Microbial chemolithotrophy mediates oxidative weathering of granitic bedrock

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Reclamation of waste coal gangue activated by Stenotrophomonas maltophilia for mine soil improvement: Solubilizing behavior of bacteria on nutrient elements

The coal gangue has occupied the farmland and caused severe pollution to the surrounding environment, which was discharged with vast amount as a by-product of coal mining and washing. A sustainable and ecological microorganism activation method was proposed to disposal coal gangue as mineral fertilizer. A Stenotrophomonas maltophilia YZ1 bacteria was separated and found to be useful in solubilizing nutrient elements in coal gangue. The contents of available P, available K and available Si in the treated coal gangue reached 278.4 mg/kg, 1305.3 mg/kg and 522.7 mg/kg, respectively. The YZ1 bacteria dissolved the minerals of monetite (CaHPO₄), muscovite and annite by the organic acids, which were the metabolism product of YZ1 bacteria. The solubilizing mechanisms of phosphate minerals included the release of protic and the chelation of organic acid with calcium. The microbial activation method can provide nutrient elements for soil, which may realize the reclamation of coal gangue in a harmless way.

Potential environmental risk of natural particulate cadmium and zinc in sphalerite- and smithsonite-spiked soils

Cadmium (Cd)-bearing sphalerite and smithsonite ore particles are ubiquitous in soils near metal-mining areas. Previous studies indicate that smithsonite is more readily dissolved in acidic waters and soils than sphalerite but the mobility of Cd and zinc (Zn) derived from these ores in soils is unknown. Using microcosm incubation experiments and microscopic and spectroscopic analysis, we found that the mobility of Cd and Zn derived from smithsonite is higher than from sphalerite. The mobilization rates of Cd (16.6%) and Zn (13.7%) released from smithsonite in soils after 30-day incubation experiments were higher than those from sphalerite (Cd, ~ 1.42%; Zn, ~ 0.75%). Moreover, the percentages of Cd²⁺ and Zn²⁺ in soil pore water showed a dynamic increase in smithsonite-spiked treatments but a decrease in sphalerite-spiked treatments. HRTEM-EDX-SAED analysis further indicates the occurrence of dynamic transformation of amorphous Cd and Zn species in soil pore water to crystalline ZnS and iron oxides in sphalerite-spiked soil but crystalline ZnCO₃ nanoparticles were dynamically transformed to amorphous metal-bearing species in smithsonite-spiked soil. The opposite transformation trends in pore water of Zn ore-spiked soils provide new insights into the Cd environmental risks in soils affected by Zn mining.

Microbial chemolithotrophic oxidation of pyrite in a subsurface shale weathering environment: Geologic considerations and potential mechanisms

Oxidative weathering of pyrite plays an important role in the biogeochemical cycling of Fe and S in terrestrial environments. While the mechanism and occurrence of biologically accelerated pyrite oxidation under acidic conditions are well established, much less is known about microbially mediated pyrite oxidation at circumneutral pH. Recent work (Percak-Dennett et al., 2017, Geobiology, 15, 690) has demonstrated the ability of aerobic chemolithotrophic microorganisms to accelerate pyrite oxidation at circumneutral pH and proposed two mechanistic models by which this phenomenon might occur. Here, we assess the potential relevance of aerobic microbially catalyzed circumneutral pH pyrite oxidation in relation to subsurface shale weathering at Susquehanna Shale Hills Critical Zone Observatory (SSHCZO) in Pennsylvania, USA. Specimen pyrite mixed with native shale was incubated in groundwater for 3 months at the inferred depth of in situ pyrite oxidation. The colonized materials were used as an inoculum for pyrite-oxidizing enrichment cultures. Microbial activity accelerated the release of sulfate across all conditions. 16S rRNA gene sequencing and metagenomic analysis revealed the dominance of a putative chemolithoautotrophic sulfur-oxidizing bacterium from the genus Thiobacillus in the enrichment cultures. Previously proposed models for aerobic microbial pyrite oxidation were assessed in terms of physical constraints, enrichment culture geochemistry, and metagenomic analysis. Although we conclude that subsurface pyrite oxidation at SSCHZO is largely abiotic, this work nonetheless yields new insight into the potential pathways by which aerobic microorganisms may accelerate pyrite oxidation at circumneutral pH. We propose a new "direct sulfur oxidation" pathway, whereby sulfhydryl-bearing outer membrane proteins mediate oxidation of pyrite surfaces through a persulfide intermediate, analogous to previously proposed mechanisms for direct microbial oxidation of elemental sulfur. The action of this and other direct microbial pyrite oxidation pathways have major implications for controls on pyrite weathering rates in circumneutral pH sedimentary environments where pore throat sizes permit widespread access of microorganisms to pyrite surfaces.

Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria

Mineral weathering bacteria play essential roles in nutrient cycling and plant nutrition. However, we are far from having a comprehensive view of the factors regulating their distribution and the molecular mechanisms involved. In this review, we highlight the extrinsic factors (i.e., nutrient availability, carbon source) and the intrinsic properties of minerals explaining the distribution and functioning of these functional communities. We also present and discuss the progress made in understanding the molecular mechanisms and genes that are used by bacteria during the mineral weathering process, or regulated during their interaction with minerals, that have been recently unraveled by omics approaches.

Deep weathering in the semi-arid Coastal Cordillera, Chile

The weathering front is the boundary beneath Earth’s surface where pristine rock is converted into weathered rock. It is the base of the “critical zone”, in which the lithosphere, biosphere, and atmosphere interact. Typically, this front is located no more than 20 m deep in granitoid rock in humid climate zones. Its depth and the degree of rock weathering are commonly linked to oxygen transport and fluid flow. By drilling into fractured igneous rock in the semi-arid climate zone of the Coastal Cordillera in Chile we found multiple weathering fronts of which the deepest is 76 m beneath the surface. Rock is weathered to varying degrees, contains core stones, and strongly altered zones featuring intensive iron oxidation and high porosity. Geophysical borehole measurements and chemical weathering indicators reveal more intense weathering where fracturing is extensive, and porosity is higher than in bedrock. Only the top 10 m feature a continuous weathering gradient towards the surface. We suggest that tectonic preconditioning by fracturing provided transport pathways for oxygen to greater depths, inducing porosity by oxidation. Porosity was preserved throughout the weathering process, as secondary minerals were barely formed due to the low fluid flow.

Correlative Microscopy: a tool for understanding soil weathering in modern analogues of early terrestrial biospheres

Correlative imaging provides a method of investigating complex systems by combining analytical (chemistry) and imaging (tomography) information across dimensions (2D-3D) and scales (centimetres-nanometres). We studied weathering processes in a modern cryptogamic ground cover from Iceland, containing early colonizing, and evolutionary ancient, communities of mosses, lichens, fungi, and bacteria. Targeted multi-scale X-ray Microscopy of a grain in-situ within a soil core revealed networks of surficial and internal features (tunnels) originating from organic-rich surface holes. Further targeted 2D grain characterisation by optical microscopy (OM), scanning electron microscopy (SEM), and energy dispersive X-ray spectroscopy (SEM-EDS), following an intermediate manual correlative preparation step, revealed Fe-rich nodules within the tunnels. Finally, nanotomographic imaging by focussed ion beam microscopy (FIB-SEM) revealed coccoid and filamentous-like structures within subsurface tunnels, as well as accumulations of Fe and S in grain surface crusts, which may represent a biological rock varnish/glaze. We attribute these features to biological processes. This work highlights the advantages and novelty of the correlative imaging approach, across scales, dimensions, and modes, to investigate biological weathering processes. Further, we demonstrate correlative microscopy as a means of identifying fingerprints of biological communities, which could be used in the geologic rock record and on extra-terrestrial bodies.

Insights into the Geomicrobiology of Biovermiculations from Rock Billet Incubation Experiments

Biovermiculations are uniquely patterned organic rich sediment formations found on the walls of caves and other subterranean environments. These distinctive worm-like features are the combined result of physical and biological processes. The diverse microbial communities that inhabit biovermiculations may corrode the host rock, form secondary minerals, and produce biofilms that stabilize the sediment matrix, thus altering cave surfaces and contributing to the formation of these wall deposits. In this study, we incubated basalt, limestone, and monzonite rock billets in biovermiculation mixed natural community enrichments for 468–604 days, and used scanning electron microscopy (SEM) to assess surface textures and biofilms that developed over the course of the experiment. We observed alteration of rock billet surfaces associated with biofilms and microbial filaments, particularly etch pits and other corrosion features in olivine and other silicates, calcite dissolution textures, and the formation of secondary minerals including phosphates, clays, and iron oxides. We identified twelve distinct biofilm morphotypes that varied based on rock type and the drying method used in sample preparation. These corrosion features and microbial structures inform potential biological mechanisms for the alteration of cave walls, and provide insight into possible small-scale macroscopically visible biosignatures that could augment the utility of biovermiculations and similarly patterned deposits for astrobiology and life detection applications.

The Weathering Microbiome of an Outcropping Granodiorite

Microorganisms have long been recognized for their capacity to catalyze the weathering of silicate minerals. While the vast majority of studies on microbially mediated silicate weathering focus on organotrophic metabolism linked to nutrient acquisition, it has been recently demonstrated that chemolithotrophic ferrous iron [Fe(II)] oxidizing bacteria (FeOB) are capable of coupling the oxidation of silicate mineral Fe(II) to metabolic energy generation and cellular growth. In natural systems, complex microbial consortia with diverse metabolic capabilities can exist and interact to influence the biogeochemical cycling of essential elements, including iron. Here we combine microbiological and metagenomic analyses to investigate the potential interactions among metabolically diverse microorganisms in the near surface weathering of an outcrop of the Rio Blanco Quartz Diorite (DIO) in the Luquillo Mountains of Puerto Rico. Laboratory based incubations utilizing ground DIO as metabolic energy source for chemolithotrophic FeOB confirmed the ability of FeOB to grow via the oxidation of silicate-bound Fe(II). Dramatically accelerated rates of Fe(II)-oxidation were associated with an enrichment in microorganisms with the genetic capacity for iron oxidizing extracellular electron transfer (EET) pathways. Microbially oxidized DIO displayed an enhanced susceptibility to the weathering activity of organotrophic microorganisms compared to unoxidized mineral suspensions. Our results suggest that chemolithotrophic and organotrophic microorganisms are likely to coexist and contribute synergistically to the overall weathering of the in situ bedrock outcrop.

Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes

Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology.

Promotion of Microbial Oxidation of Structural Fe(II) in Nontronite by Oxalate and NTA

Iron redox cycling occurs extensively in soils and sediments. Previous research has focused on microbially mediated redox cycling of aqueous Fe. At circumneutral pH, most Fe occurs in solid phase, where Fe and organic ligands interact closely. However, the role of organic ligands in microbial oxidation of solid-phase Fe(II) is not well understood. Here, we incubated reduced nontronite NAu-2 (rNAu-2) with an iron-oxidizing bacterium and in the presence of oxalate and nitrilotriacetic acid. These ligands significantly enhanced the rate and extent of microbial oxidation of structural Fe(II) in rNAu-2. Aqueous and solid-phase analyses, coupled with biogeochemical modeling, revealed a pathway for ligand-enhanced bio-oxidation of solid-phase Fe(II): (1) dissolution of rNAu-2 to form aqueous Fe(II)-ligand complex; (2) bio-oxidation to Fe(III)-ligand complex; (3) rapid reduction of Fe(III)-ligand complex to Fe(II)-ligand complex by structural Fe(II) in rNAu-2. In this process, the Fe(II)-ligand and Fe(III)-ligand complexes effectively serve as electron shuttle to expand the bioavailable pool of solid-phase Fe(II). These results have important implications for a better understanding of the bioavailability and reactivity of solid-phase Fe pool in the environment.

Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes

We have recently argued that, because microbes have pervasive - often vital - influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology-literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513-1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public-health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well-being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of 'germs' and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination-capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision-making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology-centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre-occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.