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Context Compaction removal and organic amendment application are commonly used to mitigate the compaction-induced declines in crop yield, soil carbon (C) and soil health. However, the response of microbial activities and nutrient pools to the combination of mill-mud amendments and decompaction in the soil profile are not fully understood. Aims A field trial was conducted at Burdekin, Australia, to investigate the effects of different decompaction managements on soil nutrient cycling, associated biological activities and sugarcane yield. Methods This experiment included four treatments: control (CK, without mill-mud), mill-mud shallow furrow (MS), deep trenching without mill-mud (DT) and deep trenching mill-mud application (MD). Key results The MD treatment increased concentrations of hot water extractable organic C by 30–70% and hot water extractable total nitrogen (N) by 30–90% at the application depth. Soil microbial biomass C and N were also higher in mill-mud applied layers. Mill-mud applied treatments increased plant cane yield by 7% (MS treatment) and 14% (MD treatment) compared to CK. The DT treatment also increased plant cane yield by 11% compared to CK. Conclusion The MD treatment increased the supply of organic C and nutrients to the microbial community within the entire soil profile, enhanced nutrient cycling processes, improved soil environmental conditions and soil health for sugarcane growth and thus increased sugarcane productivity. Implications Further research should focus on microbial community composition shifts to further explore the mechanisms responsible for soil microorganism regulation of nutrient cycling in sugarcane farming systems.

Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.

The development of rare earth element (REE) production in Canada could generate significant economic benefits but also poses serious potential risks to the environment. Rare earth elements have been widely used in modern life and industries and are even indispensable in some crucial advanced technologies (e.g., permanent magnets). Increasing demand and the current United States – China trade tensions provide a commercial economic development opportunity for Canada, which has rich resources of REEs, to develop its own sector. However, environmental and health issues caused by REE production are challenges that Canada has to face given that significant environmental impacts have been reported elsewhere (e.g., China). Little literature is available on the potential environmental risks associated with the development of REE production in Canada. It is important to know what environmental issues, particularly those generated by REEs themselves, may happen in Canada in the future. Therefore, three major aspects are evaluated and summarized from multidisciplinary perspectives in this paper: (1) a general conceptual model of the transport of REEs as a group in the environment is established; (2) toxicity levels, biochemical mechanisms, and physiological effects of REEs on different organisms are reviewed, and case-studies from existing REE mining areas are briefly highlighted; and (3) considering specific environmental condition and risk factors, environmental risks that Canada may face in future REE developments are identified and discussed. This review concludes with macro-identification of potential environmental risks associated with the development of REE production in Canada considering both human and ecological health. We note that ingestion, inhalation, and dermal exposure for workers and surrounding residents (including potentially Indigenous communities) and subarctic and arctic climate conditions could increase the risks to human and ecological health in future REE production development in Canada. Finally, future research directions are proposed that could be applied to both Canadian and other geographical contexts.

Wood ash may be useful as a forest soil amendment in Canada, but trace metals can have detrimental effects if they accumulate in, or are transported from, forest ecosystems. Metal concentrations in soil water and sugar maple (Acer saccharum Marsh.) seedling tissue chemistry were measured in a north temperate hardwood forest over 4 years following a biomass boiler ash addition field trial. Twenty plots (3 m × 3 m) were established in Haliburton Forest with both fly and bottom ash treatments of 0, 4, and 8 Mg·ha−1 with four replicates, and tension lysimeters were positioned in each plot at 30, 50, and 100 cm depths. Over the 4 years, soil water metal concentrations in treated plots were not significantly different from those of the control plots. No differences in metal concentrations in foliage of sugar maple seedlings could be detected, but there were significantly higher concentrations of some metals (Al, Fe, Zn, Pb, Ni, and Sr) in roots of treated plots. Simulated drought mobilized several metals in upper mineral soil, but this mobilization occurred similarly in controls and ash-treated soils. These results suggest that doses below 8 Mg·ha−1 industrial wood ash with trace metal concentrations below Canadian regulatory limits do not cause an increase in trace metal mobility or availability in northern hardwood forests with acidic soils during the first 5 years after application.

For mass culture of photosynthetic green microalgae, industrial flue gases can represent a low-cost resource of CO2. However, flue gases are often avoided, because they often also contain high levels of SO2 and/or NO2, which cause significant acidification of media to below pH 3 due to production of sulfuric and nitric acid. This creates an unsuitable environment for the neutrophilic microalgae commonly used in large-scale commercial production. To address this issue, we have looked at selecting acid-tolerant microalgae via growth at pH 2.5 carried out with samples bioprospected from an active smelter site. Of the eight wild samples collected, one consisting mainly of Coccomyxa sp. grew at pH 2.5 and achieved a density of 640 mg L−1. Furthermore, three previously bioprospected green microalgae from acidic waters (pH 3–4.5) near abandoned mine sites were also re-acclimated down to their in-situ pH environment after approximately 4 years spent at neutral pH. Of those three, an axenic culture of Coccomyxa sp. was the most successful at re-acclimating and achieved the highest density of 293.1 mg L−1 and maximum daily productivity of 38.8 mg L−1 day−1 at pH 3. Re-acclimation of acid-tolerant species is, therefore, achievable when directly placed at their original pH, but gradual reduction in pH is recommended to give the cells time to acclimate.

Photosynthetic green microalgae are eukaryotic microorganisms that can mitigate anthropogenic carbon dioxide and generate lipids as a feedstock for production of biodiesel. Biodiesel production may not, however, compete economically with fossil fuel sourced diesel, but obtaining additional value from the biomass left after lipid extraction has the potential to help make the overall process more cost-effective. This review focuses on these additional value-added options that obtain and utilize either whole lipid-extracted biomass (LEB), which typically constitutes 60%–70% of total cell mass, or specific non-biodiesel lipid components such as polyunsaturated fatty acids, carbohydrates, and proteins.

Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.

Peatlands contain a significant fraction of global soil carbon, but how these reservoirs will respond to the changing climate is still relatively unknown. A global picture of the variations in peat organic matter chemistry will aid our ability to gauge peatland soil response to climate. The goal of this research is to test the hypotheses that 1) peat carbohydrate content, an indicator of soil organic matter reactivity, will increase with latitude and decrease with mean annual temperatures (MAT), 2) while peat aromatic content, an indicator of recalcitrance, will vary inversely, and 3) elevation will have a similar effect to latitude. We used Fourier Transform Infrared Spectroscopy (FTIR) to examine variations in the organic matter functional groups of 1034 peat samples collected from 10-20, 30-40, and 60-70 cm depths at 165 individual sites across a latitudinal gradient of 79˚N to 65˚S and from elevations of 0 to 4773 meters. Carbohydrate contents of high latitude peat were significantly greater than peat originating near the equator, while aromatic content showed the opposite trend. For peat from similar latitudes but different elevations, the carbohydrate content was greater and aromatic content was lower at higher elevations. Higher carbohydrate content at higher latitudes indicates a greater potential for mineralization, whereas the chemical composition of low latitude peat is consistent with their apparent relative stability in the face of warmer temperatures. The combination of low carbohydrates and high aromatics at warmer locations near the equator suggests the mineralization of high latitude peat until reaching recalcitrance under a new temperature regime.

Fungi are primary agents of coarse woody debris (CWD) decay in forests, playing an essential role in nutrient cycling and carbon storage. Characterizing fungal communities within CWD will promote further understanding of the fungal controls on CWD decomposition. We compared fungal community assemblages using alpha and beta diversity metrics, carbon mineralization, and physical and chemical properties of CWD across 3 tree species (trembling aspen [Populus tremuloides], black spruce [Picea mariana], and jack pine [Pinus banksiana]), 5 decay classes, and 2 stand development stages, differing in time-since-stand replacing disturbance (i.e., young/self-thinning and mature/steady-state) in Ontario’s boreal forest region. In total, we sampled 180 individual CWD logs from 6 independent stands, with 3 replicates per each species × decay class combination at each site. We found that fungal community structure significantly differed across tree species, decay stage, and stand age. Higher proportions of white rot fungi were found in trembling aspen CWD, whereas higher proportions of brown rot fungi were found in black spruce and jack pine CWD. Proportions of specialized wood decay fungi increased with decay stage and were higher in CWD located in mature forest stands. Fungal diversity was highest in decay class 4 CWD. We found that Mn and K concentrations, total carbon, C/N ratio, carbon mineralization (mg CO2 g dry CWD-1 d-1), and moisture content were important predictors of fungal composition across CWD species and/or decay stage, though how CWD chemistry influences fungal species composition (and vice versa) is unknown. Carbon mineralization was highest in trembling aspen CWD and increased with decay stage, perhaps facilitated by increased N concentrations. This study suggests that forest management guidelines that consider both deadwood quantity and quality will support a broader range of fungal species and communities through post-disturbance stand development, thereby conserving biodiversity over the longer-term in our managed forest systems.

The cost of microalgae cultivation is one of the largest limitations to achieving sustainable, large-scale microalgae production of commercially desirable lipids. Utilizing CO2 as a ‘free’ carbon source from waste industrial flue gas emissions can offer wide-ranging cost savings. However, these gas streams typically create acidic environments, in which most microalgae cannot survive due to the concentration of CO2 and the presence of other acidic gasses such as NO2 and SO2. To address this situation, we investigated growth of a mixed acid-tolerant green microalgal culture (91% dominated by a single Coccomyxa sp. taxon) bioprospected at pH 2.8 from an acid mine drainage impacted water body. The culture was grown at pH 2.5 and fed with a simulated flue gas containing 6% CO2 and 94% N2. On reaching the end of the exponential growth phase, the culture was exposed to either continued light-dark cycle conditions or continual dark conditions. After three days in the dark, the biomass consisted of 28% of lipids, which was 42% higher than at the end of the exponential phase and 55% higher than the maximum lipid content achieved under light/dark conditions. The stress caused by being continually in the dark also favoured the production of omega-3 and omega-6 polyunsaturated fatty acids (PUFAs; 19.47% and 21.04%, respectively, after 7 days) compared to 7-days of light-dark treatment (1.94% and 9.53%, respectively) and showed an increase in nitrogen content (C:N ratio of 6.4) compared to light-dark treatment (C:N ratio of 11.9). The results of the research indicate that use of acid tolerant microalgae overcomes issues using flue gasses that will create an acidic environment and that applying dark stress is a low-cost stressor stimulates production of desirable dietary lipids.

Peat accumulation in high latitude wetlands represents a natural long-term carbon sink, resulting from the cumulative excess of growing season net ecosystem production over non-growing season (NGS) net mineralization in soils. With high latitudes experiencing warming at a faster pace than the global average, especially during the NGS, a major concern is that enhanced mineralization of soil organic carbon will steadily increase CO2 emissions from northern peatlands. In this study, we conducted laboratory incubations with soils from boreal and temperate peatlands across Canada. Peat soils were pretreated for different soil moisture levels, and CO2 production rates were measured at 12 sequential temperatures, covering a range from − 10 to + 35 °C including one freeze–thaw event. On average, the CO2 production rates in the boreal peat samples increased more sharply with temperature than in the temperate peat samples. For same temperature, optimum soil moisture levels for CO2 production were higher in the peat samples from more flooded sites. However, standard reaction kinetics (e.g., Q10 temperature coefficient and Arrhenius equation) failed to account for the apparent lack of temperature dependence of CO2 production rates measured below 0 °C, and a sudden increase after a freezing event. Thus, we caution against using the simple kinetic expressions to represent the CO2 emissions from northern peatlands, especially regarding the long NGS period with multiple soil freeze and thaw events.

Sludges from pulp and paper mills represent a major ecological and environmental cost, and anaerobic digestion represents a method of waste reduction and energy recovery for these mills. This study compared methane production potential and microbial communities across 11 primary and biosludges from 5 pulp and paper mills using various mill processes. We measured methane production from sludges in anaerobic batch reactor experiments over 64d. Sludges were incubated with and without added substrate to test for organic substrate limitation versus inhibition of methanogens. Initial microbial communities and changes to community composition were determined using Illumina MiSeq for metabarcoding of bacterial and archaeal 16S rRNA genes. Mean methane production potential varied greatly between sludges (0.002–79 mL CH4 g–1 TS). Among primary sludges, kraft mill sludge produced more methane than other mill types. For these other mills, biosludge produced more methane than primary sludge, which had evidence of methanogen inhibition. Microbial communities and diversity were influenced by the initial community composition, and high methane production was only seen in sludges with high diversity. A number of sludges innately produced substantial methane and may be targets for further modelling and larger-scale testing of anaerobic digestion.

Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for arthropod biodiversity assessments from soil. Processing 15 individually collected soil samples recovered significantly higher median richness (488–614 sequence variants) than pooling the same number of samples (165–191 sequence variants) prior to DNA extraction, and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Beta diversity was robust to changes in methodological regimes. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

The purpose of our study was to determine whether earthworms facilitate the burial of surface-applied wood ash. We mixed a fluorescent tracer powder with fly ash from a commercial biomass boiler to track and quantify ash burial in microcosms containing different densities of the deep-burrowing anecic earthworm Lumbricus terrestris L. While passive incorporation of the wood ash-tracer mix from the surface in the absence of earthworms was limited (rarely penetrating more than 2 cm below the surface), earthworms increased the amount of ash-tracer found belowground and the maximum depths at which ash-tracer was observed (up to 16 cm deep). We suspect that earthworms facilitated wood ash burial primarily by creating burrows down which wood ash could be carried by water and by burying wood ash-covered leaf litter. Earthworms may help increase the efficacy of wood ash amendment in ecosystems where it is impractical to manually mix amendments into the soil (e.g. forests).

Coarse woody debris (CWD) is a dynamic source of nutrients in managed forests of eastern North America. The temporal patterns of nutrient export from CWD are challenging to study, and efficient methods are lacking. We made empirical measurements of CWD density, volume, and nutrient concentrations in 5 stages of decay, and paired them with a decay class transition model to project the long-term nutrient dynamics of CWD in a managed northern hardwood forest. The model was used to describe stand-level changes in CWD nutrient pools over 40 years following a selection harvest, and to compare CWD nutrient pools in managed and unmanaged stands. The C content of CWD decreased throughout decay, and mirrored density losses. N, P, and Ca content increased throughout decay, Mg content remained relatively constant, and K was rapidly lost. At the stand level, despite a rapid loss of mass and density, the model projected an initial gain in total N, P and Ca stored in CWD during the first 4–8 years after harvest, whereas net C, Mg, and K began to decrease immediately. The average volume, mass, C and K stocks of CWD in managed stands were approximately 10% lower than unmanaged stands, and N, P, Ca, and Mg were up to 16% lower. This is the first study to use a decay class transition model to study the dynamics of nutrients other than C, and the model serves as a template upon which other models of CWD decay can be built.

The Athabasca Oil Sands in Alberta, Canada, is one of the largest point sources of nitrogen oxides in Canada. There are concerns that elevated nitrogen (N) deposition will adversely impact forest ecosystems located downwind of emission sources. The role of the forest floor in regulating these potential eutrophication effects was investigated following a 5-year enrichment study in which N was applied as NH4NO3 above the canopy of a jack pine (Pinus banksiana Lamb) stand in northern Alberta close to Fort McMurray at rates ranging from 5 to 25 kg N ha−1 y−1 in addition to background deposition of approximately 2 kg N ha−1 y−1. Chemical analysis of lichen mats revealed that the N concentration in the apical (upper) lichen tissue and necrotic tissue increased with treatment. When expressed as a N pool, the fibric–humic material held the largest quantity of N across all treatments due to its relatively large mass (172–214 kg N ha−1), but there was no significant treatment effect. Soil net N mineralization and net nitrification rates did not differ among N treatments after five years of application. A 15N tracer applied to the forest floor showed that N is initially absorbed by the apical lichen (16.6% recovery), FH material (29.4% recovery), and the foliage of the vascular plant Vaccinium myrtilloides (31.7% recovery) in particular. After 2 years, the FH 15N pool size was elevated and all other measured pools were depleted, indicating a slow transfer of N to the FH material. Applied 15N was not detectable in mineral soil. The microbial functional gene ammonia monooxygenase (amoA) responsible for catalyzing the first step in nitrification was undetectable using PCR screening of mineral soil microbial communities in all treatments, and broad fungal/bacterial qPCR assays revealed a weak treatment effect on fungal: bacterial ratios in mineral soil with decreasing relative fungal abundance under higher N deposition. This work suggests that terricolous lichen mats, which form the majority of ground cover in upland jack pine systems, have a large capacity to effectively retain elevated N deposition in soil humus.

Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analyzed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. The methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

The use of CO2 rich industrial flue gases to support cultivation of microalgae to produce lipids for biofuel and other applications is an increasingly researched option. However, this approach presents a challenge, as whilst flue gasses typically contain 6-10% CO2, excessive medium acidification can be caused by the presence of NOx and SO2. The use of acidophilic or acid-tolerant species is a possible solution, but little is known about these microalgae. In this study we investigated the growth of a bioprospected acid-tolerant mixed photosynthetic green microalgae culture (91% dominated by a single Coccomyxa sp. taxon) at pH 2.5 and fed with a simulated flue gas containing 6% CO2 and 94% N2. At the end of the exponential growth phase, lipid accumulation and profiles, and the elemental composition of biomass were analysed over one week during which biomass was exposed to either continued light-dark cycle conditions or continual dark conditions. After three days of dark stress, the biomass consisted of approximately 28% of lipids, which was 42% higher than at the end of the exponential phase and 55% higher than the maximum lipid content achieved under light/dark conditions. Oleic acid (C18:1), pentadecanoic acid (C15:0), and palmitic acid (C16:0) were the dominant fatty acids at the end of the exponential phase, and light-dark and dark-treated biomass, respectively. Dark stress conditions favoured polyunsaturated fatty acid production and showed an increase in nitrogen content. This suggests that the use of dark stress to stimulate production of desirable lipids is a no-cost alternative to other commonly used stressors.

Calcium (Ca) concentrations in lakes have declined in many regions, and concerns have been expressed that Ca levels are falling below biologically significant thresholds. Wood ash additions to soil are typically used to combat soil acidification, and it is unclear whether wood ash additions to upland soils will lead to higher Ca leaching to surface waters. In this study we applied fly ash or bottom ash at 4 Mg ha−1 and 8 Mg ha−1 to upland soils at replicated plots in Haliburton Forest in central Ontario and measured soil water chemistry at 3 depths over 4 years. Increases in soil water Ca concentration following application were quite modest and occurred primarily in the fly ash treatments in the upper depth (0.3 m) during the first 2 years following application. There was no concomitant increase in pH or acid-neutralizing capacity primarily because of the high sulphate leaching associated with the fly ash treatments. Overall, these results show that wood ash addition to soils at moderate doses will have little impact on soil export to lakes.

Canada has extensive peat deposits in northern high latitude wetlands and permafrost ecosystems. Peat accumulation represents a natural long-term carbon sink attributed to the cumulative excess of growing season net ecosystem production over non-growing season net mineralization. However, near-surface peat deposits are vulnerable to climate change and permafrost landscape transition. One specific concern is a potential rapid increase in the non-growing season carbon loss through enhanced organic matter mineralization under a warming climate. Our experimental study explores the response of peat CO2 exchanges to (1) temperature, using the conventional Q10 parameter, and (2) moisture content. The observed responses are expected to reflect, at least in part, differential soil microbial adaptations to varying wetland conditions, across two northern ecoclimatic zones. Laboratory incubations were carried out with shallow peat samples from different depths collected at seven Canadian wetland sites and adjusted to five moisture levels. For each subsample (varying by site, depth and moisture content), CO2 fluxes were measured at 12 sequential temperature settings from -10 to 35˚C. For each subsample, the data were fitted to an exponential equation to derive a Q10 value. In general, boreal peat samples were more temperature sensitive than temperate peat. The optimum moisture level for CO2 release was determined for all the subsamples and related to variations in wetland vegetation and landform types. As a general trend, increasing water saturation reduced the CO2 release rate from a given subsample. We further tested a flexible curve-fitting equation, as recently proposed on a theoretical basis, to recompile the data by ecoclimatic peat type and to account for the non-growing season dynamics. These findings will contribute to Canada’s national carbon budget model by guiding the development and calibration of the peatland module.

Acidic, metalliferous mine tailings are hostile environments for vegetation growth. Despite this, Betula papyrifera (paper birch) has emerged as a primary colonizer in metal contaminated areas. This study assessed foliar nutrient resorption efficiency and proficiency in B. papyrifera growing on two Ni-Cu (nickel-copper) tailings sites and two smelter-impacted sites near Sudbury, Ontario, in Canada. Soils at the smelter-impacted sites were more acidic, with significantly higher OM (organic matter) and P (phosphorus), whereas soil at the tailings sites had much higher concentrations of many metals. The primary limiting nutrients in the tailings were P and K (potassium), which were below reported foliar critical thresholds for paper birch, whereas foliar nitrogen (N) concentrations indicated sufficiency. Despite much lower pre-senescence foliar P and K concentrations, trees growing on tailings did not resorb nutrients more effectively than those at smelter-impacted sites. Wide within-site variation in foliar nutrient resorption efficiency and proficiency may indicate that there are physiological constraints to nutrient resorption in contaminated sites, preventing trees from fully resorbing foliar P and K. The similarities in P resorption proficiency despite large differences in pre-senescence chemistry indicate that there may be critical physiological limits below which paper birch are incapable of resorbing nutrients.

Facilitating the establishment of native pioneer plant species on mine tailings with inherent metal and/or acid tolerance is important to speed up natural succession at minimal cost, especially in remote areas where phytoremediation can be labor intensive. We investigated vegetation community dynamics after ∼48 years of succession along two legacy Ni–Cu mine tailings and waste rock deposits in the Sudbury Basin, Ontario, Canada with and without various site amendments (i.e. liming and fertilization) and planting. Metal/acid tolerant pioneer plants (Betula papyrifera, Populus tremuloides, Pohlia nutans) appeared to facilitate the establishment of less tolerant species. Conifers and nitrogen-fixers less tolerant to site conditions were planted at the fully amended (limed, fertilized, planted) mine tailings site in the 1970s, but conifers were not propagating at the site or facilitating understory succession. The planted nitrogen-fixing leguminous species Lotus corniculatus was, however, associated with increased diversity. These findings have implications for long-term reclamation strategies in acidic mine waste deposits utilizing native species, as primary colonizing tree species are only recently emerging as candidates for phytoremediation. Novelty statement The potential for native species to act as facilitators for vegetation colonization has rarely been investigated on tailings, despite wide use in remediation of less toxic sites. This study provides a retrospective of over 40 years of plant growth following initial treatment of toxic tailings. We observed that regardless of tailings geochemical conditions, acid/metal tolerant pioneer plants were facilitating ecological succession on acidic Ni-Cu mine tailings sites.

Application of stable soil amendments is often the key to successful phytostabilization and rehabilitation of mine tailings, and microbial guilds are primary drivers of many geochemical processes promoted by these amendments. Field studies were set up at a tailings management area near Sudbury, Ontario to examine performance of blends of lime stabilized municipal biosolids and compost at nine different rates over thick (1 m) municipal compost covers planted with agricultural crops. Based on biogeochemical variability of the substrates four and ten years after application of the initial compost cover, the experimental plots could be classified into three categories: “Low” rate (0–100 t ha−1 biosolids), “Medium” rate (200–800 t ha−1), and “High” rate (1600–3200 t ha−1) treatments. The addition of biosolids materials to the thick compost cover at rates higher than 100 t ha−1 significantly reduced C:N ratio of the substrates, available phosphorus, and some of the nutrient cations, while notably increasing inorganic carbon and the potential solubility of Ni and Cu. This suggests that increasing biosolids application rates may not equivalently ameliorate soil quality and geochemical stability. Correspondingly, microbial communities were altered by biosolids additions, further intensifying the negative impacts of biosolids on long-term efficiency of the initial compost cover. Abundance of cellulose, hemicellulose, and lignocellulose decomposers (as key drivers of mineralization and humification) was significantly reduced by “Medium” and “High” rate treatments. Most DNA sequences with high affinity to denitrifiers were detected in “High” rate treatments where geochemical conditions were optimal for higher microbial denitrification activities. These findings have implications for improving the long-term efficiency of reclamation and environmental management programs in mine tailings of northern temperate climates.

For mass culture of photosynthetic green microalgae, industrial flue gases can represent a low-cost resource of CO

Shallow lake sediments harbor methanogen communities that are responsible for large amounts of CH(4) flux to the atmosphere. These communities play a major role in degrading in-fluxed terrestrial organic matter (t-OM)—much of which settles in shallow near-shore sediments. Little work has examined how sediment methanogens are affected by the quantity and quality of t-OM, and the physicochemical factors that shape their community. Here, we filled mesocosms with artificial lake sediments amended with different ratios and concentrations of coniferous and deciduous tree litter. We installed them in three boreal lakes near Sudbury, Canada that varied in trophic status and water clarity. We found that higher endogenous nutrient concentrations led to greater CH(4) production when sediment solar irradiance was similar, but high irradiance of sediments also led to higher CH(4) concentrations regardless of nutrient concentrations, possibly due to photooxidation of t-OM. Sediments with t-OM had overall higher CH(4) concentrations than controls that had no t-OM, but there were no significant differences in CH(4) concentrations with different t-OM compositions or increasing concentrations over 25%. Differences among lakes also explained variation in methanogen community structure, whereas t-OM treatments did not. Therefore, lake characteristics are important modulators of methanogen communities fueled by t-OM.

The early stages of community development influence longer-term establishment of species, traits, and ultimately ecosystem function. How this process varies with small- and large-scale abiotic and biotic conditions is poorly studied in microbes. Here we tested how different spatial scales influenced the rate at which taxonomic and functional composition of microbial communities changed over time in lake sediments, and whether these changes occurred synchronously across different environments given the same initial communities. We manipulated the small-scale environment by creating sediments with different terrestrial organic matter (t-OM) quantity and quality, and placing these in two lakes differing in trophic status to vary the large-scale environment. We found that archaeal and bacterial communities, but not fungi, became taxonomically dissimilar over two months despite being derived from the same initial leaf material, primarily because of small-scale environmental conditions. Sediment t-OM quantity consistently explained changes in community composition both temporally within mesocosms and spatially between mesocosms in different lakes. Archaea, bacteria, and fungi also varied by up to 10-times in how quickly they changed, providing among the first evidence in the same study system that they respond differently over time to abiotic and biotic conditions. Finally, functional composition was influenced by both small- and large-scale environmental conditions, with genes involved in t-OM decomposition showing some of the largest changes in abundance after one year. Our study highlights that future changes to both sediments and lake waters can modify how sediment microbial communities develop with consequences for important ecosystem functions like carbon cycling.

A growth chamber trial was conducted to investigate the effects of blends of pulp and paper mill residuals and forest humus on soil properties, microbial communities and germination rate and biomass production of annual ryegrass (Lolium multiflorum) in both acid-producing and neutral to mildly alkaline mine tailings in a mine reclamation context. The organic residual amendments improved the nutritional status of the tailings substrates, and increased pH in acid-generating tailings, leading to higher germination rates and improved plant growth. A trace addition (

How ecosystem functioning changes with microbial communities remains an open question in natural ecosystems. Both present-day environmental conditions and historical events, such as past differences in dispersal, can have a greater influence over ecosystem function than the diversity or abundance of both taxa and genes. Here, we estimated how individual and interactive effects of microbial community structure defined by diversity and abundance, present-day environmental conditions, and an indicator of historical legacies influenced ecosystem functioning in lake sediments. We studied sediments because they have strong gradients in all three of these ecosystem properties and deliver important functions worldwide. By characterizing bacterial community composition and functional traits at eight sites fed by discrete and contrasting catchments, we found that taxonomic diversity and the normalized abundance of oxidase-encoding genes explained as much variation in CO(2) production as present-day gradients of pH and organic matter quantity and quality. Functional gene diversity was not linked to CO(2) production rates. Surprisingly, the effects of taxonomic diversity and normalized oxidase abundance in the model predicting CO(2) production were attributable to site-level differences in bacterial communities unrelated to the present-day environment, suggesting that colonization history rather than habitat-based filtering indirectly influenced ecosystem functioning. Our findings add to limited evidence that biodiversity and gene abundance explain patterns of microbiome functioning in nature. Yet we highlight among the first time how these relationships depend directly on present-day environmental conditions and indirectly on historical legacies, and so need to be contextualized with these other ecosystem properties.

As the focus of soil science education in Canada and elsewhere has shifted towards nonsoil science majors, it is important to understand if and how this has affected the scope of introductory soil ...

Skid trails comprise up to 40% of managed forest areas and are subject to wide variations in disturbance intensity. Despite potential for accelerated carbon (C) and nutrient losses following use, they are under-represented in studies of forest soil biogeochemistry. To address this, we assessed soil chemistry and respiration as CO 2 efflux (FCO 2 ) on primary and tertiary skid trails relative to adjacent cut forest (control) between May and October, following a winter partial-harvest in a northern hardwood forest. Primary trails were highly mixed and compacted (bulk density: ≈1.18 g cm −3 ) relative to forest controls (≈0.53 g cm −3 ) and tertiary trails (≈0.59 g cm −3 ). FCO 2 rates corrected for higher trail temperatures (+2.5 °C) were half that of controls. An absence of root respiration likely accounted for most of this difference, with precipitation event-based moisture saturation and labile C limitations for heterotrophs accounting for the remainder. A similar but weaker pattern was found for tertiary trails: after correcting for higher temperatures (+0.7 °C), trails produced 23% less FCO 2 than controls in ruts only, suggesting compaction and/or root damage inhibited FCO 2 . Concentrations of soil C, N, and cations were 16–52% lower on frequently re-used primary skid trails and 13–30% lower on tertiary skid trails than adjacent forest controls, but 0–20 cm pool sizes were similar amongst treatments. All treatments, except for primary skid trails, expressed substantial inter-correlated declines in soil C, N, and cations (−7% to −40%) by October that were also correlated to FCO 2 rates (r 2 = 0.10, p

Intensified biomass harvesting in northern forests could potentially negatively impact soils. This study measured microbial community structure and function to assess the impacts of intensified biomass removal on soil from a managed northern jack pine (Pinus banksiana Lamb.) forest in Ontario, Canada. Four clear-cut harvesting removal intensities were compared with uncut controls and mature, fire-regenerated forest reference plots: stem-only removal, full-tree biomass removal, full-tree biomass with stump removal, and full-tree biomass with stump removal and soil blading that eliminated all aboveground and much belowground organic matter. A nearby recently burned forest site, representing common natural disturbance in the region, was also studied. Within the first two years after harvesting, there were significant differences in community structure and degradation of various C compounds among all harvested and unharvested sites, but little difference in communities across the different harvest intensities. Communities within the fire site were not comparable with those of harvested treatments, indicating that clear-cut logging may not initially produce an ecologically comparable disturbance with that of fire, although this conclusion is based on only one fire disturbance site. In the two years after harvesting, an important time for seedling establishment in managed forest systems, it appears that intensification of harvesting does not further disrupt microbial community structure and functioning beyond impacts from current harvest practices.

Terrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for soil arthropod biodiversity assessments. Processing individually collected field samples recovered significantly higher richness (539-596 ESVs) than pooling the same number of field samples (126-154 ESVs), and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Variations in the number of individual or composite samples or DNA extractions resulted in similar sample clustering based on community dissimilarities. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding of local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.

Wood ash is typically applied to soils to counteract acidification and base cation depletion, but the effects of this ash on the organic layer microbial community are rarely studied. We analyzed microbial responses to ash addition in two field-scale experiments in Ontario, Canada. One experiment was in a young boreal forest soil and the other was in an uneven-aged hardwood north-temperate forest soil. We also investigated the effects of a natural forest fire near the boreal experiment. In both cases, ash addition had no effect on overall microbial biomass and respiration, but increased the phylogenetic diversity of bacterial communities and the relative abundance of Bacteroidetes taxa, though effects on other bacterial taxa were site-specific. Eukaryotic effects also varied by experiment; at the boreal site, ash increased eukaryotic phylogenetic diversity and decreased the fungi:bacteria ribosomal marker ratio, but at the temperate site ash decreased eukaryotic diversity and did not affect the fungi:bacteria ratio. There was limited additional effect on the boreal soil microbial community of increasing ash addition from 0.7 to 5.7 t ha −1 , as determined by T-RFLP analysis, though soil pH in both experiments increased with higher addition rates. At the temperate site, ash effects were consistently stronger for fly ash than for bottom ash. In both experiments, only 14 unique bacterial taxa were found after ash addition, and the strongest driver of overall community composition was the forest type, not ash treatment. In contrast, the soil microbial community observed at the forest fire site was clearly different. Overall, these results indicate that wood ash addition has only minimal effects on the composition of the soil microbial community in sites across two distinct global forest biomes.