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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 January 2021) | Viewed by 36475

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Prof. Dr. Aleksandra Sklodowska

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Guest Editor

University of Warsaw, Faculty of Biology, Laboratory of Environmental Pollution Analysis, 02-096 Warsaw, Poland
Interests: environmental microbiology; biological wastewater treatment; molecular biology; biodeterioration of monuments; biomining; metals biorecovery; applied microbiology; environmental biotechnology

Dr. Klaudia Debiec-Andrzejewska

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Guest Editor

University of Warsaw, Faculty of Biology, Laboratory of Environmental Pollution Analysis, 02-096 Warsaw, Poland
Interests: environmental microbiology; bioremediation of contaminated environments; minerals bioweathering; plants-microbial interactions

Special Issue Information

Dear Colleagues,

Microbial activity on the surface of minerals can lead to significant changes in the ecosystems. On one hand, it contributes to supplementation of the level of macro and microelements in ecosystems; on the other hand, it is the reason for the occurrence of geochemical anomalies (e.g., arsenic or selenium compounds). Microorganisms can also significantly increase the spread of contaminations, e.g., from mineral waste dumps ,and they may be responsible for serious destruction in man-made infrastructure. Among the processes of uttermost importance in the interaction with minerals, one should list passive and active sorption (including bacterial cell immobilization on/in natural minerals), biomineralization, and microbial weathering. These processes also affect the biodiversity of microorganisms found on mineral surfaces. Possible industrial applications of microbial reactivity, e.g., in bioremediation or biorecovery processes are also noteworthy. All these aspects are of huge significance in the light of recorded climate changes due to the observed shift of climate zones, which stimulates the creation of new ecological niches and changes the growth conditions for microorganisms.

In this context, the Special Issue “Microorganisms–Minerals Interactions” invites researchers with original articles, reviews as well as short communication addressing the latest knowledge about:

Interface interaction between bacterial cells and minerals/stones;
Microbial weathering of minerals as a source of macro and microelements for oligotrophic ecosystems;
Biomineralization supporting reconstruction of stone monuments;
Utilization of minerals as a carries for microorgniasms and their applicationn in the enviroenmtnal biotechnology;
Nanowires role in pollution dissemination.

Prof. Dr. Aleksandra Sklodowska
Dr. Klaudia Debiec-Andrzejewska
Guest Editors

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Keywords

interface interactions
microbial weathering
microbial cell immobilization
pollution dissemination
biomineralization

Published Papers (12 papers)

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Research

Jump to: Review

16 pages, 2008 KiB

Open AccessArticle

Bacterial and Archaeal Structural Diversity in Several Biodeterioration Patterns on the Limestone Walls of the Old Cathedral of Coimbra

by Catarina Coelho, Nuno Mesquita, Inês Costa, Fabiana Soares, João Trovão, Helena Freitas, António Portugal and Igor Tiago

Microorganisms 2021, 9(4), 709; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040709 - 30 Mar 2021

Cited by 17 | Viewed by 2725

Abstract

The “University of Coimbra-Alta and Sofia” area was awarded the UNESCO World Heritage Site distinction in 2013. The Old Cathedral of Coimbra, a 12th-century limestone monument located in this area, has been significantly impacted during the last 800 years by physical, chemical, and biological processes. This led to the significant deterioration of some of its structures and carvings, with loss of aesthetical, cultural, and historical values. For this work, deteriorated spots of the walls of three semi-open chapels from the cloister of the Cathedral were sampled to ascertain their bacterial and archaeal structural diversity. Based on Next-Generation Sequencing (NGS) result analysis, we report the presence of microbial populations that are well adapted to an ecosystem with harsh conditions and that can establish a diverse biofilm in most cases. While it was possible to determine dominant phylogenetic groups in Archaea and Bacteria domains, there was no clear connection between specific core microbiomes and the different deterioration patterns analyzed. The distribution of these archaeal and bacterial communities within the analyzed biodeterioration spots suggests they are more influenced by abiotic factors (i.e., water availability, salinity, etc.), although they influence (and are influenced by) the algal and fungal population composition in this ecosystem. This work provides valuable information that can assist in establishing future guidelines for the preservation and conservation of this kind of historic stone monuments. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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17 pages, 3712 KiB

Open AccessArticle

Microbiological Sulfide Removal—From Microorganism Isolation to Treatment of Industrial Effluent

by Zhendong Yang, Zhenghua Liu, Aleksandra Sklodowska, Marcin Musialowski, Tomasz Bajda, Huaqun Yin and Lukasz Drewniak

Microorganisms 2021, 9(3), 611; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030611 - 16 Mar 2021

Cited by 14 | Viewed by 2940

Abstract

Management of excessive aqueous sulfide is one of the most significant challenges of treating effluent after biological sulfate reduction for metal recovery from hydrometallurgical leachate. The main objective of this study was to characterize and verify the effectiveness of a sulfide-oxidizing bacterial (SOB) consortium isolated from post-mining wastes for sulfide removal from industrial leachate through elemental sulfur production. The isolated SOB has a complete sulfur-oxidizing metabolic system encoded by sox genes and is dominated by the Arcobacter genus. XRD analysis confirmed the presence of elemental sulfur in the collected sediment during cultivation of the SOB in synthetic medium under controlled physicochemical conditions. The growth yield after three days of cultivation reached ~2.34 g_protein/mol_sulfid, while approximately 84% of sulfide was transformed into elemental sulfur after 5 days of incubation. Verification of isolated SOB on the industrial effluent confirmed that it can be used for effective sulfide concentration reduction (~100% reduced from the initial 75.3 mg/L), but for complete leachate treatment (acceptable for discharged limits), bioaugmentation with other bacteria is required to ensure adequate reduction of chemical oxygen demand (COD). Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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22 pages, 2465 KiB

Open AccessArticle

Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions

by Marika Hofmann, Thomas Heine, Luise Malik, Sarah Hofmann, Kristin Joffroy, Christoph Helmut Rudi Senges, Julia Elisabeth Bandow and Dirk Tischler

Microorganisms 2021, 9(1), 111; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010111 - 05 Jan 2021

Cited by 18 | Viewed by 5118

Abstract

To guarantee the supply of critical elements in the future, the development of new technologies is essential. Siderophores have high potential in the recovery and recycling of valuable metals due to their metal-chelating properties. Using the Chrome azurol S assay, 75 bacterial strains were screened to obtain a high-yield siderophore with the ability to complex valuable critical metal ions. The siderophore production of the four selected strains Nocardioides simplex 3E, Pseudomonas chlororaphis DSM 50083, Variovorax paradoxus EPS, and Rhodococcus erythropolis B7g was optimized, resulting in significantly increased siderophore production of N. simplex and R. erythropolis. Produced siderophore amounts and velocities were highly dependent on the carbon source. The genomes of N. simplex and P. chlororaphis were sequenced. Bioinformatical analyses revealed the occurrence of an achromobactin and a pyoverdine gene cluster in P. chlororaphis, a heterobactin and a requichelin gene cluster in R. erythropolis, and a desferrioxamine gene cluster in N. simplex. Finally, the results of the previous metal-binding screening were validated by a proof-of-concept development for the recovery of metal ions from aqueous solutions utilizing C₁₈ columns functionalized with siderophores. We demonstrated the recovery of the critical metal ions V(III), Ga(III), and In(III) from mixed metal solutions with immobilized siderophores of N. simplex and R. erythropolis. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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29 pages, 6912 KiB

Open AccessArticle

Rock Surface Fungi in Deep Continental Biosphere—Exploration of Microbial Community Formation with Subsurface In Situ Biofilm Trap

by Maija Nuppunen-Puputti, Riikka Kietäväinen, Lotta Purkamo, Pauliina Rajala, Merja Itävaara, Ilmo Kukkonen and Malin Bomberg

Microorganisms 2021, 9(1), 64; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010064 - 29 Dec 2020

Cited by 13 | Viewed by 3751

Abstract

Fungi have an important role in nutrient cycling in most ecosystems on Earth, yet their ecology and functionality in deep continental subsurface remain unknown. Here, we report the first observations of active fungal colonization of mica schist in the deep continental biosphere and the ability of deep subsurface fungi to attach to rock surfaces under in situ conditions in groundwater at 500 and 967 m depth in Precambrian bedrock. We present an in situ subsurface biofilm trap, designed to reveal sessile microbial communities on rock surface in deep continental groundwater, using Outokumpu Deep Drill Hole, in eastern Finland, as a test site. The observed fungal phyla in Outokumpu subsurface were Basidiomycota, Ascomycota, and Mortierellomycota. In addition, significant proportion of the community represented unclassified Fungi. Sessile fungal communities on mica schist surfaces differed from the planktic fungal communities. The main bacterial phyla were Firmicutes, Proteobacteria, and Actinobacteriota. Biofilm formation on rock surfaces is a slow process and our results indicate that fungal and bacterial communities dominate the early surface attachment process, when pristine mineral surfaces are exposed to deep subsurface ecosystems. Various fungi showed statistically significant cross-kingdom correlation with both thiosulfate and sulfate reducing bacteria, e.g., SRB2 with fungi Debaryomyces hansenii. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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21 pages, 7723 KiB

Open AccessArticle

Accumulation of Elements in Biodeposits on the Stone Surface in Urban Environment. Case Studies from Saint Petersburg, Russia

by Katerina V. Sazanova (nee Barinova), Marina S. Zelenskaya, Vera V. Manurtdinova, Alina R. Izatulina, Aleksei V. Rusakov, Dmitry Yu. Vlasov and Olga V. Frank-Kamenetskaya

Microorganisms 2021, 9(1), 36; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010036 - 24 Dec 2020

Cited by 6 | Viewed by 2179

Abstract

The pattern of elements accumulation in biodeposits formed by living organisms and extracellular products of their metabolism (biofouling, primary soils) on different bedrocks (of the monuments of Historical necropoleis in Saint Petersburg) were studied by a complex of biological and mineralogical methods (optical microscopy, SEM, EDX, XRD, ICP MS, XRFS). The content of 46 elements in biodeposits with various communities of microorganisms is determined. The model recreating the picture of the input and selective accumulation of elements in biodeposits on the stone surface in outdoor conditions is assumed. It is shown that the main contribution to the elemental composition of biodeposits is made by the environment and the composition of the microbial community. The contribution of leaching under the action of microbial metabolites of mineral grains, entering biodeposits from the environment, is significantly greater than that of the underlying rock. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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15 pages, 2961 KiB

Open AccessArticle

Persistent Activities of Extracellular Enzymes Adsorbed to Soil Minerals

by Folasade K. Olagoke, Klaus Kaiser, Robert Mikutta, Karsten Kalbitz and Cordula Vogel

Microorganisms 2020, 8(11), 1796; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111796 - 16 Nov 2020

Cited by 12 | Viewed by 2666

Abstract

Adsorption of extracellular enzymes to soil minerals is assumed to protect them against degradation, while modifying their activities at the same time. However, the persistence of the activity of adsorbed enzymes remains poorly understood. Therefore, we studied the persistence of cellulase and α-amylase activities after adsorption to soil amended with various amounts (+1, +5, and +10 wt.%) of three typical soil minerals, montmorillonite, kaolinite, and goethite. Soil without mineral addition (pure soil), pure minerals, and pure dissolved enzymes were used as references. Soil mineral–enzyme complexes were prepared and then incubated for 100 days; temporal changes in enzyme activities were analyzed after 0, 0.1, 1, 10, and 100 days. The specific enzyme activities (activities normalized to protein content) and their persistence (activities relative to activities at day 0) were compared to enzyme activities in solution and after sorption to the control soil. Amylase adsorption to pure minerals increased in the following order: montmorillonite > kaolinite > goethite. That of cellulase increased in the following order: goethite > montmorillonite > kaolinite. Adsorption of enzymes to soils did not increase in the same order of magnitude as the addition of reactive binding sites. Based on inverse relationships between the amount of enzyme adsorbed and the specific enzyme activity and their persistency, we showed that a limited availability of sorption sites is important for high specific activity and persistence of the enzymes. This is probably the consequence of less and weaker bonds, as compared to a high availability of sorption sites, resulting in a smaller impact on the active sites of the enzyme. Hence, we suppose that the soil mineral phase supports microorganisms in less-sorptive environments by saving energy on enzyme production, since small enzyme release could already result in sufficient activities to degrade respective target carbon substrates. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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13 pages, 2667 KiB

Open AccessArticle

Effect of Schwertmannite Surface Modification by Surfactants on Adhesion of Acidophilic Bacteria

by Agnieszka Pawlowska and Zygmunt Sadowski

Microorganisms 2020, 8(11), 1725; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111725 - 04 Nov 2020

Cited by 7 | Viewed by 1728

Abstract

Bacterial cell adhesion onto mineral surfaces is important in a broad spectrum of processes, including bioweathering, bioleaching, and bacterial cell transport in the soil. Despite many research efforts, a detailed explanation is still lacking. This work investigates the role of surface-active compounds, cetyltrimethylammonium bromide (CTAB), sodium dodecyl sulfate (SDS), and pure rhamnolipid (RH), in the process of bacteria attachment on the schwertmannite surface. The surface energy was calculated based on the wettability of the tested systems, and for bacteria it was 54.8 mJ/m², schwertmannite-SDS 54.4 mJ/m², schwertmannite-CTAB 55.4 mJ/m², and schwertmannite-RH 39.7 mJ/m². The total energy of adhesion estimated based on thermodynamic data was found to be negative, suggesting favorable conditions for adhesion for all examined suspensions. However, including electrostatic interactions allowed for a more precise description of bacterial adhesion under the tested conditions. The theoretical analysis using the extended Derjaguin-Landau-Verwey-Overbeek (DLVO) approach showed a negative value of total adsorption energy only in bacteria-mineral suspensions, where SDS and rhamnolipid were added. The calculated data were in good agreement with experimental results indicating the significance of electrostatic forces in adsorption. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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11 pages, 1632 KiB

Open AccessArticle

Assessment of Aspergillus niger Strain’s Suitability for Arsenate-Contaminated Water Treatment and Adsorbent Recycling via Bioextraction in a Laboratory-Scale Experiment

by Eva Duborská, Kinga Szabó, Marek Bujdoš, Hana Vojtková, Pavol Littera, Edmund Dobročka, Hyunjung Kim and Martin Urík

Microorganisms 2020, 8(11), 1668; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8111668 - 27 Oct 2020

Cited by 4 | Viewed by 2012

Abstract

In this work, the viability of bioaccumulation and bioextraction processes for arsenic removal from contaminated waters, as well as the recycling of arsenate-treated amorphous ferric oxyhydroxide adsorbent (FeOOH) were evaluated using the common soil microscopic filamentous fungus Aspergillus niger. After treating the contaminated arsenate solution (100 mg As L⁻¹) with FeOOH, the remaining solution was exposed to the growing fungus during a static 19-day cultivation period to further decrease the arsenic concentration. Our data indicated that although the FeOOH adsorbent is suitable for arsenate removal with up to 84% removal efficiency, the fungus was capable of accumulating only up to 13.2% of the remaining arsenic from the culture media. This shows that the fungus A. niger, although highly praised for its application in environmental biotechnology research, was insufficient for decreasing the arsenic contamination to an environmentally acceptable level. However, the bioextraction of arsenic from arsenate-treated FeOOH proved relatively effective for reuse of the adsorbent. Due to its production of acidic metabolites, which decreased pH below 2.7, the fungal strain was capable of removing of up to 98.2% of arsenic from the arsenate-treated FeOOH adsorbent. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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13 pages, 3149 KiB

Open AccessArticle

Importance of Initial Interfacial Steps during Chalcopyrite Bioleaching by a Thermoacidophilic Archaeon

by Camila Safar, Camila Castro and Edgardo Donati

Microorganisms 2020, 8(7), 1009; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8071009 - 06 Jul 2020

Cited by 5 | Viewed by 1900

Abstract

Studies of thermophilic microorganisms have shown that they have a considerable biotechnological potential due to their optimum growth and metabolism at high temperatures. Thermophilic archaea have unique characteristics with important biotechnological applications; many of these species could be used in bioleaching processes to recover valuable metals from mineral ores. Particularly, bioleaching at high temperatures using thermoacidophilic microorganisms can greatly improve metal solubilization from refractory mineral species such as chalcopyrite (CuFeS₂), one of the most abundant and widespread copper-bearing minerals. Interfacial processes such as early cell adhesion, biofilm development, and the formation of passive layers on the mineral surface play important roles in the initial steps of bioleaching processes. The present work focused on the investigation of different bioleaching conditions using the thermoacidophilic archaeon Acidianus copahuensis DSM 29038 to elucidate which steps are pivotal during the chalcopyrite bioleaching. Fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) were used to visualize the microorganism–mineral interaction. Results showed that up to 85% of copper recovery from chalcopyrite could be achieved using A. copahuensis. Improvements in these yields are intimately related to an early contact between cells and the mineral surface. On the other hand, surface coverage by inactivated cells as well as precipitates significantly reduced copper recoveries. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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17 pages, 1882 KiB

Open AccessArticle

Characterization of a Sequential UV Photolysis-Biodegradation Process for Treatment of Decabrominated Diphenyl Ethers in Sorbent/Water Systems

by Yi-Tang Chang, Wei-Liang Chao, Hsin-Yu Chen, Hui Li and Stephen A. Boyd

Microorganisms 2020, 8(5), 633; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8050633 - 27 Apr 2020

Cited by 6 | Viewed by 2675

Abstract

Decabrominated diphenyl ether (BDE-209) is a primary component of the brominated flame retardants used in a variety of industrial and domestic applications. BDE-209 bioaccumulates in aquatic organisms and has been identified as an emerging contaminant that threatens human and ecosystem health. Sequential photolysis-microbial biodegradation processes were utilized here to treat BDE-209 in clay- or soil-water slurries. The removal efficiency of BDE-209 in the clay-water slurries was high; i.e., 96.5%, while that in the soil-water slurries was minimal. In the clay-water slurries the first order rate constants for the UV photolysis and biodegradation of BDE-209 were 0.017 1/day and 0.026 1/day, respectively. UV wavelength and intensity strongly influenced the BDE-209 photolysis and the subsequent biodegradation of photolytic products. Facultative chemotrophic bacteria, including Acidovorax spp., Pseudomonas spp., Novosphingobium spp. and Sphingomonas spp., were the dominant members of the bacterial community (about 71%) at the beginning of the biodegradation; many of these organisms have previously been shown to biodegrade BDE-209 and other polybrominated diphenyl ether (PBDE) congeners. The Achromobacter sp. that were isolated (NH-2; NH-4; NH-6) were especially effective during the BDE-209 degradation. These results indicated the effectiveness of the sequential UV photolysis and biodegradation for treating certain BDE-209-contaminated solids; e.g., clays; in bioreactors containing such solids as aqueous slurries. Achieving a similar treatment effectiveness for more heterogeneous solids containing natural organic matter, e.g., surface solids, appears to be significantly more difficult. Further investigations are needed in order to understand the great difference between the clay-water or soil-water slurries. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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Review

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18 pages, 1350 KiB

Open AccessReview

Regulation of Plant Mineral Nutrition by Signal Molecules

by Vipin Chandra Kalia, Chunjie Gong, Sanjay K. S. Patel and Jung-Kul Lee

Microorganisms 2021, 9(4), 774; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9040774 - 07 Apr 2021

Cited by 29 | Viewed by 4042

Abstract

Microbes operate their metabolic activities at a unicellular level. However, it has been revealed that a few metabolic activities only prove beneficial to microbes if operated at high cell densities. These cell density-dependent activities termed quorum sensing (QS) operate through specific chemical signals. In Gram-negative bacteria, the most widely reported QS signals are acylhomoserine lactones. In contrast, a novel QS-like system has been elucidated, regulating communication between microbes and plants through strigolactones. These systems regulate bioprocesses, which affect the health of plants, animals, and human beings. This mini-review presents recent developments in the QS and QS-like signal molecules in promoting plant health. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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15 pages, 3291 KiB

Open AccessReview

A Review of Asbestos Bioweathering by Siderophore-Producing Pseudomonas: A Potential Strategy of Bioremediation

by Sébastien R. David and Valérie A. Geoffroy

Microorganisms 2020, 8(12), 1870; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8121870 - 26 Nov 2020

Cited by 12 | Viewed by 3446

Abstract

Asbestos, silicate minerals present in soil and used for building constructions for many years, are highly toxic due primarily to the presence of high concentrations of the transition metal iron. Microbial weathering of asbestos occurs through various alteration mechanisms. Siderophores, complex agents specialized in metal chelation, are common mechanisms described in mineral alteration. Solubilized metals from the fiber can serve as micronutrients for telluric microorganisms. The review focuses on the bioweathering of asbestos fibers, found in soil or manufactured by humans with gypsum (asbestos flocking) or cement, by siderophore-producing Pseudomonas. A better understanding of the interactions between asbestos and bacteria will give a perspective of a detoxification process inhibiting asbestos toxicity. Full article

(This article belongs to the Special Issue Microorganisms – Minerals Interactions)

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