Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration

Phytomanagement of iron mine soil by Ricinus communis L. and garden soil

Soil pollution and heavy metals (HMs) contamination caused by the improper management of mine soil is a major concern for the environment and the associated living beings. The present study was carried out for 90 days with iron mine soil (MS) amendment with different ratios of garden soil (GS) (0, 25, 50, 75 and 100%). The study investigates the growth performance, metal tolerance, metal accumulation (Fe, Pb, Cu and Ni) ability of R. communis L. and the improvement in soil health after harvesting the plants. The MS had a high level of Fe, Pb, Cu and Ni (2017.17, 65.34, 34.02 and 69.15 mg kg^-1 respectively) with significantly low pH, water holding capacity (WHC), organic carbon (OC), organic matter (OM) and nutrients along with microbial biomass carbon and nitrogen (Cmic and Nmic). The study found that there are higher growth rates and biomass for plants grown in all GS treatments compared to 100% MS. The relative water content (%), tolerance index and carotenoid content exhibit upwards trends with the increasing growing period. The HMs accumulation in shoot and root was found highest for Fe (1354.44 and 3989.61 mg kg^-1) and Pb (31.88 and 34.83 mg kg^-1). The metal extraction ratio for all studied metals was found maximum in 50 and 75% GS treatment plants. Further, the HMs removal percentage was recorded between 14.82 and 54.86%. The soil physicochemical and biological properties like electrical conductivity, total nitrogen, Cmic and Nmic increased up to 50% and the OC and OM improved manyfold in 100% MS. Based on the findings, it is concluded that R. communis L. has the potential to easily cultivate in mine abandoned soil and tolerate high concentrations of HMs.

Effects of recultivation on soil organic carbon sequestration in abandoned coal mining sites: a meta-analysis

Opencast coal mining results in high loss of soil organic carbon (SOC), which may be restored via recultivation. Common strategies include liming, topsoil application, and phytoremediation. It remains unclear, however, which parameters determine the effectiveness of these varying recultivation strategies especially regarding SOC sequestration. This meta-analysis analyses the effect of varying recultivation strategies on SOC sequestration under different climate and soil conditions (pH, texture, depth) as well as in relation to time, based on 404 data entries from 51 studies. All included climatic regions recorded increases in SOC stocks, with tropical soils showing the highest potential for relative gains at up to 637%. We demonstrate that loamy soils sequester twice as much newly introduced SOC than sand. Strategy-wise, the highest mean rate of SOC sequestration is achieved by forest after topsoil application (3.9 Mg ha^-1 a^-1), agriculture after topsoil application (2.3 Mg ha^-1 a^-1), and agriculture with topsoil and fertiliser application (1.9 Mg ha^-1 a^-1) with a response ratio of 304%, 281%, and 218%, respectively. Soils analysed to less then 40 cm depth show higher SOC sequestration rates (< 10 cm: 0.6 Mg ha^-1 a^-1, < 20 cm: 1.0 Mg ha^-1 a^-1, and 20-40 cm: 0.4 Mg ha^-1 a^-1; response ratio of 123%, 68%, and 73%, respectively) than those analysed to a depth of 41-80 cm (0.1 Mg ha^-1 a^-1; response ratio of 6%). In terms of pH, strongly acidic soils (pH < 4.5) and alkaline conditions (pH > 7) offer the most beneficial environment for SOC sequestration at 0.4 Mg ha^-1 a^-1 and 0.8 Mg ha^-1 a^-1, respectively (185% and 273% response). Given comparable SOC sequestration potentials of forest after topsoil application, agriculture without amendments, and forest without amendments, we recommend to weigh these strategies against each other. Potentially decisive aspects are short- vs. long-term economic gains, food security concerns, and-in case of agriculture-the risk of overintensification leading to losses in SOC. Our data suggests that amendments exert considerable influence on SOC sequestration and need to be introduced under careful consideration.

Bacterial community structure and diversity in the rhizospheric soil of Robinia pseudoacacia and Juniperus sabina planted in iron tailings matrix

Iron tailings matrix is deficient in nutrients, and phytoremediation is one of the effective methods to improve tailings nutrients. The response of phytoremediation to tailings microorganisms remains to be studied. The present study analyzed rhizospheric soil of two kinds of plants bacterial diversity and community structure and their relationship with soil environmental factors. The results indicate that the rhizospheric soil bacteria species of Robinia pseudoacacia and Juniperus sabina were not significantly different from that of bare tailings, but rhizospheric soil bacterial community compositions and abundance were significantly different from that of bare tailings. Canonical correlation analysis (CCA) showed that soil alkali-hydrolyzable nitrogen (AN), soil total nitrogen (TN), and soil organic matter (SOM) were the main environmental factors affecting bacterial community diversity. Spearman's correlation analysis showed that AN, TN, and SOM were significantly positively correlated with the relative abundance of Gemmatimonadetes and Nitrospirae, and were significantly negatively correlated with that of Firmicutes, Fusobacteria, and Bacteroidetes. FAPROTAX function prediction showed that the functional microbial communities of rhizospheric soil of the two plants were significantly different from those of bare tailings. Overall, the findings support an increase of microbial diversity, SOM, and nitrogen in rhizospheric soil of revegetated tailings compared to bare tailings. These results provide theoretical support for the development and application of phytoremediation in abandoned mines.

Understanding changes in biocrust communities following phosphate mining in the Negev Desert

Biocrusts are key ecosystem engineers that are being destroyed due to anthropogenic disturbances such as trampling, agriculture and mining. In hyper-arid regions of the Negev Desert, phosphate has been mined for over six decades, altering the natural landscape over large spatial scales. In recent years, restoration-oriented practices were mandated in mining sites, however, the impact of such practices on the ecosystem, particularly the biocrust layer, has not been tested. Here, we evaluated post-mining biocrust bacterial communities and compared them to undisturbed (reference) biocrusts. We collected samples from four mining sites (each restored at a different year) and their corresponding reference sites. We hypothesized that post-mining bacterial communities would differ significantly from reference communities, given the slow regeneration of the biocrust. We also hypothesized that bacterial communities would vary among post-mining plots based on their restoration age. To test these hypotheses, we assessed the abundance and diversity of bacterial communities by sequencing the 16S rDNA and their photosynthetic potential by quantifying the abundance of cyanobacteria and chlorophyll a. The bacterial diversity was lower, and community composition differed significantly between post-mining and reference biocrusts. In addition, cyanobacteria abundances and chlorophyll a content were lower in post-mining biocrusts, indicating lower photosynthetic potential. However, no significant changes in bacterial communities were detected, regardless of the restoration age. We suggest that the practices implemented in the Negev mines may not support the recovery of the biocrust bacterial communities, particularly the cyanobacteria. Thus, active restoration measures are needed to accelerate the regeneration time of biocrusts at the hyper-arid Negev mines.

From Rags to Enriched: Metagenomic Insights into Ammonia-oxidizing Archaea Following Ammonia Enrichment of a Denuded Oligotrophic Soil Ecosystem

Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavorable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in-silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia oxidizing archaea (AOA) can be considered as the one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates. This article is protected by copyright. All rights reserved.

Soil Properties Interacting With Microbial Metagenome in Decreasing CH4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation

Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcrA and pmoA genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcrA and pmoA genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling.

Longitudinal Survey of Fecal Microbiota in Healthy Dogs Administered a Commercial Probiotic

The aim of this longitudinal microbiome study was to investigate the effects of a commercially available veterinary synbiotic product (Blackmore's® Paw DigestiCare 60™) on the fecal microbiome of healthy dogs using 16S rRNA gene microbial profiling. Fifteen healthy, privately-owned dogs participated in a 2-week trial administration of the product. Fecal samples were collected at different time points, including baseline (prior to treatment), during administration and after discontinuation of product. Large intra- and inter-individual variation was observed throughout the study, but microbiome composition at higher phylogenetic levels, alpha and beta diversity were not significantly altered after 2 weeks of probiotic administration, suggesting an absence of probiotic impact on microbial diversity. Administration of the synbiotic preparation did, however, result in transient increases in probiotic species from Enterococacceae and Streptococacceae families as well as an increase in Fusobacteria; with the fecal microbiota partially reverting to its baseline state 3-weeks after cessation of probiotic administration.

Calcicole-calcifuge plant strategies limit restoration potential in a regional semi-arid flora

AIM

To examine calcicole and calcifuge plant strategies, as well as nutrient-acquisition strategies, as drivers of the distribution of species in response to edaphic factors, and the degree to which these strategies may act as filters to species establishment in ecological restoration on heavily altered or reconstructed substrates.

LOCATION

An 82,000-ha area within a major mining province in the Mid-West region of Western Australia, harboring vegetation communities ranging from species-poor halophytic scrub on saline flats to dense biodiverse shrubland on the skeletal soils of ancient Banded Ironstone Formations (BIF).

METHODS

Univariate and multivariate analyses were employed to examine how variation in soil chemistry and landscape position (undulating plains, slopes, and BIF crests and ridges) influenced patterns of floristic diversity, calcifuge plant strategies, and nutrient-acquisition strategies in 538 plant species from 830 relevés.

RESULTS

Landscape position was the strongest driver of species richness and vegetation functional composition. Soils became increasingly acidic and P-impoverished along an increasing elevational gradient. Vegetation from different landscape positions was not compositionally dissimilar, but vegetation of BIF crests and ridges was up to twice as biodiverse as vegetation from adjacent lower-relief areas and harbored higher proportions of calcifuge species and species with mycorrhizal associations.

MAIN CONCLUSIONS

Topographic and edaphic complexity of BIF landforms in an otherwise relatively homogenous landscape has likely facilitated species accumulation over long time periods. They represent musea of regional floristic biodiversity, excluding only species that cannot establish or are inferior competitors in heavily weathered, acidic, skeletal, and nutrient-impoverished soils. Plant strategies likely represent a major filter in establishing biodiverse, representative vegetation on postmining landforms in geologically ancient regions.

Incorporating rock in surface covers improves the establishment of native pioneer vegetation on alkaline mine tailings

BACKGROUND AND AIMS

Rates of tailings production and deposition around the world have increased markedly in recent decades, and have grown asynchronously with safe and environmentally suitable solutions for their storage. Tailings are often produced in regions harbouring biodiverse native plant communities adapted to old, highly-weathered soils. The highly-altered edaphic conditions of tailings compared with natural soils in these areas will likely select against many locally endemic plant species, making phytostabilisation, rehabilitation or ecological restoration of these landforms challenging.

METHODS

We established four substrate cover composition treatments on a dry-stacked magnetite tailings storage facility in semi-arid Western Australia, representative of standard industry practices for rehabilitating or restoring post-mining landforms in the region. Plots were seeded with a selection of locally native plant species and monitored for five years to determine whether different substrate cover treatments yielded different edaphic conditions (soil moisture, substrate surface temperature and substrate chemistry) and influenced soil development and the success of native vegetation establishment.

RESULTS

No vegetation established from seeds on unamended tailings with no surface cover, and substrate chemistry changed minimally over five years. In contrast, rock-containing surface covers allowed establishment of up to 11 native plant species from broadcast seeds at densities of ca. 1.5 seedlings m^-2, and up to 3.5 seedlings m^-2 of five native pioneer chenopods from capture of wind-dispersed seeds from surrounding undisturbed native vegetation. Greater vegetation establishment in rock-containing surface covers resulted from increased heterogeneity (e.g., lower maximum soil temperature, greater water capture and retention, surface microtopography facilitating seed capture and retention, more niches for seed germination). Soil development and bio-weathering occurred most rapidly under the canopy of native pioneer plants on rock-containing surface covers, particularly increases in organic carbon, total nitrogen, and organo-bound aluminium and iron.

CONCLUSIONS

Seed germination and seedling survival on tailings were limited by extreme thermal and hydrological conditions and a highly-altered biogeochemical environment. The design of surface cover layers appears crucial to achieving closure outcomes on tailings landforms, and designs should prioritise increasing surface heterogeneity through the incorporation of rock or other structure-improving amendments to assist the establishment of pioneer vegetation.

Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing

The ecological restoration of ecosystem services and biodiversity is a key intervention used to reverse the impacts of anthropogenic activities such as mining. Assessment of the performance of restoration against completion criteria relies on biodiversity monitoring. However, monitoring usually overlooks soil microbial communities (SMC), despite increased awareness of their pivotal role in many ecological functions. Recent advances in cost, scalability and technology has led to DNA sequencing being considered as a cost-effective biological monitoring tool, particularly for otherwise difficult to survey groups such as microbes. However, such approaches for monitoring complex restoration sites such as post-mined landscapes have not yet been tested. Here we examine bacterial and fungal communities across chronosequences of mine site restoration at three locations in Western Australia to determine if there are consistent changes in SMC diversity, community composition and functional capacity. Although we detected directional changes in community composition indicative of microbial recovery, these were inconsistent between locations and microbial taxa (bacteria or fungi). Assessing functional diversity provided greater understanding of changes in site conditions and microbial recovery than could be determined through assessment of community composition alone. These results demonstrate that high-throughput amplicon sequencing of environmental DNA (eDNA) is an effective approach for monitoring the complex changes in SMC following restoration. Future monitoring of mine site restoration using eDNA should consider archiving samples to provide improved understanding of changes in communities over time. Expansion to include other biological groups (e.g. soil fauna) and substrates would also provide a more holistic understanding of biodiversity recovery.

Field-Deployed Extruded Seed Pellets Show Promise for Perennial Grass Establishment in Arid Zone Mine Rehabilitation

Current methods of mine rehabilitation in the arid zone have a high failure rate at seedling emergence largely due to limited availability of topsoil and low water-holding capacity of alternative growth substrates such as mining overburden and tailings. Further, seedlings have consistently failed to emerge from seeds sown on the soil surface using traditional broadcasting methods. Seed pellets, formed by extruding soil mixtures and seeds into pellets, can potentially increase soil water uptake through enhanced soil-seed contact and thereby improve seedling emergence. We tested an extruded seed pelleting method in a three-factor field experiment (i.e., different pellet-soil mixtures, organic amendments, and simulated rainfall regimes) in north-western Australia. Given the observed lack of seedling emergence from broadcast seeds, the aims of the experiment were to assess: (i) the use of pellets to promote native seedling emergence and establishment and; (ii) the soil physico-chemical and microbiological changes that occur with this method of rehabilitation. The effects of pellet-soil mixtures, organic amendment, and rainfall regime on seedling emergence and survival of three native plant species suggest trade-offs among responses. Pellets made with a 1:1 blend of topsoil and a loamy-sand waste material had the highest seedling emergence, while 100% topsoil pellets had lower emergence probably because of hardsetting. Triodia pungens (a native grass) survived to the end of the experiment while Indigofera monophylla and Acacia inaequilatera (native shrubs) emerged but did not survive. Adding an organic amendment in the extruded pellet inhibited Triodia seedling emergence but increased soil microbial activity. Overall, extruded pellets made from a 1:1 blend showed promise for the establishment of Triodia seeds and beneficially, incorporates mine waste overburden and lesser amounts of topsoil. Further research is needed to improve pelleting production and to test the applicability of the method at scale, for different species and other ecosystem types.

Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar

Abandoned unrestored mines are an important environmental concern as they typically remain unvegetated for decades, exposing vast amounts of mine waste to erosion. Several factors limit the revegetation of these sites, including extreme abiotic and unfavorable biotic conditions. However, some pioneer tree species having high levels of genetic diversity, such as balsam poplar (Populus balsamifera), can naturally colonize these sites and initiate plant succession. This suggests that some tree genotypes are likely more suited for acclimation to the conditions of mine wastes. In this study, we selected two contrasting mine waste storage facilities (waste rock from a gold mine and tailings from a molybdenum mine) from the Abitibi region of Quebec (Canada), on which poplars were found to have grown naturally. First, we assessed in situ the impact of vegetation presence on each mine waste type. The presence of balsam poplars improved soil health locally by modifying the physicochemical properties (e.g., higher nutrient content and pH) of the mine wastes and causing an important shift in their bacterial and fungal community compositions, going from lithotrophic communities that dominate mine waste environments to heterotrophic communities involved in nutrient cycling. Next, in a greenhouse experiment we assessed the impact of plant genotype when grown in these mine wastes. Ten genotypes of P. balsamifera were collected locally, found growing either at the mine sites or in the surrounding natural forest. Tree growth was monitored over two growing seasons, after which the effects of genotype-by-environment interactions were assessed by measuring the physicochemical properties of the substrates and the changes in microbial community assembly. Although substrate type was identified as the main driver of rhizosphere microbiome diversity and community structure, a significant effect due to tree genotype was also detected, particularly for bacterial communities. Plant genotype also influenced aboveground tree growth and the physicochemical properties of the substrates. These results highlight the influence of balsam poplar genotype on the soil environment and the potential importance of tree genotype selection in the context of mine waste revegetation.

Reconditioning Degraded Mine Site Soils With Exogenous Soil Microbes: Plant Fitness and Soil Microbiome Outcomes

Mining of mineral resources substantially alters both the above and below-ground soil ecosystem, which then requires rehabilitation back to a pre-mining state. For belowground rehabilitation, recovery of the soil microbiome to a state which can support key biogeochemical cycles, and effective plant colonization is usually required. One solution proposed has been to translate microbial inocula from agricultural systems to mine rehabilitation scenarios, as a means of reconditioning the soil microbiome for planting. Here, we experimentally determine both the aboveground plant fitness outcomes and belowground soil microbiome effects of a commercially available soil microbial inocula (SMI). We analyzed treatment effects at four levels of complexity; no SMI addition control, Nitrogen addition alone, SMI addition and SMI plus Nitrogen addition over a 12-week period. Our culture independent analyses indicated that SMIs had a differential response over the 12-week incubation period, where only a small number of the consortium members persisted in the semi-arid ecosystem, and generated variable plant fitness responses, likely due to plant-microbiome physiological mismatching and low survival rates of many of the SMI constituents. We suggest that new developments in custom-made SMIs to increase rehabilitation success in mine site restoration are required, primarily based upon the need for SMIs to be ecologically adapted to both the prevailing edaphic conditions and a wide range of plant species likely to be encountered.

Bacterial Community Structure Recovery in Reclaimed Coal Mined Soil under Two Vegetative Regimes

Coal mining can be deleterious to the soil physical and chemical makeup, but also to the soil microbial community. Effectively, the removal of nearly all organic matter from the upper soil horizons reduces the effectiveness of any soil to support vegetation, and up until recently, microbial community parameters were not considered in the successful reclamation of overburden. Thus, our study proposes to measure the uncultivated bacterial community using 16S ribosomal RNA (rRNA) high-throughput sequencing in a chronosequence of reclaimed overburden in Mississippi. The study sites comprised samplings of pasture and wooded reclamation sites consisting of 1 to 13 yr post reclamation time, as well as reference sites. Overall, the primary driver of bacterial community dynamics was vegetative cover, although time also influenced dynamics. Richness estimations for operational taxonomic units (OTUs) showed that recently reclaimed (∼1 yr) and Pasture sites were more OTU rich with levels of >1400 compared with reference site levels of ∼1000. Diversity levels also followed a similar trend. Community structure typically differed between time points and vegetative cover; however, membership was similar between sites and reference, indicating that new communities still shared some membership from the previous community. Overall, physicochemical properties trended toward more positive for soil health as time progressed, but bacterial community recovery was still not structurally recovered, although richness and diversity values exceeded reference. Overall, this study demonstrated that mine reclamation using pasture and/or wood restoration can reestablish the bacterial community to approximate reference conditions, but vegetation is still the dominating environmental factor dictating microbial community.

Streptomyces Dominate the Soil Under Betula Trees That Have Naturally Colonized a Red Gypsum Landfill

The successful restoration of well-engineered tailings storage facilities is needed to avoid mine tailings problems. This study characterized the bacterial communities from vegetated and non-vegetated soils from a red gypsum landfill resulting from the industrial extraction of titanium. A set of 275 bacteria was isolated from vegetated soil and non-vegetated soil areas and taxonomically characterized using BOX-PCR. The study also evaluated the ability of a subset of 88 isolated bacteria on their ability to produce plant growth promoting (PGP) traits [indoleacetic acid (IAA) production, phosphate solubilization, and siderophore production] and their tolerance to potentially toxic elements (PTEs). Twenty strains were chosen for further analysis to produce inoculum for birch-challenging experiments. Principal component analysis (PCA) showed that the set of pedological parameters (pH, granulometry, carbon, organic matter, and Mg content) alone explained approximately 40% of the differences between the two soils. The highest density of total culturable bacteria was found in the vegetated soil, and it was much higher than that in the non-vegetated soil. The Actinobacteria phyla dominated the culturable soil community (70% in vegetated soil and 95% in non-vegetated soil), while the phyla Firmicutes (including the genus Bacillus) and Bacteroides (including the genera Pedobacter and Olivibacter) were found only in the vegetated soil fraction. Additional genera (Rhizobium, Variovorax, and Ensifer) were found solely in the vegetated soil. The vegetated soil bacteria harbored the most beneficial PGP bacteria with 12% of the isolates showing three or more PGP traits. The strains with higher metal tolerances in our study were Phyllobacterium sp. WR140 (RO1.15), Phyllobacterium sp. WR140 (R01.34), and Streptomyces sp. (R04.15), all isolated from the vegetated soil. Among the isolates tested in challenging experiments, Phyllobacterium (R01.34) and Streptomyces sp. (R05.33) have the greatest potential to act as PGP rhizobacteria and therefore to be used in the biological restoration of tailings dumps.

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

BACKGROUND

The use of shotgun metagenomics to analyse low-complexity microbial communities in foods has the potential to be of considerable fundamental and applied value. However, there is currently no consensus with respect to choice of species classification tool, platform, or sequencing depth. Here, we benchmarked the performances of three high-throughput short-read sequencing platforms, the Illumina MiSeq, NextSeq 500, and Ion Proton, for shotgun metagenomics of food microbiota. Briefly, we sequenced six kefir DNA samples and a mock community DNA sample, the latter constructed by evenly mixing genomic DNA from 13 food-related bacterial species. A variety of bioinformatic tools were used to analyse the data generated, and the effects of sequencing depth on these analyses were tested by randomly subsampling reads.

RESULTS

Compositional analysis results were consistent between the platforms at divergent sequencing depths. However, we observed pronounced differences in the predictions from species classification tools. Indeed, PERMANOVA indicated that there was no significant differences between the compositional results generated by the different sequencers (p = 0.693, R² = 0.011), but there was a significant difference between the results predicted by the species classifiers (p = 0.01, R² = 0.127). The relative abundances predicted by the classifiers, apart from MetaPhlAn2, were apparently biased by reference genome sizes. Additionally, we observed varying false-positive rates among the classifiers. MetaPhlAn2 had the lowest false-positive rate, whereas SLIMM had the greatest false-positive rate. Strain-level analysis results were also similar across platforms. Each platform correctly identified the strains present in the mock community, but accuracy was improved slightly with greater sequencing depth. Notably, PanPhlAn detected the dominant strains in each kefir sample above 500,000 reads per sample. Again, the outputs from functional profiling analysis using SUPER-FOCUS were generally accordant between the platforms at different sequencing depths. Finally, and expectedly, metagenome assembly completeness was significantly lower on the MiSeq than either on the NextSeq (p = 0.03) or the Proton (p = 0.011), and it improved with increased sequencing depth.

CONCLUSIONS

Our results demonstrate a remarkable similarity in the results generated by the three sequencing platforms at different sequencing depths, and, in fact, the choice of bioinformatics methodology had a more evident impact on results than the choice of sequencer did.

Young calcareous soil chronosequences as a model for ecological restoration on alkaline mine tailings

Tailings are artificial soil-forming substrates that have not been created by the natural processes of soil formation and weathering. The extreme pH environment and corresponding low availability of some macro- and micronutrients in alkaline tailings, coupled with hostile physical and geochemical conditions, present a challenging environment to native biota. Some significant nutritional constraints to ecosystem reconstruction on alkaline tailings include i) predominant or complete absence of combined nitrogen (N) and poor soil N retention; ii) the limited bioavailability of some micronutrients at high soil pH (e.g., Mn, Fe, Zn and Cu); and iii) potentially toxic levels of biologically available soil phosphorus (P) for P-sensitive plants. The short regulatory time frames (years) for mine closure on tailings landforms are at odds with the long time required for natural pedogenic processes to ameliorate these factors (thousands of years). However, there are similarities between the chemical composition and nutrient status of alkaline tailings and the poorly-developed, very young calcareous soils of biodiverse regions such as south-western Australia. We propose that basic knowledge of chronosequences that start with calcareous soils may provide an informative model for understanding the pedogenic processes required to accelerate soil formation on tailings. Development of a functional, stable root zone is crucial to successful ecological restoration on tailings, and three major processes should be facilitated as early as possible during processing or in the early stages of restoration to accelerate soil development on alkaline tailings: i) acidification of the upper tailings profile; ii) establishment of appropriate and resilient microbial communities; and iii) the early development of appropriate pioneer vegetation. Achieving successful ecological restoration outcomes on tailings landforms is likely one of the greatest challenges faced by restoration ecologists and the mining industry, and successful restoration on alkaline tailings likely depends upon careful management of substrate chemical conditions by targeted amendments.