Jack W. McFarland

A first comprehensive census of fungi in soil reveals both hyperdiversity and fine‐scale niche partitioning

Fungi play key roles in ecosystems as mutualists, pathogens, and decomposers. Current estimates of global species richness are highly uncertain, and the importance of stochastic vs. deterministic forces in the assembly of fungal communities is unknown. Molecular studies have so far failed to reach saturated, comprehensive estimates of fungal diversity. To obtain a more accurate estimate of global fungal diversity, we used a direct molecular approach to census diversity in a boreal ecosystem with precisely known plant diversity, and we carefully evaluated adequacy of sampling and accuracy of species delineation. We achieved the first exhaustive enumeration of fungi in soil, recording 1002 taxa in this system. We show that the fungus : plant ratio in Picea mariana forest soils from interior Alaska is at least 17:1 and is regionally stable. A global extrapolation of this ratio would suggest 6 million species of fungi, as opposed to leading estimates ranging from 616 000 to 1.5 million. We also find that clos...

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.

Cycling Dynamics of NH4+ and Amino Acid Nitrogen in Soils of a Deciduous Boreal Forest Ecosystem

AbstractConventional 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.

THE EVOLUTIONARY HISTORY OF MYCORRHIZAL SPECIFICITY AMONG LADY'S SLIPPER ORCHIDS

Abstract 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 ladys 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.

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

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.

Estimating aboveground biomass in interior Alaska with Landsat data and field measurements

a b s t r a c t Terrestrial plant biomass is a key biophysical parameter required for understanding ecological systems in Alaska. An accurate estimation of biomass at a regional scale provides an important data input for ecological modeling in this region. In this study, we created an aboveground biomass (AGB) map at 30-m resolution for the Yukon Flats ecoregion of interior Alaska using Landsat data and field measurements. Tree, shrub, and herbaceous AGB data in both live and dead forms were collected in summers and autumns of 2009 and 2010. Using the Landsat-derived spectral variables and the field AGB data, we generated a regression model and applied this model to map AGB for the ecoregion. A 3-fold cross-validation indicated that the AGB estimates had a mean absolute error of 21.8 Mg/ha and a mean bias error of 5.2 Mg/ha. Additionally, we validated the mapping results using an airborne lidar dataset acquired for a portion of the ecoregion. We found a significant relationship between the lidar-derived canopy height and the Landsat-derived AGB (R 2 = 0.40). The AGB map showed that 90% of the ecoregion had AGB values ranging from 10 Mg/ha to 134 Mg/ha. Vegetation types and fires were the primary factors controlling the spatial AGB patterns in this ecoregion. Published by Elsevier B.V.

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer‐tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Following cloning and colony restriction fragment length polymorphism analysis, we found no significant difference in representation in 19 of the 23 tested primers. We also generated a clone library from two soil DNA extracts using two primers for each extract and compared 456 clone sequences. Community diversity statistics and contingency table tests applied to counts of operational taxonomic units revealed that the two DNA extracts differed significantly, while the pairs of tagged primers from each extract were indistinguishable. Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig‐tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi.

Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions

ABSTRACT Wetland 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. IMPORTANCE Wetlands 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. Wetlands 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.

Spatially explicit estimation of aboveground boreal forest biomass in the Yukon River Basin, Alaska

Quantification of aboveground biomass (AGB) in Alaska’s boreal forest is essential to the accurate evaluation of terrestrial carbon stocks and dynamics in northern high-latitude ecosystems. Our goal was to map AGB at 30 m resolution for the boreal forest in the Yukon River Basin of Alaska using Landsat data and ground measurements. We acquired Landsat images to generate a 3-year (2008–2010) composite of top-of-atmosphere reflectance for six bands as well as the brightness temperature (BT). We constructed a multiple regression model using field-observed AGB and Landsat-derived reflectance, BT, and vegetation indices. A basin-wide boreal forest AGB map at 30 m resolution was generated by applying the regression model to the Landsat composite. The fivefold cross-validation with field measurements had a mean absolute error (MAE) of 25.7 Mg ha−1 (relative MAE 47.5%) and a mean bias error (MBE) of 4.3 Mg ha−1 (relative MBE 7.9%). The boreal forest AGB product was compared with lidar-based vegetation height data; the comparison indicated that there was a significant correlation between the two data sets.