Prokaryotic diversity in stream sediments affected by acid mine drainage

Assembly patterns and key taxa of bacterial communities in the rhizosphere soil of moso bamboo (Phyllostachys pubescens) under different Cd and Pb pollution

Moso bamboo is excellent candidate for cadmium (Cd)/lead (Pb) phytoremediation, while rhizosphere microbiome has significant impact on phytoremediation efficiency of host plant. However, little is known about the rhizosphere bacterial communities of moso bamboo in Cd/Pb contaminated soils. Therefore, this study investigated the assembly patterns and key taxa of rhizosphere bacterial communities of moso bamboo in Cd/Pb polluted and unpolluted soils, by field sampling, chemical analysis, and 16S rRNA gene sequencing. The results indicated α-diversity between Cd/Pb polluted and unpolluted soils showed a similar pattern (p > 0.05), while β-diversity was significantly different (p < 0.05). The relative abundance analysis indicated α-proteobacteria (37%) and actinobacteria (31%) were dominant in Cd/Pb polluted soils, while γ-proteobacteria (40%) and α-proteobacteria (22%) were dominant in unpolluted soils. Co-occurrence network analysis indicated microbial networks were less complex and more negative in polluted soils than in unpolluted soils. Mantel analysis indicated soil available phosphorus, organic matter, and available Pb were the most important environmental factors affecting microbial community structure. Correlation analysis showed 11 bacterial genera were significantly positively related to Cd/Pb. Overall, this study identified the bacterial community composition of bamboo rhizosphere in responding to Cd/Pb contamination and provides a theoretical basis for microbe-assistant phytoremediation in the future.

Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil)

Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Evaluation of nutrient characteristics and bacterial community in agricultural soil groups for sustainable land management

The soil bacterial community is critical for understanding biological processes in soils and is used for agricultural soil management. The understanding of microorganisms and ecology in different soil groups classified based on soil properties (e.g., minerals, soil texture, location, nitrogen, phosphorus, organic carbon and pH, among others), is limited. To suggest soil management strategies using bacterial data, we classified soils into four groups based on physical-chemical characteristics and elucidated their relationships with soil nutrient characteristics and the bacterial community in agricultural fields in Saraburi Province, Thailand. Results show that soil groups with high bacterial diversity had positive correlations with total Kjeldahl nitrogen and available phosphorus but were negatively affected by total organic carbon and pH levels. Dominant bacterial genera included Lactobacillus, Phascolarctobacterium, Prevotella, Clostridium, Gaiellales and Blautia. Significant key biomarkers were found (p < 0.05). Nutrient-rich soil groups (high available P, acidic pH) were found with genus Agromyces, while low nutrient soil groups (low available P, basic pH) were found with Hydrogenispora, Ignavibacterium and Bauldia. Based on co-occurrence networks, organic degrading bacteria functioned with other bacteria at high degrees of interconnections, suggesting organic amendment, biostimulation and biodegradation using nutrient-rich organic substrates could be used for agricultural soil improvements.

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3)

The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO₄²⁻, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg²⁺ and SO₄²⁻ were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg²⁺ and SO₄²⁻, Ca²⁺, temperature, and Fe²⁺, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg²⁺ and SO₄²⁻ concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.

Microbial Community Diversity Dynamics in Acid Mine Drainage and Acid Mine Drainage-Polluted Soils: Implication on Mining Water Irrigation Agricultural Sustainability

Environmental degradation related to mining-generated acid mine drainage (AMD) is a major global concern, contaminating surface and groundwater sources, including agricultural land. In the last two decades, many developing countries are expanding agricultural productivity in mine-impacted soils to meet food demand for their rapidly growing population. Further, the practice of AMD water (treated or untreated) irrigated agriculture is on the increase, particularly in water-stressed nations around the world. For sustainable agricultural production systems, optimal microbial diversity, and functioning is critical for soil health and plant productivity. Thus, this review presents up-to-date knowledge on the microbial structure and functional dynamics of AMD habitats and AMD-impacted agricultural soils. The long-term effects of AMD water such as soil acidification, heavy metals (HM), iron and sulfate pollution, greatly reduces microbial biomass, richness, and diversity, impairing soil health plant growth and productivity, and impacts food safety negatively. Despite these drawbacks, AMD-impacted habitats are unique ecological niches for novel acidophilic, HM, and sulfate-adapted microbial phylotypes that might be beneficial to optimal plant growth and productivity and bioremediation of polluted agricultural soils. This review has also highlighted the impact active and passive treatment technologies on AMD microbial diversity, further extending the discussion on the interrelated microbial diversity, and beneficial functions such as metal bioremediation, acidity neutralization, symbiotic rhizomicrobiome assembly, and plant growth promotion, sulfates/iron reduction, and biogeochemical N and C recycling under AMD-impacted environment. The significance of sulfur-reducing bacteria (SRB), iron-oxidizing bacteria (FeOB), and plant growth promoting rhizobacteria (PGPRs) as key players in many passive and active systems dedicated to bioremediation and microbe-assisted phytoremediation is also elucidated and discussed. Finally, new perspectives on the need for future studies, integrating meta-omics and process engineering on AMD-impacted microbiomes, key to designing and optimizing of robust active and passive bioremediation of AMD-water before application to agricultural production is proposed.

Influence of Extremophiles on the Generation of Acid Mine Drainage at the Abandoned Pan de Azúcar Mine (Argentina)

The risk of generation of acid drainages in the tailings of the Pan de Azúcar mine that closed its activities more than three decades ago, was evaluated through biooxidation studies using iron- and sulfur-oxidizing extremophilic leaching consortia. Most of tailings showed a high potential for generating acid drainage, in agreement with the results from net acid generation (NAG) assays. In addition, molecular analysis of the microbial consortia obtained by enrichment of the samples, demonstrated that native leaching microorganisms are ubiquitous in the area and they seemed to be more efficient in the biooxidation of the tailings than the collection microorganisms. The acid drainages detected at the site and those formed by oxidation of the tailings, produced a significant ecotoxicological effect demonstrated by a bioassay. These drainages, even at high dilutions, could seriously affect a nearby Ramsar site (Laguna de Pozuelos) that is connected to the Pan de Azúcar mine through a hydrological route (Cincel River).