The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

The Effect of Cysteine on the Removal of Cadmium in Paddy Soil by Combination with Bioremediation and the Response of the Soil Microbial Community

Bioremediation is widely recognized as a promising and efficient approach for the elimination of Cd from contaminated paddy soils. However, the Cd removal efficacy achieved through this method remains unsatisfactory and is accompanied by a marginally higher cost. Cysteine has the potential to improve the bioleaching efficiency of Cd from soils and decrease the use cost since it is green, acidic and has a high Cd affinity. In this study, different combination modes of cysteine and microbial inoculant were designed to analyze their effects on Cd removal and the soil microbial community through the sequence extraction of Cd fraction and high-throughput sequencing. The results demonstrate that the mixture of cysteine and the microbial inoculant was the best mode for increasing the Cd removal efficiency. And a ratio of cysteine to microbial inoculant of 5 mg:2 mL in a 300 mL volume was the most economically efficient matching. The Cd removal rate increased by 7.7-15.1% in comparison with the microbial inoculant treatment. This could be ascribed to the enhanced removal rate of the exchangeable and carbonate-bound Cd, which achieved 94.6% and 96.1%, respectively. After the treatment, the contents of ammonium nitrogen (NH3-N), total phosphorus (TP), available potassium (AK), and available phosphorus (AP) in the paddy soils were increased. The treatment of combinations of cysteine and microbial inoculant had an impact on the soil microbial diversity. The relative abundances of Alicyclobacillus, Metallibacterium, and Bacillus were increased in the paddy soils. The microbial metabolic functions, such as replication and repair and amino acid metabolism, were also increased after treatment, which benefitted the microbial survival and adaptation to the environment. The removal of Cd was attributed to the solubilizing, complexing, and ion-exchanging effects of the cysteine, the intra- and extracellular adsorption, and the production of organic acids of functional microorganisms. Moreover, cysteine, as a carbon, nitrogen, and sulfur source, promoted the growth and metabolism of microorganisms to achieve the effect of the synergistic promotion of microbial Cd removal. Therefore, this study underscored the potential of cysteine to enhance the bioremediation performance in Cd-contaminated paddy soils, offering valuable theoretical and technical insights for this field.

Urban mining of municipal solid waste incineration (MSWI) residues with emphasis on bioleaching technologies: a critical review

Metals are essential in our daily lives and have a finite supply, being simultaneously contaminants of concern. The current carbon emissions and environmental impact of mining are untenable. We need to reclaim metals sustainably from secondary resources, like waste. Biotechnology can be applied in metal recovery from waste streams like fly ashes and bottom ashes of municipal solid waste incineration (MSWI). They represent substantial substance flows, with roughly 46 million tons of MSWI ashes produced annually globally, equivalent in elemental richness to low-grade ores for metal recovery. Next-generation methods for resource recovery, as in particular bioleaching, give the opportunity to recover critical materials and metals, appropriately purified for noble applications, in waste treatment chains inspired by circular economy thinking. In this critical review, we can identify three main lines of discussion: (1) MSWI material characterization and related environmental issues; (2) currently available processes for recycling and metal recovery; and (3) microbially assisted processes for potential recycling and metal recovery. Research trends are chiefly oriented to the potential exploitation of bioprocesses in the industry. Biotechnology for resource recovery shows increasing effectiveness especially downstream the production chains, i.e., in the waste management sector. Therefore, this critical discussion will help assessing the industrial potential of biotechnology for urban mining of municipal, post-combustion waste.

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

The interaction of acidophiles driving community functional responses to the re-inoculated chalcopyrite bioleaching process

Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe³⁺ coupling with S⁰ oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or sulfur oxidizers (SO) were inoculated to chalcopyrite microcosm, then they were crossly re-inoculated again to characterize the interspecific interaction patterns. The results showed that the dominant species in Fe groups were Acidithiobacillus ferrooxidans, while A. thiooxidans predominated in S groups. Introducing FeO resulted in a great disturbance by shifting the community diversity and evenness significantly (p < 0.05). In comparison, the communities intensified by SO maintained the original composition and structures. Microbial networks were constructed positively and modularly. The networks intensified by FeO were less connected and complex with less nodes and edges, but showed faster responses to the re-inoculation disturbance reflected by shorter average path length. Interestingly, the genus Leptospirillum were identified as keystones in S groups, playing critical roles in iron-oxidizing with lots of sulfur oxidizers. The introduced sulfur oxidizers enhanced microbial cooperation, formed robust community with strong bio-dissolution capability, and harbored the highest bioleaching efficiency. These findings improved our understanding about the acidophiles interactions, which drive community functional responses to the re-inoculated bioleaching process.

Microplastic pollution alters forest soil microbiome

The impact of microplastic pollution on terrestrial biota is an emerging research area, and this is particularly so for soil biota. In this study, we addressed this knowledge gap by examining the impact of aged low-density polyethylene (LDPE) and polyester fibres (i.e. polyethylene terephthalate, PET) on a forest microbiome composition and activity. We also measured the corresponding physicochemical changes in the soil. We observed that bacteria community composition diverged in PET and LDPE treated soils from that of the control by day 42. These changes occurred at 0.2% and 0.4% (w/w) of PET and at 3% LDPE. Additionally, soil respiration was 8-fold higher in soil that received 3% LDPE compared to other treatments and control. There were no clear patterns linking these biological changes to physicochemical changes measured. Taken together, we concluded that microplastics aging in the environment may have evolutionary consequences for forest soil microbiome and there is immediate implication for climate change if the observed increase in soil respiration is reproducible in multiple ecosystems.

Genomic Insights into the Aquatic Fusarium spp. QHM and BWC1 and Their Application in Phenol Degradation

Fusarium species are widely distributed in ecosystems with wide pH ranges and play pivotal roles in aquatic communities through xenobiotic degradation. It is necessary to explore genomic insights for the application of Fusarium species. In this study, the aquatic Fusarium strains QHM and BWC1 were isolated from a coal mine and a subterranean river, respectively, cultured under acidic conditions and sequenced genomically. Phylogenetic analysis of the isolates was conducted based on the sequences of internal transcripts and sequences encoding β-microtubulin, translation elongation factors and the second large subunit of the RNA polymerase. Fusarium QHM demonstrates close relationships to the type strains of Fusarium ramigenum and Fusarium napiforme in Fusarium fujikuroi species complex. Fusarium BWC1 is predicted to be Fusarium subglutinans. A total of 479 and 2352 scaffolds, corresponding to 14,814 and 15,295 genes, were obtained for Fusarium spp. QHM and BWC1, respectively. Genomic analyses revealed that they harbored biodegradation pathways for aromatic compounds. Phenol stress experiments indicated that Fusarium spp. QHM and BWC1 exhibited optimal degradation at a density of 300 mg/L to achieve a phenol degradation rate of 39.91-43.65% at pH 3.5-4.0. Fusarium spp. QHM and BWC1 were applied to mock phenol-water, and an average phenol degradation rate of 51.71-65.55% indicated the feasibility of these species. The findings of this study have important implications for Fusarium spp. QHM and BWC1 applied to phenol wastewater in acidic or neutral pH environments.

Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs

The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

Microbiomes in extremely acidic environments: functionalities and interactions that allow survival and growth of prokaryotes at low pH

Extremely acidic environments have global distribution and can have natural or, increasingly, anthropogenic origins. Extreme acidophiles grow optimally at pH 3 or less, have multiple strategies for tolerating stresses that accompany high levels of acidity and are scattered in all three domains of the tree of life. Metagenomic studies have expanded knowledge of the diversity of extreme acidophile communities, their ecological networks and their metabolic potentials, both confirmed and inferred. High resolution compositional and functional profiling of these microbiomes have begun to reveal spatial diversity patterns at global, regional, local, zonal and micro-scales. Future integration of genomic and other meta-omic data will offer new opportunities to utilize acidic microbiomes and to engineer beneficial interactions within them in biotechnologies.

Isotope and microbiome data provide complementary information to identify natural nitrate attenuation processes in groundwater

Natural attenuation processes alleviate the impact of fertilization practices on groundwater resources. Therefore, identifying the occurrence of denitrification has become a requirement for water quality management. Several approaches are useful for this purpose, such as isotopic and microbiological methods, each of them providing distinct but complementary information about denitrification reactions, attenuation rates and their occurrence in the aquifer. In this paper, we investigate the contribution of both approaches to describe denitrification in a consolidated rock aquifer (limestone and marls), with a porosity related to fracture networks located in the northeastern sector of the Osona basin (NE Spain). Isotopic methods indicated the origin of nitrate (fertilization using manure) and that denitrification occurred, reaching a reduction of near 25% of the nitrate mass in groundwater. The studied area could be divided in two zones with distinct agricultural pressures and, consequently, nitrate concentrations in groundwater. Denitrification occurred in both zones and at different levels, indicating that attenuation processes took place all along the whole hydrogeological unit, and that the observed levels could be attributed to a larger flow path or, in a minor extent, to mixing processes that mask the actual denitrification rates. Microbiological data showed a correlation between denitrifier genes and the isotopic composition. However, the groundwater microbiome and the distribution of denitrifying bacteria did not reveal a major influence on the denitrification level observed by isotopic methods. This focuses the interest of microbiological analysis to identify functional genes within the bacteria present in the aquifer. Results indicated that isotopic methods provide information of the overall denitrification ability of the hydrogeological unit, and that genomic data represent the processes actually acting nearby the well. A combination of both approaches is advised to support induced in situ attenuation actions in polluted sites.