Microorganisms meet solid minerals: interactions and biotechnological applications

Ecological responses and functional significance of paddy crust in the southern Chinese environment

Paddy Crusts (PC) play a pivotal role in the migration and transformation of heavy metals within paddy ecosystems, situated at the critical intersection of air, water, and soil. This study focused on PC samples from heavy metal-contaminated rice paddies in six southern Chinese provinces. It's the first time we've screened and quantified the impact of nutrition, physicochemical properties, and heavy metals on bacterial diversity in PC. Our results highlight the significant influence of zinc, total nitrogen, and soil manganese on bacterial diversity. Using structural equation models, we identified the pathways through which these three types of environmental factors shape bacterial diversity. Heavy metal indicators and physical and chemical indicators exerted a direct negative effect on bacterial diversity in PC, while nutritional indicators had a direct and significant positive effect on bacterial diversity. Variance partitioning analysis revealed heavy metals had the most significant impact, accounting for 7.77% of the total effect. Moreover, the influence of heavy metals on bacterial diversity increased as diversity decreased, ranging from 3.81% to 42.09%. To remediate specific heavy metal pollution, our proposed method involves cultivating indigenous bacteria by controlling these environmental factors, based on an analysis of the interplay among bacterial diversity, environmental variables, and heavy metal bioconcentration factors. These findings enhance our understanding of PC and provide insights into rice field heavy metal pollution mitigation.

Goethite adaptation prompts alterations in antibiotic susceptibility and suppresses development of antibiotic resistance in bacteria

Understanding the impact of environmental factors on antibiotic sensitivity and the emergence of antibiotic resistance in microorganism is crucial for antibiotics management and environmental risk assessment. Natural materials, like mineral particles, are prevalent in aquatic and terrestrial ecosystems. However, it remains unclear how microorganism adapt to the physical stress of mineral particles and whether this adaptation influences antibiotic sensitivity and the evolution of antibiotic resistance. In this study, the model bacterium Escherichia coli (E. coli) was exposed to the mineral particle goethite for 30 generations. Adaptive morphogenesis, including an increase in the fraction of spherical bacteria, variations in bacterial mobility, a slightly increased cell membrane thickness, and genome-wide changes in the transcriptomic profile, were observed in adapted E. coli samples to counteract the stress. Moreover, the goethite adapted E. coli showed increased susceptibility to antibiotics including amoxicillin and tetracycline, and decreased susceptibility to kanamycin compared to its ancestral counterparts. These alterations in antibiotic susceptibility in the adapted E. coli were not heritable, as evidenced by the gradual recovery of antibiotic tolerance in cells with the cessation of goethite exposure. Transcriptomic data and a series of experiments suggested that these changes may be associated with variations in cell membrane property and iron metabolism. In addition, the evolution of antibiotic resistance in adapted cells occurred at a slower rate compared to their ancestral counterparts. For instance, E. coli adapted to goethite at a concentration of 1 mg/mL did not acquire antibiotic resistance even after 13 generations, probably due to its poor biofilm-formation capacity. Our findings underscore the occurrence of microbial adaptation to goethite, which influenced antibiotic sensitivity and decelerated the development of resistance in microorganisms. This insight contributes to our comprehension of the natural dynamics surrounding the evolution of antibiotic resistance and opens new perspectives for addressing this issue through nanotechnology-based approaches.

Terrestrial algae: pioneer organisms of carbonate rock solutional weathering in South China karst

The formation of soil in karst ecosystem has always been a scientific problem of great concern to human beings. Algae can grow on the exposed and non-nutrition carbonate surface, inducing and accelerating weathering of rock substrates, thus promoting soil formation. Yet the actual contribution of algae to solutional weathering intensity remains unclear. In this study, we performed weathering simulation experiment on two algae species (Klebsormidium dissectum (F.Gay) H.Ettl & G.Gärtner and Chlorella vulgaris Beijerinck), which were screened from carbonated rock surfaces from a typical karst region in South China. The results showed: (1) both algae have solutional weathering effect on carbonate rock, (2) there is no difference of solutional intensity observed, yet the solutional modes are different, suggesting different ecological adaptative strategies, (3) algae on carbonate rocks have higher carbonic anhydrase activity (CAA) and secrete more extracellular polysaccharide (EPS), accelerating rock weathering. (4) The absolute dissolution amount of carbonate rock with algae participation is 3 times of that of without algae. These results indicate the significant impact of terrestrial algae on carbonate rock solutional weathering and provides quantitative evidence that terrestrial algae are pioneer species. It also contributes to our further understanding of soil formation in karst ecosystems in South China.

Reciprocal Interactions of Abiotic and Biotic Dechlorination of Chloroethenes in Soil

Chloroethenes (CEs) as common organic pollutants in soil could be attenuated via abiotic and biotic dechlorination. Nonetheless, information on the key catalyzing matter and their reciprocal interactions remains scarce. In this study, FeS was identified as a major catalyzing matter in soil for the abiotic dechlorination of CEs, and acetylene could be employed as an indicator of the FeS-mediated abiotic CE-dechlorination. Organohalide-respiring bacteria (OHRB)-mediated dechlorination enhanced abiotic CEs-to-acetylene potential by providing dichloroethenes (DCEs) and trichloroethene (TCE) since chlorination extent determined CEs-to-acetylene potential with an order of trans-DCE > cis-DCE > TCE > tetrachloroethene/PCE. In contrast, FeS was shown to inhibit OHRB-mediated dechlorination, inhibition of which could be alleviated by the addition of soil humic substances. Moreover, sulfate-reducing bacteria and fermenting microorganisms affected FeS-mediated abiotic dechlorination by re-generation of FeS and providing short chain fatty acids, respectively. A new scenario was proposed to elucidate major abiotic and biotic processes and their reciprocal interactions in determining the fate of CEs in soil. Our results may guide the sustainable management of CE-contaminated sites by providing insights into interactions of the abiotic and biotic dechlorination in soil.

Mineral weathering of iron ore tailings primed by Acidithiobacillus ferrooxidans and elemental sulfur under contrasting pH conditions

The acidophilic sulfur oxidizing bacterium (SOB), Acidithiobacillus ferrooxidans, has been found to stimulate elemental sulfur (S⁰) oxidation and mineral weathering in alkaline Fe ore tailings. However, A. ferrooxidans growth and activities depend on the pH conditions surrounding their interfaces with minerals. The present study aimed to investigate how pH influences bacterial growth and functions in Fe ore tailings. A simulated aquatic 'homogeneous' incubation system was initially adjusted into acidic (pH 4), neutral (pH 7) and alkaline (pH 9) conditions, which mimicked the microenvironmental conditions of the water-cell-mineral interfaces in the tailings. It was found that A. ferrooxidans grew well and oxidised S⁰ under the prevailing and initially acidic conditions (pH < 6). These stimulated the weathering of biotite and amphibole-like minerals and the formation of nanosized jarosite and ferrihydrite-like minerals mediated by extracellular polymer substrate (EPS). In contrast, the initially neutral/alkaline pH conditions (i.e., pH > 7) with the presence of the alkaline tailings restricted SOB growth and functions in S⁰-oxidation and mineral weathering. These findings suggest that it is essential to prime acidic conditions in microenvironments to support SOB growth, activities, and functions toward mineral weathering in tailings, providing critical basis for involving SOB in eco-engineered pedogenesis in tailings.

Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.

Microbial Networks Reveal the Structure of Water Microbial Communities in Kalamaili Mountain Ungulate Nature Reserve

Water microorganisms contribute to the key components of ecosystems in dryland waters, which are extremely important for wildlife. However, the distribution patterns of water microbes across different basal water sources are still largely unknown. This study was conducted to compare microorganisms in the water bodies of different types of water sources in the Kalamaili Mountain Ungulate Nature Reserve in China. Bioinformatic analysis revealed that the undirected microbial co-existence network consisted of 15 main modules referring to different water sources, which indicated specific molecular co-existence relationships. It was found that the most dominant phyla (namely Proteobacteria, Patescibacteria, Firmicutes, Bacteroidota, and Actinobacteriota) of the molecular ecological network shared the same structures as the microbial community, which justified the construction of the network via a random network formation. Principal coordinate analysis (PCoA) based on Bray–Curtis distances revealed that there were still considerable variations among different habitats, showing separate sample clusters. Additionally, the different topological roles of subnetworks trimmed to a uniform size indicated different co-existence patterns in the microbiome. The artificially recharged water from concrete pond substrate (ARC) subnetworks had a relatively discrete co-occurrence, while the natural water sources (NRE) and artificially recharged water from earthen pond substrate (ARE) groups were more compact with giant modules. The NRE and ARE groups were also richer in microbial composition and had a higher number of species with low abundance. Consequently, concrete substrates may contribute to dysfunction in water microbiomes. Moreover, the functional diversity of the NRE and ARE groups is due to more intra-module connections and more inter-module connections, indirectly leading to a stable function resilient to external environmental influences. In conclusion, the microecology of the NRE was more stable than that of the concrete substrate, and artificial transportation had less effect on the microbial community.

Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock

The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.

Investigation on Microbial Biodeterioration of the Stone Monuments in Yildiz Technical University-Yildiz Campus-Istanbul-Turkey

The stone samples of historical monuments around Yıldız Technical University Besiktas Campus were investigated using DNA extraction-PCR-DGGE methods, scanning electron microscopy (SEM), XRF, and other analytical methods to assess stone decay over the centuries. Microbial diversity was examined by classical cultivation and modern diagnostic methods besides modern analysis techniques. The number of the microorganisms in per gram of stone samples was calculated by microbial culture methods. SEM analysis showed that stone surfaces have too many pores, decaying pieces and microbial colony. It is put forth by XRF analysis that stone materials have some elements serving the growth of microorganisms. It was concluded that there is a close connection the stone structure and microbial growth, most likely mineralogical composition, hardness and porosity of stone. Cyanobacterial microorganisms lived on stone surfaces were also determined using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. It was revealed DNA-based molecular analysis of 16S rRNA that 23 bacterial/Cyanobacterial clones were inhabited to stone materials.

Developments in the study and applications of bacterial transformations of selenium species

Microbial bio-transformations of the essential trace element selenium are now recognized to occur among a wide variety of microorganisms. These transformations are used to convert this element into its assimilated form of selenocysteine, which is at the active center of a number of key enzymes, and to produce selenium nanoparticles, quantum dots, metal selenides, and methylated selenium species that are indispensable for biotechnological and bioremediation applications. The focus of this review is to present the state-of-the-art of all aspects of the investigations into the bacterial transformations of selenium species, and to consider the characterization and biotechnological uses of these transformations and their products.

Green Infrastructure Design Influences Communities of Urban Soil Bacteria

The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree pits), and an urban forest. The design of ROWB GI features directly connects with the road to manage street runoff, which can increase the Technosol saturation and exposure to urban contaminants washed from the street and carried into the GI feature. This GI design specifically accommodates dramatic pulses of water that influence the bacterial community composition and diversity through the selective pressure of contaminants or by disturbance. The ROWB had the highest biodiversity, but no significant correlation with levels of soil organic matter and microbially-mediated biogeochemical functions. Another important biogeochemical parameter for soil bacterial communities is pH, which influenced the bacterial community composition, consistent with studies in non-urban soils. Bacterial community composition in GI features showed signs of anthropogenic disturbance, including exposure to animal feces and chemical contaminants, such as petroleum products. Results suggest the overall design and management of GI features with a channeled connection with street runoff, such as ROWB, have a comprehensive effect on soil parameters (particularly organic matter) and the bacterial community. One key consideration for future assessments of GI microbial community would be to determine the source of organic matter and elucidate the relationship between vegetation, Technosol, and bacteria in the designed GI features.

The detoxification potential of ferric ions for bioleaching of the chalcopyrite associated with fluoride-bearing gangue mineral

Fluoride toxicity to microorganisms was a predominant factor contributing to the failure of a commercial scale bioleach heap. An integrated control strategy for fluoride complexation without jarosite generation by stepwise adding ferric ions was first proposed to enable the bioleaching of the chalcopyrite associated with fluoride-bearing gangue mineral by Acidithiobacillus ferrooxidans. Chemical speciation calculation revealed that with the presence of Fe³⁺, the concentration of the main lethal fluoride to microorganism, HF, decreased dramatically. The pure culture study showed that the detrimental effect of fluoride on microorganism was eliminated by increasing the molar ratio of Fe³⁺/F^- to 3:1. Furthermore, chalcopyrite bioleaching experiment revealed the minimum Fe³⁺/F^- molar ratio that enabled the bioleaching was 6:1. Stepwise addition was an effective way to promote a balanced system and avoid the formation of jarosite caused by the excessive Fe³⁺. Above all, the introduction of Fe³⁺ is a feasible method for reducing the fluoride toxicity during the bioleaching of chalcopyrite, shedding light on the industrial applications.

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes

Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.

Artificial inorganic biohybrids: The functional combination of microorganisms and cells with inorganic materials

Biohybrids can be defined as the functional combination of proteins, viable cells or microorganisms with non-biological materials. This article reviews recent findings on the encapsulation of microorganisms and eukaryotic cells in inorganic matrices such as silica gels or cements. The entrapment of biological entities into a support material is of great benefit for processing since the encapsulation matrix protects sensitive cells from shear forces, unfavourable pH changes, or cytotoxic solvents, avoids culture-washout, and simplifies the separation of formed products. After reflecting general aspects of such an immobilization as well as the chemistry of the inorganic matrices, we focused on manufacturing aspects and the application of such biohybrids in biotechnology, medicine as well as in environmental science and for civil engineering purpose.

STATEMENT OF SIGNIFICANCE

The encapsulation of living cells and microorganisms became an intensively studied and rapidly expanding research field with manifold applications in medicine, bio- and environmental technology, or civil engineering. Here, the use of silica or cements as encapsulation matrices have the advantage of a higher chemical and mechanical resistance towards harsh environmental conditions during processing compared to their polymeric counterparts. In this perspective, the article gives an overview about the inorganic material systems used for cell encapsulation, followed by reviewing the most important applications. The future may lay in a combination of the currently achieved biohybrid systems with additive manufacturing techniques. In a longer perspective, this would enable the direct printing of cell loaded bioreactor components.

Commercial silicate phosphate sequestration and desorption leads to a gradual decline of aquatic systems

Laboratory desorption behaviour, function and elemental composition of commercially marketed silicate minerals used to sequester phosphorus pollution as well as Zeolite, Smectite, and Kaolinite were determined to see whether their use by environmental scientists and water managers in eutrophic waterways has the potential to contribute to longer-term environmental impacts. As expected, lower phosphorus concentrations were observed, following treatment. However, data relating to desorption, environmental fate and bioavailability of phospho-silicate complexes (especially those containing rare earth elements) appear to be underrepresented in product testing and trial publications. Analysis of desorption of phosphate (P) was > 5 μg[P]/L for all three non-commercial samples and 0 > μg[P]/L > 5 for all commercial silicates for a range of concentrations from 0 to 300 μg[P]/L. Based on a review of bioaccumulation data specific to the endangered Cherax tenuimanus (Hairy Marron) and other endemic species, this is significant considering anything > 20 μg[La]/L is potentially lethal to the hairy marron, other crustaceans and even other phyla. Where prokaryotic and eukaryotic effects are underreported, this represents a significant challenge. Especially where product protocols recommend continual reapplication, this is significant because both the forward and reverse reactions are equally important. The users of silicate minerals in water columns should accept the dynamic nature of the process and pay equal attention to both adsorption and desorption because desorption behaviour is an inherent trait. Even if broader desorption experimentation is difficult, expensive and time-consuming, it is a critical consideration nonetheless.

Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential

Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.

Insights into Nitrate-Reducing Fe(II) Oxidation Mechanisms through Analysis of Cell-Mineral Associations, Cell Encrustation, and Mineralogy in the Chemolithoautotrophic Enrichment Culture KS

Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic and depend on organic cosubstrates for growth. Encrustation of cells in Fe(III) minerals has been observed for mixotrophic NRFeOB but not for autotrophic phototrophic and microaerophilic Fe(II) oxidizers. So far, little is known about cell-mineral associations in the few existing autotrophic NRFeOB. Here, we investigate whether the designated autotrophic Fe(II)-oxidizing strain (closely related to Gallionella and Sideroxydans) or the heterotrophic nitrate reducers that are present in the autotrophic nitrate-reducing Fe(II)-oxidizing enrichment culture KS form mineral crusts during Fe(II) oxidation under autotrophic and mixotrophic conditions. In the mixed culture, we found no significant encrustation of any of the cells both during autotrophic oxidation of 8 to 10 mM Fe(II) coupled to nitrate reduction and during cultivation under mixotrophic conditions with 8 to 10 mM Fe(II), 5 mM acetate, and 4 mM nitrate, where higher numbers of heterotrophic nitrate reducers were present. Two pure cultures of heterotrophic nitrate reducers (Nocardioides and Rhodanobacter) isolated from culture KS were analyzed under mixotrophic growth conditions. We found green rust formation, no cell encrustation, and only a few mineral particles on some cell surfaces with 5 mM Fe(II) and some encrustation with 10 mM Fe(II). Our findings suggest that enzymatic, autotrophic Fe(II) oxidation coupled to nitrate reduction forms poorly crystalline Fe(III) oxyhydroxides and proceeds without cellular encrustation while indirect Fe(II) oxidation via heterotrophic nitrate-reduction-derived nitrite can lead to green rust as an intermediate mineral and significant cell encrustation. The extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible under environmental conditions in most habitats.IMPORTANCE Most described nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOB) are mixotrophic (their growth depends on organic cosubstrates) and can become encrusted in Fe(III) minerals. Encrustation is expected to be harmful and poses a threat to cells if it also occurs under environmentally relevant conditions. Nitrite produced during heterotrophic denitrification reacts with Fe(II) abiotically and is probably the reason for encrustation in mixotrophic NRFeOB. Little is known about cell-mineral associations in autotrophic NRFeOB such as the enrichment culture KS. Here, we show that no encrustation occurs in culture KS under autotrophic and mixotrophic conditions while heterotrophic nitrate-reducing isolates from culture KS become encrusted. These findings support the hypothesis that encrustation in mixotrophic cultures is caused by the abiotic reaction of Fe(II) with nitrite and provide evidence that Fe(II) oxidation in culture KS is enzymatic. Furthermore, we show that the extent of encrustation caused by indirect Fe(II) oxidation by reactive nitrogen species depends on Fe(II) concentrations and is probably negligible in most environmental habitats.