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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.

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.

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.

Phytoremediation can be a cost-effective method of restoring contaminated soils using plants and associated microorganisms. Most studies follow the impacts of phytoremediation solely across the treatment period and have not explored long-term ecological effects. In 1995, a phytoremediation study was initiated near Fairbanks, Alaska, to determine how the introduction of annual grasses and/or fertilizer would influence degradation of petroleum hydrocarbons (PHCs). After one year, grass and/or fertilizer treated soils showed greater decreases in PHC concentrations compared to untreated plots. The site was then left for 15 years with no active site management. In 2011, we re-examined the site to explore the legacy of phytoremediation on contaminant disappearance, as well as plant and soil microbial ecology. We found that the recruited vegetation, along with current bulk soil microbial community structure and function were all heavily influenced by initial phytoremediation treatment. The number of diesel-degrading microorganisms (DDM) was positively correlated with increasing amounts of vegetation on the site, and inversely correlated with PHC concentrations. Even 15 years later, the initial use of fertilizer had significant effects on microbial biomass and microbial community structure activities. We conclude that phytoremediation treatment has long-term, legacy effects on the plant community, which, in turn, impacts microbial community structure, function, and continued TPH disappearance. It is therefore important to consider phytoremediation strategies that not only influence site remediation rates in the short-term, but that also prime the site for restoration of vegetation across the long-term. [ABSTRACT FROM AUTHOR]

The re-vegetation of mining wastes with native plants is a comparatively low-cost solution for mine reclamation. However, re-vegetation fails when extreme pH values, low organic matter, or high concentrations of phytotoxic elements inhibit plant establishment and growth. Our aim was to determine whether the combined addition of municipal waste compost and diazotrophic endophytes (i.e., microorganisms that fix atmospheric N2 and live within plants) could improve plant growth, organic matter accumulation, and phytostabilization of trace element contaminants in two types of hard rock mine waste. We grew a widespread native perennial grass, Bouteloua curtipendula, for one month in alkaline waste rock (porphyry copper mine) and tailings (Ag-Pb-Au mine, amended with dolomite) sourced from southeastern Arizona, United States. B. curtipendula tolerated elevated concentrations of multiple phytotoxic trace elements in the tailings (Mn, Pb, Zn), stabilizing them in roots without foliar translocation. Adding compost and endophyte seed coats improved plant growth, microbial biomass, and organic matter accumulation despite stark differences in the geochemical and physical characteristics of the mining wastes. The widespread grass B. curtipendula is a potential candidate for re-vegetating mine wastes when seeded with soil additives to increase pH and with microbial and organic amendments to increase plant growth. This study quantifies improvements to plant growth, soil fertility, and trace element stabilization with a municipal waste compost topdressing and diazotrophic endophyte seed coating in two common hard rock mining wastes of the western United States. It establishes that a widespread perennial grass, Bouteloua curtipendula, can grow despite high concentrations of phytotoxic trace elements and minimal soil nutrients, and stabilizes trace elements on or in its roots, making it a suitable option for re-vegetation or phytostabilization of hard rock mining wastes. [ABSTRACT FROM AUTHOR]

CH 4 oxidation in landfill cover soils plays a significant role in mitigating CH 4 release to the atmosphere. Oxygen availability and the presence of co-contaminants are potentially important factors affecting CH 4 oxidation rate and the fate of CH 4 -derived carbon. In this study, microbial populations that oxidize CH 4 and the subsequent conversion of CH 4 -derived carbon into CO 2 , soil organic C and biomass C were investigated in landfill cover soils at two O 2 tensions, i.e., O 2 concentrations of 21% ("sufficient") and 2.5% ("limited") with and without toluene. CH 4 -derived carbon was primarily converted into CO 2 and soil organic C in the landfill cover soils, accounting for more than 80% of CH 4 oxidized. Under the O 2 -sufficient condition, 52.9%-59.6% of CH 4 -derived carbon was converted into CO 2 (CE CO2-C ), and 29.1%-39.3% was converted into soil organic C (CE organic-C ). A higher CE organic-C and lower CE CO2-C occurred in the O 2 -limited environment, relative to the O 2 -sufficient condition. With the addition of toluene, the carbon conversion efficiency of CH 4 into biomass C and organic C increased slightly, especially in the O 2 -limited environment. A more complex microbial network was involved in CH 4 assimilation in the O 2 -limited environment than under the O 2 -sufficient condition. DNA-based stable isotope probing of the community with 13 CH 4 revealed that Methylocaldum and Methylosarcina had a higher relative growth rate than other type I methanotrophs in the landfill cover soils, especially at the low O 2 concentration, while Methylosinus was more abundant in the treatment with both the high O 2 concentration and toluene. These results indicated that O 2 -limited environments could prompt more CH 4 -derived carbon to be deposited into soils in the form of biomass C and organic C, thereby enhancing the contribution of CH 4 -derived carbon to soil community biomass and functionality of landfill cover soils (i.e. reduction of CO 2 emission)., (Copyright © 2019 Elsevier Ltd. All rights reserved.)