Microbial Reducibility of Fe(III) Phases Associated with the Genesis of Iron Ore Caves in the Iron Quadrangle, Minas Gerais, Brazil

Subterranean fauna associated with mesovoid shallow substratum in canga formations from southeastern Brazil: invertebrate biodiversity of a highly threatened ecosystem

Iron Formations (IF) are threatened by mining, particularly the Mesovoid Shallow Substratum (MSS), an understudied subterranean environment. We evaluate the spatiotemporal patterns of subterranean fauna in MSS of iron duricrust (canga) in the Iron Quadrangle and Southern Espinhaço Range, southeastern Brazil. Samplings took place between July 2014 and June 2022 using five trap types. We sampled 108,005 individuals, 1,054 morphospecies, and seven phyla, globally the largest dataset on MSS in IF. Arthropoda represented 97% of all invertebrates sampled. We identified 31 troglomorphic organisms, primarily Arthropoda and Platyhelminthes. MSS traps were the most efficient method, capturing 80% of all invertebrates. Morphospecies were more prevalent in each locality than shared among localities. Species replacement was the main processes to spatial differences. Over time, we found a decrease of total dissimilarity and importance of species replacement for troglomorphic organisms. A positive correlation between spatial distance and compositional dissimilarity of invertebrates was found. Iron Quadrangle and Southern Espinhaço Range showed marked differences in the spatiotemporal patterns of subterranean fauna. Brazilian IF are threatened, with their biological significance not fully understood but highly endangered due their limited distribution. Conservation efforts require a comprehensive understanding of both biotic and abiotic factors shaping the entire IF ecosystem.

The role of plants in ironstone evolution: iron and aluminium cycling in the rhizosphere

The Carajás plateaus in Brazil host endemic epilithic vegetation ("campo rupestre") on top of ironstone duricrusts, known as canga. This capping rock is primarily composed of iron(III) oxide minerals and forms a physically resistant horizon. Field observations reveal an intimate interaction between canga's surface and two native sedges (Rhynchospora barbata and Bulbostylis cangae). These observations suggest that certain plants contribute to the biogeochemical cycling of iron. Iron dissolution features at the root-rock interface were characterised using synchrotron-based techniques, Raman spectroscopy and scanning electron microscopy. These microscale characterisations indicate that iron is preferentially leached in the rhizosphere, enriching the comparatively insoluble aluminium around root channels. Oxalic acid and other exudates were detected in active root channels, signifying ligand-controlled iron oxide dissolution, likely driven by the plants' requirements for goethite-associated nutrients such as phosphorus. The excess iron not uptaken by the plant can reprecipitate in and around roots, line root channels and cement detrital fragments in the soil crust at the base of the plants. The reprecipitation of iron is significant as it provides a continuously forming cement, which makes canga horizons a 'self-healing' cover and contributes to them being the world's most stable continuously exposed land surfaces. Aluminium hydroxide precipitates ("gibbsite cutans") were also detected, coating some of the root cavities, often in alternating layers with goethite. This alternating pattern may correspond with oscillating oxygen concentrations in the rhizosphere. Microbial lineages known to contain iron-reducing bacteria were identified in the sedge rhizospheric microbiome and likely contribute to the reductive dissolution of iron(III) oxides within canga. Drying or percolation of oxygenated water to these anaerobic niches have led to iron mineralisation of biofilms, detected in many root channels. This study sheds light on plants' direct and indirect involvement in canga evolution, with possible implications for revegetation and surface restoration of iron mine sites.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

Bats as ecosystem engineers in iron ore caves in the Carajás National Forest, Brazilian Amazonia

Ecosystem engineers are organisms able to modify their environment by changing the distribution of materials and energy, with effects on biotic and abiotic ecosystem components. Several ecosystem engineers are known, but for most of them the mechanisms behind their influence are poorly known. We detail the role of bats as ecosystem engineers in iron ore caves in the Carajás National Forest, Brazilian Amazonia, an area with > 1,500 caves, some holding ~150,000 bats. We analyzed the chemical composition of guano deposits in bat caves, radiocarbon-dated those deposits, and elucidated the chemical mechanisms involved and the role the bat guano has on modifying those caves. The insect-composed guano was rich in organic matter, with high concentrations of carbon, nitrogen, phosphorus pentoxide and ferric oxide, plus potassium oxide, calcium and sulfur trioxide. Radiocarbon dating indicated guano deposits between 22,000 and 1,800 years old. The guano pH was mainly acid (from 2.1 to 5.6). Percolating waters in those bat caves were also acid (pH reaching 1.5), with the presence of phosphate, iron, calcium, nitrate and sulfate. Acid solutions due to guano decomposition and possible microbial activity produced various forms of corrosion on the caves´ floor and walls, resulting in their enlargement. Bat caves or caves with evidence of inactive bat colonies had, on average, lengths six times larger, areas five times larger, and volumes five times bigger than the regional average, plus more abundant, diversified and bigger speleothems when compared with other caves. In an example of bioengineering, the long-term presence of bats (> 22,000 years) and the guano deposits they produce, mediated by biological and chemical interactions over millennia, resulted in very unique ecological, evolutionary and geomorphological processes, whose working are just beginning to be better understood by science. However, the current expansion of mineral extraction activities coupled with the loosening of licensing and cave protection rules is a real conservation threat to the bat caves in Carajás. The destruction of those caves would represent an unacceptable loss of both speleological and biological heritage and we urge that, whenever they occur, bat caves and their colonies must be fully protected and left off-limits of mineral extraction.

Application of Inductively Coupled Plasma Spectrometric Techniques and Multivariate Statistical Analysis in the Hydrogeochemical Profiling of Caves-Case Study Cloșani, Romania

The aim of the study was to develop the hydrogeochemical profiling of caves based on the elemental composition of water and silty soil samples and a multivariate statistical analysis. Major and trace elements, including rare earths, were determined in the water and soil samples. The general characteristics of water, anions content, inorganic and organic carbon fractions and nitrogen species (NO₃⁻ and NH₄⁺) were also considered. The ANOVA—principal component analysis (PCA) and two-way joining analysis were applied on samples collected from Cloșani Cave, Romania. The ANOVA-PCA revealed that the hydrogeochemical characteristics of Ca²⁺-HCO₃⁻ water facies were described by five factors, the strongest being associated with water-carbonate rock interactions and the occurrence of Ca, Mg and HCO₃⁻ (43.4%). Although organic carbon fractions have a lower influence (20.1%) than inorganic ones on water characteristics, they are involved in the chemical processes of nitrogen and of the elements involved in redox processes (Fe, Mn, Cr and Sn). The seasonal variability of water characteristics, especially during the spring, was observed. The variability of silty soil samples was described by four principal components, the strongest influence being attributed to rare earth elements (52.2%). The ANOVA-PCA provided deeper information compared to Gibbs and Piper diagrams and the correlation analysis.

Hydrologic Alteration and Enhanced Microbial Reductive Dissolution of Fe(III) (hydr)oxides Under Flow Conditions in Fe(III)-Rich Rocks: Contribution to Cave-Forming Processes

Previous work demonstrated that microbial Fe(III)-reduction contributes to void formation, and potentially cave formation within Fe(III)-rich rocks, such as banded iron formation (BIF), iron ore and canga (a surficial duricrust), based on field observations and static batch cultures. Microbiological Fe(III) reduction is often limited when biogenic Fe(II) passivates further Fe(III) reduction, although subsurface groundwater flow and the export of biogenic Fe(II) could alleviate this passivation process, and thus accelerate cave formation. Given that static batch cultures are unlikely to reflect the dynamics of groundwater flow conditions in situ, we carried out comparative batch and column experiments to extend our understanding of the mass transport of iron and other solutes under flow conditions, and its effect on community structure dynamics and Fe(III)-reduction. A solution with chemistry approximating cave-associated porewater was amended with 5.0 mM lactate as a carbon source and added to columns packed with canga and inoculated with an assemblage of microorganisms associated with the interior of cave walls. Under anaerobic conditions, microbial Fe(III) reduction was enhanced in flow-through column incubations, compared to static batch incubations. During incubation, the microbial community profile in both batch culture and columns shifted from a Proteobacterial dominance to the Firmicutes, including Clostridiaceae, Peptococcaceae, and Veillonellaceae, the latter of which has not previously been shown to reduce Fe(III). The bacterial Fe(III) reduction altered the advective properties of canga-packed columns and enhanced permeability. Our results demonstrate that removing inhibitory Fe(II) via mimicking hydrologic flow of groundwater increases reduction rates and overall Fe-oxide dissolution, which in turn alters the hydrology of the Fe(III)-rich rocks. Our results also suggest that reductive weathering of Fe(III)-rich rocks such as canga, BIF, and iron ores may be more substantial than previously understood.

Co-occurrence pattern and function prediction of bacterial community in Karst cave

Background

Karst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats.

Results

The bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed.

Conclusion

These results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.

Biogeochemical cycling of iron oxides in the rhizosphere of plants grown on ferruginous duricrust (canga)

Goethite-cemented duricrusts, also known as canga, commonly occur as a capping rock protecting underlying iron ore deposits. The processes that govern canga formation are still unclear but include recurrent partial dissolution and recrystallisation of goethite through biogeochemical cycling of iron, hypothesised to be catalysed by plants and bacteria. In the present study, the effect of plant exudates on mobilisation of iron in canga was examined using model plants grown on crushed canga in RHIZOtest devices, which separate roots from substrate by a semi-permeable membrane. Moderate plant-induced acidification of the canga was detected, however the primary driver of mineral dissolution was the synergistic effect of reductive and ligand-promoted dissolution, identified by an increase in organic acids concentration and the presence of low concentrations of free ferrous iron. Whilst organic acids exudation lasted, iron cations were stabilised in solution; once the organic acids were degraded by microorganisms, the free cations precipitated as iron oxy-hydroxides. Mineralogical analysis and high-resolution microscopy confirmed our hypothesis that plants that grow in this iron-rich substrate contribute to iron dissolution indirectly (e.g., during phosphate solubilisation), and that the resulting surplus iron not taken up by the plants is redeposited, promoting the cementation of the residual minerals. Understanding the contribution of plants to the iron cycling in canga is crucial when formulating post-mining rehabilitation strategies for iron ore sites.

Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum

In tropical iron ore regions, biologically mediated reduction of crystalline iron oxides drives ongoing iron cycling that contributes to the stability of surface duricrusts. This represents a biotechnological opportunity with respect to post-mining rehabilitation attempts, requiring re-formation of these duricrusts. However, cultivated dissimilatory iron reducing bacteria typically reduce crystalline iron oxides quite poorly. A glucose-fermenting microbial consortium capable of reducing at least 27 mmol/L goethite was enriched from an iron duricrust region. Metagenome analysis led to the recovery of a metagenome assembled genome (MAG) of an iron reducer belonging to the alphaproteobacterial genus Telmatospirillum. This is the first report of iron reduction within the Telmatospirillum and the first reported genome of an iron-reducing, neutrophilic member of the Alphaproteobacteria. The Telmatospirillum MAG encodes putative metal transfer reductases (MtrA, MtrB) and a novel, multi-heme outer membrane cytochrome for extracellular electron transfer. In the presence of goethite, short chain fatty acid production shifted significantly in favor of acetate rather than propionate, indicating goethite is a hydrogen sink in the culture. Therefore, the presence of fermentative bacteria likely promotes iron reduction via hydrogen production. Stimulating microbial fermentation has potential to drive reduction of crystalline iron oxides, the rate limiting step for iron duricrust re-formation.

Microbial diversity and biosignatures of amorphous silica deposits in orthoquartzite caves

Chemical mobility of crystalline and amorphous SiO₂ plays a fundamental role in several geochemical and biological processes, with silicate minerals being the most abundant components of the Earth's crust. Although the oldest evidences of life on Earth are fossilized in microcrystalline silica deposits, little is known about the functional role that bacteria can exert on silica mobility at non-thermal and neutral pH conditions. Here, a microbial influence on silica mobilization event occurring in the Earth's largest orthoquartzite cave is described. Transition from the pristine orthoquartzite to amorphous silica opaline precipitates in the form of stromatolite-like structures is documented through mineralogical, microscopic and geochemical analyses showing an increase of metals and other bioessential elements accompanied by permineralized bacterial cells and ultrastructures. Illumina sequencing of the 16S rRNA gene describes the bacterial diversity characterizing the consecutive amorphization steps to provide clues on the biogeochemical factors playing a role in the silica solubilization and precipitation processes. These results show that both quartz weathering and silica mobility are affected by chemotrophic bacterial communities, providing insights for the understanding of the silica cycle in the subsurface.

A review and statistical assessment of the criteria for determining cave significance

Determining the significance of caves is challenging due to a lack of consensus on which parameters to consider and their relative importance, in addition to difficulties in applying the parameters in a repeatable way. However, classifying caves by levels of significance is unequivocally important because it allows the prioritization of caves for future environmental protection. In countries where the subsurface belongs to the government, such as Brazil, the decision process is coordinated at the government level and a comprehensive approach balancing environmental protection and economic/social interests should be applied. Brazil has the most comprehensive set of criteria for assessing the significance of caves, encompassing parameters applied in other countries. A sample of 401 Brazilian caves in limestone and iron-rich rocks was analysed statistically to infer the relative frequency of each criterion in assigning significance to caves. The analysis included 70 parameters; 30 were present in caves, but on average less than five of these parameters occurred together at each cave. Subjective parameters tended to be less represented. Biotic parameters were dominant and both abiotic and biotic parameters displayed a correlation with length and area, suggesting that these parameters could be good indicators of cave significance. Applying the set of criteria proposed by the Brazilian government to our sample, there was no marked difference between caves in different rock types. A better approach to defining cave relevance is required, with an emphasis on science-based parameters.

The interactions between nanoscale zero-valent iron and microbes in the subsurface environment: A review

Nanoscale zero-valent iron (NZVI) particles, applied for in-situ subsurface remediation, are inevitable to interact with various microbes in the remediation sites directly or indirectly. This review summarizes their interactions, including the effects of NZVI on microbial activity and growth, the synergistic effect of NZVI and microbes on the contaminant removal, and the effects of microbes on the aging of NZVI. NZVI could exert either inhibitive or stimulative effects on the growth of microbes. The mechanisms of NZVI cytotoxicity (i.e., the inhibitive effect) include physical damage and biochemical destruction. The stimulative effects of NZVI on certain bacteria are associated with the creation of appropriate living environment, either through providing electron donor (e.g., H₂) or carbon sources (e.g., the engineered organic surface modifiers), or through eliminating the noxious substances that can cause bactericidal consequence. As a result of the positive interaction, the combination of NZVI and some microbes shows synergistic effect on contaminant removal. Additionally, the aged NZVI can be utilized by some iron-reducing bacteria, resulting in the transformation of Fe(III) to Fe(II), which can further contribute to the contaminant reduction. However, the Fe(III)-reduction process can probably induce environmental risks, such as environmental methylation and remobilization of the previously entrapped heavy metals.