Near‐neutral surface charge and hydrophilicity prevent mineral encrustation of Fe‐oxidizing micro‐organisms

Microbial survival in mineralizing environments depends on the ability to evade surface encrustation by minerals, which could obstruct nutrient uptake and waste output. Some organisms localize mineral precipitation away from the cell; however, cell surface properties – charge and hydrophobicity – must also play a role in preventing surface mineralization. This is especially relevant for iron‐oxidizing bacteria (FeOB), which face an encrustation threat from both biotic and abiotic mineralization. We used electron microscopy and surface characterization techniques to study the surfaces of two stalk‐forming neutrophilic FeOB: the marine Zetaproteobacterium Mariprofundus ferrooxydans PV‐1 and the recently isolated freshwater Betaproteobacterium Gallionellales strain R‐1. Both organisms lack detectable iron on cell surfaces. Live and azide‐inhibited M. ferrooxydans PV‐1 cells had small negative zeta potentials (?0.34 to ?2.73 mV), over the pH range 4.2–9.4; Gallionellales strain R‐1 cells exhibited an even smaller zeta potential (?0.10 to ?0.19 mV) over pH 4.2–8.8. Cells have hydrophilic surfaces, according to water contact angle measurements and microbial adhesion to hydrocarbons tests. Thermodynamic and extended Derjaguin–Landau–Verwey–Overbeek (XDLVO) calculations showed that as low charge causes low electrostatic attraction, hydrophilic repulsion dominates cell–mineral interactions. Therefore, we conclude that surface properties help enable these FeOB to survive in highly mineralizing environments. Given both mineral‐repelling surface properties and the ability to sequester Fe(III) biominerals in an organomineral stalk, these two FeOB have a well‐coordinated system to localize both biotic and abiotic mineral distribution.     

Microaerophilic Fe‐oxidizing micro‐organisms in Middle Jurassic ferruginous stromatolites and the paleoenvironmental context of their formation (Southern Carpathians,Romania)

Ferruginous stromatolites occur associated with Middle Jurassic condensed deposits in several Tethyan and peri‐Tethyan areas. The studied ferruginous stromatolites occurring in the Middle Jurassic condensed deposits of Southern Carpathians (Romania) preserve morphological, geochemical, and mineralogical data that suggest microbial iron oxidation. Based on their macrofabrics and accretion patterns, we classified stromatolites: (1) Ferruginous microstromatolites associated with hardground surfaces and forming the cortex of the macro‐oncoids and (2) Domical ferruginous stromatolites developed within the Ammonitico Rosso‐type succession disposed above the ferruginous microstromatolites (type 1). Petrographic and scanning electron microscope (SEM) examinations reveal that different types of filamentous micro‐organisms were the significant framework builders of the ferruginous stromatolitic laminae. The studied stromatolites yield a large range of δ⁵⁶Fe values, from ?0.75‰ to +0.66‰ with predominantly positive values indicating the prevalence of partial ferrous iron oxidation. The lowest negative δ⁵⁶Fe values (up to ?0.75‰) are present only in domical ferruginous stromatolites samples and point to initial iron mobilization where the Fe(II) was produced by dissimilatory Fe(III) reduction of ferric oxides by Fe(III)‐reducing bacteria. Rare‐earth elements and yttrium (REE + Y) are used to decipher the nature of the seawater during the formation of the ferruginous stromatolites. Cerium anomalies display moderate to small negative values for the ferruginous microstromatolites, indicating weakly oxygenated conditions compatible with slowly reducing environments, in contrast to the domical ferruginous stromatolites that show moderate positive Ce anomalies suggesting that they formed in deeper, anoxic–suboxic waters. The positive Eu anomalies from the studied samples suggest a diffuse hydrothermal input on the seawater during the Middle Jurassic on the sites of ferruginous stromatolite accretion. This study presents the first interpretation of REE + Y in the Middle Jurassic ferruginous stromatolites of Southern Carpathians, Romania.     

Biotransformations of monoterpenes by photoautotrophic micro‐organisms

Monoterpenes are widely used in food technology, cosmetic and pharmaceutical industries and as compounds of agricultural importance. It is known that compounds comprising this class can be transformed by a variety of organisms, namely by: bacteria, fungi, yeasts, plants or isolated enzymes. Biotransformations, as one of the most important tools of green chemistry, allow obtaining new products using whole cells of micro‐organisms or isolated enzymes in mild reaction conditions. Therefore, biotransformations of monoterpenes, by different type of reaction such as: epoxidation, oxidation and stereoselective hydroxylation, resulted in the production of so desired, enantiomerically defined compounds that can be advised as natural seem to be interesting. Bearing in mind that such processes are carried out also by easy to maintain, photoautotrophic micro‐organisms cultivated at large scale, this paper is focused on biotransformations of acyclic, monocyclic and bicyclic monoterpenes by freshwater or haliphylic cyanobacteria and microalgae on the way of mainly stereoselective hydroxylation. Moreover, aspects of potential industrial application of obtained products in medicine, perfume, cosmetics and food industry are discussed.     

Screening and characterization of butanol‐tolerant micro‐organisms

Aims: Poor butanol tolerance of solventogenic stains directly limits their butanol production during industrial‐scale fermentation process. This study was performed to search for micro‐organisms possessing elevated tolerance to butanol. Methods and Results: Two strains, which displayed higher butanol tolerance compared to commonly used solventogenic Clostridium acetobutylicum, were isolated by evolution and screening strategies. Both strains were identified as lactic acid bacteria (LAB). On this basis, a LAB culture collection was tested for butanol tolerance, and 60% of the strains could grow at a butanol concentration of 2·5% (v/v). In addition, an isolated strain with superior butanol tolerance was transformed using a certain plasmid. Conclusions: The results indicate that many strains of LAB possessed inherent tolerance of butanol. Significance and Impact of the Study: This study suggests that LAB strains may be capable of producing butanol to elevated levels following suitable genetic manipulation.     

Colonisation of soft lining materials by micro‐organisms

doi:10.1111/j.1741‐2358.2009.00300.x
Colonisation of soft lining materials by micro‐organisms Objective: This study evaluated the in vitro adherence of pathogenic micro‐organisms, Candida albicans, Staphylococcus aureus and Pseudomonas aeruginosa, to soft lining materials and their inhibitory effect on these micro‐organisms. Materials and Methods: To measure adherence, specimens of Molloplast B and Ufi Gel P were inoculated [10⁷ colony‐forming units per millimetre (cfu/ml)] with TSB media containing the micro‐organisms. To determine the number of micro‐organisms in the 10^?2–10^?5 dilutions, 25 μl of the suspension were transferred to plates of selective media. Colony counts of each specimen were quantified (cfu/ml). The surface roughness was measured with a perfilometer to assess the relationship between the adherence of micro‐organisms and surface roughness of each material. For the inhibition test, specimens of materials were placed in agar plates inoculated individually with the micro‐organisms. After 48 h, the inhibition zones around the specimens were measured. Results: None of the materials exhibited inhibition zones. The number of cfu/ml of S. aureus and P. aeruginosa were significantly greater than C. albicans for both materials. The Ufi Gel P exhibited greater adherence of C. albicans than Molloplast B. No correlation was observed between the adherence of micro‐organisms and surface roughness. Conclusion: The surface roughness of the materials is not the only factor governing micro‐organism adherence.     

Phosphogenesis in the 2460 and 2728 million‐year‐old banded iron formations as evidence for biological cycling of phosphate in the early biosphere

The banded iron formation deposited during the first 2 billion years of Earth's history holds the key to understanding the interplay between the geosphere and the early biosphere at large geological timescales. The earliest ore‐scale phosphorite depositions formed almost at ~2.0–2.2 billion years ago bear evidence for the earliest bloom of aerobic life. The cycling of nutrient phosphorus and how it constrained primary productivity in the anaerobic world of Archean–Palaeoproterozoic eons are still open questions. The controversy centers about whether the precipitation of ultrafine ferric oxyhydroxide due to the microbial Fe(II) oxidation in oceans earlier than 1.9 billion years substantially sequestrated phosphate, and whether this process significantly limited the primary productivity of the early biosphere. In this study, we report apatite radial flowers of a few micrometers in the 2728 million‐year‐old Abitibi banded iron formation and the 2460 million‐year‐old Kuruman banded iron formation and their similarities to those in the 535 million‐year‐old Lower Cambrian phosphorite. The lithology of the 535 Million‐year‐old phosphorite as a biosignature bears abundant biomarkers that reveal the possible similar biogeochemical cycling of phosphorus in the Later Archean and Palaeoproterozoic oceans. These apatite radial flowers represent the primary precipitation of phosphate derived from the phytoplankton blooms in the euphotic zones of Neoarchean and Palaoeproterozoic oceans. The unbiased distributions of the apatite radial flowers within sub‐millimeter bands do not support the idea of an Archean Crisis of Phosphate. This is the first report of the microbial mediated mineralization of phosphorus before the Great Oxidation Event when the whole biosphere was still dominated by anaerobic microorganisms.     

Recent strategies for efficient production of polyhydroxyalkanoates by micro‐organisms

Polyhydroxyalkanoates (PHAs) are polyesters accumulated by many bacteria under unbalanced growth conditions, and have been used to meet the various demands in areas of agriculture, medicine, and materials especially belong to a rapidly expanding area of biomedical research. Unfortunately, the high production cost than the traditional synthetic materials has greatly limited the wide application of PHA. Here, we systematically summarized recent progress in production of PHAs and a series of optimization strategies such as supplying renewable carbon substrates, developing better bacterial strains, optimization of fermentation processes, engineering new pathways and etc., were applied to reduce production cost, therefore providing many new ideas and methods for the production of PHAs in economically viable processes. This is believed to be a comprehensive report to show different strategies and methods for low‐cost production of PHAs. Further studies are still needed to make PHAs more and more economically viable to meet a wide range of applicability.     

Potential applications of nonthermal plasmas against biofilm‐associated micro‐organisms in vitro

Biofilms as complex microbial communities attached to surfaces pose several challenges in different sectors, ranging from food and healthcare to desalination and power generation. The biofilm mode of growth allows microorganisms to survive in hostile environments and biofilm cells exhibit distinct physiology and behaviour in comparison with their planktonic counterparts. They are ubiquitous, resilient and difficult to eradicate due to their resistant phenotype. Several chemical‐based cleaning and disinfection regimens are conventionally used against biofilm‐dwelling micro‐organisms in vitro. Although such approaches are generally considered to be effective, they may contribute to the dissemination of antimicrobial resistance and environmental pollution. Consequently, advanced green technologies for biofilm control are constantly emerging. Disinfection using nonthermal plasmas (NTPs) is one of the novel strategies having a great potential for control of biofilms of a broad spectrum of micro‐organisms. This review discusses several aspects related to the inactivation of biofilm‐associated bacteria and fungi by different types of NTPs under in vitro conditions. A brief introduction summarizes prevailing methods in biofilm inactivation, followed by introduction to gas discharge plasmas, active plasma species and their inactivating mechanism. Subsequently, significance and aspects of NTP inactivation of biofilm‐associated bacteria, especially those of medical importance, including opportunistic pathogens, oral pathogenic bacteria, foodborne pathogens and implant bacteria, are discussed. The remainder of the review discusses majorly about the synergistic effect of NTPs and their activity against biofilm‐associated fungi, especially Candida species.     

The potential significance of microbial Fe(III) reduction during deposition of Precambrian banded iron formations

During deposition of late Archean–early Palaeoproterozoic Precambrian banded iron formations (BIFs) the downward flux of ferric hydroxide (Fe(OH)₃) and phytoplankton biomass should have facilitated microbial Fe(III) reduction. However, quantifying the significance of such a metabolic pathway in the Precambrian is extremely difficult, considering the post‐depositional alteration of the rocks and the lack of ideal modern analogues. Consequently, we have very few constraints on the Fe cycle at that time, namely (i) the concentration of dissolved Fe(II) in the ocean waters; (ii) by what mechanisms Fe(II) was oxidized (chemical, photochemical or biological, the latter using either O₂ or light); (iii) where the ferric hydroxide was precipitated (over the shelf vs. open ocean); (iv) the amount of phytoplankton biomass, which relates to the nutrient status of the surface waters; (v) the relative importance of Fe(III) reduction vs. the other types of metabolic pathways utilized by sea floor microbial communities; and (vi) the proportion of primary vs. diagenetic Fe(II) in BIF. Furthermore, although estimates can be made regarding the quantity of reducing equivalents necessary to account for the diagenetic Fe(II) component in Fe‐rich BIF layers, those same estimates do not offer any insights into the magnitude of Fe(III) actually generated within the water column, and hence, the efficiency of Fe and C recycling prior to burial. Accordingly, in this study, we have attempted to model the ancient Fe cycle, based simply on conservative experimental rates of photosynthetic Fe(II) oxidation in the euphotic zone. We estimate here that under ideal growth conditions, as much as 70% of the biologically formed Fe(III) could have been recycled back into the water column via fermentation and organic carbon oxidation coupled to microbial Fe(III) reduction. By comparing the potential amount of biomass generated phototrophically with the reducing equivalents required for Fe(III) reduction and magnetite formation, we also hypothesize that another anaerobic metabolic pathway might have been utilized in the surface sediment to oxidize the fermentation by‐products. Based on the premise that the deep ocean waters were anoxic, this role could have been fulfilled by methanogens, and maybe even methanotrophs that employed Fe(III) reduction.     

On the biogenicity of Fe‐oxyhydroxide filaments in silicified low‐temperature hydrothermal deposits: Implications for the identification of Fe‐oxidizing bacteria in the rock record

Microaerophilic Fe(II)‐oxidizing bacteria produce biomineralized twisted and branched stalks, which are promising biosignatures of microbial Fe oxidation in ancient jaspers and iron formations. Extracellular Fe stalks retain their morphological characteristics under experimentally elevated temperatures, but the extent to which natural post‐depositional processes affect fossil integrity remains to be resolved. We examined siliceous Fe deposits from laminated mounds and chimney structures from an extinct part of the Jan Mayen Vent Fields on the Arctic Mid‐Ocean Ridge. Our aims were to determine how early seafloor diagenesis affects morphological and chemical signatures of Fe‐oxyhydroxide biomineralization and how extracellular stalks differ from abiogenic features. Optical and scanning electron microscopy in combination with focused ion beam‐transmission electron microscopy (FIB‐TEM) was used to study the filamentous textures and cross sections of individual stalks. Our results revealed directional, dendritic, and radial arrangements of biogenic twisted stalks and randomly organized networks of hollow tubes. Stalks were encrusted by concentric Fe‐oxyhydroxide laminae and silica casings. Element maps produced by energy dispersive X‐ray spectroscopy (EDS) in TEM showed variations in the content of Si, P, and S within filaments, demonstrating that successive hydrothermal fluid pulses mediate early diagenetic alteration and modify the chemical composition and surface features of stalks through Fe‐oxyhydroxide mineralization. The carbon content of the stalks was generally indistinguishable from background levels, suggesting that organic compounds were either scarce initially or lost due to percolating hydrothermal fluids. Dendrites and thicker abiotic filaments from a nearby chimney were composed of nanometer‐sized microcrystalline iron particles and silica and showed Fe growth bands indicative of inorganic precipitation. Our study suggests that the identification of fossil stalks and sheaths of Fe‐oxidizing bacteria in hydrothermal paleoenvironments may not rely on the detection of organic carbon and demonstrates that abiogenic filaments differ from stalks and sheaths of Fe‐oxidizing bacteria with respect to width distribution, ultrastructure, and textural context.     

Bacterial paleontology of the Neoarchean banded iron formations of Karelia and the Kola Peninsula

Probable microfossils, presumably of bacterial origin, were found in the banded iron formations of Karelia and the Kola Peninsula. The age of these formations is 2.7–2.8 Ga. Based on the organic carbon content and balance estimations it was established that these banded iron formations were deposited in environments rich in organic matter. Comparative analysis of the morphology of Recent and Neoarchean microorganisms suggests a bacterial origin for some magnetite in the studied quartzites.     

Acid‐tolerant microaerophilic Fe(II)‐oxidizing bacteria promote Fe(III)‐accumulation in a fen

The ecological importance of Fe(II)‐oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O₂ where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ～5) located in northern Bavaria, Germany. Mean O₂ penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid‐tolerant FeOB cultivated in gradient tubes were most abundant (10⁶ cells g^?1 peat) at the 10–20 cm depth interval. A stable enrichment culture was active at up to 29% O₂ saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid‐tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD‐1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale‐goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid‐tolerant population of FeOB is thriving at redox interfaces formed by diffusion‐limited O₂ transport in acidic peatlands. Furthermore, this well‐adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle.     

Development of a colorimetric colony‐screening assay for detection of defluorination by micro‐organisms

Aims: To develop a colorimetric colony‐screening assay to facilitate the isolation of micro‐organisms capable of defluorination. Methods and Results: A metal‐dye chelate, zirconium‐xylenol orange was used to detect fluoride ions released from a fluorinated substrate through microbial metabolism. Depolymerised zirconium reagent gave the greatest visual contrast for the presence of fluoride compared to more polymerised forms of zirconium reagent. The sensitivity of the assay was greatest when the molar ratio of depolymerised zirconium to xylenol orange was 1 : 2. Using depolymerised zirconium and xylenol orange (150 and 300 nmol l^?1 respectively), the assay could detect a fluoride application spot (5 mmol l^?1) containing 50 nmoles of fluoride ions. Most media constituents were well tolerated by the assay, although phosphate ions needed to be restricted to 0·1 g l^?1 and some proteins digest to between 1 and 5 g l^?1. A microbial enrichment culture growing on solidified medium containing 20 mmol l^?1 fluoroacetate was screened using the assay, and defluorinating bacteria belonging to the genus Burkholderia isolated. Conclusions: A method was developed that is sensitive, rapid and reliable for detecting defluorination by micro‐organisms growing on solidified medium. Significance and Impact of the Study: This method can be used to facilitate the isolation of micro‐organisms capable of defluorination.     

Biodegradation of 1080: Testing soils in south‐eastern Australia for sodium fluoroacetate‐degrading micro‐organisms

Sodium fluoroacetate (1080) is a vertebrate poison commonly used for the control of vertebrate pests in Australia. Long‐term environmental persistence of 1080 from baiting operations has likely nontarget species and environmental impacts and is a matter of public concern. Defluorinating micro‐organisms have been detected in soils of Western and central Australia, and Queensland, but not in south‐eastern Australia. The presence or absence of defluorinating micro‐organisms in soils from south‐eastern Australia will assist in determining whether long‐term environmental persistence of 1080 is or is not occurring. Soils from the Central West Slopes and Plains and Central Tablelands of New South Wales were sampled to investigate the presence and capability of 1080 defluorinating soil micro‐organisms. Thirty‐one species of micro‐organisms were isolated from soils from each site after 10 days incubation in a 20 mM 1080 solution. Of these, 13 isolates showed measurable defluorinating ability when grown in a 1080 and sterile soil suspension. Two species, the bacteria Micromonospora, and the actinomycete Streptosporangium, have not been previously reported for their defluorinating ability. These results indicate that defluorinating micro‐organisms are present in soils in south‐eastern Australia, which adds weight to other studies that found that 1080 is subject to microbiological degradative processes following removal from the bait substrate. Soil micro‐organism defluorination, in combination with physical breakdown and uptake by plants, indicates that fluoroacetate in soils and natural water ways is unlikely to persist. This has implications for the better informed use of 1080 in pest animal management programmes in south‐eastern Australia.