Case studies associated with the 10 major geodiversity-related topics.

This paper outlines the 10 major topics related to geodiversity that have emerged since the concept was first introduced in 1993, 30 years ago. After a short introduction, each of the 10 topics is then illustrated by a relevant case study. The 10 topics (italics) and their case studies (bold) are as follows: 1. Celebrating, International Geodiversity Day; 2. Measurement/Assessment, Potential role of remote sensing; 3. Natural Capital and Geosystem Services, Coastal geosystem services; 4. Biodiversity, Mangue de Pedra, Brazil; 5. Geomaterials, The circular economy; 6. Geotourism, World's top geotourism sites?; 7. Geoheritage, Landscape restoration; 8. National Geoconservation, Trump golf course and an SSSI, Scotland; 9. World Heritage Sites and Global Geoparks, Azores Global Geopark, Portugal; 10. Sustainability, Xitle Volcano, Mexico City. It is concluded that, given the way in which geodiversity has developed as a concept, leading to new insights and avenues of research and advancing our understanding of the world since its first use, it clearly now constitutes a significant, geoscientific paradigm. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

Towards a taxonomy of geodiversity.

Geodiversity is a topical concept in earth and environmental sciences. Geodiversity information is needed to conserve nature, use ecosystem services and achieve sustainable development goals. Despite the increasing demand for geodiversity data, there exists no comprehensive system for categorizing geodiversity. Here, we present a hierarchically structured taxonomy that is potentially applicable in mapping and quantifying geodiversity across different regions, environments and scales. In this taxonomy, the main components of geodiversity are geology, geomorphology, hydrology and pedology. We propose a six-level hierarchical system where the components of geodiversity are classified at progressively lower taxonomic levels based on their genesis, physical-chemical properties and morphology. This comprehensive taxonomy can be used to compile geodiversity information for scientific research and various applications of value to society and nature conservation. Ultimately, this hierarchical system is the first step towards developing a global geodiversity taxonomy. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

The status and future of essential geodiversity variables.

Rapid environmental change, natural resource overconsumption and increasing concerns about ecological sustainability have led to the development of 'Essential Variables' (EVs). EVs are harmonized data products to inform policy and to enable effective management of natural resources by monitoring global changes. Recent years have seen the instigation of new EVs beyond those established for climate, oceans and biodiversity (ECVs, EOVs and EBVs), including Essential Geodiversity Variables (EGVs). EGVs aim to consistently quantify and monitor heterogeneity of Earth-surface and subsurface abiotic features, including geology, geomorphology, hydrology and pedology. Here we assess the status and future development of EGVs to better incorporate geodiversity into policy and sustainable management of natural resources. Getting EGVs operational requires better consensus on defining geodiversity, investments into a governance structure and open platform for curating the development of EGVs, advances in harmonizing in situ measurements and linking heterogeneous databases, and development of open and accessible computational workflows for global digital mapping using machine-learning techniques. Cross-disciplinary collaboration and partnerships with governmental and private organizations are needed to ensure the successful development and uptake of EGVs across science and policy. This article is part of the Theo Murphy meeting issue 'Geodiversity for science and society'.

Boundary of ecosystem services: A response to.

Chen et al. (2023) have proposed a scheme to define which services should be included as ecosystem services and which should be excluded so as to avoid "an all-encompassing metaphor that captures any benefit". We discuss the proposals, drawing attention in particular to definitions of 'natural capital' and 'ecosystems', the complexities of separating biotic from abiotic flows, and the importance of geodiversity and geosystem services in delivering societal benefits. We conclude that rather than trying to separate out bits of nature in order to draw the boundary of ecosystem services, it is perhaps time to avoid using 'nature' and 'biodiversity' as synonyms and think instead of a more holistic and integrated approach involving 'environmental', 'natural' or 'nature's services', in which the role of abiotic nature is fully recognised in both ecosystem services and non-ecosystem domains.

Scalable, chromatography-free synthesis of alkyl-tethered pyrene-based materials. Application to first-generation "archipelago model" asphaltene compounds.

In this paper, we report a highly efficient, scalable approach to the total synthesis of conformationally unrestricted, electronically isolated arrays of alkyl-tethered polycyclic aromatic chromophores. This new class of modular molecules consists of polycyclic aromatic "islands" comprising significant structural fragments present in unrefined heavy petroleum, tethered together by short saturated alkyl chains, as represented in the "archipelago model" of asphaltene structure. The most highly branched archipelago compounds reported here share an architecture with first-generation dendrimeric constructs, making the convergent, chromatography-free synthesis described herein particularly attractive for further extensions in scope and applications to materials chemistry. The syntheses are efficient, selective, and readily adaptable to a multigram scale, requiring only inexpensive, "earth-abundant" transition-metal catalysts for cross-coupling reactions and extraction and fractional crystallization for purification. This approach avoids typical limitations in cost, scale, and operational practicality. All of the archipelago compounds and synthetic intermediates have been fully characterized spectroscopically and analytically. The solid-state structure of one archipelago model compound has been determined by X-ray crystallography.

Why geodiversity matters in valuing nature's stage.

Geodiversity--the variability of Earth's surface materials, forms, and physical processes-is an integral part of nature and crucial for sustaining ecosystems and their services. It provides the substrates, landform mosaics, and dynamic physical processes for habitat development and maintenance. By determining the heterogeneity of the physical environment in conjunction with climate interactions, geodiversity has a crucial influence on biodiversity across a wide range of scales. From a literature review, we identified the diverse values of geodiversity; examined examples of the dependencies of biodiversity on geodiversity at a site-specific scale (for geosites <1 km(2) in area); and evaluated various human-induced threats to geosites and geodiversity. We found that geosites are important to biodiversity because they often support rare or unique biota adapted to distinctive environmental conditions or create a diversity of microenvironments that enhance species richness. Conservation of geodiversity in the face of a range of threats is critical both for effective management of nature's stage and for its own particular values. This requires approaches to nature conservation that integrate climate, biodiversity, and geodiversity at all spatial scales.

Evaluating steady-state and time-resolved fluorescence as a tool to study the behavior of asphaltene in toluene.

A combination of steady-state fluorescence, fluorescence lifetime measurements and the determination of time-resolved emission spectra were employed to characterize asphaltene toluene solutions. Lifetime measurements were shown to be insensitive to the source of asphaltene or the alkane solvent from which asphaltene was precipitated. This insensitivity suggests that either the composition of Athabasca and Cold Lake asphaltene is very similar or that the fluorescence behavior is dominated by the same sub-set of fluorophores for the different samples. These results highlight the limitations in using fluorescence to characterize asphaltene solutions. Different dependencies were observed for the average lifetimes with the asphaltene concentration when measured at two different emission wavelengths (420 nm and 520 nm). This result suggests that different fluorophores underwent diverse interactions with other asphaltene molecules as the asphaltene concentration was raised, suggesting that models for asphaltene aggregation need to include molecular diversity.

Selective sorting of cargo proteins into bacterial membrane vesicles.

In contrast to the well established multiple cellular roles of membrane vesicles in eukaryotic cell biology, outer membrane vesicles (OMV) produced via blebbing of prokaryotic membranes have frequently been regarded as cell debris or microscopy artifacts. Increasingly, however, bacterial membrane vesicles are thought to play a role in microbial virulence, although it remains to be determined whether OMV result from a directed process or from passive disintegration of the outer membrane. Here we establish that the human oral pathogen Porphyromonas gingivalis has a mechanism to selectively sort proteins into OMV, resulting in the preferential packaging of virulence factors into OMV and the exclusion of abundant outer membrane proteins from the protein cargo. Furthermore, we show a critical role for lipopolysaccharide in directing this sorting mechanism. The existence of a process to package specific virulence factors into OMV may significantly alter our current understanding of host-pathogen interactions.

The EmhABC efflux pump decreases the efficiency of phenanthrene biodegradation by Pseudomonas fluorescens strain LP6a.

Pseudomonas fluorescens strain LP6a, designated here as strain WEN (wild-type PAH catabolism, efflux positive), utilizes the polycyclic aromatic hydrocarbon phenanthrene as a carbon source but also extrudes it into the extracellular medium using the efflux pump EmhABC. Because phenanthrene is considered a nontoxic carbon source for P. fluorescens WEP, its energy-dependent efflux seems counter-productive. We hypothesized that the efflux of phenanthrene would decrease the efficiency of its biodegradation. Indeed, an emhB disruptant strain, wild-type PAH catabolism, efflux negative (WEN), biodegraded 44% more phenanthrene than its parent strain WEP during a 6-day incubation. To determine whether efflux affected the degree of oxidation of phenanthrene, we quantified the conversion of ¹4C-phenanthrene to radiolabeled polar metabolites and ¹4CO2. The emhB⁻ WEN strain produced approximately twice as much ¹4CO2 and radiolabeled water-soluble metabolites as the WEP strain. In contrast, the mineralization of ¹4C-glucose, which is not a known EmhB efflux substrate, was equivalent in both strains. An early open-ring metabolite of phenanthrene, trans-4-(1-hydroxynaphth-2-yl)-2-oxo-3-butenoic acid, also was found to be a substrate of the EmhABC pump and accumulated in the supernatant of WEP but not WEN cultures. The analogous open-ring metabolite of dibenzothiophene, a heterocyclic analog of phenanthrene, was extruded by EmhABC plus a putative alternative efflux pump, whereas the end product 3-hydroxy-2-formylbenzothiophene was not actively extruded from either WEP or WEN cells. These results indicate that the active efflux of phenanthrene and its early metabolite(s) decreases the efficiency of phenanthrene degradation by the WEP strain. This activity has implications for the bioremediation and biocatalytic transformation of polycyclic aromatic hydrocarbons and heterocycles.

Carbon disulfide reagent allows the characterization of nonpolar analytes by atmospheric pressure chemical ionization mass spectrometry.

While atmospheric pressure ionization methodologies have revolutionized the mass spectrometric analysis of nonvolatile analytes, limitations native to the chemistry of these methodologies hinder or entirely inhibit the analysis of certain analytes, specifically, many nonpolar compounds. Examination of various analytes, including asphaltene and lignin model compounds as well as saturated hydrocarbons, demonstrates that atmospheric pressure chemical ionization (APCI) using CS(2) as the reagent produces an abundant and stable molecular ion (M(+•)) for all model compounds studied, with the exception of completely saturated aliphatic hydrocarbons and the two amino acids tested, arginine and phenylalanine. This reagent substantially broadens the applicability of mass spectrometry to nonvolatile nonpolar analytes and also facilitates the examination of radical cation chemistry by mass spectrometry.

Influence of adhesion on aerobic biodegradation and bioremediation of liquid hydrocarbons.

Biodegradation of poorly water-soluble liquid hydrocarbons is often limited by low availability of the substrate to microbes. Adhesion of microorganisms to an oil-water interface can enhance this availability, whereas detaching cells from the interface can reduce the rate of biodegradation. The capability of microbes to adhere to the interface is not limited to hydrocarbon degraders, nor is it the only mechanism to enable rapid uptake of hydrocarbons, but it represents a common strategy. This review of the literature indicates that microbial adhesion can benefit growth on and biodegradation of very poorly water-soluble hydrocarbons such as n-alkanes and large polycyclic aromatic hydrocarbons dissolved in a non-aqueous phase. Adhesion is particularly important when the hydrocarbons are not emulsified, giving limited interfacial area between the two liquid phases. When mixed communities are involved in biodegradation, the ability of cells to adhere to the interface can enable selective growth and enhance bioremediation with time. The critical challenge in understanding the relationship between growth rate and biodegradation rate for adherent bacteria is to accurately measure and observe the population that resides at the interface of the hydrocarbon phase.

Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production.

Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production ('souring') caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers (≤10(3) MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5-20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50-60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50-60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is added.

Adhesion to the hydrocarbon phase increases phenanthrene degradation by Pseudomonas fluorescens LP6a.

Microbial adhesion is an important factor that can influence biodegradation of poorly water soluble hydrocarbons such as phenanthrene. This study examined how adhesion to an oil-water interface, as mediated by 1-dodecanol, enhanced phenanthrene biodegradation by Pseudomonas fluorescens LP6a. Phenanthrene was dissolved in heptamethylnonane and added to the aerobic aqueous growth medium to form a two phase mixture. 1-Dodecanol was non-toxic and furthermore could be biodegraded slowly by this strain. The alcohol promoted adhesion of the bacterial cells to the oil-water interface without significantly changing the interfacial or surface tension. Introducing 1-dodecanol at concentrations from 217 to 4,100 mg l(-1) increased phenanthrene biodegradation by about 30% after 120 h incubation. After 100 h incubation, cultures initially containing 120 or 160 mg l(-1) 1-dodecanol had mineralized >10% of the phenanthrene whereas those incubated without 1-dodecanol had mineralized only 4.5%. The production and accumulation of putative phenanthrene metabolites in the aqueous phase of cultures likewise increased in response to the addition of 1-dodecanol. The results suggest that enhanced adhesion of bacterial cells to the oil-water interface was the main factor responsible for enhanced biodegradation of phenanthrene to presumed polar metabolites and to CO(2).

Structures of water molecules at solvent/silica interfaces.

The adsorption of water at solvent/silica interfaces was studied using IR-visible sum frequency generation (SFG) vibrational spectroscopy. We discovered a water layer between toluene and silica with no detectable free OHs. The water layer without free OHs showed resistance against further adsorption of water molecules. This "water-resistant" water surface was very stable at room temperature and did not become a regular water layer with free OH over a period of 12 h in water-saturated toluene. However, this special structure of water was not observed at heptane/silica interfaces, at which free OHs were observed. The study indicates that interactions between solvents and water molecules can significantly change the interfacial water properties.

Sulfide persistence in oil field waters amended with nitrate and acetate.

Nitrate amendment is normally an effective method for sulfide control in oil field-produced waters. However, this approach has occasionally failed to prevent sulfide accumulation, despite the presence of active nitrate-reducing bacterial populations. Here, we report our study of bulk chemical transformations in microcosms of oil field waters containing nitrate-reducing, sulfide-oxidizing bacteria, but lacking denitrifying heterotrophs. Amendment with combinations of nitrate, acetate, and phosphate altered the microbial sulfur and nitrogen transformations. Elemental sulfur produced by chemotrophic nitrate-reducing bacteria was re-reduced heterotrophically to sulfide. Ammonification, rather than denitrification, was the predominant pathway for nitrate reduction. The application of nitrite led to transient sulfide depletion, possibly due to higher rates of nitrite reduction. The addition of molybdate suppressed both the accumulation of sulfide and the heterotrophic reduction of nitrate. Therefore, sulfidogenesis was likely due to elemental sulfur-reducing heterotrophic bacteria, and the nitrate-reducing microbial community consisted mainly of facultatively chemotrophic microbes. This study describes one set of conditions for continued sulfidogenesis during nitrate reduction, with important implications for nitrate control of sulfide production in oil fields.

Two different mechanisms for adhesion of Gram-negative bacterium, Pseudomonas fluorescens LP6a, to an oil-water interface.

Microbial adhesion to the oil-water interface is an important parameter in biodegradation of hydrocarbons to enhance uptake and metabolism of compounds with very low aqueous solubility, but the mechanisms of adhesion are not well understood. Our approach was to study a range of compounds and mechanisms to promote the adhesion of a hydrophilic bacterium, Pseudomonas fluorescens strain LP6a, to an oil-water interface. The cationic surfactants cetylpyridinium chloride (CPC), poly-l-lysine and chlorhexidine gluconate (CHX) and the long chain alcohols 1-dodecanol and farnesol increased the adhesion of P. fluorescens LP6a to n-hexadecane from ca. 30 to 90% of suspended cells adhering. In contrast, adjusting the ionic strength of the suspending medium only increased the adhesion from about 8 to 30%. The alcohols, 1-dodecanol and farnesol, also caused a dramatic change in the oil-water contact angle of the cell surface, increasing it from 24 degrees to 104 degrees , whereas the cationic compounds had little effect. In contrast, cationic compounds changed the electrophoretic mobility of the bacteria, reducing the mean zeta potential from -23 to -7 mV in 0.01 M potassium phosphate buffer, but the alcohols, 1-dodecanol and farnesol, had no effect on zeta potential. Even though both types of compounds promoted cell adhesion to the n-hexadecane interface, the mechanisms were different. Alcohols acted through altering the cell surface hydrophobicity, whereas cationic surfactants changed the surface charge density.

Mechanical properties of hexadecane-water interfaces with adsorbed hydrophobic bacteria.

This study focuses on how intact, hydrophobic bacteria in their stationary (i.e., non-dividing) phase could adsorb onto the hexadecane-water interface and alter its mechanical properties. The two strains of bacteria used in forming the interfacial films were Acinetobacter venetianus RAG-1 and Rhodococcus erythropolis 20S-E1-c. Using the dynamic pendant drop technique, the film interfacial tension was monitored as the surface area was made to undergo transient changes. Under static conditions, both types of bacteria had no effect on the interfacial tension. When subjected to transient excitations, however, the two bacterial films exhibited clear and qualitatively similar rheological properties: they responded as two-dimensional Maxwellian materials when the interfacial areas were dilated suddenly, but appeared to be purely elastic upon rapid area compression. Such rheological behaviours are "non-linear" in that the responses of the tension to area dilation and contraction are not mirror images of one another. Despite their qualitative similarities, the two types of film had very distinct film elasticities and relaxation times. The most striking difference between the two bacterial films was revealed under continuous reduction of area, when the A. venetianus RAG-1 system displayed a "paper-like" interface, whereas the interface of the R. erythropolis 20S-E1-c system was "soap film-like". These macroscopic observations could be explained by the surface ultrastructures of the two cell strains determined using transmission electron microscopy.

Hydrophobic bacteria at the hexadecane-water interface: examination of micrometre-scale interfacial properties.

Hydrophobic bacteria, like colloidal solids, can spontaneously adsorb onto fluid-fluid interfaces and modify their mechanical properties. In this study, two strains of bacteria--Acinetobacter venetianus RAG-1 and Rhodococcus erythropolis 20S-E1-c--were prepared in their stationary (i.e. non-dividing) phase in the absence of biosurfactants; the cells were then used as emulsifiers to stabilize n-hexadecane droplets in aqueous environments. Using the micropipette technique, colloidal stability of the bacteria-coated droplets was examined through direct-contact experiments. Both types of bacteria were seen to function as effective stabilizers, although the Acinetobacter venetianus RAG-1 film provided stronger resistance to droplet-droplet coalescence. In addition to creating steric barriers, the adsorbed bacteria also interacted with one another at the interface, giving rise to higher order rheological properties. A technique of directly probing the mechanical properties of the emulsion drop surfaces (i.e. the adsorbed films) on the micrometre-scale revealed that (a) the films behaved as purely elastic sheets, and (b) with a reduction in cell concentration in the aqueous phase, less oil was emulsified, but the elastic moduli of the adsorbed films remained unchanged (suggesting an "all or none" adsorption process). These results are in contrast to a previous macroscopic (i.e. millimetre-scale) study, which showed that the absorbed films were viscoelastic, with the apparent elastic moduli depending strongly on cell concentration. The rheological properties of these bacteria-adsorbed interfaces appeared therefore to be length scale-dependent.

Aerobic biotransformation of decalin (decahydronaphthalene) by Rhodococcus spp.

Mixed bacterial cultures aerobically transformed decalin (decahydronaphthalene) dissolved in an immiscible carrier phase (heptamethylnonane; HMN) in liquid medium. Conversion was enhanced in the presence of decane, a readily degraded n-alkane, and/or HMN. Four Rhodococcus spp. isolates purified from one of the mixed cultures were active against decalin in the presence of n-decane, but their ability to use decalin as a sole carbon source for growth could not be sustained. Isolate Iso 1a oxidized decalin under co-metabolic conditions with decane vapours as the primary carbon source. Mass spectrometry and comparison to authentic standards showed that the oxidized products of decalin biotransformation were 2-decahydronaphthol and 2-decalone. Some evidence of ring-opening was obtained, but the possible ring-opened product was not definitively identified. These results are consistent with co-metabolic oxidation of decalin by enzymes active toward n-alkanes.