Iron oxidizing bacteria: insights on diversity, mechanism of iron oxidation and role in management of metal pollution

Handwashing basins and healthcare associated infections: Bacterial diversity in biofilms on faucets and drains

BACKGROUND

Increasingly, hospital handwashing basins have been identified as a source of healthcare-associated infections. Biofilms formed on the faucet and drains of handbasins can potentially harbour pathogenic microbes and promote the dissemination of antimicrobial resistance. However, little is known about the diversity of these biofilm communities and the routes of contamination.

AIM

The aim of this paper was to use 16S rRNA gene amplicon sequencing to investigate the diversity of prokaryote communities present in faucet and drain biofilm samples taken from hospital and residential handbasins.

FINDINGS

The biofilm prokaryotes communities were diverse, with high abundances of potentially corrosive, biofilm forming and pathogenic genera, including those that are not typically waterborne. The β-diversity showed statistically significant differences in the variation of bacterial communities on the basis on building type (hospital vs residential p = 0.0415). However, there was no statistically significant clustering based on sampling site (faucet vs drain p = 0.46). When examining the β-diversity between individual factors, there was a significant difference between drain biofilms of different buildings (hospital drain vs residential drain p = 0.0338).

CONCLUSION

This study demonstrated that biofilms from hospital and residential handbasins contain complex and diverse microbial communities that differ significantly by building type. It also showed biofilms formed on the faucet and drain of a hospital's handbasins were not significantly different. Future research is needed to understand the potential mechanisms of transfer between drains and faucets of hospital handbasins. This information will inform improved infection control guidelines to control this underrecognized source of infections.

Chapter 6: The Breadth and Limits of Life on Earth

Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.

Iron oxide nanoparticles in the soil environment: Adsorption, transformation, and environmental risk

Iron oxide nanoparticles (IONPs) have great application potential due to their multifunctional excellence properties, leading to the possibility of their release into soil environments. IONPs exhibit different adsorption properties toward environmental pollutants (e.g., heavy metals and organic compounds), thus the adsorption performance for various contaminants and the molecular interactions at the IONPs-pollutants interface are discussed. After solute adsorption, the change in the environmental behavior of IONPs is an important transformation process in the natural environments. The aggregation, aging process, and chemical/biological transformation of IONPs can be altered by soil solution chemistry, as well as by the presence of dissolved organic matter and microorganisms. Upon exposure to soil environments, IONPs have both positive and negative impacts on soil organisms (e.g., bacteria, plants, nematodes, and earthworms). Moreover, we compared the toxicity of IONPs alone to combined toxicity with environmental pollutants and pristine IONPs to aged IONPs, and the mechanisms of IONPs toxicity at the cellular level are also reviewed. Given the unanswered questions, future research should include prediction and design of IONPs, new characterization technology for monitoring IONPs transformation in soil ecosystems, and further refinement the environmental risk assessment of IONPs. This review will greatly enhance our knowledge of the performance and impact of IONPs in soil systems.

Iron transport mechanisms and their evolution focusing on chloroplasts

Iron (Fe) is an essential element for photosynthetic organisms, required for several vital biological functions. Photosynthesis, which takes place in the chloroplasts of higher plants, is the major Fe consumer. Although the components of the root Fe uptake system in dicotyledonous and monocotyledonous plants have been extensively studied, the Fe transport mechanisms of chloroplasts in these two groups of plants have received little attention. This review focuses on the comparative analysis of Fe transport processes in the evolutionary ancestors of chloroplasts (cyanobacteria) with the processes in embryophytes and green algae (Viridiplantae). The aim is to summarize how chloroplasts are integrated into cellular Fe homeostasis and how Fe transporters and Fe transport mechanisms have been modified by evolution.

Removal of Fe and Mn from the groundwater by using zeolite with Rossellomorea sp

Groundwater is one of the alternatives to surface water that can be used for drinking water; however, it normally exists with high iron and manganese content. In this study, a column study was conducted to observe the elimination of iron (Fe) and manganese (Mn) in the groundwater under different retention times by using zeolite immobilized with iron-oxidizing bacteria (IOB). Rossellomorea sp., representing an IOB, was found from the isolation process and was further cultured in the laboratory for immobilization into the natural zeolite as replacement materials for the sand filter. When the zeolite assisted with the Rossellomorea sp. was used, the elimination of Fe and Mn were 99.34% and 88.92%, respectively, compared to the removal of Fe and Mn, which were 93.62% and 93.73%, respectively, for media without immobilization. The presence of Rossellomorea sp. enhances the Fe oxidation, resulting in high removal of Fe. The Thomas and Yoon-Nelson models were performed in both raw zeolite and zeolite with IOB. The total coliform (most probable number [MPN]) increased from 70.8 to 307.6 MPN/100 mL because of the Rossellomorea sp. present that promotes the growth of coliform bacteria. In conclusion, the immobilization of zeolite with IOB is a potential technique to extract the Fe and Mn in the groundwater. PRACTITIONER POINTS: Zeolite incorporated with Rossellomorea sp. has higher removal performance of Fe, whereas the removal of Mn reduced compared to the raw zeolite. The presence of Rossellomorea sp. enhances the oxidation of ferrous iron and improves the removal of Fe in the groundwater because the ferric iron is the priority ion to be exchanged. The removal of UV254 increase when Rossellomorea sp. present in the zeolite because the Rossellomorea sp. consume the natural organic matter as carbon source.

Intestinal bacteria diversity of suckermouth catfish (Pterygoplichthys pardalis) in the Cd, Hg, and Pb contaminated Ciliwung River, Indonesia

The contamination of aquatic environments with heavy metals poses a serious threat to fish, potentially leading to diseases or even death. Therefore, there is an urgent need for studies to investigate the adaptability of fish in heavy metal-contaminated environments. Several studies have explored the adaptability of suckermouth catfish (P. pardalis) to survive in the contaminated Ciliwung River. The findings obtained showed that the presence of intestinal bacteria helped these fish overcome the heavy metals in their intestines, thereby enabling the fish to survive. Analysis using the Next Generation Sequencing (NGS) technology has succeeded in identifying diversity of these bacteria in P. pardalis living in the Ciliwung River, which contaminated with Cd (0.3-1.6 ppm in the water & 0.9-1.6 ppm in the sediment), Hg (0.6-2 ppm in the water & 0.6-1.8 ppm in the sediment), and Pb (59.9-73.8 ppm in the water & 26.1-58.6 ppm in the sediment). Diversity index of intestinal bacteria in P. pardalis was relatively high, but it had a negative correlation with the presence of these contaminants. Actinobacteria, Firmicutes, and Proteobacteria were abundant in the intestines of P. pardalis from the upstream to downstream of the river, with an overall abundance range of 15-48%. Furthermore, Mycobacterium along with 6 other genera were identified as core intestinal bacteria. The presence of these bacterial communities in all the samples affected their survival in heavy metals-contaminated rivers. The fish's adaptability to live in this harsh environment indicated that it has the potential to be utilized as a bioremediator of heavy metals in river sediments.

Moving towards the enhancement of extracellular electron transfer in electrogens

Electrogens are very common in nature and becoming a contemporary theme for research as they can be exploited for extracellular electron transfer. Extracellular electron transfer is the key mechanism behind bioelectricity generation and bioremediation of pollutants via microbes. Extracellular electron transfer mechanisms for electrogens other than Shewanella and Geobacter are less explored. An efficient extracellular electron transfer system is crucial for the sustainable future of bioelectrochemical systems. At present, the poor extracellular electron transfer efficiency remains a decisive factor in limiting the development of efficient bioelectrochemical systems. In this review article, the EET mechanisms in different electrogens (bacteria and yeast) have been focused. Apart from the well-known electron transfer mechanisms of Shewanella oneidensis and Geobacter metallireducens, a brief introduction of the EET pathway in Rhodopseudomonas palustris TIE-1, Sideroxydans lithotrophicus ES-1, Thermincola potens JR, Lysinibacillus varians GY32, Carboxydothermus ferrireducens, Enterococcus faecalis and Saccharomyces cerevisiae have been included. In addition to this, the article discusses the several approaches to anode modification and genetic engineering that may be used in order to increase the rate of extracellular electron transfer. In the side lines, this review includes the engagement of the electrogens for different applications followed by the future perspective of efficient extracellular electron transfer.

Niche differentiation of sulfur-oxidizing bacteria (SUP05) in submarine hydrothermal plumes

Hydrothermal plumes transport reduced chemical species and metals into the open ocean. Despite their considerable spatial scale and impact on biogeochemical cycles, niche differentiation of abundant microbial clades is poorly understood. Here, we analyzed the microbial ecology of two bathy- (Brothers volcano; BrV-cone and northwest caldera; NWC) and a mesopelagic (Macauley volcano; McV) plumes on the Kermadec intra-oceanic arc in the South Pacific Ocean. The microbial community structure, determined by a combination of 16S rRNA gene, fluorescence in situ hybridization and metagenome analysis, was similar to the communities observed in other sulfur-rich plumes. This includes a dominance of the vent characteristic SUP05 clade (up to 22% in McV and 51% in BrV). In each of the three plumes analyzed, the community was dominated by a different yet uncultivated chemoautotrophic SUP05 species, here, provisionally named, Candidatus Thioglobus vadi (McV), Candidatus Thioglobus vulcanius (BrV-cone) and Candidatus Thioglobus plumae (BrV-NWC). Statistical analyses, genomic potential and mRNA expression profiles suggested a SUP05 niche partitioning based on sulfide and iron concentration as well as water depth. A fourth SUP05 species was present at low frequency throughout investigated plume samples and may be capable of heterotrophic or mixotrophic growth. Taken together, we propose that small variations in environmental parameters and depth drive SUP05 niche partitioning in hydrothermal plumes.

Intracellular silicification by early-branching magnetotactic bacteria

Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.

A novel colorimetric technique for estimating iron in magnetosomes of magnetotactic bacteria based on linear regression

Magnetotactic bacteria (MTB) use iron from their habitat to create magnetosomes, a unique organelle required for magnetotaxis. Due to a lack of cost-effective assay methods for estimating iron in magnetosomes, research on MTB and iron-rich magnetosomes is limited. A systemized assay was established in this study to quantify iron in MTB using ferric citrate colorimetric estimation. With a statistically significant R² value of 0.9935, the iron concentration range and wavelength for iron estimation were optimized using linear regression. This colorimetric approach and the inductively coupled plasma optical emission spectrometry (ICP-OES) exhibited an excellent correlation R² value of 0.961 in the validatory correlative study of the iron concentration in the isolated magnetotactic bacterial strains. In large-scale screening studies, this less-expensive strategy could be advantageous.

Survival and activity of an indigenous iron-reducing microbial community from MX80 bentonite in high temperature / low water environments with relevance to a proposed method of nuclear waste disposal

MX80 bentonite clay has been selected as the buffer and backfill in a proposed method for long-term deep geological storage of nuclear waste. Extensive studies have been carried out on the geomechanical properties of the clay; however, it is not clear what effect microbes, specifically iron-reducing bacteria, will have on its ability to function as an affective barrier. Iron-reducing bacteria can reduce structural or external Fe(III) to Fe(II) and have been previously identified in the indigenous microbial community of MX80 bentonite. Experiments to assess bacterial survival at the high temperature and low water conditions likely to exist in the repository were carried out at different temperatures with the addition of steel to represent a nuclear waste canister. The resulting microbial enrichments were analysed, and mineralogical and geomechnical analysis was carried out on the clay. Microbial sequencing revealed that iron-reducing bacteria, and other indigenous species can survive these conditions in MX80 bentonite in either an active or dormant state. Microbial influenced mineralogical changes may lead to a loss of silica from the clay and reduction of Fe(III) to Fe(II). These changes could alter the ability of the clay to act as an effective barrier in nuclear waste disposal. Furthermore, evidence of reduced steel corrosion when microbes were present suggested that microbial activity may lead to either a protective coating on the steel or depletion of oxygen to slow corrosion. The production of such a layer would benefit nuclear waste disposal by inhibiting corrosion of a metal waste canister.

Microbiology of a multi-layer biosolid/desulfurized tailings cover on a mill tailings impoundment

The Strathcona Waste Water Treatment System (SWWTS; Sudbury, ON, Canada) has received mill tailings from Ni/Cu ore processing from 1970 to present. Demonstration-scale, multi-layer cover systems were installed on selected tailings deposition cells at the SWWTS. The cover systems are comprised of an upper layer of organic carbon-rich material, composed of a layer biosolids fertilizer along with composted municipal food and yard waste, then a layer of desulfurized, fine-grained tailings. Organic carbon components used in these covers promote microbial communities that consume O₂, thus decreasing sulfide oxidation rates in the underlying tailings. The aim of this study was to investigate the microbiology of the cover systems and the underlying tailings, using a combination of culture-dependent (most probable number) and culture-independent (16S rRNA gene amplicon sequencing) techniques, and assess the impact of the organic component of the cover system four to six years after implementation. Most tailings samples were characterized by circumneutral bulk pH and low concentrations of dissolved metals. The presence of the organic cover resulted in elevated counts of sulfate-reducers (by two orders of magnitude, compared to control samples) immediately below the organic cover, as well as an increased abundance of heterotrophic species (∼10⁸ cells g^-1) at greater depth (∼4 m) in the tailings profile. Mineral-oxidizing microorganisms were also present in the tailings, with neutrophilic sulfur-oxidizers dominating the samples (mean ∼10⁶ cells g^-1). Relative abundances of sulfur- and/or iron-oxidizers determined by sequencing ranged from 0.5 to 18.3% of total reads (mean ∼5.6% in amended tailings) and indicated the presence of local microenvironments with ongoing sulfide oxidation. This work provides a detailed characterization of the microbiology of a tailings impoundment with an organic cover, highlighting the opportunities associated with monitoring microbial processes in such remediation systems.

Potential use of a novel actinobacterial species to ameliorate tungsten nanoparticles induced oxidative damage in cereal crops

Tungsten nanoparticles (WNPs) could induce hazard impact on plant growth and development; however, no study investigated their phytotoxicity. On the other hand, plant growth-promoting bacteria (PGPB) can effectively reduce WNPs toxicity. To this end, Nocardiopsis sp. was isolated and employed to mitigate the phytotoxic effect of WNPs on three crops (wheat, barley, and oat). Soil contamination with WPNs induced the W accumulation in all tested crops, inhibited both growth and photosynthesis and induced oxidative damage. On the other hand, pre-inoculation with Nocardiopsis sp. significantly reduced W level in treated plants. Concomitantly, Nocardiopsis sp. strikingly mitigated the inhibitory effect of WNPs by augmenting both growth and reactive oxygen species (ROS) homeostasis. To cope with heavy metal stress, all the tested species orchestrated their antioxidant homeostasis through enhancing the production of antioxidant metabolites (e.g., phenolics, flavonoids and tocopherols) and elevated the activities of ROS-scavenging enzymes (e.g., APX, POX, CAT, as well as the enzymes involved in AsA/GSH cycle). Moreover, pre-inoculation with Nocardiopsis sp. improved the detoxification metabolism by enhancing the accumulation of phytochelatins (PCs), metallothionein (MTC) and glutathione-S-transferase (GST) in grasses grown in WNPs-contaminated soils. Overall, restrained ROS homeostasis and improved WNPs detoxification systems were the bases underlie the WNPs stress mitigating impact of Nocardiopsis sp treatment.

The differential inhibitive effects and fates of As(III) and As(V) mediated by Sulfobacillus thermosulfidooxidans grown on S0, Fe2+ and FeS2

Arsenic often coexists with metal sulfide minerals and occurs in different speciation and different toxicity in responding to Fe/S biooxidation. The differential inhibitive effects and fates of As(III) and As(V) during biooxidations of elemental sulfur (S⁰), ferrous ions (Fe²⁺) and pyrite (FeS₂) by Sulfobacillus thermosulfidooxidans were studied. The results revealed that the arsenic species hardly changed for the biooxidation of S⁰, but dramatically changed for the biooxidation of Fe²⁺ and FeS₂. Different transformation degree between As(III) and As(V) occurred for biooxidation of FeS₂ in the presence of arsenic, where about 72% of As(III) was transformed to As(V) for the group with As(III) added, and 16% of As(V) was transformed to As(III) for that with As(V) added. Both formation and dissolution of amorphous ferric arsenate occurred during biooxidation of FeS₂ with the addition of As(III) or As(V) and for the group grown on Fe²⁺ with added As(V), which were controlled by the changes of Fe/As molar ratio and pH value in the solution. Jarosite was detected for the group grown on Fe²⁺ and could adsorb As(III) and As(V). The inhibitive effects of As(V) were higher than As(III) when the strain grew on FeS₂, which was contrary to those when the strain grew on S⁰ and Fe²⁺. The above results signify that the fates and inhibitive effects of arsenic are much related to each other, and such a relationship is significantly affected by the utilization of Fe/S energy substrates by the sulfur- and ferrous-oxidizing microorganisms.

Investigation into the Cause of Iron-Related Clogging of Groundwater Bores Used for Viticulture in the Limestone Coast, South Australia

Iron-related clogging of boreholes, pumps and dripper lines is a significant and costly problem for irrigators worldwide. The primary cause of iron-related clogging is still debated. Previous studies have described complex interactions between biological clogging and inorganic iron/manganese oxide precipitation. This case study examined groundwater bores used for viticulture irrigation in the Limestone Coast region, a highly productive wine growing area in the SE of South Australia. Iron clogging of bore screens, pumps and dripper systems has been a persistent problem in the region and the issue is perceived to be growing, with irrigators suggesting the widespread introduction of iron-related bacteria (IRB) through drilling equipment to be the root cause of the problem. Analysis of the groundwater microbiology and inorganic chemistry found no apparent correlation between the presence of IRB and the clogging status of wells. In fact, IRB proved to be widespread throughout the limestone aquifer. However, a clear correlation could be found between clogging affected bores and the redox potential of the groundwater with the most severely affected bores strongly oversaturated in respect to iron oxide minerals. Elevated dissolved concentrations of Fe(II) thereby tended to be found in deeper bores, which also were generally more recently drilled. Following decades of less than average rainfall, a tendency to deepen bores in response to widespread declines in water levels has been documented for the SE of South Australia. The gradually widening clogging problem in the region is postulated to be related to the changes in climate in the region, with irrigators increasingly driven to rely on deeper, anoxic iron-rich groundwater resources.

Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria

Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.