Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale

Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.

Biological nitrogen fixation in logging residue piles of different tree species after final felling

Logging residues influence the nitrogen cycling processes that play a key role in risks for nitrogen losses from the ecosystem after the clear cut. Therefore, our aim was to identify the potential ability of logging residues to gain external nitrogen via biological nitrogen fixation. We measured biological nitrogen fixation as nitrogenase activity in logging residues of three different tree species (Norway spruce (Picea abies (L.) Karst.), Scots pine (Pinus sylvestris L.), and silver birch (Betula pendula Roth.). The study site was located in south-eastern Finland and was clear cut in 2014 and piles of logging residues were established. Sampling was performed in June 2016, September 2018, and August 2019 and nitrogenase activity in branches and needles or leaves was measured using the acetylene (C₂H₂) reduction assay. Nitrogenase activity (ethylene production) was shown in all residue types. Nitrogenase activity tended to be higher in branches than in needles or leaves and in coniferous residues than in birch. C-to-N ratios were higher in branches than in needles/leaves and in coniferous residues than in birch. Our results indicate that logging residues can acquire external nitrogen from the atmosphere via biological nitrogen fixation and can thus bring nitrogen to the forest ecosystem and substitute some part of the N losses occurring when residues are retained at the site after clear cutting.

Nitrate Uptake from an Aquifer by Two Plantation Forests: Plausibility Strengthened by Process-Based Modelling

Forest plantations can access water from some unconfined aquifers that also contain nitrate at concentrations that could support hydroponic culture, but the separate effects of such additional water and nitrogen availability on tree growth have not hitherto been quantified. We demonstrate these effects using simulation modelling at two contrasting sites supporting Eucalyptus globulus Labill. or Pinus radiata D.Don plantations. The APSIM Eucalyptus and Pinus models simulated plantation growth within 2% of observed growth where the water table was at 4 m depth for eucalypts (height 28 m, MAI 32 m3 ha−1 year−1) and at 23 m for pines (height 37 m, MAI 20 m3 ha−1 year−1). In simulations without an aquifer, observed growth could only be matched using unrealistically high surface soil nitrogen (N) supply, suggesting this is an unlikely mechanism. Simulated aquifer N concentrations, evapotranspiration, and net N mineralization and leaching (emergent properties of modelling) were similar to measured values. These results strengthen the plausibility that aquifer N uptake by plantations could be contributing to tree growth. This hypothesis warrants further research that quantifies these processes at multiple sites. Simulations included growth of herbaceous and tree weed species, and pasture, which demonstrated the utility of the process-based APSIM modelling framework for dynamically simulating carbon, water and N of plantations and other mixed-species systems.

Substrate stoichiometry determines nitrogen fixation throughout succession in southern Chinese forests

The traditional view holds that biological nitrogen (N) fixation often peaks in early- or mid-successional ecosystems and declines throughout succession based on the hypothesis that soil N richness and/or phosphorus (P) depletion become disadvantageous to N fixers. This view, however, fails to support the observation that N fixers can remain active in many old-growth forests despite the presence of N-rich and/or P-limiting soils. Here, we found unexpected increases in N fixation rates in the soil, forest floor, and moss throughout three successional forests and along six age-gradient forests in southern China. We further found that the variation in N fixation was controlled by substrate carbon(C) : N and C : (N : P) stoichiometry rather than by substrate N or P. Our findings highlight the utility of ecological stoichiometry in illuminating the mechanisms that couple forest succession and N cycling.

Assessing Forest Ecosystems across the Vertical Edge of the Mid-Latitude Ecotone Using the BioGeoChemistry Management Model (BGC-MAN)

The mid-latitude ecotone (MLE)—a transition zone between boreal and temperate forests, which includes the regions of Northeast Asia around 30°–60° N latitudes—delivers different ecosystem functions depending on different management activities. In this study, we assessed forest volume and net primary productivity changes in the MLE of Northeast Asia under different ecological characteristics, as well as various current management activities, using the BioGeoChemistry Management Model (BGC-MAN). We selected five pilot sites for pine (Scots pine and Korean red pine; Pinus sylvestris and P. densiflora), oak (Quercus spp.), and larch forests (Dahurian larch and Siberian larch; Larix gmelinii and L. sibirica), respectively, which covered the transition zone across the MLE from Lake Baikal, Russia to Kyushu, Japan, including Mongolia, Northeast China, and the Korean Peninsula. With site-specific information, soil characteristics, and management descriptions by forest species, we established their management characteristics as natural preserved forests, degraded forests, sandy and cold forest stands, and forests exposed to fires. We simulated forest volume (m3) and net primary productivity (Mg C ha−1) during 1960–2005 and compared the results with published literature. They were in the range of those specified in previous studies, with some site-levels under or over estimation, but unbiased estimates in their mean values for pine, oak, and larch forests. Annual rates of change in volume and net primary productivity differed by latitude, site conditions, and climatic characteristics. For larch forests, we identified a high mountain ecotype which warrants a separate model parameterization. We detected changes in forest ecosystems, explaining ecological transition in the Northeast Asian MLE. Under the transition, we need to resolve expected problems through appropriate forest management and social efforts.

Nitrogen fixation does not balance fire-induced nitrogen losses in longleaf pine savannas

Fire is a critical force in structuring ecosystems, but it also removes substantial amounts of nitrogen (N), which can limit plant growth. Biological N fixation (BNF) may alleviate fire-induced N deficiencies that inhibit ecosystem recovery, yet if and how BNF achieves this under frequent fire is unclear. This problem is further complicated in the context of modern human influences (such as land-use history and atmospheric N deposition), which may confound the relationship between fire and fixation. Here, we investigate whether BNF supplies the N necessary to replace fire-induced N losses in restored longleaf pine savannas, and, if so, what factors control fixation. We established 54 1-ha plots of longleaf pine capturing 227 yr of forest recovery and a broad gradient of fire return interval (1.5-20 yr) at two sites in the southeastern United States. We quantified N fixation from three functional groups (herbaceous legumes, soil crusts, and asymbiotic N fixing bacteria), N losses from individual fire events and ecosystem dynamics of N supply and demand. We found that BNF rates were low but sustained over stand age but were substantially below estimated rates of atmospheric N deposition. While fire temporarily stimulated BNF from herbaceous legumes, neither BNF nor atmospheric N deposition were sufficient to balance N losses from fire and soil N stocks declined over stand age. However, rates of N mineralization were surprisingly high and tree productivity was unrelated to N availability, questioning the importance of N limitation in these temperate savannas. While it is possible that progressive N losses signal a decline in ecosystem resiliency, N enrichment from multiple land-use transitions and anthropogenic N deposition may suppress rates of BNF or diminish its importance as a long-term N balancing source in these pyrogenic ecosystems. In this case, fire may be acting as relief mechanism, critical for returning the modern longleaf pine landscape to its historical oligotrophic condition.

Nitrogen-induced new net primary production and carbon sequestration in global forests

Nitrogen (N) deposition and biological N fixation (BNF) are main external N inputs into terrestrial ecosystems. However, few studies have simultaneously quantified the contribution of these two external N inputs to global NPP and consequent C sequestration. Based on literature analysis, we estimated new net primary production (NPP) due to external N inputs from BNF and N deposition and the consequent C sinks in global boreal, temperate and tropical forest biomes via a stoichiometric scaling approach. Nitrogen-induced new NPP is estimated to be 3.48 Pg C yr^-1 in global established forests and contributes to a C sink of 1.83 Pg C yr^-1. More specifically, the aboveground and belowground new NPP are estimated to be 2.36 and 1.12 Pg C yr^-1, while the external N-induced C sinks in wood and soil are estimated to be 1.51 and 0.32 Pg C yr^-1, respectively. BNF contributes to a major proportion of N-induced new NPP (3.07 Pg C yr^-1) in global forest, and accounts for a C sink of 1.58 Pg C yr^-1. Compared with BNF, N deposition only makes a minor contribution to new NPP (0.41 Pg C yr^-1) and C sinks (0.25 Pg C yr^-1) in global forests. At the biome scale, rates of N-induced new NPP and C sink show an increase from boreal forest towards tropical forest, as mainly driven by an increase of BNF. In contrast, N deposition leads to a larger C sink in temperate forest (0.11 Pg C yr^-1) than boreal (0.06 Pg C yr^-1) and tropical forest (0.08 Pg C yr^-1). Our estimate of total C sink due to N-induced new NPP approximately matches an independent assessment of total C sink in global established forests, suggesting that external N inputs by BNF and atmospheric deposition are key drivers of C sinks in global forests.

Effect of Fertilization on Growth and Mortality of Jack Pine Growing on Poor, Sandy Soils in Michigan, USA: Implications for Sustainable Management

Our understanding of nutrient limitations to jack pine (Pinus banksiana Lamb.) growth is lacking across the Lake States of the USA (Michigan, Wisconsin and Minnesota), where this species makes up an important forest cover type on nutrient poor sands. Currently this cover type is managed using whole-tree harvesting (WTH) across large areas of state and federal forestland, which raises concerns for long-term declines in soil fertility and future productivity. In this study, I carried out a factorial fertilization experiment to better understand potential nutrient limitations to jack pine growth on excessively drained sandy soils in northern Lower Michigan. Treatments were nitrogen (N), phosphorus (P) and base cations applied singly and in all factorial combinations. In addition, I constructed input-output nutrient budgets for jack pine management in northern Lower Michigan using existing data on atmospheric deposition, weathering and harvest nutrient removals. In no case did I observe an increase in tree growth rate to fertilization, instead I observed an overall decline in growth rates, and an increase in mortality rates, in trees fertilized with N. Nitrogen-induced imbalances of foliar N: potassium (K) were strongly correlated with decreased growth in N amended plots. Together with nutrient budget analysis, which indicated that harvest removals of K greatly exceed inputs over the planned rotation, this suggests that WTH may not be sustainable over multiple rotations. Furthermore, the impacts of WTH on ecosystem K status are likely to be exacerbated over time by anthropogenic N deposition.

Dry-hot stress significantly reduced the nitrogenase activity of epiphytic cyanolichen

Nitrogen (N) fixed by epiphytic cyanolichens (i.e. lichens that contain cyanobacterial symbionts) is thought to be the most important resource of this nutrient in some natural forest ecosystems. Although a great deal of work has been carried out to evaluate the biomass of this group as well as its contribution to ecosystem N budgets, empirical studies are needed to confirm the N input responses by cyanolichens under climate change conditions (dry-hot stress) as well as to determine the factors that control this process. We simulated climate change conditions by transplanting Lobaria retigera, a common cyanolichen in the area, to lower elevations, and measured nitrogenase activity in response to warmer and drier conditions. In addition, we conducted a series of laboratory and greenhouse experiments to determine the dominant factors influencing nitrogenase activity in this species. The results of this study show that mean annual nitrogenase activity at the higher site was 1.5 and 2.4 times that at the simulated warmer and drier (middle and lower) sites, respectively. Combining laboratory experimental conclusions, we show that thallus water content is a key factor determining the nitrogenase activity of L. retigera in early transplantation while insufficient carbon storage resulting from a combination of warming and desiccation was likely responsible for reducing nitrogenase activity in later months of the transplant experiment. The results of this study imply that the negative impact of climate change (dry-hot stress) on ecosystems not only impacts the distribution and growth of species, but also nutrient circles and budgets.

Bacteria in decomposing wood and their interactions with wood-decay fungi

The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.

Multimodel simulations of forest harvesting effects on long‐term productivity and CN cycling in aspen forests

The effects of forest management on soil carbon (C) and nitrogen (N) dynamics vary by harvest type and species. We simulated long-term effects of bole-only harvesting of aspen (Populus tremuloides) on stand productivity and interaction of CN cycles with a multiple model approach. Five models, Biome-BGC, CENTURY, FORECAST, LANDIS-II with Century-based soil dynamics, and PnET-CN, were run for 350 yr with seven harvesting events on nutrient-poor, sandy soils representing northwestern Wisconsin, United States. Twenty CN state and flux variables were summarized from the models' outputs and statistically analyzed using ordination and variance analysis methods. The multiple models' averages suggest that bole-only harvest would not significantly affect long-term site productivity of aspen, though declines in soil organic matter and soil N were significant. Along with direct N removal by harvesting, extensive leaching after harvesting before canopy closure was another major cause of N depletion. These five models were notably different in output values of the 20 variables examined, although there were some similarities for certain variables. PnET-CN produced unique results for every variable, and CENTURY showed fewer outliers and similar temporal patterns to the mean of all models. In general, we demonstrated that when there are no site-specific data for fine-scale calibration and evaluation of a single model, the multiple model approach may be a more robust approach for long-term simulations. In addition, multimodeling may also improve the calibration and evaluation of an individual model.

Regional constraints to biological nitrogen fixation in post-fire forest communities

Biological nitrogen fixation (BNF) is a key ecological process that can restore nitrogen (N) lost in wildfire and shape the pace and pattern of post-fire forest recovery. To date, there is limited information on how climate and soil fertility interact to influence different pathways of BNF in early forest succession. We studied asymbiotic (forest floor and soil) and symbiotic (the shrub Ceanothus integerrimus) BNF rates across six sites in the Klamath National Forest, California, USA. We used combined gradient and experimental phosphorus (P) fertilization studies to explore cross-site variation in BNF rates and then related these rates to abiotic and biotic variables. We estimate that our measured BNF rates 22 years after wildfire (6.1-12.1 kg N x ha(-1) x yr(-1)) are unlikely to fully replace wildfire N losses. We found that asymbiotic BNF is P limited, although this is not the case for symbiotic BNF in Ceanothus. In contrast, Ceanothus BNF is largely driven by competition from other vegetation: in high-productivity sites with high potential evapotranspiration (Et), shrub biomass is suppressed as tree biomass increases. Because shrub biomass governed cross-site variation in Ceanothus BNF, this competitive interaction led to lower BNF in sites with high productivity and Et. Overall, these results suggest that the effects of nutrients play a larger role in driving asymbiotic than symbiotic fixation across our post-fire sites. However, because symbiotic BNF is 8-90x greater than asymbiotic BNF, it is interspecific plant competition that governs overall BNF inputs in these forests.

Suillus mycelia under elevated atmospheric CO2 support increased bacterial communities and scarce nifH gene activity in contrast to Hebeloma mycelia

Bacterial communities associated with mycorrhizal roots are likely to respond to rising atmospheric CO(2) levels in terms of biomass, community composition and activity since they are supported by the carbon (C) flow outside the root tips, especially by exudation of low molecular weight organic compounds. We studied how general bacterial and diazotrophic communities associated with ectomycorrhizal (ECM) fungi respond to different belowground C supply conditions, mediated by elevated atmospheric CO(2) concentration under nitrogen (N) limited conditions. Microcosm systems were constructed using forest soil and Scots pine seedlings, which were either pre-inoculated with one of the ECM fungal species Hebeloma velutipes or Suillus variegatus, or non-inoculated. These fungal species differ in C allocation and exudation patterns. Seedlings were maintained under ambient (380 ppm) or elevated (700 ppm) CO(2) levels for 6 months. Quantitative polymerase chain reaction (PCR) showed a significant increase in 16S rRNA gene copy numbers for Suillus-inoculated microcosms under elevated CO(2) compared to ambient CO(2). The copy numbers of the nitrogenase reductase (nifH) gene were under the detection limit in all samples regardless the CO(2) treatments. Denaturing gradient gel electrophoresis analysis of PCR-amplified nifH genes revealed simple and consistent communities in all samples throughout the incubation period. A nested reverse transcription PCR approach revealed that expression of nifH genes were detected in some microcosms. Our findings suggest that the effect of mycorrhizal fungi on soil bacteria may vary depending on C supply and fungal species.

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.