Nutrient input influences fungal community composition and size and can stimulate manganese (II) oxidation in caves

Unveiling the Subterranean Symphony: A Comprehensive Study of Cave Fungi Revealed Through National Center for Biotechnology Sequences

Caves can be regarded as extreme environments, and fungi are known as omnipresent and highly adaptable organisms that can easily colonize such environments. The primary objective of this study was to use the statistical analysis of sequences stored in the NCBI database, together with related metadata, to find and uncover statistically significant distribution patterns of fungi occupying different substrata inside the caves. The obtained list included a total of 1447 sequences corresponding to fungi isolated from various substrata within cave environments around the world, which corresponds to 445 fungal species, members of the 394 genera. Ascomycota was the most dominant phylum and Eurotiomycetes the dominant class of fungal dwellers in these environments. The highest species richness is detected for the genus Penicillium (57), followed by Aspergillus (51). On the other hand, the most frequently documented single species was Pseudogymnoascus destructans, isolated mostly from hibernating bats and guano, followed by Penicillium chrysogenum. Because caves have stable, nutrient-limited, low-competition microhabitats that support unusual or cryptic species, many new fungal taxa have been reported as well (such as Aspergillus, Apiotrichum, and Cephalotrichum species). Finally, cutting-edge molecular technologies and better sampling methods are revealing hitherto undiscovered fungal diversity in caves worldwide.

Subterranean marvels: microbial communities in caves and underground mines and their promise for natural product discovery

Covering: 2014 to 2024Since the dawn of human history, caves have played an intimate role in our existence. From our earliest ancestors seeking shelter from the elements to more recent generations harnessing cave substances for medicinal purposes, caves have served as essential resources and havens. The last 40 years of geomicrobiology research has replaced the outdated perception of subterranean environments as lifeless and unchanging with the realization that vibrant microbial communities have adapted to thrive in extreme conditions over millions of years. The ability of subterranean microbial communities to withstand nutrient deprivation and darkness creates a unique reservoir of untapped biosynthetic potential. These communities offer exciting prospects for medicine (e.g., antimicrobial and antitumor therapies) and biotechnology (e.g., redox chemical properties and biomineralization). This article highlights the significance of caves and mines as reservoirs of microbial diversity, the potential impact of their bioactive compounds on the fields of healthcare and biotechnology, and the significant challenges that must be overcome to access and harness the biotechnological potential of subterranean microbial communities. Additionally, it emphasizes the conservation efforts needed to protect these delicate ecosystems, ensuring the preservation of both ancient traditions and tomorrow's medicines.

Biogenic Mn Oxide Generation and Mn(II) Removal by a Manganese Oxidizing Bacterium Bacillus sp. Strain M2

Mn(II)-oxidizing bacteria (MOB) are widely distributed in natural environments and can convert soluble Mn(II) into insoluble Mn(III) and Mn(IV). The biogenic manganese oxides (BioMnOx) produced by MOB have been considered for remediating heavy metal pollution and degrading organic pollutants in an eco-friendly manner. In this study, a manganese-oxidizing bacterium was isolated from Mn-polluted rivulet sediment and identified as Bacillus sp. strain M2 by PCR, phylogenetic tree construction, transmission electron microscopy (TEM), and physiological and biochemical indices. Strain M2 grew well under Mn(II) stress. BioMnOx with nanosized irregular geometric shapes and loose structures generated by strain M2 were found on the surface of the bacterial cells. The content of Mn in the bacteria was as high as 5.36%. Approximately 71.24% and 47.52% of Mn(II) was oxidized to Mn(III/IV) in the cell and in the deposits, respectively, within 3 d of cultivation with Mn(II). Extracellular enzymes contributed to the Mn removal and oxidation. In conclusion, Bacillus sp. strain M2 has a high potential for use in the remediation of Mn-contaminated sites.

Manganese: From Soil to Human Health-A Comprehensive Overview of Its Biological and Environmental Significance

Background: Manganese is an essential micronutrient that plays a pivotal role in environmental systems, plant physiology, and human health. This review comprehensively examines the manganese cycle in the environment, its absorption and transport mechanisms in plants, and the implications of manganese exposure to human health. Objectives: The objectives of this review are to (i) analyze the environmental cycling of manganese and its bioavailability, (ii) evaluate the role of manganese in plant metabolism and disease resistance, and (iii) assess the impact of manganese toxicity and deficiency on human health. Conclusion: This review highlights that while manganese is crucial for photosynthesis, enzyme activation, and resistance to plant diseases, both its deficiency and toxicity can have severe consequences. In plants, manganese deficiency can lead to impaired growth and reduced crop yields, while toxicity, particularly in acidic soils, can inhibit photosynthesis and stunt development. In humans, manganese is necessary for various physiological processes, but overexposure, especially in occupational settings, can result in neurodegenerative conditions such as manganism. The conclusion emphasizes the importance of managing manganese levels in agriculture and industry to optimize its benefits while minimizing health risks. A multidisciplinary approach is advocated to enhance agricultural productivity and ensure public health safety.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

Formation of Biogenic Manganese Oxide Nodules on Hyphae of a New Fungal Isolate of Periconia That Immobilizes Aqueous Copper

Mn(II)-oxidizing microorganisms are considered to play significant roles in the natural geochemical cycles of Mn and other heavy metals because the insoluble biogenic Mn oxides (BMOs) that are produced by these microorganisms adsorb other dissolved heavy metals and immobilize them as precipitates. In the present study, a new Mn(II)-oxidizing fungal strain belonging to the ascomycete genus Periconia, a well-studied plant-associating fungal genus with Mn(II)-oxidizing activity that has not yet been exami-ned in detail, was isolated from natural groundwater outflow sediment. This isolate, named strain TS-2, was confirmed to oxidize dissolved Mn(II) and produce insoluble BMOs that formed characteristic, separately-located nodules on their hyphae while leaving major areas of the hyphae free from encrustation. These BMO nodules also adsorbed and immobilized dissolved Cu(II), a model analyte of heavy metals, as evidenced by elemental mapping ana-lyses of fungal hyphae-BMO assemblages using a scanning electron microscope with energy-dispersive X-ray spectroscopy (SEM-EDX). Analyses of functional genes within the whole genome of strain TS-2 further revealed the presence of multiple genes predicted to encode laccases/multicopper oxidases that were potentially responsible for Mn(II) oxidation by this strain. The formation of BMO nodules may have functioned to prevent the complete encrustation of fungal hyphae, thereby enabling the control of heavy metal concentrations in their local microenvironments while maintaining hyphal functionality. The present results will expand our knowledge of the physiological and morphological traits of Mn(II)-oxidizing Periconia, which may affect the natural cycle of heavy metals through their immobilization.

Dispersal Limitation Controlling the Assembly of the Fungal Community in Karst Caves

As a unique ecosystem, Karst caves harbor an impressive diversity of specific fungi. However, the factors and mechanisms that shape fungal biodiversity in caves remain elusive. In this study, we explored the assembly patterns of fungal communities based on our previous research in eight representative Karst caves in Southwest China. Our results indicated that dispersal limitation plays a crucial role in shaping the overall fungal community as well as specific communities in rock, sediment, and water samples. However, "Undominated" processes contributed more than dispersal limitation in air samples. Interestingly, the dominant assembly processes varied between caves. Consistently, environmental selection had a minor impact on the assembly of fungal communities. Among the examined spatial and environmental variables, latitude, longitude, altitude, and temperature were found to significantly influence fungal communities irrespective of substrate type. These findings provide valuable insights into the ecological factors governing fungal community assembly in Karst caves.

Microbial diversity and proxy species for human impact in Italian karst caves

To date, the highly adapted cave microbial communities are challenged by the expanding anthropization of these subterranean habitats. Although recent advances in characterizing show-caves microbiome composition and functionality, the anthropic effect on promoting the establishment, or reducing the presence of specific microbial guilds has never been studied in detail. This work aims to investigate the whole microbiome (Fungi, Algae, Bacteria and Archaea) of four Italian show-caves, displaying different environmental and geo-morphological conditions and one recently discovered natural cave to highlight potential human-induced microbial traits alterations. Results indicate how show-caves share common microbial traits in contrast to the natural one; the first are characterized by microorganisms related to outdoor environment and/or capable of exploiting extra inputs of organic matter eventually supplied by tourist flows (i.e. Chaetomium and Phoma for fungi and Pseudomonas for bacteria). Yet, variation in microalgae assemblage composition was reported in show-caves, probably related to the effect of the artificial lighting. This study provides insights into the potential microbiome cave contamination by human-related bacteria (e.g. Lactobacillus and Staphylococcus) and commensal/opportunistic human associated fungi (e.g. Candida) and dermatophytes. This work is critical to untangle caves microbiome towards management and conservation of these fragile ecosystems.

Microbial roles in cave biogeochemical cycling

Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.

Microbial ecology of tourist Paleolithic caves

Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.

Spatial Patterns of Soil Fungal Communities Are Driven by Dissolved Organic Matter (DOM) Quality in Semi-Arid Regions

Soil fungi are ecologically important as decomposers, pathogens, and symbionts in nature. Understanding their biogeographic patterns and driving forces is pivotal to predict alterations arising from environmental changes in ecosystem. Dissolved organic matter (DOM) is an essential resource for soil fungi; however, the role of its quality in structuring fungal community patterns remains elusive. Here using Illumina MiSeq sequencing, we characterized total fungi and their functional groups in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China, which are currently suffering great pressure from climate change. Total fungi and their functional groups were all observed to exhibit significant biogeographic patterns which were primarily driven by environmental variables. DOM quality was the best and consistent predictor of diversity of both total fungi and functional groups. Specifically, plant-derived DOM was associated with greater diversity relative to microbe-dominated origins. In addition, fungal diversity linearly increased with increases in degree of humification in DOM. Similarly, among all measured environmental variables, DOM quality had the strongest effects on the community composition of total fungi and functional groups. Together, our work contributes to the factors underlying fungal biogeographic patterns and adds detail to the importance of DOM quality in structuring fungal communities.

Microbial community composition in iron deposits and manganese crusts formed in riverine environments around the Aso area in Japan

The Kurokawa river flowing through the Aso Caldera in Southwest Japan is influenced by groundwater containing high concentration of dissolved metals (Fe²⁺ and Mn²⁺) and is associated with orange deposits in the upstream and thick black crusts on the wall of artificial waterway tunnel with several km lengths in the midstream regions. X-ray fluorescence analysis revealed that the orange deposits contained up to 34.4% Fe and black crusts comprised up to 25.4% and 10.6% Mn and Fe, respectively. Although naturally occurring Mn-oxides and crusts are considered biogenic in pH-neutral freshwater environments, the whole microbial community in Mn crust and their contribution to Mn crust formation in these environments remain unclear. High-throughput molecular sequencing for bacteria and eukaryotes including fungi revealed black Mn crusts had a high abundance of Sphingomonas, Hyphomicrobium, Bacillus, Pseudomonas, and Mortierella, previously reported genera including several species with Mn-oxidizing activity in Mn crusts or nodules of other marine and freshwater environments. In addition, one bacterial isolate and one fungal isolate with Mn-oxidizing activity were obtained from black Mn crust. These results suggest that multiple Mn-oxidizing bacteria including Pseudomonas and fungi are involved in Mn crust formation on the wall of dark waterway tunnel in the oligotrophic environment of the Kurokawa river.

A manganese-oxidizing bacterial consortium and its biogenic Mn oxides for dye decolorization and heavy metal adsorption

Manganese (Mn) contamination is a common environmental problem in the world and manganese oxidizing bacteria (MOB) play important roles in bioremediation of heavy metal and organic pollution. In this study, a novel MOB consortium AS containing core microbes of Sphingobacterium and Bacillus was acclimated from Mn-contaminated rivulet sediments. The MOB consortium AS presented good Mn(II) removal performance under 500-10,000 mg/L Mn(II), with Mn(II) removal capacities ranging from 481 to 3478 mg/L. In coexistence systems of Mn(II) and Fe(II), Ni(II), Cu(II), and Zn(II), the MOB consortium AS removed 98%, 91%, 99%, and 76% of Mn(II), respectively. Additionally, the MOB consortium AS could utilize multiple carbon sources (e.g., Chitosan, β-Cyclodextrin, and Phenanthrene) to remove Mn(II), with Mn(II) removal efficiencies ranging from 11% to 97%. Meanwhile, XRD, XPS, FTIR, SEM, and EDS analyses reflected that biogenic Mn oxides (bio-MnOx-C) contained C, O, Mn (Mn(II) and Mn(IV)) and embodied in rhodochrosite and birnessite. The bio-MnOx-C exhibited second-order kinetic reaction for removal of dye, with corresponding decolorization capacities of 22.0 mg/g for methylene blue and 23.8 mg/g for crystal violet. In addition, bio-MnOx-C showed adsorption capacities of 159.0 mg/g for Cu(II), 130.7 mg/g for Zn(II), and 123.3 mg/g for Pb(II). Overall, this study illustrates consortium AS and bio-MnOx-C have great potentials in remediation of pollution caused by heavy metals and organic pollutants.

Molecular Cloning and Heterologous Expression of Manganese(II)-Oxidizing Enzyme from Acremonium strictum Strain KR21-2

Diverse ascomycete fungi oxidize manganese(II) [Mn(II)] and produce Mn(III, IV) oxides in terrestrial and freshwater environments. Although multicopper oxidase (MCO) is considered to be a key catalyst in mediating Mn(II) oxidation in ascomycetes, the responsible gene and its product have not been identified. In this study, a gene, named mco1, encoding Mn(II)-oxidizing MCO from Acremonium strictum strain KR21-2 was cloned and heterologously expressed in the methylotrophic yeast Pichia pastoris. Based on the phylogenetic relationship, similarity of putative copper-binding motifs, and homology modeling, the gene product Mco1 was assigned to a bilirubin oxidase. Mature Mco1 was predicted to be composed of 565 amino acids with a molecular mass of 64.0 kDa. The recombinant enzyme oxidized Mn(II) to yield spherical Mn oxides, several micrometers in diameter. Zinc(II) ions added to the reaction mixture were incorporated by the Mn oxides at a Zn/Mn molar ratio of 0.36. The results suggested that Mco1 facilitates the growth of the micrometer-sized Mn oxides and affects metal sequestration through Mn(II) oxidation. This is the first report on heterologous expression and identification of the Mn(II) oxidase enzyme in Mn(II)-oxidizing ascomycetes. The cell-free, homogenous catalytic system with recombinant Mco1 could be useful for understanding Mn biomineralization by ascomycetes and the sequestration of metal ions in the environment

Neighboring plants divergently modulate effects of loss-of-function in maize mycorrhizal phosphate uptake on host physiology and root fungal microbiota

Maize, a main crop worldwide, establishes a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi providing nutrients to the roots from soil volumes which are normally not in reach of the non-colonized root. The mycorrhizal phosphate uptake pathway (MPU) spans from extraradical hyphae to root cortex cells housing fungal arbuscules and promotes the supply of phosphate to the mycorrhizal host in exchange for photosynthetic carbon. This symbiotic association with the mycobiont has been shown to affect plant host nutritional status and growth performance. However, whether and how the MPU affects the root microbial community associated with mycorrhizal hosts in association with neighboring plants, remains to be demonstrated. Here the maize germinal Mu transposon insertion mutant pht1;6, defective in mycorrhiza-specific Pi transporter PHT1;6 gene, and wild type B73 (wt) plants were grown in mono- and mixed culture and examined under greenhouse and field conditions. Disruption of the MPU in pht1;6 resulted in strongly diminished growth performance, in reduced P allocation to photosynthetic source leaves, and in imbalances in leaf elemental composition beyond P. At the microbial community level a loss of MPU activity had a minor effect on the root-associated fungal microbiome which was almost fully restricted to AM fungi of the Glomeromycotina. Moreover, while wt grew better in presence of pht1;6, pht1;6 accumulated little biomass irrespective of whether it was grown in mono- or mixed culture and despite of an enhanced fungal colonization of its roots in co-culture with wt. This suggested that a functional MPU is prerequisite to maintain maize growth and that neighboring plants competed for AM fungal Pi in low P soil. Thus future strategies towards improving yield in maize populations on soils with low inputs of P fertilizer could be realized by enhancing MPU at the individual plant level while leaving the root-associated fungal community largely unaffected.

Nutrient availability in tropical caves influences the dynamics of microbial biomass

Few studies have evaluated the trophic level in tropical caves, and none related the microbial biomass dynamics in the immobilization of carbon and nitrogen. Here, four tropical caves of Terra Ronca State Park, Brazil, were studied: Angélica, São Bernardo, Terra Ronca I, and Terra Ronca II caves. Physical, chemical, and microbiological parameters (microbial biomass and respiration) were estimated in the dry and wet seasons. São Bernardo, Terra Ronca I, and Terra Ronca II caves presented higher nitrogen and microbial biomass nitrogen (MBN) values in the wet season than in the dry season. On the other hand, the Angélica cave showed larger amounts of nitrogen and lower MBN values in the dry season. These results indicate that caves can be adjusted in two ecological theories known as "stoichiometric decomposition" and "microbial nitrogen mining"-to the effects of nutrient availability on organic matter decomposition. The caves studied showed different environmental dynamics in relation to organic matter decomposition, which allows them to be considered unique and possess specific characteristics. Microbial biomass dynamics can be an important parameter to evaluate the availability of nutrients and ecological dynamics of the trophic network in subterranean environments.