial community. Co-treatment sludge had slightly higher settleability and a lower bound water content, but notable changes in sludge morphology was observed. This study demonstrates co-treatment allows for continuous mitigation of AMD without adversely impacting MWW treatment performance in conventional biological MWW processes.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes

Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C. Sampling approaches range in their representation of wetland C from short to long timeframes and local to landscape spatial scales. This review summarizes common and cutting-edge methodological approaches for quantifying wetland C pools and fluxes. We first define each of the major C pools and fluxes and provide rationale for their importance to wetland C dynamics. For each approach, we clarify what component of wetland C is measured and its spatial and temporal representativeness and constraints. We describe practical considerations for each approach, such as where and when an approach is typically used, who can conduct the measurements (expertise, training requirements), and how approaches are conducted, including considerations on equipment complexity and costs. Finally, we review key covariates and ancillary measurements that enhance the interpretation of findings and facilitate model development. The protocols that we describe to measure soil, water, vegetation, and gases are also relevant for related disciplines such as ecology. Improved quality and consistency of data collection and reporting across studies will help reduce global uncertainties and develop management strategies to use wetlands as nature-based climate solutions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13157-023-01722-2.

Prior exposure of microbial communities to seawater reduces resilience but increases compositional and functional resistance to flooding events

Storm surges, flooding, and the encroachment of seawater onto agricultural land are predicted to increase with climate change. These flooding events fundamentally alter many soil properties and have knock-on effects on the microbial community composition and its functioning. The hypotheses tested in this study were (1) that the extent of change (resistance) of microbial community functioning and structure during seawater flooding is a factor of pre-adaptation to the stress, and (2) if structure and function are altered, the pre-adaptation will result in communities returning to previous state prior to flooding (resilience) faster than unexposed communities. We chose a naturally occurring saltmarsh-terrestrial pasture gradient from which three elevations were selected to create mesocosms. By selecting these sites, we were able to incorporate the legacy of differing levels of seawater ingress and exposure. Mesocosms were submerged in seawater for 0, 1, 96- and 192-h, with half of the mesocosms sacrificed immediately after flooding, and the other half taken after a 14 day "recovery" period. The following parameters were monitored: 1) changes in soil environmental parameters, 2) prokaryotic community composition, and 3) microbial functioning. Our results indicated that any length of seawater inundation significantly altered the physicochemical properties of all the soils, although a greater change is observed in the pasture site compared to the saltmarsh sites. These changes remained following a recovery period. Interestingly, our results indicated that for community composition, there was a high degree of resistance for the Saltmarsh mesocosms, with the Pasture mesocosm displaying higher resilience. Further, we observed a functional shift in the enzyme activities with labile hemicellulose being preferentially utilised over cellulose, with the effect increasing with longer floods. These results suggest that changing bacterial physiology is more critical to understanding the impact of storm surges on agricultural systems than bulk community change.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Rapid oxidative removal of Fe2+ and Mn2+ from acidic mining wastewater by a new-type biofilter system: application and mechanism

Aimed at the problem of excessive concentration of Fe2+ and Mn2+ in acidic mining wastewater during mining and utilization, a new rapid oxidative removal technology of Fe2+ and Mn2+ by a new-type biofilter system was designed and tested. The new-type biofilter system was constructed using a bioreactor filled with special mature bioceramic pellets after continuous biofilm cultivation as the filter layers. The results indicated that the biofilter system could efficiently treat five times its volume of wastewater per hour. The Fe2+ concentration of the influent wastewater was about 500 mg/L, and its Mn2+ concentration was about 20 mg/L. The average Fe2+ and Mn2+ removal rates could reach 99.7% and 90.8%, respectively. In addition, scanning electron microscopy and energy dispersive spectroscopy-energy dispersive spectroscopy and X-ray photoelectron spectroscopy were applied to analyze the migration distribution and valence change of Fe and Mn ions to clarify the removal mechanism of Fe2+ and Mn2+ using the biofilter system. The results showed that iron oxidation products were mainly coated at the surface of the mature bioceramic pellets and could be easily washed out from the filter layer with flowing water, while manganese oxidation products tended to accumulate between the pores of the mature bioceramic pellets. Furthermore, the final filtration products were multivalent complex oxides, indicating that the high-valent oxidation products could adsorb Fe and Mn ions, which were mainly removed by the oxidation effect.

Culturable heterotrophic bacterial diversity study from an Indian lignite mine habitat

Diversity lifts the productivity of any ecosystem as all the species have a vital role to play that is present within the ecosystem. The characterization is essential to delve into the ecological functions of microbial communities and discover the type of microorganisms present within the ecosystem. As microbial diversity in ecosystems responds to environmental disturbances, it functions as a marker to indicate the change in such ecosystems. Mine ecology differs significantly from other habitats due to the presence of acidic runoff. This paper provides insight into the diversity of cultivable bacteria isolated from lignite mines located in south Gujarat. A total of 67 heterotrophic isolates were successfully cultivated from the collected solid and water samples of the Rajpardi and Tadkeshwar Lignite mine sites. The isolates were characterized morphologically and biochemically, and intra- and extracellular enzyme synthesis were studied. Moreover, the relative density and frequency of cultivated isolates from the samples were calculated. The similarity and evenness of the heterotrophic isolated were studied by calculating diversity indices such as Shannon and Simpson. Alpha diversity was calculated in PAST software to analyse the similarity between the selected two mine sites. This research also explored the relationship between the variance in heterotrophic microbial diversity and substrate utilization richness of the studied lignite mines of Gujarat.

Both species richness and growth forms affect nutrient removal in constructed wetlands: A mesocosm experiment

Introduction

Plant richness is thought to improve the function of constructed wetlands (CWs), but most CWs are planted with monocultures, with only a few employed polycultures, which have drawn contradictory conclusions. We suppose functional diversity is the key to better performance of plant communities and hypothesize that CWs planted with diverse growth forms are superior in plant growth and nutrient removal.

Methods

In this study, six emergent plant species categorized into slender type (Schoenoplectus tabernaemontani, Typha orientalis), fan type (Iris sibirica, Acorus calamus) and large type (Canna indica and Thalia dealbata) were planted in monocultures, combinations (two species of the same growth form) and mixed polycultures (six species of three growth forms). We then compared how plant growth and nutrient uptake differed among treatments.

Results

It showed that the polyculture considerably increased the removal of total nitrogen (TN) and total phosphorus (TP), but the combination did not outperform monoculture. High consistency in the patterns between underground biomass and total biomass indicated that plant roots were essential for nutrient consumption. Compared with slender and fan plants, the large plants had a greater biomass increase in polycultures, which greatly accelerated the absorption and assimilation of TN and TP.

Conclusion

Our study indicated that plant community with various growth forms reduced the intensity of interspecific competition, increased the functional diversity, and greatly enhanced the ability of pollutant removal. Our results also provide some suggestions for plant selection and combination designs in CWs.

Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches

Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.

Lead and cadmium removal with native yeast from coastal wetlands

Water bodies affected by heavy metals have been characterized in some natural ecosystems such as coastal wetlands in Peru. For this reason, in the present study, the determination of heavy metals lead (Pb), cadmium (Cd), and others was carried out in the water bodies of the Regional Conservation Area (RCA) Wetlands of Ventanilla using the Induction Coupled Plasma method. Water samples were collected at the six most critical stations for Pb and Cd, for the isolation of lead-tolerant microorganisms in 2022 with the aim of evaluating native microorganisms with removal potential of Pb and Cd. Yeasts such as Candida guilliermondii, Candida famata, Cryptococcus laurentii, Cryptococcus humicola, and Rhodotorula mucilaginosa with tolerance to high concentrations of Pb were isolated. The yeast with the best Pb tolerance result was Candida guilliermondii isolated from groundwater (piezometer sampling J1); Pb sorption was conducted with active yeast (living biomass), whereas both Pb and Cd sorption were conducted with inactive yeast (dead biomass). The results were compared with those of a reference standard yeast strain Saccharomyces cerevisiae: the native yeast proved to have optimum behavior for the process.

Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data

The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome‐assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Relevance of the microbial community to Sb and As biogeochemical cycling in natural wetlands

Mining activities lead to elevated levels of antimony (Sb) and arsenic (As) in river systems, having adverse effects on the aquatic environment and human health. Microbes inhabiting river sediment can mediate the transformation of Sb and As, thus changing the toxicity and mobility of Sb and As. Compared to river sediments, natural wetlands could introduce distinct geochemical conditions, leading to the formation of different sedimentary microbial compositions between river sediments and wetland sediments. However, whether such changes in microbial composition could influence the microbially mediated geochemical behavior of Sb or As remains poorly understood. In this study, we collected samples from a river contaminated by Sb tailings and a downstream natural wetland to study the influence of microorganisms on the geochemical behavior of Sb and As after the Sb/As-contaminated river entered the natural wetland. We found that the microbial compositions in the natural wetland soil differed from those in the river sediment. The Sb/As contaminant components (Sb(III), As(III), As(V), As_exe) and nutrients (TC) were important determinants of the difference in the compositions of the microbial communities in the two environments. Taxonomic groups were differentially enriched between the river sediment and wetland soil. For example, the taxonomic groups Xanthomonadales, Clostridiales and Desulfuromonadales were important in the wetland and were likely to involve in Sb/As reduction, sulfate reduction and Fe(III) reduction, whereas Burkholderiales, Desulfobacterales, Hydrogenophilales and Rhodocyclales were important taxonomic groups in the river sediments and were reported to involve in Sb/As oxidation and sulfide oxidation. Our results suggest that microorganisms in both river sediments and natural wetlands can affect the geochemical behavior of Sb/As, but the mechanisms of action are different.

Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem

Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3)

The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO₄²⁻, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg²⁺ and SO₄²⁻ were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg²⁺ and SO₄²⁻, Ca²⁺, temperature, and Fe²⁺, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg²⁺ and SO₄²⁻ concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.

Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality

Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.

Passive Treatment for Acid Mine Drainage Partially Restores Microbial Community Structure in Different Stream Habitats

The assessment of the degree to which biological communities in streams impaired by acid mine drainage (AMD) are restored by passive treatment has focused primarily on eukaryotic-cell organisms and microbial processes. The responses of microbial community structure to passive treatment have received much less attention, even though functional processes such as nutrient cycling and organic matter decomposition depend on taxonomic composition. Our objective was to determine the degree to which passive treatment restored microbial communities in three types of habitats: aqueous, leaf, and sediment. To assess their recovery, we compared the community composition in these habitats based on 16S rRNA gene sequencing at three different stream sites: an untreated AMD site (U), a remediated site below AMD passive treatment (T), and an unimpaired reference site (R). The acidity, conductivity, and soluble metal concentrations at T were found to be elevated compared to R, but generally 1–2 orders of magnitude less than at U. Microbial community composition was found to be synergistically affected by habitat type and AMD impact, with the similarity among communities in the three habitats increasing with the severity of the AMD. Sediment- and leaf-associated microbial communities at U were characterized by taxa that are tolerant to severe AMD. The absence of the nitrogen oxidizing bacterium Nitrospira in sediment communities at T and U was found to correspond to higher NH4+ concentrations compared to R, possibly because of the presence of iron oxyhydroxide precipitate. In contrast, the microbial composition was found to be similar between the T and R sites for both aqueous and leaf communities, indicating that passive treatment was more able to restore these communities to the reference condition than sediment communities. The remediation of AMD streams should consider the habitat-specific responses of microbial community composition and be guided by future studies that empirically couple changes in taxonomic composition to measured functional processes.

Microorganisms that participate in biochemical cycles in wetlands

Several biochemical cycles are performed in natural wetlands (NWs) and constructed wetlands (CWs). The knowledge of the microorganisms could be used to monitor the restoration of wetlands or the performance of the wastewater treatment. Regarding bacteria, Proteobacteria phylum is the most abundant in NWs and CWs, which possesses a role in N, P, and S cycles, and in the degradation of organic matter. Other phyla are present in lower abundance. Archaea participate in methanogenesis, methane oxidation, and the methanogenic N2 fixation. Sulfur and phosphorus cycles are also performed by other microorganisms, such as Chloroflexi or Nitrospirae phyla. In general, there is more information about the N cycle, especially nitrification and denitrification. Processes where archaea participate (e.g. methane oxidation, methanogenic N2 fixation) are still unclear their metabolic role and several of these microorganisms have not been isolated so far. The study can use 16S rDNA genes or functional genes. The use of functional genes gives information to monitor specific microbial populations and 16S rDNA is more suitable to perform the taxonomic classification. Also, there are several Candidatus microorganisms, which have not been isolated so far. However, it has been described their metabolic role in the biochemical cycles in wetlands.

Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments

Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have recently been developed which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alternative to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥1,200 m from Norwegian salmon farms, and three metabolic inference approaches (Paprica, Picrust2 and Tax4Fun2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed between approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomic data ranged from 0.52 and 0.60 to 0.76 and 0.79, respectively. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for Paprica and Tax4Fun2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

Inoculation of Bacillus spp. Modulate the soil bacterial communities and available nutrients in the rhizosphere of vetiver plant irrigated with acid mine drainage

Acid mine drainage (AMD) is one of an important pollution sources associated with mining activities and often inhibits plant growth. Plant growth promoting bacteria has received extensive attention for enhancing adaptability of plants growing in AMD polluted soils. The present study investigated the effect of plant growth promoting Bacillus spp. (strains UM5, UM10, UM13, UM15 and UM20) to improve vetiver (Chrysopogon zizanioides L.) adaptability in a soil irrigated with 50% AMD. Bacillus spp. exhibited P-solubilization, IAA and siderophore production. The Bacillus spp. strains UM10 and UM13 significantly increased shoot (4.2-2.5%) and root (3.4-1.9%) biomass in normal and AMD-impacted soil, respectively. Bacillus sp. strain UM20 significantly increased soil AP (379.93 mg/kg) while strain UM13 increased TN (1501.69 mg/kg) and WEON (114.44 mg/kg) than control. Proteobacteria, Chloroflexi, Acidobacteria and Bacteroidetes are the dominant phyla, of which Acidobacteria (12%) and Bacteroidetes (8.5%) were dominated in soil inoculated with Bacillus sp. strain UM20 while Proteobacteria (70%) in AMD soil only. However, the Chao1 and evenness indices were significantly increased in soil inoculated with Bacillus sp. strain UM13. Soil pH, AP and N fractions were positively correlated with the inoculation of bacterial strains UM13 and UM20. Plant growth promoting Bacillus spp. strains UM13 and UM20 were the main contributors to the variations in the rhizosphere bacterial community structure, improving soil available P, TN, WEON, NO₃^--N thus could be a best option to promote C. zizanioides adaptability in AMD-impacted soils.

Simultaneous removal of iron and manganese from acid mine drainage by acclimated bacteria

A bacterial consortium for efficient decontamination of high-concentration Fe-Mn acid mine drainage (AMD) was successfully isolated. The removal efficiencies of Fe and Mn were effective, reaching 99.8 % and 98.6 %, respectively. High-throughput sequencing of the 16S rRNA genes demonstrated that the microbial community had changed substantially during the treatment. The Fe-Mn oxidizing bacteria Flavobacterium, Brevundimonas, Stenotrophomonas and Thermomonas became dominant genera, suggesting that they might play vital roles in Fe and Mn removal. Moreover, the pH of culture increased obviously after incubation, which was benefit for depositing Fe and Mn from AMD. The specific surface area of the biogenic Fe-Mn oxides was 108-121 m²/g, and the surface contained reactive oxygen functional groups (-OH and -COOH), which also improved Fe and Mn removal efficiency. Thus, this study provides an alternative method to treat AMD containing high concentrations of Fe and Mn.

Synthetic Naphthofuranquinone Derivatives Are Effective in Eliminating Drug-Resistant Candida albicans in Hyphal, Biofilm, and Intracellular Forms: An Application for Skin-Infection Treatment

Candida albicans is the most common cause of fungal infection. The emergence of drug resistance leads to the need for novel antifungal agents. We aimed to design naphthofuranquinone analogs to treat drug-resistant C. albicans for topical application on cutaneous candidiasis. The time-killing response, agar diffusion, and live/dead assay of the antifungal activity were estimated against 5-fluorocytosine (5-FC)- or fluconazole-resistant strains. A total of 14 naphthofuranquinones were compared for their antifungal potency. The lead compounds with hydroxyimino (TCH-1140) or O-acetyl oxime (TCH-1142) moieties were the most active agents identified, showing a minimum inhibitory concentration (MIC) of 1.5 and 1.2 μM, respectively. Both compounds were superior to 5-FC and fluconazole for killing planktonic fungi. Naphthofuranquinones efficiently diminished the microbes inside and outside the biofilm. TCH-1140 and TCH-1142 were delivered into C. albicans-infected keratinocytes to eradicate intracellular fungi. The compounds did not reduce the C. albicans burden inside the macrophages, but the naphthofuranquinones promoted the transition of fungi from the virulent hypha form to the yeast form. In the in vivo skin mycosis mouse model, topically applied 5-FC and TCH-1140 reduced the C. albicans load from 1.5 × 10⁶ to 5.4 × 10⁵ and 1.4 × 10⁵ CFU, respectively. The infected abscess diameter was significantly decreased by TCH-1140 (3-4 mm) as compared to the control (8 mm). The disintegrated skin-barrier function induced by the fungi was recovered to the baseline by the compound. The data support the potential of TCH-1140 as a topical agent for treating drug-resistant C. albicans infection without causing skin irritation.

Dynamics of bacterioplankton community structure in response to seasonal hydrological disturbances in Poyang Lake, the largest wetland in China

Bacterioplankton communities play a critical role in biogeochemical cycling in freshwater environments, but how the hydrological regime impacts the assembly of bacterioplankton communities remains unclear. This study examined differences in bacterioplankton community structures between wet (July and September) and dry (October and November) seasons in two consecutive years (2016 and 2017) in Poyang Lake, the largest seasonal freshwater lake in China. Our results revealed no overall difference in bacterioplankton compositions and their predicted functions among spatially separated sites. However, bacterioplankton communities did show significant temporal shifts, mainly between samples in November and other months. Transitions from the dry to the wet season were observed in October in both sampling years. Meanwhile, insignificant spatial but significant temporal differences were also found for physicochemical variables. Moreover, redundancy analysis indicates that compared with water depth, water temperature was found to better explain changes in the bacterioplankton community. These findings consistently indicate that the bacterioplankton community in Poyang Lake is relatively less sensitive to annual hydrology shifts than water temperature and nutrient conditions.

Relationships Between Chemical Defenses of Common Toad (Bufo bufo) Tadpoles and Bacterial Community Structure of their Natural Aquatic Habitat

Many organisms synthesize secondary metabolites against natural enemies. However, to which environmental factors the production of these metabolites is adjusted to is poorly investigated in animals, especially so in vertebrates. Bufadienolides are steroidal compounds that are present in a wide range of plants and animals and, if present in large quantities, can provide protection against natural enemies, such as pathogens. In a correlative study involving 16 natural populations we investigated how variation in bufadienolide content of larval common toads (Bufo bufo) is associated with the bacterial community structure of their aquatic environment. We also evaluated pond size, macrovegetation cover, and the abundance of predators, conspecifics and other larval amphibians. We measured toxin content of tadpoles using HPLC-MS and determined the number of bufadienolide compounds (NBC) and the total quantity of bufadienolides (TBQ). AICc-based model selection revealed strong relationships of NBC and TBQ with bacterial community structure of the aquatic habitat as well as with the presence of conspecific tadpoles. The observed relationships may have arisen due to adaptation to local bacterial communities, phenotypic plasticity, differential biotransformation of toxin compounds by different bacterial communities, or a combination of these processes. Bacterial groups that contribute to among-population variation in toxin content remain to be pinpointed, but our study suggesting that toxin production may be influenced by the bacterial community of the environment represents an important step towards understanding the ecological and evolutionary processes leading to microbiota-mediated variation in skin toxin profiles of aquatic vertebrates.

Bacterial response to sharp geochemical gradients caused by acid mine drainage intrusion in a terrace: Relevance of C, N, and S cycling and metal resistance

A unique terrace with sharp gradient of environmental conditions was selected to study the microbial response and survival strategies to the extreme environments introduced by acid mine drainage (AMD) contamination. A combination of geochemical analyses, metagenomic sequencing, ex-situ microcosm setups, and statistical analyses were used to investigate the environment-microbe interactions. The microbial communities and metabolic potentials along the terrace were studied by focusing on the genes associated with important biogeochemical processes (i.e., C, N, S cycling and metal resistance). Results show that the variations of geochemical parameters substantially shaped the indigenous microbial communities. Sharp environmental gradients also impacted the microbial metabolic potentials, especially for C, N, and S cycling. Although the relative abundances of carbon fixing genes did not significantly vary along the environmental gradients, the taxa for carbon fixation varied significantly in more contaminated fields versus less contaminated fields, indicating the effects of AMD contamination on the autotrophic microbial communities. AMD input also influenced the N cycling, especially for nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). In addition, ex situ experiments were undertaken to evaluate the effects of AMD contamination on nitrogen fixation rates. Random Forest (RF) analysis indicated that nitrate, pH, total N, TOC exhibited positive correlations with the rates of nitrogen fixation while total Fe, Fe(III), and sulfate showed negative effects. Two co-occurrence networks at taxonomic and genomic levels indicated that geochemical parameters such as pH, TOC, total N, total S, and total Fe substantially influenced the innate microbial communities and their metabolic potentials. The current study provides an understanding for microbial response to AMD contamination and lays the foundation for future potential AMD bioremediation.

Bacterial dominance is due to effective utilisation of secondary metabolites produced by competitors

Interactions between bacteria govern the progression of respiratory infections; however, the mechanisms underpinning these interactions are still unclear. Understanding how a bacterial species comes to dominate infectious communities associated with respiratory infections has direct relevance to treatment. In this study, Burkholderia, Pseudomonas, and Staphylococcus species were isolated from the sputum of an individual with Cystic Fibrosis and assembled in a fully factorial design to create simple microcosms. Measurements of growth and habitat modification were recorded over time, the later using proton Nuclear Magnetic Resonance spectra. The results showed interactions between the bacteria became increasingly neutral over time. Concurrently, the bacteria significantly altered their ability to modify the environment, with Pseudomonas able to utilise secondary metabolites produced by the other two isolates, whereas the reverse was not observed. This study indicates the importance of including data about the habitat modification of a community, to better elucidate the mechanisms of bacterial interactions.

A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems

Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.

Macroalgae as spatial and temporal bioindicators of coastal metal pollution following remediation and diversion of acid mine drainage

Acid mine drainage (AMD) is a significant contributor of metal pollution leading to ecosystem damage. Bioindicator organisms such as intertidal brown macroalgae have an important role in quantifying the risks of metal bioaccumulation in coastal locations exposed to AMD contamination. Measurement of As, Cd, Cu, Fe, Pb, and Zn accumulation was performed in Fucus serratus, Fucus vesiculosus and Ascophyllum nodosum sampled from two marine locations near to an abandoned Cu mine in Anglesey, Wales, UK. Transect samples were taken from a coastal location (Amlwch) that has seen a substantial increase in AMD contamination over 15 years, in comparison to a nearby estuarine location (Dulas Estuary leading to Dulas Bay) with a historic legacy of pollution. These were compared with samples from the same sites taken 30 years earlier. Some of the Dulas macroalgae samples had Cd, Cu and Zn concentrations that were above background but in general indicated a non-polluted estuary in comparison to substantial pollution over previous decades. In contrast, Fucus samples collected from directly below an AMD outflow at Amlwch showed extremely elevated metal bioaccumulation (>250 mg Fe g^-1, >6 mg Cu g^-1, >2 mg Zn g^-1, >190 μg As g^-1) and evidence of macroalgae toxicity, indicating severe pollution at this site. However, the pollution dispersed within 200 m of the outflow source. This study has demonstrated the efficiency of three brown macroalgae species as indicators for metal bioavailability at high spatial resolution and over time.

Characterization of a pH-Tolerant Strain Cobetia sp. SASS1 and Its Phenol Degradation Performance Under Salinity Condition

Biological treatment of complex saline phenolic wastewater remains a great challenge due to the low activity of bacterial populations under stressful conditions. Acid mine drainage (AMD) as a typically extreme environment, shaped unique AMD microbial communities. Microorganisms survived in the AMD environment have evolved various mechanisms of resistance to low pH, high salinity and toxic heavy metals. The primary goal of this work was to determine whether a strain isolated from an AMD could degrade phenol under stressful conditions such as low pH, high salinity and heavy metals. The results suggested that the strain Cobetia sp. SASS1 isolated from AMD presented different physiological characteristics in comparison with five most closely related species. SASS1 can efficiently degrade phenol at wide ranges of pH (3.0-9.0) and NaCl concentration (0-40 g/L), as well as the existence of Cu2+ and Mn2+. Specifically, the SASS1 could completely degrade 1500 mg/L phenol in 80 h at 10 g/L NaCl. Meanwhile, mineralization of phenol was achieved with complete degradation of 900 mg/L phenol and simultaneously COD decreasing from 2239 mg/L to 181.6 mg/L in 36 h. Based on biodegradation metabolites identification and enzyme activities analysis, both ortho-cleavage pathway and benzoic acid pathway for phenol degradation were proposed. These findings suggested that SASS1 was an efficient phenol degrader under salinity and acidic conditions, and could be considered as key population for bioremediation of industrial phenolic wastewaters under stressful conditions.

The association of microbial activity with Fe, S and trace element distribution in sediment cores within a natural wetland polluted by acid mine drainage

Natural recovery and remediation of acid mine drainage (AMD) reduces the generation of acidity and transport of trace elements in the runoff. A natural wetland that receives and remediates AMD from an abandoned copper mine at Parys Mountain (Anglesey, UK) was investigated for better understanding of the remediation mechanisms. Water column concentrations of dissolved Fe and S species, trace metal (loid)s and acidity decreased markedly as the mine drainage stream passed through the wetland. The metal (loid)s were removed from the water column by deposition into the sediment. Fe typically accumulated to higher concentrations in the surface layers of sediment while S and trace metal (loid)s were deposited at higher concentration within deeper (20-50 cm) sediments. High resolution X-ray fluorescence scans of sediment cores taken at three sites along the wetland indicates co-immobilization of Zn, Cu and S with sediment depth as each element showed a similar core profile. To examine the role of bacteria in sediment elemental deposition, marker genes for Fe and S metabolism were quantified. Increased expression of marker genes for S and Fe oxidation was detected at the same location within the middle of the wetland where significant decrease in SO₄^2- and Fe²⁺ was observed and where generation of particulate Fe occurs. This suggests that the distribution and speciation of Fe and S that mediates the immobilization and deposition of trace elements within the natural wetland sediments is mediated in part by bacterial activity.

Metabolic adaptation of a Chlamydomonas acidophila strain isolated from acid mine drainage ponds with low eukaryotic diversity

The diversity and biological characteristics of eukaryotic communities within acid mine drainage (AMD) sites is less well studied than for prokaryotic communities. Furthermore, for many eukaryotic extremophiles the potential mechanisms of adaptation are unclear. This study describes an evaluation of eight highly acidic (pH 1.6-3.1) and one moderately acidic (pH 5.6) metal-rich acid mine drainage ponds at a disused copper mine. The severity of AMD pollution on eukaryote biodiversity was examined, and while the most species-rich site was less acidic, biodiversity did not only correlate with pH but also with the concentration of dissolved and particulate metals. Acid-tolerant microalgae were present in all ponds, including the species Chlamydomonas acidophila, abundance of which was high in one very metal-rich and highly acidic (pH 1.6) pond, which had a particularly high PO₄-P concentration. The C. acidophila strain named PM01 had a broad-range pH tolerance and tolerance to high concentrations of Cd, Cu and Zn, with bioaccumulation of these metals within the cell. Comparison of metal tolerance between the isolated strain and other C. acidophila strains previously isolated from different acidic environments found that the new strain exhibited much higher Cu tolerance, suggesting adaptation by C. acidophila PM01 to excess Cu. An analysis of the metabolic profile of the strains in response to increasing concentrations of Cu suggests that this tolerance by PM01 is in part due to metabolic adaptation and changes in protein content and secondary structure.