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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.

Decadal scale lake drying in interior Alaska results in lake margin colonization by willow shrub and graminoid vegetation, but the effects of these changes on plant production, biodiversity, soil properties, and soil microbial communities are not well known. We studied changes in soil organic carbon (SOC) and nitrogen (N) storage, plant and microbial community composition, and soil microbial activities in drying and non‐drying lakes in the Yukon Flats National Wildlife Refuge. Historic changes in lake area were determined using Landsat imagery. Results showed that SOC storage in drying lake margins declined by 0.13 kg C m−2 yr−1 over 30 years of exposure of lake sediments, with no significant change in soil N. Lake drying resulted in an increase in graminoid and shrub aboveground net primary production (ANPP, +3% yr−1) with little change in plant functional composition. Increases in ANPP were similar in magnitude (but opposite in sign) to losses in SOC over a 30‐year drying trend. Potential decomposition rates and soil enzyme activities were lower in drying lake margins compared to stable lake margins, possibly due to high salinities in drying lake margin soils. Microbial communities shifted in response to changing plant communities, although they still retained a legacy of the previous plant community. Understanding how changing lake hydrology impacts the ecology and biogeochemistry of lake margin terrestrial ecosystems is an underexamined phenomenon with large impacts to landscape processes. Plain Language Summary: Lake dominated ecosystems in Alaska have experienced periods of widespread lake drying in the past. We understand little of what occurs on these new nearshore habitats following lake drying, especially changes in soil properties and soil microbial communities. Using a combination of remote sensing and field sampling on hundreds of lakes in the Yukon Flats National Wildlife Refuge, we learned that lake margin soils lose significant quantities of soil C in the decades following lake drying, and at the same time soils become increasingly saline and soil microbial activites are reduced. Overall, lake drying has large impacts on the surrounding ecosystems and it is important to understand these changes for management. Key Points: Lake drying in the Yukon Flats National Wildlife Refuge triggers a succession of plant and microbial communities and losses of lake margin soil organic carbon (SOC)Lake drying also results in increases in the salinity of lake margin soils, slowing rates of microbial activitiesAlthough lake drying resulted in losses of SOC, increases in Aboveground Net Primary Production (ANPP) compensated for these losses [ABSTRACT FROM AUTHOR]

UnlabelledWetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest.ImportanceWetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities that mediate carbon cycling in wetlands is critical to accurately predicting their responses to changes in land management and climate. Here, we studied a restored wetland and revealed substantial spatial heterogeneity in biogeochemistry, methane production, and microbial communities, largely associated with the wetland hydraulic design. We observed patterns in microbial community composition and functions correlated with biogeochemistry and methane production, including diverse microorganisms involved in methane production and consumption. We found that methanogenesis gene abundance is inversely correlated with genes from pathways exploiting other electron acceptors, yet the ubiquitous presence of genes from all these pathways suggests that diverse electron acceptors contribute to the energetic balance of the ecosystem. These investigations represent an important step toward effective management of wetlands to reduce methane flux to the atmosphere and enhance belowground carbon storage.

Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle.

This paper outlines molecular analyses of soil fungi within the Bonanza Creek Long Term Ecological Research program. We examined community structure in three studies in mixed upland, black spruce (Picea mariana (Mill.) BSP), and white spruce (Picea glauca (Moench) Voss) forests and examined taxa involved in cellulose degradation at one upland site. We found that soil horizon was the factor by which fungal communities were most strongly structured and that predictable turnover in upland fungal species occurred through succession. Communities from consecutive summers were not significantly different, indicating that interannual variation was small in relation to differences between forest types and soil horizons, yet the community at a seasonal study site underwent significant changes within a year. In each study, mycorrhizal fungi dominated the community. Fungi rather than bacteria appeared to dominate [[.sup.13]C]cellulose degradation, with strongest growth in taxa that were not dominant members of the untreated community, including members of the genus Sebacina. Overall, our results point to considerable interannual resilience juxtaposed with narrow niche partitioning and the capacity of individual taxa in these hyperdiverse communities to respond strongly to resource inputs and changes in other abiotic environmental parameters such as temperature. Our data double the cumulative total of fungal sequences in GenBank and together achieve a better picture of fungal communities here than for any other ecosystem on earth at this time. Resume: Cet article decrit les analyses moleculaires effectuees sur les champignons du sol dans le cadre du programme de recherche a long terme en ecologie de Bonanza Creek. Nous avons etudie la structure des communautes par le biais de trois etudes portant sur des forets mixtes en milieu sec, d'epinette noire (Picea mariana (Mill.) BSP) et d'epinette blanche (Picea glauca (Moench) Voss) et nous avons etudie les taxons impliques dans la degradation de la cellulose dans une station seche. Nous avons trouve que l'horizon du sol etait le facteur preponderant dans la structuration des communautes fongiques et que le renouvellement previsible des especes fongiques en milieu sec se produisait par l'entremise de la succession. Les communautes presentes d'un ete a l'autre n'etaient pas significativement differentes indiquant que la variation interannuelle etait faible comparativement aux differences entre les types de foret et les horizons du sol. Par contre, la communaute presente sur le site d'une etude saisonniere a subi des changements significatifs a l'interieur d'une annee. Dans chaque etude, les champignons mycorhiziens dominaient la communaute. Les champignons plutot que les bacteries semblaient dominer la degradation de la [[.sup.13]C]cellulose; la plus forte croissance a ete observee parmi les taxons qui n'etaient pas des membres dominants de la communaute non traitee, incluant des membres du genre Sebacina. Globalement, nos resultats font ressortir la grande resilience interannuelle juxtaposee a d'etroites niches ecologiques ainsi que la capacite de taxons particuliers dans ces communautes hyper diversifiees de reagir fortement aux apports de ressources et a la variation d'autres parametres environnementaux. Nos donnees viennent doubler le total cumulatif de sequences fongiques dans GenBank et ensemble donnent a ce jour une meilleure image des communautes fongiques ici que dans n'importe quel autre ecosysteme ailleurs dans le monde. [Traduit par la Redaction], Introduction Fungi play integral roles in terrestrial ecosystems and hence putatively influence the resilience of boreal systems in the midst of environmental changes such as global warming. Soil fungi impact [...]

Abstract: Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2 gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the direct (microaerobiosis) and indirect (loss of plant C inputs) effects of elevated soil CO2 flux have significant impacts on the composition and overall structural trajectory of soil microbial populations within disturbed areas. [Copyright &y& Elsevier]

Plant and microbial use of nitrogen (N) can be simultaneously mutualistic and competitive, particularly in ecosystems dominated by mycorrhizal fungi. Our goal was to quantify plant uptake of organic and inorganic N across a broad latitudinal gradient of forest ecosystems that varied with respect to overstory taxon, edaphic characteristics, and dominant mycorrhizal association. Using 13C and 15N, we observed in situ the cycling dynamics of NH4 + and glycine through various soil pools and fine roots over 14 days. Recovery of 15N as soil N varied with respect to N form, forest type, and sampling period; however, there were similarities in the cycling dynamics of glycine and NH4 + among all forest types. Microbial immobilization of 15N was immediately apparent for both treatments and represented the largest sink (~25%) for 15N among extractable soil N pools during the first 24 h. In contrast, fine roots were a relatively small sink (<10%) for both N forms, but fine root 13C enrichment indicated that plants in all forest types absorbed glycine intact, suggesting that plants and microbes effectively target the same labile soil N pools. Relative uptake of amino acid-N versus NH4 + varied significantly among sites and approximately half of this variation was explained by mycorrhizal association. Estimates of plant uptake of amino acid-N relative to NH4 + were 3× higher in ectomycorrhizal-dominated stands (1.6 ± 0.2) than arbuscular mycorrhizae-dominated stands (0.5 ± 0.1). We conclude that free amino acids are an important component of the N economy in all stands studied; however, in these natural environments plant uptake of organic N relative to inorganic N is explained as much by mycorrhizal association as by the availability of N forms per se. [ABSTRACT FROM AUTHOR]

Plant and microbial use of nitrogen (N) can be simultaneously mutualistic and competitive, particularly in ecosystems dominated by mycorrhizal fungi. Our goal was to quantify plant uptake of organic and inorganic N across a broad latitudinal gradient of forest ecosystems that varied with respect to overstory taxon, edaphic characteristics, and dominant mycorrhizal association. Using 13C and 15N, we observed in situ the cycling dynamics of NH4 + and glycine through various soil pools and fine roots over 14 days. Recovery of 15N as soil N varied with respect to N form, forest type, and sampling period; however, there were similarities in the cycling dynamics of glycine and NH4 + among all forest types. Microbial immobilization of 15N was immediately apparent for both treatments and represented the largest sink (~25%) for 15N among extractable soil N pools during the first 24 h. In contrast, fine roots were a relatively small sink (<10%) for both N forms, but fine root 13C enrichment indicated that plants in all forest types absorbed glycine intact, suggesting that plants and microbes effectively target the same labile soil N pools. Relative uptake of amino acid-N versus NH4 + varied significantly among sites and approximately half of this variation was explained by mycorrhizal association. Estimates of plant uptake of amino acid-N relative to NH4 + were 3× higher in ectomycorrhizal-dominated stands (1.6 ± 0.2) than arbuscular mycorrhizae-dominated stands (0.5 ± 0.1). We conclude that free amino acids are an important component of the N economy in all stands studied; however, in these natural environments plant uptake of organic N relative to inorganic N is explained as much by mycorrhizal association as by the availability of N forms per se. [ABSTRACT FROM AUTHOR]

Although coevolution is acknowledged to occur in nature, coevolutionary patterns in symbioses not involving species-to-species relationships are poorly understood. Mycorrhizal plants are thought to be too generalist to coevolve with their symbiotic fungi; yet some plants, including some orchids, exhibit strikingly narrow mycorrhizal specificity. Here, we assess the evolutionary history of mycorrhizal specificity in the lady's slipper orchid genus, Cypripedium. We sampled 90 populations of 15 taxa across three continents, using DNA methods to identify fungal symbionts and quantify mycorrhizal specificity. We assessed phylogenetic relationships among sampled Cypripedium taxa, onto which we mapped mycorrhizal specificity. Cypripedium taxa associated almost exclusively with fungi within family Tulasnellaceae. Ancestral specificity appears to have been narrow, followed by a broadening after the divergence of C. debile. Specificity then narrowed, resulting in strikingly narrow specificity in most of the taxa in this study, with no taxon rewidening to the same extant as basal members of the genus. Sympatric taxa generally associated with different sets of fungi, and most clades of Cypripedium-mycorrhizal fungi were found throughout much of the northern hemisphere, suggesting that these evolutionary patterns in specificity are not the result of biogeographic lack of opportunity to associate with potential partners. Mycorrhizal specificity in genus Cypripedium appears to be an evolvable trait, and associations with particular fungi are phylogenetically conserved. [ABSTRACT FROM AUTHOR]

Conventional studies of nitrogen (N) cycling in forest ecosystems have focused on inorganic N uptake as the primary source of N for plant metabolism. More recently, however, alternative sources of N for plant nutrition, such as free amino acids, have gained attention, particularly in nutrient-limited systems. Using a multiple stable isotope (13C and 15N) design, that allowed us to simultaneously assess root uptake of ammonium (NH4 +) and glycine, we compared the cycling dynamics of NH4 + and amino acid N within the soils of several interior Alaskan floodplain balsam poplar stands. Our design included multiple sampling periods extending from 45 min to 14 days, which permitted us to study interpool transfers of our carbon (C) and N isotopes over time. Microbial biomass N was the largest sink of both 15N-ammonium and glycine. Percent recovery of 15N for this pool was an order of magnitude larger than fine-root 15N uptake for most sampling periods. Although recovery of 15N in fine-root biomass was small, amino acid N and NH4 + were assimilated at approximately the same rate irrespective of sampling period, and total recovery was still increasing 2 weeks after application. Recovery of 15N in bulk soil samples did not vary significantly over time for either treatment. However, bulk soil 13C declined steadily during the experiment, measuring less than 30% recovery of added label after 14 days. We suspect that the majority of 13C lost from our soils was respired. Soil microorganisms strongly outcompeted plants in the short term for both NH4 + and amino acid N. However, amino acid N appears to cycle through soil N pools at approximately the same rate as inorganic N forms. The similarity in uptake patterns for inorganic and organic N suggests that these stands are meeting part of their N requirements directly from amino acids. [ABSTRACT FROM AUTHOR]