Composition and functional profiles of microbial communities in two geochemically and mineralogically different caves

Identification of polychlorinated biphenyls (PCBs) and PCB metabolites associated with changes in the gut microbiome of female mice exposed to an environmental PCB mixture

Polychlorinated biphenyls (PCBs) are neurotoxic hazardous materials that may cause toxicity via the gut-liver-brain axis. This study investigated PCB × microbiome interactions in adult female mice exposed orally to an environmental PCB mixture. Female mice (6-week-old) were exposed daily for 7 weeks to peanut butter containing 0, 0.1, 1, or 6 mg/kg/day of PCBs. Twenty hours after the final exposure, the cecal content was collected to characterize the microbiome composition and predicted function. PCB and its metabolites in feces were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS), while cecal content was assessed with liquid chromatography-high resolution mass spectrometry (LC-HRMS). PCB exposure influenced the abundance of microbial taxa and predicted functions within the cecal content. Complex PCB and metabolite mixtures were detected in the gastrointestinal tract. Network analysis revealed associations between specific parent PCBs and metabolites with changes in the abundance of bacteria in the gastrointestinal tract. These findings demonstrate that individual PCBs and their metabolites significantly influence the abundance of specific bacteria in the gastrointestinal tract following oral PCB exposure. These findings inform further research targeting the microbiome to attenuate the adverse health outcomes of PCB exposure.

Characterization and Enzymatic Potential of Bacteria and Fungi From Mwakirunge Dumpsite, Kenya

Accumulation of solid waste is a major global challenge. The conventional waste disposal methods are often ineffective in mitigating solid waste pollution, highlighting the need for other sustainable alternatives. This study is aimed at isolating and identifying potential waste-degrading microorganisms from Mwakirunge dumpsite in Mombasa, Kenya. A total of 16 soil samples were collected using a randomized block design. The samples were inoculated in enriched basal media containing mixed municipal solid waste and incubated at 37°C for 21 days. Microbial identification was conducted using standard morphological, biochemical, and molecular approaches. DNA was extracted using organic isolation methods, and PCR amplification of the 16S rRNA gene for bacteria and the ITS gene for fungi was performed. Phylogenetic analysis grouped bacterial isolates into phylum Bacillota (Firmicutes), Pseudomonadota (Proteobacteria), and Actinomycetota (Actinobacteria) that included members of the genera bacilli, Pseudomonas, brevibacilli, Microbacterium, Ochrobactrum, Paenibacillus, Staphylococcus, Isoptericola, and Streptomyces. Fungal isolates belonged to the genus Aspergillus within the phylum Ascomycota. Three bacterial isolates B4S2 b (MZ571886), B3S1 (MZ571907), and B3S4 B (MZ571915) and one fungal isolate B2S2 a1 (MZ569413) had low sequence similarities with their closely known taxonomic relatives. The ability of the isolates to produce lipase, esterase, cellulase, amylase, and gelatinase enzymes was tested using the agar diffusion method. The results showed a significant level of enzyme production (p < 0.05). Bacillus cereus (MZ571899) exhibited the highest esterase activity; Streptomyces thermocarboxydus (MZ571882) exhibited the highest lipase activity, Bacillus subtilis (MZ571887) exhibited the highest amylase activity, and Bacillus licheniformis (MZ571888) exhibited the highest cellulase activity, while Pseudomonas stutzeri (MZ571900) exhibited the highest gelatinase activity. We recommend further studies to characterize the isolates with low sequence percentage similarities to establish their true identities. In addition, further enzymatic studies are required to quantify, characterize, and purify these enzymes for industrial applications.

Exploring bioactive compound origins: Profiling gene cluster signatures related to biosynthesis in microbiomes of Sof Umer Cave, Ethiopia

Sof Umer Cave is an unexplored extreme environment that hosts novel microbes and potential genetic resources. Microbiomes from caves have been genetically adapted to produce various bioactive metabolites, allowing them to survive and tolerate harsh conditions. However, the biosynthesis-related gene cluster signatures in the microbiomes of Sof Umer Cave have not been explored. Therefore, high-throughput shotgun sequencing was used to explore biosynthesis-related gene clusters (BGCs) in the microbiomes of Sof Umer Cave. The GeneAll DNA Soil Mini Kit was used to extract high-molecular-weight DNA from homogenized samples, and the purified DNA was sequenced using a NovaSeq PE150. According to the Micro-RN database, the most common microbial genera in Sof Umer Cave are Protobacteria, Actinobacteria, Verrucomicrobiota, and Cyanobacteria. The biosynthesis-related gene clusters were annotated and classified, and the BGCs were predicted using antiSMASH and NAPDOS1. A total of 460 putative regions of BGCs encoding a wide range of secondary metabolites were identified, including RiPP (47.82%), terpene (19.57%), NRPS (13.04%), hybrid (2.18%), and other newly annotated (10.87%) compounds. Additionally, the NAPDOS pipeline identified a calcium-dependent antibiotic gene cluster from Streptomyces coelicolor, an actinomycin gene cluster from Streptomyces chrysomallus, and a bleomycin gene cluster from Streptomyces verticillus. These findings highlight the untapped biosynthetic potential of the Sof Umer Cave microbiome, as well as its potential for the discovery of natural products.

Isolation and characterization of cadmium-resistant Bacillus cereus strains from Cd-contaminated mining areas for potential bioremediation applications

Cadmium (Cd) is a naturally occurring heavy metal found in the soil. However, its concentrations can be substantially increased by anthropogenic activities, presenting considerable environmental challenges. One effective remediation strategy is soil bioremediation, which employs indigenous bacteria to mitigate contamination. This study aimed to identify Cd-resistant bacteria and assess their potential for bioremediating Cd-contaminated soil. Two Cd-resistant bacterial strains, designated C9 and C27, were isolated from Cd-contaminated soil at concentrations ranging from 100 to 500 mg/L. Morphological analysis and 16S rDNA sequencing identified both strains as Bacillus cereus. The strains' capacity to adsorb and remove Cd from solutions was assessed, as well as their resistance to other heavy metals, including Zinc (Zn) and Thallium (Tl). Optimal Cd adsorption was observed at 36 h for strain C9 and at 48 h for strain C27, with maximum removal rates achieved at a Cd concentration of 70 μM. Both strains demonstrated substantial resistance to heavy metals in the order Zn > Cd > Tl on solid media. Additionally, they exhibited strong salt tolerance, starch hydrolysis, citrate utilization, and ammonia production capabilities. Notably, both strains produced significantly higher levels of siderophores compared to the model bacterium Bacillus subtilis 3,610, with strain C9 exhibiting superior siderophore production. This enhanced siderophore activity is hypothesized to contribute to Cd resistance. Collectively, these findings suggest that strains C9 and C27 have significant potential for the bioremediation of Cd-contaminated environments. Future research will focus on elucidating the molecular mechanisms underlying heavy-metal resistance and optimizing their application in large-scale bioremediation strategies.

Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives

Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.

Eight novel cave fungi in Thailand's Satun Geopark

Karst caves are unique oligotrophic ecosystems characterised by the scarcity of organic litter, darkness, low to moderate temperatures, and high humidity, supporting diverse fungal communities. Despite their importance, little is known about the fungi in karst caves in Thailand. In 2019, we explored the culturable mycobiota associated with three selected types of substrates (air, soil/sediment and organic litter samples) from two karst caves, the Le Stegodon and Phu Pha Phet Caves, in the Satun UNESCO Global Geopark in southern Thailand. Based on morphological characters and multilocus phylogenetic analyses, eight new species (Actinomortierella caverna, Hypoxylon phuphaphetense, Leptobacillium latisporum, Malbranchea phuphaphetensis, Scedosporium satunense, Sesquicillium cavernum, Thelonectria satunensis and Umbelopsis satunensis) were described, illustrated, and compared to closely related species. These new fungal taxa form independent lineages distinct from other previously described species and classified into eight different families across six orders and two phyla (Ascomycota and Mucoromycota). This paper provides additional evidence that the karst caves located within the Satun UNESCO Global Geopark, situated in the southern region of Thailand, harbour a diverse range of newly discovered species. Citation: Preedanon S, Suetrong S, Srihom C, Somrithipol S, Kobmoo N, Saengkaewsuk S, Srikitikulchai P, Klaysuban A, Nuankaew S, Chuaseeharonnachai C, Chainuwong B, Muangsong C, Zhang ZF, Cai L, Boonyuen N (2023). Eight novel cave fungi in Thailand's Satun Geopark. Fungal Systematics and Evolution 12: 1-30. doi: 10.3114/fuse.2023.12.01.

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

Introduction

Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).

Materials and Methods

To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.

Results and Discussion

Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.

Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis

Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.

Calcium carbonate precipitation by cave bacteria isolated from Kashmir Cave, Khyber Pakhtunkhwa, Pakistan

The participation of numerous physicochemical and biological functions maintains the evolution and expansion of the remarkable nature. Due to its vast applicability in several engineering disciplines, naturally occurring bio-mineralization or microbially induced calcium carbonate (MICP) precipitation is attracting more interest. Cave bacteria contribute to the precipitation of calcium carbonate (CaCO₃ ). In the present study, soil sediments were collected from Kashmir cave, KPK, Pakistan, and plated on B4 specific nutrients limited medium for bacterial isolation and the viable bacterial count was calculated. Three bacterial strains named GSN-11, TFSN-14, and TFSN-15 were capable of precipitating CaCO₃ . These bacterial isolates were identified through 16S rRNA gene sequencing and strain GSN-11 was identified as Bacillus toyonensis, TFSN-14 as Paracoccus limosus and TFSN-15 as Brevundimonas diminuta. Enhanced CaCO₃ precipitation potential of these bacteria strains was observed at 25°C and pH 5. The precipitated CaCO₃ was confirmed by scanning electron microscopy, X-ray powder diffraction, and Fourier transform infra-red spectroscopy. The findings showed that the precipitates were dominated by calcite, aragonite, and nanosize vaterite. Current research suggests that precipitation of CaCO₃ by proteolytic cave bacteria is widespread in Kashmir cave and these bacterial communities can actively contribute to the formation of CaCO₃ by enhancing the pH of the microenvironment.