Bacterial and fungal diversity in the lorandite (TlAsS2) mine 'Allchar' in the Republic of North Macedonia

Dissolved organic matter mediates the interactions between bacterial community and heavy metal fractionation in contaminated coal mine soils

Heavy metal (HM) contamination in coal mine soils disrupts local bacterial networks, leading to prolonged soil deterioration. Dissolved organic matter (DOM), a crucial soil component, actively modulates both bacterial metabolism and HM mobilization. Despite its significance, our understanding of the complex interactions among bacterial communities, soil chemical and DOM properties, and HM fractionation remains limited. In this study, DOM and bacterial communities from three contaminated mines with varying HM levels and soil properties were analyzed using optical methods and high-throughput sequencing technique. Our results revealed pH and DOM composition, especially the ratio of recalcitrant to labile substances, as key environmental drivers of HM mobilization. Moreover, the composition of bacterial community, particularly the keystone and abundant species, exhibits pronounced site-specificity and HM-dependency. Distinct characteristic genera that are pertinent to HM tolerance/mobility were identified across three mines. Specifically, in Zibo (ZB) soils, Rhodococcus, Acinetobacter, and Pseudomonas significantly regulated the fractionation of Pb, Cu, Se, and Hg possibly via protein-like exudates releasing. In Zaozhuang (ZZ) soils, relationships were recognized between Reyranella, oxides associated Pb, and soil cation exchange capacity. Paenibacillus and Fictibacillus contributed to Se mobilization/tolerance in Linyi (LY) soils. Based on these field findings, two mechanisms were identified for how DOM mediates interactions between HM fractionation and bacterial communities. First, metal-resistant bacteria can produce labile DOM compounds, modifying HM fractionation and reducing metal bioavailability, as observed in ZB soils. Second, humic substances in DOM promoted the development of cohesive bacterial networks featuring metal-resistant keystone bacteria, thereby enhancing community resistance to metal contamination, as evidenced in LY and ZZ soils. Overall, this study provides field evidence elucidating the multilateral interactions among bacterial communities, soil chemical and DOM properties, and HM fractionation, underscoring the significant role of DOM in connecting soil bacterial activity and HM mobilization.

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.

Biochemical transformation and bioremediation of thallium in the environment

Thallium (Tl) is a toxic element associated with minerals, and its redistribution is facilitated by both geological and anthropogenic activities. In the natural environment, the transformation and migration of Tl mediated by (micro)organisms have attracted increasing attention. This review presents an overview of the biochemical transformation of Tl and the bioremediation strategies for Tl contamination. In the environment, Tl exists in various forms and originates from diverse sources. The global distribution characteristics of Tl in various media are summarized here, while its speciation and toxicity mechanism to organisms are elucidated. Interactions between (micro)organisms and Tl are commonly observed in the environment. Microbial response mechanisms to typical Tl exposure are analyzed at both species and gene levels, and the possibility of microorganisms as bio-indicators for monitoring Tl contamination is also highlighted. The processes and mechanisms involved in the microbial and benthic mediated transformation of Tl, as well as its enrichment by plants, are discussed. Additionally, in situ bioremediation strategies for Tl contamination and bio-treatment techniques for Tl-containing wastewater are summarized. Finally, the existing knowledge gaps and future research challenges are emphasized, including Tl distribution characteristics in the atmosphere and ocean, the key molecular mechanisms underlying Tl transformation by organisms, the screening of potential Tl oxidizing microorganisms and hyperaccumulators, as well as the revelation of global biogeochemical cycling pathways of Tl.

Microbial electrochemical Cr(VI) reduction in a soil continuous flow system

Microbial electrochemical technologies represent innovative approaches to contaminated soil and groundwater remediation and provide a flexible framework for removing organic and inorganic contaminants by integrating electrochemical and biological techniques. To simulate in situ microbial electrochemical treatment of groundwater plumes, this study investigates Cr(VI) reduction within a bioelectrochemical continuous flow (BECF) system equipped with soil-buried electrodes, comparing it to abiotic and open-circuit controls. Continuous-flow systems were tested with two chromium-contaminated solutions (20-50 mg Cr(VI)/L). Additional nutrients, buffers, or organic substrates were introduced during the tests in the systems. With an initial Cr(VI) concentration of 20 mg/L, 1.00 mg Cr(VI)/(L day) bioelectrochemical removal rate in the BECF system was observed, corresponding to 99.5% removal within nine days. At the end of the test with 50 mg Cr(VI)/L (156 days), the residual Cr(VI) dissolved concentration was two orders of magnitude lower than that in the open circuit control, achieving 99.9% bioelectrochemical removal in the BECF. Bacteria belonging to the orders Solirubrobacteriales, Gaiellales, Bacillales, Gemmatimonadales, and Propionibacteriales characterized the bacterial communities identified in soil samples; differently, Burkholderiales, Mycobacteriales, Cytophagales, Rhizobiales, and Caulobacterales characterized the planktonic bacterial communities. The complexity of the microbial community structure suggests the involvement of different microorganisms and strategies in the bioelectrochemical removal of chromium. In the absence of organic carbon, microbial electrochemical removal of hexavalent chromium was found to be the most efficient way to remove Cr(VI), and it may represent an innovative and sustainable approach for soil and groundwater remediation. Integr Environ Assess Manag 2024;20:2033-2049. © 2024 The Author(s). Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Diversity of Fungal Community and Its Constraints in the Yifeng Lithium Mines, Eastern China

It is well accepted that biodiversity and ecosystem functions are strongly shaped by environmental conditions; however, relatively little is known about how they depend on the mineralogical assemblage of local environments, especially in mines. This study aims to reveal the diversity characteristics of the fungal community in the surface of granite lithium ores and their weathering products sampled from the Yifeng lithium mines in Jiangxi Province, eastern China. According to the analysis of internal transcribed spacer1 (ITS1) high-throughput sequencing, significant differences in fungal community diversity on the surface of lithium ores and their weathering products have been revealed. The operational taxonomic unit (OTU) of the ore surface and its weathering products ranged from 280 to 624, which may depend on the mineral composition as well as the degree of weathering. The community composition of each sample was significantly different at the phylum level, especially between the weathering products in Ascomycota and Basidiomycota. Although Ascomycota and Basidiomycota were the dominant fungal communities in all samples, each sample has its own distinctive fungi. The trophic modes of the fungi were more complex than that of the bacteria. 10 different fungal trophic modes and 25 dominant functional fungal groups were disclosed, and the saprophytic community was found to be the dominant group. These fungi could accelerate the decomposition of environmental organic matter in the environment by producing hydrolases and oxidases. Chytridiomycota with the function of producing and regulating secondary metabolites were the representative fungi in all samples. Our findings would provide theoretical basis and research clues for understanding the relationship between weathering of granite lithium and fungal communities.

Unraveling assemblage of microbial community dwelling in Dabaoshan As/Pb/Zn mine-impacted area: A typical mountain mining area of South China

Microbial community assemblage includes microorganisms from the three domains including Bacteria, Archaea, and Eukarya (Fungi), which play a crucial role in geochemical cycles of metal(loid)s in mine tailings. Mine tailings harbor vast proportions of metal(loid)s, representing a unique source of co-contamination of metal(loid)s that threaten the environment. The elucidation of the assembly patterns of microbial communities in mining-impacted ecospheres has received little attention. To decipher the microbial community assembly processes, the microbial communities from the five sites of the Dabaoshan mine-impacted area were profiled by the MiSeq sequencing of 16S rRNA (Bacteria and Archaea) genes and internal transcribed spacers (Fungi). Results indicated that the coexistence of 31 bacterial, 10 fungal, and 3 archaeal phyla, were mainly dominated by Mucilaginibacter, Cladophialophora, and Candidatus Nitrosotalea, respectively. The distribution of microorganisms was controlled by deterministic processes. The combination of Cu, Pb, and Sb was the main factor explaining the structure of microbial communities. Functional predicting analysis of bacteria and archaea based on the phylogenetic investigation of communities by reconstruction of unobserved states analyses revealed that the metabolic pathways related to arsenite transporter, arsenate reductase, and FeS cluster were important for metal detoxification. Furthermore, the ecological guilds (pathogens, symbiotrophs, and saprotrophs) of fungal communities explained 44.5 % of functional prediction. In addition, metal-induced oxidative stress may be alleviated by antioxidant enzymes of fungi communities, such as catalase. Such information provides new insights into the microbial assembly rules in co-contaminated sites.

Metagenomic insights into the influence of thallium spill on sediment microbial community

Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.

Mycorrhizal inoculation effects on growth and the mycobiome of poplar on two phytomanaged sites after 7-year-short rotation coppicing

AIMS

Afforestation of trace-element contaminated soils, notably with fast growing trees, has been demonstrated to be an attractive option for bioremediation due to the lower costs and dispersion of contaminants than conventional cleanup methods. Mycorrhizal fungi form symbiotic associations with plants, contributing to their tolerance towards toxic elements and actively participating to the biorestoration processes. The aim of this study was to deepen our understanding on the effects of mycorrhizal inoculation on plant development and fungal community at two trace-element contaminated sites (Pierrelaye and Fresnes-sur-Escaut, France) planted with poplar (Populus trichocarpa x Populus maximowiczii).

METHODS

The 2 sites were divided into 4 replicated field blocks with a final plant density of 2200 tree h^-1. Half of the trees were inoculated with a commercial inoculum made of a mix of mycorrhizal species. The sites presented different physico-chemical characteristics (e.g., texture: sandy soil versus silty-loam soil and organic matter: 5.7% versus 3.4% for Pierrelaye and Fresnes-sur-Escaut, respectively) and various trace element contamination levels.

RESULTS

After 7 years of plantation, inoculation showed a significant positive effect on poplar biomass production at the two sites. Fungal composition study demonstrated a predominance of the phylum Ascomycota at both sites, with a dominance of Geopora Arenicola and Mortierella elongata, and a higher proportion of ectomycorrhizal and endophytic fungi (with the highest values observed in Fresnes-sur-Escaut: 45% and 28% for ECM and endophytic fungi, respectively), well known for their capacity to have positive effects on plant development in stressful conditions. Furthermore, Pierrelaye site showed higher frequency (%) of mycorrhizal tips for ectomycorrhizal fungi (ECM) and higher intensity (%) of mycorrhizal root cortex colonization for arbuscular mycorrhizal fungi (AMF) than Fresnes-sur-Escaut site, which translates in a higher level of diversity.

CONCLUSIONS

Finally, this study demonstrated that this biofertilization approach could be recommended as an appropriate phytomanagement strategy, due to its capacity to significantly improve poplar productivity without any perturbations in soil mycobiomes.

Interactions between bacteria and eukaryotic microorganisms and their response to soil properties and heavy metal exchangeability nearby a coal-fired power plant

Persistent heavy metal (HM) contaminated soil provides special habitat for microorganisms, HM stress and complex abiotic factors bring great uncertainty for the development of bacteria and eukaryotic microbes. Despite numerous studies about HMs' effect on soil microorganisms, the key factors affecting microbial communities in severe HM contaminated soil and their interactions are still not definite. In this study, the effect of HM fractions and soil properties on the interaction between bacterial communities and eukaryotic microorganisms was studied by high-throughput Illumina sequencing and simplified continuous extraction of HM in severe HM contaminated soil. Based on amplification and sequencing of the 18S rRNA gene, this study revealed that protists and algae were the most predominant eukaryotic microorganisms, and the dominant phyla were SAR, Opisthokonta and Archaeplastida in HM seriously polluted soil. These results also showed that exchangeable As was negatively correlated with bacterial Shannon and Simpson indexes, while exchangeable Zn was positively correlated with Shannon and Simpson indexes of eukaryotic microbes. Moreover, the structural equation model illustrated that pH, moisture content, available potassium and phosphorus, and exchangeable Cd, As and Zn were the dominant factors shaping bacterial communities, while total organic carbon and exchangeable Zn made the predominant contributions to variations in eukaryotic microbes. In addition, eukaryotic microbes were intensely affected by the bacterial communities, with a standardized regression weight of 0.53, which exceeded the influence of other abiotic factors. It was suggested that community-level adaptions through cooperative interactions under serious HM stress in soil.

Quantification of smelter-derived contributions to thallium contamination in river sediments: Novel insights from thallium isotope evidence

Thallium(Tl), an extremely toxic metal, is posing great hazards to water safety through anthropogenic activities (e.g., Pb-Zn smelter) and natural weathering in riverine systems. However, the relative contribution from each source remains obscure. This study investigated enrichment pattern of Tl and its isotopic compositions in sediment profiles from a recipient river, which was continuously collecting various Tl-bearing wastes discharged from a large Pb-Zn smelter in South China. Results show that high Tl content and ultra-fine particles (~ μm) of Tl-bearing mineral assemblages, probably derived from Pb-Zn smelting wastes, were ubiquitously observed in both of the depth profiles. In addition, the sediments generally yielded intermediate ε²⁰⁵Tl values of -3.76 to 1.01, which resembled those found in smelting wastes. A ternary mixing model was for the first time proposed for quantifying relative Tl contributions from each possible source. The calculation suggests that the smelter wastes are the major contributors, contributing approximately 80% of Tl contamination. All these results indicate that Tl isotope can be used as powerful proxies for quantitatively identifying potential different contributors in the environment. This is of critical importance to further implementation of pollution control and remediation strategy for the riverine systems in the near future.

Genome Sequence of Litorilinea aerophila, an Icelandic Intertidal Hot Springs Bacterium

The hot springs bacterium Litorilinea aerophila PRI-4131^T (= ATCC BAA-2444^T) was found in Isafjardardjup, in northwest Iceland. In this paper, we present a draft genome sequence for the type strain, with a total predicted genome length of 6,043,010 bp, 4,608 protein-coding sequences, 54 RNAs, 9 CRISPR arrays, and a G+C content of 64.61%.