Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and ...their responses to global change are a major uncertainty in the global C cycle. Here, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.
Most tree roots on Earth form a symbiosis with either ecto‐ or arbuscular mycorrhizal fungi. Nitrogen fertilization is hypothesized to favor arbuscular mycorrhizal tree species at the expense of ...ectomycorrhizal species due to differences in fungal nitrogen acquisition strategies, and this may alter soil carbon balance, as differences in forest mycorrhizal associations are linked to differences in soil carbon pools. Combining nitrogen deposition data with continental‐scale US forest data, we show that nitrogen pollution is spatially associated with a decline in ectomycorrhizal vs. arbuscular mycorrhizal trees. Furthermore, nitrogen deposition has contrasting effects on arbuscular vs. ectomycorrhizal demographic processes, favoring arbuscular mycorrhizal trees at the expense of ectomycorrhizal trees, and is spatially correlated with reduced soil carbon stocks. This implies future changes in nitrogen deposition may alter the capacity of forests to sequester carbon and offset climate change via interactions with the forest microbiome.
Responses of arbuscular and ectomycorrhizal trees to atmospheric nitrogen deposition.
As land use leaves massive tracts of land vacant for recovery, restoration must undergo a substantial shift to incorporate a complexity perspective beyond the traditional community, biodiversity or ...functional views. With an interaction–function perspective, we may be able to achieve ecosystems with better chances to adapt to current environmental changes and, especially, to climate change. We explore combined approaches that include still unused and underexplored techniques that will soon go mainstream and produce massive amounts of information to address the complexity gap. As we understand how complexity reassembles after the end of agriculture, we will be able to design actions to restore or enhance it at unprecedented spatial scales while increasing its adaptability to environmental changes.
Moreno and Bhatnagar argue in favor of using an ‘interaction–function’ perspective to understand the dynamics of ecosystem recovery after land-use change, especially in the light of climate change.
Mycorrhizal fungi are critical members of the plant microbiome, forming a symbiosis with the roots of most plants on Earth. Most plant species partner with either arbuscular or ectomycorrhizal fungi, ...and these symbioses are thought to represent plant adaptations to fast and slow soil nutrient cycling rates. This generates a second hypothesis, that arbuscular and ectomycorrhizal plant species traits complement and reinforce these fungal strategies, resulting in nutrient acquisitive vs. conservative plant trait profiles. Here we analyzed 17,764 species level trait observations from 2,940 woody plant species to show that mycorrhizal plants differ systematically in nitrogen and phosphorus economic traits. Differences were clearest in temperate latitudes, where ectomycorrhizal plant species are more nitrogen use- and phosphorus use-conservative than arbuscular mycorrhizal species. This difference is reflected in both aboveground and belowground plant traits and is robust to controlling for evolutionary history, nitrogen fixation ability, deciduousness, latitude, and species climate niche. Furthermore, mycorrhizal effects are large and frequently similar to or greater in magnitude than the influence of plant nitrogen fixation ability or deciduous vs. evergreen leaf habit. Ectomycorrhizal plants are also more nitrogen conservative than arbuscular plants in boreal and tropical ecosystems, although differences in phosphorus use are less apparent outside temperate latitudes. Our findings bolster current theories of ecosystems rooted in mycorrhizal ecology and support the hypothesis that plant mycorrhizal association is linked to the evolution of plant nutrient economic strategies.
ABSTRACT
Ecologists have frequently observed a pattern of fungal succession during litter decomposition, wherein different fungal taxa dominate different stages of decay in individual ecosystems. ...However, it is unclear which biological features of fungi give rise to this pattern. We tested a longstanding hypothesis that fungal succession depends on the evolutionary history of species, such that different fungal phyla prefer different decay stages. To test this hypothesis, we performed a meta-analysis across studies in 22 different ecosystem types to synthesize fungal decomposer abundances at early, middle and late stages of plant litter decay. Fungal phyla varied in relative abundance throughout decay, with fungi in the Ascomycota reaching highest relative abundance during early stages of decay (P < 0.001) and fungi in the Zygomycota reaching highest relative abundance during late stages of decay (P < 0.001). The best multiple regression model to explain variation in abundance of these fungal phyla during decay included decay stage, as well as plant litter type and climate factors. Most variation in decay-stage preference of fungal taxa was observed at basal taxonomic levels (phylum and class) rather than finer taxonomic levels (e.g. genus). For many finer-scale taxonomic groups and functional groups of fungi, plant litter type and climate factors were better correlates with relative abundance than decay stage per se, suggesting that the patchiness of fungal community composition in space is related to both resource and climate niches of different fungal taxa. Our study indicates that decomposer fungal succession is partially rooted in fungal decomposers’ deep evolutionary history, traceable to the divergence among phyla.
The evolutionary history of fungal decomposers contributes to the structure of complex microbial decomposer communities.
Niche differentiation among species is a key mechanism by which biodiversity may be linked to ecosystem function. We tested a set of widely invoked hypotheses about the extent of niche ...differentiation in one of the most diverse communities on Earth, decomposer microorganisms, by measuring their response to changes in three abundant litter resources: lignin, cellulose, and nitrogen (N). To do this, we used the model system Arabidopsis thaliana to manipulate lignin, cellulose, and N availability and then used high-throughput sequencing to measure the response of microbial communities during decay. Resequencing the decomposer communities after incubation of decomposed litter with pure substrates showed that groups of species had unique substrate use profiles, such that species organized into functional "guilds" of decomposers that were associated with individual litter chemicals. Low concentrations of lignin, cellulose, or N in the litter caused unique shifts in decomposer community composition after 1 yr of decay. Low cellulose plants had low levels of fungi in all decomposer guilds, low lignin plants had high levels of fungi in all decomposer guilds, and low N plants had low levels of fungi in decomposer guilds associated with sucrose and lignin. The relative abundance of decomposer guilds correlated with the total loss of individual litter chemicals during litter decay in the field. In addition, N fertilization shifted decomposer communities during both the early and later stages of decay to those dominated by decomposers in the cellulose guild. Our results contrast the assumption that major carbon (C) and N degradation mechanisms are uniform across whole decomposer communities and instead suggest that decomposition arises from complementarity among groups of metabolically distinct taxa.
Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune ...activities that regulate the long‐term stabilization of carbon in ecosystems. In this review, we outline the process of environmental engineering and synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community and modify an ecosystem function target. Recent work, enabled by high‐throughput technologies and modeling approaches, indicate that microbial inocula designed from the top‐down, particularly through directed evolution, may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering. We address outstanding questions about the determinants of inocula establishment and provide suggestions for further research about the possibilities and challenges of environmental microbiome engineering as a tool to combat climate change.
Environmental microbiome engineering is emerging as a potential avenue for climate change mitigation. In this process, microbial inocula are introduced to natural microbial communities to tune activities that regulate the stabilization of carbon in ecosystems. We synthesize key considerations about ecosystem functions to target, means of sourcing microorganisms, strategies for designing microbial inocula, methods to deliver inocula, and the factors that enable inocula to establish within a resident community. Microbial inocula designed from the top‐down may generally have a higher chance of establishing within existing microbial communities than other historical approaches to microbiome engineering.
Nitrogen (N) availability relative to plant demand has been declining in recent years in terrestrial ecosystems throughout the world, a phenomenon known as N oligotrophication. The temperate forests ...of the northeastern U.S. have experienced a particularly steep decline in bioavailable N, which is expected to be exacerbated by climate change. This region has also experienced rapid urban expansion in recent decades that leads to forest fragmentation, and it is unknown whether and how these changes affect N availability and uptake by forest trees. Many studies have examined the impact of either urbanization or forest fragmentation on nitrogen (N) cycling, but none to our knowledge have focused on the combined effects of these co‐occurring environmental changes. We examined the effects of urbanization and fragmentation on oak‐dominated (Quercus spp.) forests along an urban to rural gradient from Boston to central Massachusetts (MA). At eight study sites along the urbanization gradient, plant and soil measurements were made along a 90 m transect from a developed edge to an intact forest interior. Rates of net ammonification, net mineralization, and foliar N concentrations were significantly higher in urban than rural sites, while net nitrification and foliar C:N were not different between urban and rural forests. At urban sites, foliar N and net ammonification and mineralization were higher at forest interiors compared to edges, while net nitrification and foliar C:N were higher at rural forest edges than interiors. These results indicate that urban forests in the northeastern U.S. have greater soil N availability and N uptake by trees compared to rural forests, counteracting the trend for widespread N oligotrophication in temperate forests around the globe. Such increases in available N are diminished at forest edges, however, demonstrating that forest fragmentation has the opposite effect of urbanization on coupled N availability and demand by trees.
Bio‐available nitrogen (N) has been declining in temperate forests throughout the world, but we find that urbanization may relieve this N decline through increased soil N cycling rates and subsequent N uptake by trees. However, conditions at the forest edge, which are often created during urban expansion, negate increases in soil N cycling rates.
Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and ...soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.
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