Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp. nov. dominates South African commercial biooxidation tanks that operate at 40 degrees C

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

Nutrient optimization in bioleaching: are we overdosing?

The general trend in biomining (i.e., bioleaching and biooxidation) is the use of media with high concentrations of the nutrients (nitrogen as ammonium, phosphorous as phosphate, and K), which are considered to be essential for microbial growth. The depletion of any of the nutrients would affect negatively the bioleaching (and biooxidation) capacity of the microorganisms, so the formulation of the different media ensures that there is a surplus of nutrients. However, some of these nutrients (e.g., phosphate, K) may be already present in the ore and are made available to the microorganisms when the ore is exposed to the low-pH media used during bioleaching. The effect of phosphate addition (109 mg/L) and depletion on the bioleaching of low-grade sulfidic ore alongside the determination of ammonium (i.e., 25 mg/L, 50 mg/L, 109 mg/L, 409 mg/L, and 874 g/L) requirements were studied. The results of the experiments presented showed that the addition of phosphate did not have any effect on the bioleaching of the low-grade sulfidic ore while the addition of ammonium was necessary to obtain higher redox potentials (>650 mV vs. Ag/AgCl) and higher metal (Co, Cu, Ni, and Zn) dissolutions. Temperature was the factor that shaped the microbial communities, at 30°C, the microbial community at the end of all the experiments was dominated by Acidithiobacillus sp. as well as at 42°C, except when nutrients were not added and Sulfobacillus sp. was the dominant microorganism. At 55°C, DNA recovery was unsuccessful, and at 60°C, the microbial communities were dominated by Sulfolobus sp. In conclusion, the amount of nutrients in bioleaching could be reduced significantly to achieve the redox potentials and metal dissolution desired in bioleaching without affecting the microbial communities and bioleaching efficiencies.

Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature

In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite-arsenopyrite concentrate at temperatures of 40-50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov.

Resource Recycling, Recovery, and Xenobiotic Remediation from E-wastes Through Biofilm Technology: A Review

Around 50 million tonnes of electronic waste has been generated globally per year, causing an environmental hazard and negative effects on human health, such as infertility and thyroid disorders in adults, endocrine and neurological damage in both animals and humans, and impaired mental and physical development in children. Out of that, only 15% is recycled each year and the remaining is disposed of in a landfill, illegally traded or burned, and treated in a sub-standard way. The processes of recycling are challenged by the presence of brominated flame retardants. The different recycling technologies such as the chemical and mechanical methods have been well studied, while the most promising approach is the biological method. The process of utilizing microbes to decontaminate and degrade a wide range of pollutants into harmless products is known as bioremediation and it is an eco-friendly, cost-effective, and sustainable method. The bioremediation process is significantly aided by biofilm communities attached to electronic waste because they promote substrate bioavailability, metabolite transfer, and cell viability, all of which accelerate bioleaching and biodegradation. Microbes existing in biofilm mode relatable to free-floating planktonic cells are advantageous of bioremediation due to their tolerant ability to environmental stress and pollutants through diverse catabolic pathways. This article discusses the harmful effects of electronic waste and its management using biological strategies especially biofilm-forming communities for resource recovery.

A classical modelling of abandoned mine tailings' bioleaching by an autochthonous microbial culture

The aim of this study was to study and model the bioleaching of abandoned mine tailings at different pulp densities 1-20% w/v by using an autochthonous mesophilic microbial culture. Because of the importance of the ferrous-iron oxidation as sub-process on the bioleaching of sulphide mineral ores, the ferrous-iron oxidation process by the autochthonous microbial culture was studied at different ferrous-iron concentrations. A mathematical model fitted to the experimental results and the main kinetic and stoichiometric parameters were determined, being the most relevant the maximum ferrous-iron oxidation rate 5.1 (mmol Fe²⁺/mmol C·h) and the biomass yield, 0.01 mmol C/mmol Fe²⁺, values very similar to that of mixed cultured dominated by Leptospirillum strains. This autochthonous culture was used in the bioleaching experiment carried out at different pulp densities, obtaining a maximum metal recovery in the tests carried out at 1% w/v, recovering a 90% of Cd, 60% of Zn, 30% of Cu, 25% Fe and 6% of Pb. Finally, the different leaching mechanisms were modelled by using the pyrite as ore model obtaining a bioleaching rate of 0.316 mmol Fe²⁺/(L·h) for the direct mechanisms and a bioleaching rate for the indirect and cooperative leaching mechanisms of 0.055 Fe²⁺/(L·h).

Bulk flotation followed by selective leaching with biogenic ferric iron is a promising solution for eco-friendly processing of complex sulfidic ores

The development of cost-effective environmentally friendly technologies is of current importance for the intensification of metal recovery. Here, we propose a new direction in the use of a two-step process for the treatment of complex sulfidic ores. In the first step, ore flotation allows the obtainment of a bulk copper-zinc concentrate and low-toxicity waste. In the second step, zinc is selectively extracted by chemical leaching with a biogenic ferric iron solution, while copper is accumulated in the leach residue. Importantly, the efficiency of this step depends on the chemical and mineralogical composition of polymetallic concentrates. Four samples of the copper-zinc sulfide concentrate with various contents of copper and zinc have been leached in multiple cycles at 80 °C, 10% of pulp density, and pH 1.3-1.5. The leaching of the concentrate that contained 14.7% of copper and 5.0% of zinc for three leaching cycles (total duration, 5.75 h) allowed the obtainment of a leach residue containing 15.3 and 0.14% of copper and zinc, respectively. At the same time, the leaching of another concentrate that contained 19.2% of copper and 2.64% of zinc after one leaching cycle (total duration, 0.67 h) led to copper and zinc contents of 19.1 and 0.72%, respectively, in the leach residue. Therefore, the treatment of only two concentrates allowed the obtainment of high-grade copper concentrates containing low amounts of zinc. Ferric iron, the oxidant of sulfide minerals, was fully regenerated in leachate within 30-35 h at 40 °C using an acidophilic microbial community dominated by Leptospirillum ferriphilum, Sulfobacillus spp., and Ferroplasma acidiphilum. The loss of copper and zinc in solid waste of the bioregeneration did not exceed 1.0% and 1.8%, respectively. The proposed flowsheet of bulk concentrate processing has several important advantages over conventional technologies, including short duration of leaching, formation of low-toxicity solid waste, and pyrometallurgical processing of only high-grade copper concentrates. This approach can be a promising solution for the efficient processing of polymetallic bulk concentrates.

Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation

Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.

Carbon Sources as a Factor Determining the Activity of Microbial Oxidation of Sulfide Concentrate at Elevated Temperature

The goal of the present work was to evaluate the possibility of improving the efficiency of the stirred tank reactor biooxidation of sulfide gold-bearing concentrate by means of addition of carbon sources required for the constructive metabolism of microorganisms. Biooxidation experiments were performed on gold-bearing pyrite-arsenopyrite concentrate in continuous mode at 45 °C to determine the influence of additional carbon sources (carbon dioxide and molasses) on sulfide mineral oxidation. The use of CO2 allowed increasing the efficiency of the biooxidation and the extents of sulfide sulfur (Ss) oxidation and gold recovery were 79% and 84%, respectively. Biooxidation in a control experiment (without additional carbon sources) and when using molasses allowed achieving 39% and 66% oxidation of Ss as well as 73% and 81% of gold recovery. Analysis of the microbial populations formed in biooxidation reactors using NGS methods demonstrated that CO2 application led to an increase in the relative abundance of the genus Sulfobacillus. Thus, it was determined that application of additional carbon source makes it possible to manage the biooxidation process, affecting both sulfide mineral oxidation and microbial population composition.

Effect of Carbon Sources on Pyrite-Arsenopyrite Concentrate Bio-oxidation and Growth of Microbial Population in Stirred Tank Reactors

Tank bio-oxidation is a biohydrometallurgical technology widely used for metal recovery from sulfide concentrates. Since carbon availability is one of the key factors affecting microbial communities, it may also determine the rate of sulfide concentrate bio-oxidation. The goal of the present work was to evaluate the effect of carbon sources on the bio-oxidation of the concentrate containing 56% pyrite and 14% arsenopyrite at different temperatures (40 and 50 °C) in stirred tank reactors. CO2 was supplied into the pulp of the first reactor (about 0.01 L/min) and 0.02% (w/v) molasses was added to the pulp of the second one, and no additional carbon sources were used in the control tests. At 40 °C, 77% of pyrite and 98% of arsenopyrite were oxidized in the first reactor, in the second one, 73% of pyrite and 98% of arsenopyrite were oxidized, while in the control reactor, 27% pyrite and 93% arsenopyrite were oxidized. At 50 °C, in the first reactor, 94% of pyrite and 99% of arsenopyrite were oxidized, in the second one, 21% of pyrite and 94% of arsenopyrite were oxidized, while in the control reactor, 10% pyrite and 92% arsenopyrite were oxidized. The analysis of the microbial populations in the reactors revealed differences in the total number of microorganisms and their species composition. Thus, it was shown that the use of various carbon sources made it possible to increase the intensity of the concentrate bio-oxidation, since it affected microbial populations performing the process.

Phylogenetically divergent bacteria consortium from neutral activated sludge showed heightened potential on bioleaching spent lithium-ion batteries

Recycling of spent lithium-ion batteries (LIBs) has become a global issue because of the potential environment risks raised by spent LIBs as well as high valuable metal content remaining in them. Although bioleaching is an environmentally friendly method to recover metals from spent LIBs, the commonly utilized bioleaching bacterial consortia or strains enriched/isolated from acidic environments cannot be applied at large scales owing to their long leaching cycle and poor tolerance to organic compounds. Here, two bioleaching consortia were enriched in 60 days from neutral activated sludge and were identified phylogenetically divergent from the documented bioleaching bacteria. The results showed that the novel consortia shortened the leaching cycle almost by half when compared to the previous reported consortia or strains, of which one consortium dominated by Acidithiobacillus ferrooxidans displayed high bioleaching efficiency on LiMn₂O₄, as 69.46% lithium (Li) and 67.60% manganese (Mn) were leached out in seven days. This consortium was further domesticated using cathodic materials for 100 days and proved consisted of three mixotrophs and two chemoautotrophs, three of which were novel species from the genera Sulfobacillus and Leptospirillum. More genes coding for proteins that utilize organic compounds were annotated in the metagenomic assembled genomes (MAGs) than previously reported. A mutualistic relationship between mixotrophs and chemoautotrophs was suggested to help the consortium surviving under either organic- rich or shortage environments. The results discovered that novel bioleaching bacteria with shorter leaching cycle and higher tolerance to organics could be enriched from non-acidic environments, which showed high potential for the metal recovering from spent LIBs or other organic-rich environments.

Bioleaching of E-Waste: Influence of Printed Circuit Boards on the Activity of Acidophilic Iron-Oxidizing Bacteria

Bioleaching is a promising strategy to recover valuable metals from spent printed circuit boards (PCBs). The performance of the process is catalyzed by microorganisms, which the toxic effect of PCBs can inhibit. This study aimed to investigate the capacity of an acidophilic iron-oxidizing culture, mainly composed of Leptospirillum ferriphilum, to oxidize iron in PCB-enriched environments. The culture pre-adapted to 1% (w/v) PCB content successfully thrived in leachates with the equivalent of 6% of PCBs, containing 8.5 g L^–1 Cu, 8 g L^–1 Fe, 1 g L^–1 Zn, 92 mg L^–1 Ni, 12.6 mg L^–1 Pb, and 4.4 mg L^–1 Co, among other metals. However, the inhibiting effect of PCBs limited the microbial activity by delaying the onset of the exponential iron oxidation. Successive subcultures boosted the activity of the culture by reducing this delay by up to 2.6 times under batch conditions. Subcultures also favored the rapid establishment of high microbial activity in continuous mode.

The biology of thermoacidophilic archaea from the order Sulfolobales

Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.

Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli

Bioleaching of metal sulfide ores involves acidophilic microbes that catalyze the chemical dissolution of the metal sulfide bond that is enhanced by attached and planktonic cell mediated oxidation of iron(II)-ions and inorganic sulfur compounds. Leptospirillum spp. often predominate in sulfide mineral-containing environments, including bioheaps for copper recovery from chalcopyrite, as they are effective primary mineral colonizers and oxidize iron(II)-ions efficiently. In this study, we demonstrated a functional diffusible signal factor interspecies quorum sensing signaling mechanism in Leptospirillum ferriphilum and Leptospirillum ferrooxidans that produces (Z)-11-methyl-2-dodecenoic acid when grown with pyrite as energy source. In addition, pure diffusible signal factor and extracts from supernatants of pyrite grown Leptospirillum spp. inhibited biological iron oxidation in various species, and that pyrite grown Leptospirillum cells were less affected than iron grown cells to self inhibition. Finally, transcriptional analyses for the inhibition of iron-grown L. ferriphilum cells due to diffusible signal factor was compared with the response to exposure of cells to N- acyl-homoserine-lactone type quorum sensing signal compounds. The data suggested that Leptospirillum spp. diffusible signal factor production is a strategy for niche protection and defense against other microbes and it is proposed that this may be exploited to inhibit unwanted acidophile species.

Homogeneous Cytochrome 579 Is an Octamer That Reacts Too Slowly With Soluble Iron to Be the Initial Iron Oxidase in the Respiratory Chain of Leptospirillum ferriphilum

The exact role that cytochrome 579 plays in the aerobic iron respiratory chain of Leptospirillum ferriphilum is unclear. This paper presents genomic, structural, and kinetic data on the cytochrome 579 purified from cell-free extracts of L. ferriphilum cultured on soluble iron. Electrospray mass spectrometry of electrophoretically homogeneous cytochrome 579 yielded two principal peaks at 16,015 and 16,141 Daltons. N-terminal amino acid sequencing of the purified protein yielded data that were used to determine the following: there are seven homologs of cytochrome 579; each homolog possesses the CXXCH heme-binding motif found in c-type cytochromes; each of the seven sequenced strains of L. ferriphilum expresses only two of the seven homologs of the cytochrome; and each homolog contains an N-terminal signal peptide that directs the mature protein to an extra-cytoplasmic location. Static light scattering and macroion mobility measurements on native cytochrome 579 yielded masses of 125 and 135 kDaltons, respectively. The reduced alkaline pyridine hemochromogen spectrum of the purified cytochrome had an alpha absorbance maximum at 567 nm, a property not exhibited by any known heme group. The iron-dependent reduction and oxidation of the octameric cytochrome exhibited positively cooperative kinetic behavior with apparent Hill coefficients of 5.0 and 3.7, respectively, when the purified protein was mixed with mM concentrations of soluble iron. Consequently, the extrapolated rates of reduction at sub-mM iron concentrations were far too slow for cytochrome 579 to be the initial iron oxidase in the aerobic respiratory chain of L. ferriphilum. Rather, these observations support the hypothesis that the acid-stable cytochrome 579 is a periplasmic conduit of electrons from initial iron oxidation in the outer membrane of this Gram-negative bacterium to a terminal oxidase in the plasma membrane.

RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite

Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.

Acid mine drainage at the Bahia Gold Belt (Brazil): microbial isolation and characterization

Acid mine drainage occurs due to the chemical and microbiological oxidation of sulfide minerals and can be a source of potentially toxic elements contamination of groundwater and surface water. The objective of this study was to identify microorganisms involved in sulfide oxidation in the tailings of a Bahia Gold Belt mine (Brazil). Samples of solids and water were collected at the mine tailings dam and characterized. The microorganisms were isolated after enrichment and subsequent purification. The major constituents of the tailings are Si, Fe, Al, S, and K. The sulfur content of the tailings is 0.98%. The major phases are quartz, muscovite, and clinochlore. Gravity concentrates of the tailings show several particles of pyrite, that is, the major sulfide phase. Molecular analysis identified the microorganisms isolated in the acid mine drainage process in this region. Five bacterium species were found: Acidithiobacillus spp., Acidithiobacillus ferrooxidans, Acidiphilium spp., Leptospirillum type II, and Sulfobacillus spp. No organisms of the archaea or eukaryote domains were found. The isolate was used in the bioleaching of copper sulfide ore, and the copper extraction was about 60% in 60 days for ground ore.

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia

Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30 °C and 48 °C, but not 42 °C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48 °C endogenous consortium (80%), then the 42 °C exogenous BRGM-KCC consortium (71%), and finally the 30 °C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48 °C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.

Systems biology of acidophile biofilms for efficient metal extraction

Society’s demand for metals is ever increasing while stocks of high-grade minerals are being depleted. Biomining, for example of chalcopyrite for copper recovery, is a more sustainable biotechnological process that exploits the capacity of acidophilic microbes to catalyze solid metal sulfide dissolution to soluble metal sulfates. A key early stage in biomining is cell attachment and biofilm formation on the mineral surface that results in elevated mineral oxidation rates. Industrial biomining of chalcopyrite is typically carried out in large scale heaps that suffer from the downsides of slow and poor metal recoveries. In an effort to mitigate these drawbacks, this study investigated planktonic and biofilm cells of acidophilic (optimal growth pH < 3) biomining bacteria. RNA and proteins were extracted, and high throughput “omics” performed from a total of 80 biomining experiments. In addition, micrographs of biofilm formation on the chalcopyrite mineral surface over time were generated from eight separate experiments. The dataset generated in this project will be of great use to microbiologists, biotechnologists, and industrial researchers.

Measurement(s)	biofilm formation • Proteome • protein expression data • RNA • transcriptome
Technology Type(s)	fluorescence microscopy • mass spectrometry • RNA sequencing
Sample Characteristic - Organism	Leptospirillum ferriphilum • Sulfobacillus thermosulfidooxidans • Acidithiobacillus caldus
Sample Characteristic - Environment	mine

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12173637

Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities' profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

Evolution of Predicted Acid Resistance Mechanisms in the Extremely Acidophilic Leptospirillum Genus

Organisms that thrive in extremely acidic environments (≤pH 3.5) are of widespread importance in industrial applications, environmental issues, and evolutionary studies. Leptospirillum spp. constitute the only extremely acidophilic microbes in the phylogenetically deep-rooted bacterial phylum Nitrospirae. Leptospirilli are Gram-negative, obligatory chemolithoautotrophic, aerobic, ferrous iron oxidizers. This paper predicts genes that Leptospirilli use to survive at low pH and infers their evolutionary trajectory. Phylogenetic and other bioinformatic approaches suggest that these genes can be classified into (i) "first line of defense", involved in the prevention of the entry of protons into the cell, and (ii) neutralization or expulsion of protons that enter the cell. The first line of defense includes potassium transporters, predicted to form an inside positive membrane potential, spermidines, hopanoids, and Slps (starvation-inducible outer membrane proteins). The "second line of defense" includes proton pumps and enzymes that consume protons. Maximum parsimony, clustering methods, and gene alignments are used to infer the evolutionary trajectory that potentially enabled the ancestral Leptospirillum to transition from a postulated circum-neutral pH environment to an extremely acidic one. The hypothesized trajectory includes gene gains/loss events driven extensively by horizontal gene transfer, gene duplications, gene mutations, and genomic rearrangements.

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium

Possibilities for the recovery of non-ferrous and precious metals from Kapan polymetallic mine tailings (Armenia) were studied. The aim of this paper was to study the possibilities of bioleaching of samples of concentrated tailings by the natural microbial consortium of drainage water. The extent of extraction of metals from the samples of concentrated tailings by natural microbial consortium reached 41-55% and 53-73% for copper and zinc, respectively. Metal leaching efficiencies of pure culture Leptospirillum ferrooxidans Teg were higher, namely 47-93% and 73-81% for copper and zinc, respectively. The content of gold in solid phase of tailings increased about 7-16% and 2-9% after bio-oxidation process by L. ferrooxidans Teg and natural microbial consortium, respectively. It was shown that bioleaching of the samples of tailings could be performed using the natural consortium of drainage water. However, to increase the intensity of the recovery of valuable metals, natural consortium of drainage water combined with iron-oxidizing L. ferrooxidans Teg has been proposed.

Validation of Genetic Markers Associated to Oxygen Availability in Low-Grade Copper Bioleaching Systems: An Industrial Application

Forced aeration is one of the major energy consumption factors of the bioleaching process of run-of-mine ore. The effect of aeration in the microbial community has scarcely been studied at industrial level. Leptospirillum ferriphilum is one of the most representative species of the Fe³⁺ producing population in this kind of systems. We analyzed the effect of oxygen availability on L. ferriphilum by growth activity and transcriptional dynamics of its two terminal oxidases (cbb3 and bd complexes) under different experimental test: culture reactor, bioleaching column, and industrial heap tests. Relatively low O₂ availability triggered important changes in the microbial community composition, cell growth, microbial activity and cydAB genes transcription in all cases of study. We assessed the potential role of the terminal oxidases on the adaptation to variable aeration conditions in different lifestyles of L. ferriphilum and identified transcriptional markers associated to oxygen metabolism in an industrial system. An interesting hypothesis about the possible role of the cbb3 complex in the response to oxidative stress as well as their role as a high oxygen-affinity oxidase in L. ferriphilum is proposed and discussed. This study successfully proves the function of the cydAB genes as valid genetic markers for low-grade copper industrial bioleaching systems.

Idiomarina mangrovi sp. nov., isolated from rhizosphere soil of a mangrove Avicennia marina forest

A Gram-staining negative, aerobic, motile and rod-shaped bacterium, designated ZQ330^T, was isolated from rhizosphere soil of a mangrove (Avicennia marina) forest of Zhangzhou, Fujian Province, China. The growth range of NaCl concentration was 0.5-10.0 % (w/v), with an optimum at 2.5-3.0 % (w/v), the temperature range for growth was 10-40 °C, with an optimum at 28-30 °C, the pH range for growth was pH 6.0-9.5, with an optimum at pH 7.5. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ330^T exhibited less than 97.0 % sequence similarity to all type strains with validly published names and revealed that strain ZQ330^T formed a distinct lineage in the genus Idiomarina. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain ZQ330^T and the reference strains were 64.8-69.9 % and 27.5-28.4 %, respectively. Chemotaxonomic analysis indicated that the main respiratory quinone was Q-8, the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c), iso-C15 : 1F, C16 : 0, C18 : 0, summed feature 3 (C16 : 1ω8c and/or iso-C16 : 1 2-OH) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. Based on the genotypic, phenotypic, chemotaxonomic and phylogenetic features, strain ZQ330^T is considered to represent a novel species, for which the name Idiomarina mangrovi sp. nov. is proposed. The type strain is ZQ330^T (=MCCC 1K03495^T=KCTC 62455^T).

Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition

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Deep learning has become widely used in different fields of computer science such as face recognition, but also in biology, for example to detect malignant skin cancers based on images.

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Deep learning applied to microscopy images of biofilm colonization patterns accurately characterized its bacterial composition.

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Deep learning applications only rarely outperform human experts in classification tasks. Here however, deep learning reached an accuracy of 90%, therefore clearly outperforming human experts (50% accurate).

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Our method provides an accurate alternative to standard, time-consuming biochemical methods, using visual information only.

Background

Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases.

Methods

The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles.

Results

A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts.

Conclusions

Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods.

Adhesion to Mineral Surfaces by Cells of Leptospirillum, Acidithiobacillus and Sulfobacillus from Armenian Sulfide Ores

Bioleaching of metal sulfides is an interfacial process where adhesion and subsequent biofilm formation are considered to be crucial for this process. In this study, adhesion and biofilm formation by several acidophiles (Acidithiobacillus, Leptospirillum and Sulfobacillus) isolated from different biotopes with sulfide ores in Armenia were studied. Results showed that: (1) these bacteria adhere to pyrite surfaces to various extents. A correlation between pyrite biooxidation and adhesion of S. thermosulfidooxidans 6, L. ferriphilum CC, L. ferrooxidans ZC on pyrite surfaces is shown. It is supposed that bioleaching of pyrite by S. thermosulfidooxidans 6, L. ferriphilum CC, L. ferrooxidans ZC occurs by means of indirect leaching: by ferric iron of bacterial origin; (2) cells of At. ferrooxidans 61, L. ferrooxidans ZC and St. thermosulfidooxidans 6 form a monolayer biofilm on pyrite surfaces. The coverage of pyrite surfaces varies among these species. The order of the biofilm coverage is: L. ferrooxidans ZC ≥ At. ferrooxidans 61 > St. thermosulfidooxidans 6; (3) the extracellular polymeric substances (EPS) analysis indicates that the tested strains produce EPS, if grown either on soluble ferrous iron or solid pyrite. EPS are mainly composed of proteins and carbohydrates. Cells excrete higher amounts of capsular EPS than of colloidal EPS. In addition, cells grown on pyrite produce more EPS than ones grown on ferrous iron.

Weak Iron Oxidation by Sulfobacillus thermosulfidooxidans Maintains a Favorable Redox Potential for Chalcopyrite Bioleaching

Bioleaching is an emerging technology, describing the microbially assisted dissolution of sulfidic ores that provides a more environmentally friendly alternative to many traditional metal extraction methods, such as roasting or smelting. Industrial interest is steadily increasing and today, circa 15-20% of the world's copper production can be traced back to this method. However, bioleaching of the world's most abundant copper mineral chalcopyrite suffers from low dissolution rates, often attributed to passivating layers, which need to be overcome to use this technology to its full potential. To prevent these passivating layers from forming, leaching needs to occur at a low oxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult and costly. As an alternative, selected weak iron-oxidizers could be employed that are incapable of scavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onset of bioleaching, but not high enough to allow for the occurrence of passivation. In this study, we report that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications. Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole iron oxidizer exhibited significantly lower redox potentials and higher release of copper compared to communities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic response to single and co-culture of these two iron oxidizers was studied and revealed a greatly decreased number of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured in the presence of L. ferriphilum. This allowed for the identification of genes potentially responsible for S. thermosulfidooxidans' weaker iron oxidation to be studied in the future, as well as underlined the need for new mechanisms to control the microbial population in bioleaching heaps.

Automated Microscopic Analysis of Metal Sulfide Colonization by Acidophilic Microorganisms

Industrial biomining processes are currently focused on metal sulfides and their dissolution, which is catalyzed by acidophilic iron(II)- and/or sulfur-oxidizing microorganisms. Cell attachment on metal sulfides is important for this process. Biofilm formation is necessary for seeding and persistence of the active microbial community in industrial biomining heaps and tank reactors, and it enhances metal release. In this study, we used a method for direct quantification of the mineral-attached cell population on pyrite or chalcopyrite particles in bioleaching experiments by coupling high-throughput, automated epifluorescence microscopy imaging of mineral particles with algorithms for image analysis and cell quantification, thus avoiding human bias in cell counting. The method was validated by quantifying cell attachment on pyrite and chalcopyrite surfaces with axenic cultures of Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans. The method confirmed the high affinity of L. ferriphilum cells to colonize pyrite and chalcopyrite surfaces and indicated that biofilm dispersal occurs in mature pyrite batch cultures of this species. Deep neural networks were also applied to analyze biofilms of different microbial consortia. Recent analysis of the L. ferriphilum genome revealed the presence of a diffusible soluble factor (DSF) family quorum sensing system. The respective signal compounds are known as biofilm dispersal agents. Biofilm dispersal was confirmed to occur in batch cultures of L. ferriphilum and S. thermosulfidooxidans upon the addition of DSF family signal compounds.IMPORTANCE The presented method for the assessment of mineral colonization allows accurate relative comparisons of the microbial colonization of metal sulfide concentrate particles in a time-resolved manner. Quantitative assessment of the mineral colonization development is important for the compilation of improved mathematical models for metal sulfide dissolution. In addition, deep-learning algorithms proved that axenic or mixed cultures of the three species exhibited characteristic biofilm patterns and predicted the biofilm species composition. The method may be extended to the assessment of microbial colonization on other solid particles and may serve in the optimization of bioleaching processes in laboratory scale experiments with industrially relevant metal sulfide concentrates. Furthermore, the method was used to demonstrate that DSF quorum sensing signals directly influence colonization and dissolution of metal sulfides by mineral-oxidizing bacteria, such as L. ferriphilum and S. thermosulfidooxidans.

Identification of trehalose as a compatible solute in different species of acidophilic bacteria

The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response or adaptation to osmotic stress. In order to investigate the response to osmotic stress in these microorganisms, six species of acidophilic bacteria were grown at elevated osmotic strength in liquid media, and the compatible solutes synthesised were identified using ion chromatography and MALDI-TOF mass spectrometry. Trehalose was identified as one of, or the sole, compatible solute in all species and strains, apart from Acidithiobacillus thiooxidans where glucose and proline levels increased at elevated osmotic potentials. Several other potential compatible solutes were tentatively identified by MALDITOF analysis. The same compatible solutes were produced by these bacteria regardless of the salt used to produce the osmotic stress. The results correlate with data from sequenced genomes which confirm that many chemolithotrophic and heterotrophic acidophiles possess genes for trehalose synthesis. This is the first report to identify and quantify compatible solutes in acidophilic bacteria that have important roles in biomining technologies.

Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation

Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647^T (here referred to as Leptospirillum ferriphilum ^T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum ^T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS₂). Adaptations of Leptospirillum ferriphilum ^T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum ^T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum ^T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.

Antimicrobial resistance, heavy metal resistance and integron content in bacteria isolated from a South African tilapia aquaculture system

Antibacterial compounds and metals co-select for antimicrobial resistance when bacteria harbour resistance genes towards both types of compounds, facilitating the proliferation and evolution of antimicrobial and heavy metal resistance. Antimicrobial and heavy metal resistance indices of 42 Gram-negative bacteria from a tilapia aquaculture system were determined to identify possible correlations between these phenotypes. Agar dilution assays were carried out to determine susceptibility to cadmium, copper, lead, mercury, chromate and zinc, while susceptibility to 21 antimicrobial agents was investigated by disk diffusion assays. Presence of merA, the mercury resistance gene, was determined by dot-blot hybridizations and PCR. Association of mercury resistance with integrons and transposon Tn21 was also investigated by PCR. Isolates displayed a high frequency of antimicrobial (erythromycin: 100%; ampicillin: 85%; trimethoprim: 78%) and heavy metal (Zn2+: 95%; Cd2+: 91%) resistance. No correlation was established between heavy metal and multiple antibiotic resistance indices. Significant positive correlations were observed between heavy metal resistance profiles, indices, Cu2+ and Cr3+ resistance with erythromycin resistance. Significant positive correlations were observed between merA (24%)/Tn21 (24%) presence and heavy metal resistance profiles and indices; however, significant negative correlations were obtained between integron-associated qacE∆1 (43%) and sulI (26%) gene presence and heavy metal resistance indices. Heavy metal and antimicrobial agents co-select for resistance, with fish-associated, resistant bacteria demonstrating simultaneous heavy metal resistance. Thus, care should be taken when using anti-fouling heavy metals as feed additives in aquaculture facilities.

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.