Ecological mechanisms and effectiveness of bioremediation in Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 2014What drives microbial community structure and function is a fundamental question of microbial ecology. Soil microbial communities have wide ranging metabolic capabilities, which include performing oxidation-reduction reactions responsible for cycling of nutrients and organic compounds and biodegradation of pollutants. One major determinant of microbial function in soils is vegetation type. Considering plants are diverse in chemical composition, they impact the quantity and quality of carbon and nutrients available to microbes through root turnover, root leachates, as well as by altering pH and soil microclimate (moisture, temperature). Rhizosphere interactions, in the form of phytoremediation, can be capitalized upon to provide a potentially cost effective method for detoxifying contaminated soils using plants and associated soil microorganisms. The remote locations and cold climate of Alaska provide unique challenges associated with phytoremediation such as finding effective plant species that can achieve successful site clean-up despite the extreme environmental conditions that includes minimal site management. Here we investigate the potential mechanisms and related effectiveness of microbial communities and native boreal vegetation associated with contaminant degradation and biogeochemical cycling. We examined three different soil systems to understand how dominant vegetation type, historical treatment and contamination shape the microbial community structure and functional potential. First, we used stable isotope probing to understand how microbial communities act in concert to biotransform the recalcitrant contaminants, polychlorinated biphenyls. Second, we sought to understand if dominant vegetation type controls microbial community structure and function either through direct impacts of plant root exudates and detritus or indirectly through the influence of plants on soil chemistry, composition, and structure. Finally, we conducted a forensic investigation of a petroleum contaminated site with no active site management for 15 years to assess the long-term effects of phytoremediation on soil petroleum concentrations, microbial community and vegetation colonization. The results of these experiments provide novel insights into the mechanisms of contaminant removal in boreal forest soils and the role of plants in ecosystem resilience to contamination, and demonstrates that phytoremediation using native and local plants can be an effective means to treat petroleum contaminated soils.Chapter 1: Introduction -- Chapter 2: Aromatic compound processing in PCB-contaminated soil: carbon flow through the microbial ecosystem -- Chapter 3: Microbial community structure and functional potential associated with four boreal forest vegetation types -- Chapter 4: Long-term effects of nutrient addition and phytoremediation on diesel and crude oil contaminated soils in subarctic Alaska -- Chapter 5: Conclusions

The native shrub, Piliostigma reticulatum , as an ecological “resource island” for mango trees in the Sahel

African farmers are increasingly adopting sustainable agricultural practices including use of native shrub intercropping approaches. In one village of Sénégal (near Thiès) it was reported that farmers planted mango (Mangifera indica) seedlings within the canopies of a native shrub (Piliostigma reticulatum). Anecdotal information and qualitative observations suggested that the presence of P. reticulatum promoted soil quality and a competitive advantage for establishing mango plantations. We hypothesized that soil chemical and microbial properties of mango rhizosphere soil growing in the presence of P. reticulatum would be significantly improved over soils associated with mango growing outside the influence of P. reticulatum. The results showed that mango-shrub interplanting significantly lowered pH, and increased arbuscular mycorrhizal fungi (AMF) colonization of mango roots, enzyme activities, and microbial biomass compared to mango alone. Phylogenetic analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that community structures of fungi, bacteria, and bacterial genes responsible for denitrification (nirK) of the soil from the rooting zone of the mango-shrub intercropping system were distinct from all other soil outside the influence of P. reticulatum. It is concluded that P. reticulatum enhances soil biological functioning and that there is a synergistic effect of intercropping mango with the native shrub, P. reticulatum, in soil quality with a more diverse community, greater AMF infection rates, and greater potential to perform decomposition and mineralize nutrients

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Abstract Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy

Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.

Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions

Microbiome assembly in thawing permafrost and its feedbacks to climate

The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post‐thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw‐mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well‐suited to thrive in changing environmental conditions. We predict that on a short timescale and following high‐disturbance thaw (e.g., thermokarst), stochasticity dominates post‐thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower‐intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post‐thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change