Bioremediation Applications Research Articles

High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines

Abstract. Siblos SKV, Tabugo SR. 2023. High-throughput analysis using 16S rRNA sequencing of bacterial communities associated in selected mangrove species from Bayug Island, Iligan City, Philippines. Biodiversitas 25: 53-61. Mangrove ecosystems are recognized globally as highly productive ecosystems, that play a crucial role in carbon sequestration, erosion control, water purification, and as essential breeding grounds for diverse aquatic life. They also offer specialized ecological niches, accommodating a diverse range of organisms, including bacterial communities. This study aimed to investigate bacterial communities of Bayug Island in Iligan City, Philippines, inhabiting six mangrove species, namely Rhizophora stylosa Griffith, Rhizophora apiculata Blume, Rhizophora mucronata Lam., Sonneratia alba Sm., Ceriops tagal (Perr.) C.B.Rob., and Nypa fruticans Wurmb and their possible functions within the mangrove forests. Genomic DNA was extracted from the six pooled soil samples, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Six amplicon libraries, corresponding to the mangrove species were analyzed with Parallel Meta Suite software, yielding 173,270 amplicon sequence variants (ASVs) after quality control. The study identified the top five most abundant ASVs in the mangrove rhizosphere, linked to the genera Vibrio, Stenotrophomonas, Serratia, Pseudoalteromonas, and Achromobacter. Among the mangrove species, S. alba exhibited higher alpha diversity according to the Shannon index. PICRUSt analysis revealed that microorganisms are involved in biodegradation, xenobiotic metabolism, and other metabolic processes within the mangroves. These bacteria could find applications in environmental cleanup, bioremediation, waste treatment, and soil health improvement. This result contributes to the ongoing ecological restoration of mangrove forests at the research site.

Riverine mycobiome dynamics: From South African tributaries to laboratory bioreactors

ABSTRACT Riverine fungi have the capacity for both pathogenicity, pertinent for countries with elevated immunosuppressed individuals, and bioremediation potential. The purpose was (i) to screen for the presence of clinically relevant riverine fungi and associations with anthropogenic influence, and (ii) the acclimatisation of environmental communities toward potential bioremediation application. Communities were harvested from polluted rivers in Stellenbosch, South Africa, and mycobiomes characterised by high-throughput amplicon sequencing. The remainder of the biomass was inoculated into continuous bioreactors with filtered river water or sterile minimal medium. Seven weeks later, the mycobiomes were re-sequenced. At least nine clinically relevant species were detected, including agents of mycoses belonging to the genus Candida. The occurrence of genera that harbour opportunisticstrains was significantly higher (P = 0.04) at more polluted sites. Moreover, positive correlations occured between some genera and pollution indices, demonstrating the potential of fungi for addition to water quality indicators. Despite biomass increase, almost all pathogens were undetectable after seven weeks, demonstrating less resilience in conditions mimicking rivers. Thus, when screening riverine biomes for bioremediation potential, ambient reactors select against human pathogens. This indicates a transient introduction of allochthonous opportunistic species into rivers due to insufficient sanitation, and the potential of bioremediation strategies that selects for environmental rather than pathogenic traits..

Investigating the impact of chitosan nanocarrier for different dilution factors of Cornus circinata for bioremediation and antimicrobial applications

Investigating the impact of chitosan nanocarrier for different dilution factors of Cornus circinata for bioremediation and antimicrobial applications

A Review of Environmental Challenges Facing Martian Colonisation and the Potential for Terrestrial Microbes to Transform a Toxic Extraterrestrial Environment

Mars is a focus of New Space Age exploration and colonisation, but there are significant challenges to successful colonisation by humankind. Environmental microbes play a key role in supporting the ecosystems of Earth, especially within the biodegradation and bioremediation sectors. However, the repurposed roles of microbes on Mars and their associated uses to colonists remain incompletely defined. The aim of this review was to examine the key roles of microbes on Earth and how they have been employed by humans to tackle four pivotal environmental challenges associated with the colonisation of Mars, namely the physical environment, the creation of a hospitable environment via terraforming, environmental sustainability and life support, and finally, renewable processing technologies. Some species of microbes were found to be tolerant of the ever-changing physical environment on Mars (freeze–thaw and UVC exposure) making them useful for bioremediation applications. Employing perchlorate-remediating microbes for their ability to bioremediate the soils of sodium perchlorate, which is present in Martian soils, in addition to their innate ability to cycle nutrients through the biosphere showed promise in establishing sustained crops to support colonists. The employment of terrestrial environmental microbes is a necessary part of overcoming key environmental challenges to successfully colonise Mars. Without this, future New Space exploration is unlikely to be successful.

Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens

The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5–20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.

An overview on trehalolipids: a promising eco-friendly bio-surfactant

Abstract Amphiphilic surfactants, which are currently used mainly for cleaning purposes, are produced in large quantities from petroleum, but are often harmful to the environment and poorly biodegradable. Therefore, the importance of environmentally friendly, non-toxic and skin-friendly biosurfactants is increasing. Different types of biosurfactants exist depending on their molecular structure. Trehalolipids belong to the low molecular weight glycolipids. Compared to other microbial glycolipids, they often show different properties and performances, including inhibition and enhancement of biodegradation rates. Optimisation of their production and downstream processing is one of the major obstacles to the potential use of trehaloselipids in a range of applications. This review provides an overview of different substrates and microorganisms used for trehalose lipid production, as well as various applications in bioremediation, biomedicine and microbial enhanced oil recovery.

Strain-level diversity in sulfonamide biodegradation: adaptation of Paenarthrobacter to sulfonamides.

The widespread occurrence of sulfonamides raises significant concerns about the evolution and spread of antibiotic resistance genes. Biodegradation represents not only a resistance mechanism but also a clean-up strategy. Meanwhile, dynamic and diverse environments could influence the cellular function of individual sulfonamide-degrading strains. Here, we present Paenarthrobacter from different origins that demonstrated diverse growth patterns and sulfonamide-degrading abilities. Generally, the degradation performance was largely associated with the number of sadA gene copies and also relied on its genotype. Based on the survey of sad genes in the public database, an independent mobilization of transposon-borne genes between chromosome and plasmid was observed. Insertions of multiple sadA genes could greatly enhance sulfonamide-degrading performance. Moreover, the sad gene cluster and sadA transposable element showed phylogenetic conservation currently, being identified only in two genera of Paenarthrobacter (Micrococcaceae) and Microbacterium (Microbacteriaceae). Meanwhile, Paenarthrobacter exhibited a high capacity for genome editing to adapt to the specific environmental niche, opening up new opportunities for bioremediation applications.

The nexus of phyto-assisted plant growth-promoting bacterial application for bioremediation of azo dye

The nexus of phyto-assisted plant growth-promoting bacterial application for bioremediation of azo dye

Unveiling the PCB biodegradation potential and stress survival strategies of resuscitated strain Pseudomonas sp. HR1

The exploration of resuscitated strains, facilitated by the resuscitation promoting factor (Rpf), has substantially expanded the pool of cultivated degraders, enhancing the screening of bio-inoculants for bioremediation applications. However, it remains unknown whether these resuscitated strains can re-enter the viable but non-culturable (VBNC) state and the specific stress conditions that trigger such a transition. In this work, the whole genome, and polychlorinated biphenyl (PCB)-degrading capabilities of a resuscitated strain HR1, were investigated. Notably, the focus of this exploration was on elucidating whether HR1 would undergo a transition into the VBNC state when exposed to low temperature and PCBs, with and without the presence of heavy metals (HMs). The results suggested that the resuscitated strain Pseudomonas sp. HR1 harbored various functional genes related to xenobiotic biodegradation, demonstrating remarkable efficiency in Aroclor 1242 degradation and strong resistance against stress induced by low temperature and PCBs. Nevertheless, when exposed to the combined stress of low temperature, PCBs, and HMs, HR1 underwent a transition into the VBNC state. This transition was characterized by significant decreases in enzyme activities and notable changes in both morphological and physiological traits when compared to normal cells. Gene expression analysis revealed molecular shifts underlying the VBNC state, with down-regulated genes showed differential expression across multiple pathways and functions, including oxidative phosphorylation, glycolysis, tricarboxylic acid cycle, amino acid metabolism, translation and cytoplasm, while up-regulated genes predominantly associated with transcription regulation, membrane function, quorum sensing, and transporter activity. These findings highlighted the great potential of resuscitated strains as bio-inoculants in bioaugmentation and shed light on the survival mechanisms of functional strains under stressful conditions, which should be carefully considered during bioremediation processes.

Applications of Bioremediation in Biomedical Waste Management: Current and Future Prospects

Applications of Bioremediation in Biomedical Waste Management: Current and Future Prospects

Microalgae: A Biological Tool for Removal and Recovery of Potentially Toxic Elements in Wastewater Treatment Photobioreactors.

Potentially toxic elements (PTE) pollution in water bodies is an emerging problem in recent decades due to uncontrolled discharges from human activities. Copper, zinc, arsenic, cadmium, lead, mercury, and uranium are considered potentially toxic and carcinogenic elements that threaten human health. Microalgae-based technologies for the wastewater treatment have gained importance in recent years due to their biomass high growth rates and effectiveness. Also, these microalgae-bacteria systems are cost-effective and environmentally friendly, utilize sunlight and CO2, and simultaneously address multiple environmental challenges, such as carbon mitigation, bioremediation, and generation of valuable biomass useful for biofuel production. Additionally, microalgae possess a diverse array of extracellular and intracellular mechanisms that enable them to remove and mitigate the toxicity of PTE present in wastewater. Therefore, photobioreactors are promising candidates for practical applications in bioremediation of wastewater containing toxic elements. Despite the increasing amount of research in this field in recent years, most studies are conducted in laboratory scale and there is a scarcity of large-scale studies under real and variable environmental conditions. Besides, the limited understanding of the multiple mechanisms controlling PTE biosorption in wastewater containing high organic matter loads and potentially toxic elements requires further studies. This chapter provides a schematic representation of the mechanisms and factors involved in the remediation of potentially toxic elements by microalgae, as well as the main results obtained in recent years.

Enhancement on migration and biodegradation of Diaphorobacter sp. LW2 mediated by Pythium ultimum in soil with different particle sizes.

The composition and structure of natural soil are very complex, leading to the difficult contact between hydrophobic organic compounds and degrading-bacteria in contaminated soil, making pollutants hard to be removed from the soil. Several researches have reported the bacterial migration in unsaturated soil mediated by fungal hyphae, but bacterial movement in soil of different particle sizes or in heterogeneous soil was unclear. The remediation of contaminated soil enhanced by hyphae still needs further research. In this case, the migration and biodegradation of Diaphorobacter sp. LW2 in soil was investigated in presence of Pythium ultimum. Hyphae could promote the growth and migration of LW2 in culture medium. It was also confirmed that LW2 was able to migrate in the growth direction and against the growth direction along hyphae. Mediated by hyphae, motile strain LW2 translocated over 3 cm in soil with different particle size (CS1, 1.0-2.0 mm; CS2, 0.5-1.0mm; MS, 0.25-0.5 mm and FS, <0.25 mm), and it need shorter time in bigger particle soils. In inhomogeneous soil, hyphae participated in the distribution of introduced bacteria, and the total number of bacteria increased. Pythium ultimum enhanced the migration and survival of LW2 in soil, improving the bioremediation of polluted soil. The results of this study indicate that the mobilization of degrading bacteria mediated by Pythium ultimum in soil has great potential for application in bioremediation of contaminated soil.

Characterization and performance of a new lipopeptide biosurfactant producing strain Bacillus Subtilis R1-2

Biosurfactants produced by native microorganisms have excellent surface activity and ideal environmental compatibility, and the mining of the biosurfactant-producing strains has become a key focus in the field of applied and environmental biotechnology. In this paper, we report a new lipopeptide-producing strain isolated from the production water of Daqing oilfield in China and identified as Bacillus Subtilis R1-2 based on 16S rRNA gene sequence analyses. A combination of ESI-MS and FT-IR analyses revealed that the strain R1-2 produced the surfactin family containing four members of the C12-surfactin, C13-surfactin, C14-surfactin and C15-surfactin, which is a representative family of the lipopeptide biosurfactants. The lipopeptide biosurfactant produced by the strain R1-2 exhibits excellent surface activity and good thermal stability over a temperature range between 20°C and 100°C and pH range between 3 and 14, and has a strong salt tolerance to NaCl concentration up to 140 g/L. In addition, the lipopeptide biosurfactant demonstrates significant properties in changing the contact angles of oil reservoir core slices from 86.2° to 39.0° and the wettability from strong oil-wet to strong water-wet, and therefore, resulted in a good oil removing ability with an efficiency of 64.84%, suggesting that the lipopeptide-producing strain R1-2 is promising in applications in environmental bioremediation and enhanced oil recovery.

Defluorination of PFAS by Acidimicrobium sp. strain A6 and potential applications for remediation.

Acidimicrobium sp. strain A6 is a recently discovered autotrophic bacterium that is capable of oxidizing ammonium while reducing ferric iron and is relatively common in acidic iron-rich soils. The genome of Acidimicrobium sp. strain A6 contains sequences for several reductive dehalogenases, including a gene for a previously unreported reductive dehalogenase, rdhA. Incubations of Acidimicrobium sp. strain A6 in the presence of perfluorinated substances, such as PFOA (perfluorooctanoic acid, C8HF15O2) or PFOS (perfluorooctane sulfonic acid, C8HF17O3S), have shown that fluoride, as well as shorter carbon chain PFAAs (perfluoroalkyl acids), are being produced, and the rdhA gene is expressed during these incubations. Results from initial gene knockout experiments indicate that the enzyme associated with the rdhA gene plays a key role in the PFAS defluorination by Acidimicrobium sp. strain A6. Experiments focusing on the defluorination kinetics by Acidimicrobium sp. strain A6 show that the defluorination kinetics are proportional to the amount of ammonium oxidized. To explore potential applications for PFAS bioremediation, PFAS-contaminated biosolids were augmented with Fe(III) and Acidimicrobium sp. strain A6, resulting in PFAS degradation. Since the high demand of Fe(III) makes growing Acidimicrobium sp. strain A6 in conventional rectors challenging, and since Acidimicrobium sp. strain A6 was shown to be electrogenic, it was grown in the absence of Fe(III) in microbial electrolysis cells, where it did oxidize ammonium and degraded PFAS.

Ecological significance and multifaceted roles of macrofungi in a changing world. A review

Macro-fungi, members of the Basidiomycota and Ascomycota groups, are large fungi with visible fruiting bodies, significant for their ecological roles. They serve as decomposers, mutualistic partners, and pathogens, influencing nutrient cycling, ecosystem functions, and biodiversity. The diverse phylum Basidiomycota comprises many macro-fungi with above-ground or below-ground fruiting bodies. Among approximately 100,000 fungal species, around 6,000 produce observable fruiting bodies and sclerotia. They engage in various lifestyles, including symbiotic and saprophytic relationships, impacting ecosystems and offering applications in biotechnology, medicine, and ecology. Macro-fungi influence forest services directly through food and resources, and indirectly by participating in ecological processes like nitrogen cycling. Global changes, such as climate shifts and habitat fragmentation, affect macro-fungi, potentially disrupting ecosystem dynamics. However, the conservation of macro-fungi is often overlooked, with limited understanding of their roles and vulnerability. Understanding their interactions with plants, animals, and substrates is crucial for effective conservation. Macro-fungi can influence nutrient cycling through mycorrhizal associations and contribute to ecological restoration. Despite challenges in studying them, macro-fungi hold promise for bio-remediation and technological applications. Preserving their diversity is essential for maintaining ecosystem balance and harnessing their benefits.

Perspectives of pteridophytes microbiome for bioremediation in agricultural applications.

The microbiome is the synchronised congregation of millions of microbial cells in a particular ecosystem. The rhizospheric, phyllospheric, and endospheric microbial diversity of lower groups of plants like pteridophytes, which includes the Ferns and Fern Allies, have also given numerous alternative opportunities to achieve greener and sustainable agriculture. The broad-spectrum bioactivities of these microorganisms, including bioremediation of heavy metals (HMs) in contaminated soil, have been drawing the attention of agricultural researchers for the preparation of bioformulations for applications in climate-resilient and versatile agricultural production systems. Pteridophytes have an enormous capacity to absorb HMs from the soil. However, their direct application in the agricultural field for HM absorption seems infeasible. At the same time, utilisation of Pteridophyte-associated microbes having the capacity for bioremediation have been evaluated and can revolutionise agriculture in mining and mineral-rich areas. In spite of the great potential, this group of microbiomes has been less studied. Under these facts, this prospective review was carried out to summarise the basic and applied research on the potential of Pteridophyte microbiomes for soil bioremediation and other agricultural applications globally. Gaps have also been indicated to present scopes for future research programmes.

Issues about application of bioremediation for cleaning up of contaminated sites

Bioremediation as a cleaning up technology is less predictable and efficient for application on site. An apparent gap is still evident between the laboratory results with pure culture or mixed culture of microorganisms and their biochemical capability including genes and enzymes involved, and the effectiveness at cleaning up the pollutants in soil and sediment on site. Associated issues include the characteristics of the site, ageing of the chemical pollutants and sequestration into soil as one, and activity and competitive of the degradative microorganisms under the actual contaminated conditions of natural environment. Because of these, the favorable conditions for the active growth of degradative microorganisms have not been investigated well enough with the available technology, so a simple inoculation of the pure culture effective under laboratory conditions cannot guarantee an expected efficiency and positive results at on site testing. In addition, the soil or sediment physical and chemical conditions under the natural environment play an important role in the removal or mineralization of organic pollutants, but inadequate attention has been given to these factors involved from ecology. It is the objectives here to bring the attention to the bioavailable concentration of the pollutants and also the active metabolism of the organisms in situ to advance and demonstrate the effective cleaning up of contaminated sites.

In vitro chronic phytotoxicity of heavy metals and metalloids to Lepidium sativum (garden cress).

The paper presents the results of studies on the influence of selected concentrations (10-100 mg L-1) of heavy metals (Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Pb, Zn) and metalloids (As, Sb, Se) on the germination and root elongation of garden cress (Lepidium sativum L). There are not many studies on phytotoxicity of heavy metals and metalloids with the complex use of single plant species so far. On the basis of the germination index (GI) and inhibition concentration IC50, the following order of phytotoxicity of the tested elements was determined: Se> As> Hg> Sb > Mo > Cd> Co > Zn > Ni. The other metals showed no phytotoxicity or even stimulating effect. In our study the stimulating effect of the majority of Pb concentrations and the lowest concentrations of Cd and Hg has been revealed. These metals do not play any role in living organisms, however some authors confirm their stimulating effect on plants at low concentrations. Toxic concentration of metals and metalloids calculated as IC50 are lower than the concentration calculated as GI (not phytotoxic). It is well known that seeds are more independent and tolerant to toxicants when they contain reserve substances which are used during the germination period. On the basis of conducted research, high tolerance of L. sativum to heavy metals and metalloids was found, which may indicate its usefulness for phytotoxicity assessment of leachate from contaminated soil or waste (e.g. foundry waste) and its application for bioremediation to manage heavy metal pollution of soils or foundry wastes containing heavy metals and metalloids. The understanding of heavy metal and metalloids toxicity will facilitate bioremediation.

Purification and characterization of a Rieske oxygenase and its NADH-regenerating partner proteins.

The Rieske non-heme iron oxygenases (Rieske oxygenases) comprise a class of metalloenzymes that are involved in the biosynthesis of complex natural products and the biodegradation of aromatic pollutants. Despite this desirable catalytic repertoire, industrial implementation of Rieske oxygenases has been hindered by the multicomponent nature of these enzymes and their requirement for expensive reducing equivalents in the form of a reduced nicotinamide adenine dinucleotide cosubstrate (NAD(P)H). Fortunately, however, some Rieske oxygenases co-occur with accessory proteins, that through a downstream reaction, recycle the needed NAD(P)H for catalysis. As these pathways and accessory proteins are attractive for bioremediation applications and enzyme engineering campaigns, herein, we describe methods for assembling Rieske oxygenase pathways in vitro. Further, using the TsaMBCD pathway as a model system, in this chapter, we provide enzymatic, spectroscopic, and crystallographic methods that can be adapted to explore both Rieske oxygenases and their co-occurring accessory proteins.

Crude Oil Degradation in Temperatures Below the Freezing Point by Bacteria from Hydrocarbon-Contaminated Arctic Soils and the Genome Analysis of Sphingomonas sp. AR_OL41.

Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas-previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago-as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from -1.5 °C to 35 °C in the presence of 0-8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA-DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.