TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Nitrogen transformation pathways, rates, and isotopic signatures in Lake Lugano

The consequences of detrimental alterations caused to the natural nitrogen (N) cycle are manifold. To tackle problems, such as eutrophication of coastal marine and lacustrine environments, or increasing emissions of greenhouse gas nitrous oxide (N2O), requires a clear understanding of the microbial N cycle. A promising tool to study N transformations is the measurement of the stable isotope composition of N compounds. The overall goal of this project was to improve the understanding of N transformation pathways and associated isotope effects, using the meromictic northern and the monomictic southern basins of Lake Lugano as natural model systems. Toward this goal, we collected samples from the water column of both basins for dissolved inorganic nitrogen (DIN) analyses (including N2:Ar, N2O), molecular microbiological phylogenetic analyses, 15N-labeling experiments (water column and sediments), and stable N and O isotope (and N2O isotopomer) measurements. First, we identified the main processes responsible for fixed N elimination in the Lake Lugano north basin. The stable redox transition zone (RTZ) in the mid-water column provides environmental conditions that are favorable for both, anaerobic ammonium oxidation (anammox), as well as sulfur-driven denitrification. Previous marine studies suggested that sulfide (H2S) inhibits the anammox reaction. In contrast to this we demonstrated that anammox bacteria coexist with sulfide-dependent denitrifiers in the water column of the Lake Lugano north basin. The maximum potential rates of both processed were comparatively low, but consistent with nutrient fluxes calculated from concentration gradients. Furthermore, we showed that organotrophic denitrification is a negligible nitrate-reducing pathway in the Lake Lugano north basin. Based on these findings, we next interpreted the N and O isotope signatures in the Lake Lugano north basin. Anammox and sulfide-dependent denitrification left clear N (in NO3- and NH4+) and O (in NO3-) isotope patterns in the water column. However, the associated isotope effects were low compared to previous reports on isotope fractionation by organotrophic denitrification and aerobic ammonium oxidation. We attribute this apparent under-expression to two possible explanations: 1) The biogeochemical conditions (i.e., substrate limitation, low cell specific N transformation rates) that are particularly conducive in the Lake Lugano RTZ to an N isotope effect under-expression at the cellular-level, or 2) a low process-specific isotope fractionation at the enzyme-level. Moreover, an 18O to 15N enrichment ratio of ~0.89 associated with NO3- reduction suggested that the periplasmic dissimilatory nitrate reductase Nap was more important than the membrane-bound dissimilatory Nar. While in the meromictic north basin, most fixed N elimination took place within the water column RTZ, seasonal mixing and re-oxygenation of the water column in the south basin suggests N2 production within the sediments. We showed that denitrification was the major benthic NO3- reduction pathway in the southern basin. Benthic anammox and dissimilatory nitrate reduction to ammonium (DNRA) rates remained close to the detection limit. A comparison between benthic N2 production rates and water column N2 fluxes revealed that during anoxic bottom water conditions, ~40% of total N2 production was associated with benthic and ~60% with pelagic processes. This quantitative partitioning was confirmed by N isotope analysis of water column NO3-. The N isotope enrichment factor associated with total NO3- reduction was ~14‰. This translates into a sedimentary N2 contribution of 36-51%, if canonical assumptions for N isotope fractionation associated with water column (15εwater = 20-25‰) and sedimentary (15εsed = 1.5-3‰) denitrification are made. Finally, we compared the N2O production and consumption pathways in the northern and southern basin and found contrasting N2O dynamics. Maximum N2O concentrations in the south basin (>900 nmol L-1) greatly exceeded maximum concentrations in the north basin (32‰ in the south basin indicated nitrification via hydroxylamine (NH2OH) oxidation as the prime N2O source, whereas in the north basin N2O production was attributed to nitrifier denitrification. In the north basin, N2O was completely reduced within the RTZ. This chemolithotrophic N2O reduction occurred with an 18O to 15N enrichment ratio of ~2.5, which is consistent with previous reports for organotrophic N2O reduction. In conclusion, our study highlights the importance of chemolithotrophic processes in aquatic ecosystems. Moreover, the expression of N isotope fractionation can be variable in nature and depends on various factors such as the pathways of NO3- dissimilation (organotrophic vs. chemolithotrophic), the main catalyzing enzymes, the pathways of NH4+ oxidation (nitrification vs. anammox), and the controlling environmental conditions (e.g., substrate limitation, cell specific N transformation rates). Hence, this study suggests to refrain from universal, canonical assumptions of N isotope fractionation in N budget calculations. Additional stable isotope measurements such as O isotopes in NO3-, or the 15N site preference in N2O are powerful tools to identify and quantify microbial N transformation pathways occurring simultaneously or in close vicinity. For a successful interpretation of such data, however, a mechanistic understanding of the processes leading to certain characteristic isotopic signatures in the environment is needed

Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations

Dissimilatory sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth’s history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation—the electron carriers selected for survival under energy-limited conditions. Employing a quantitative biochemical-isotopic model, we find that the large S isotope fractionations (>55‰) observed in a wide range of natural environments and culture experiments at low respiration rates are only possible when the standard-state Gibbs free energy ( ΔG′° ) of all steps during DSR is more positive than −10 kJ mol −1 . This implies that at low respiration rates, only electron carriers with modestly negative reduction potentials are involved, such as menaquinone, rubredoxin, rubrerythrin or some flavodoxins. Furthermore, the constraints from S isotope fractionation imply that ferredoxins with a strongly negative reduction potential cannot be the direct electron donor to S intermediates at low respiration rates. Although most sulfate reducers have the genetic potential to express a variety of electron carriers, our results suggest that a key physiological adaptation of sulfate reducers to low-energy environments is to use electron carriers with modestly negative reduction potentials

Nitrogen cycling in the subsurface biosphere: Nitrate isotopes in porewaters underlying the oligotrophic North Atlantic

Nitrogen (N) is a key component of fundamental biomolecules. Hence, its cycling and availability are central factors governing the extent of ecosystems across the Earth. In the organic-lean sediment porewaters underlying the oligotrophic ocean, where low levels of microbial activity persist despite limited organic matter delivery from overlying water, the extent and modes of nitrogen transformations have not been widely investigated. Here we use the N and oxygen (O) isotopic composition of porewater nitrate (NO₃^−) from a site in the oligotrophic North Atlantic (Integrated Ocean Drilling Program – IODP) to determine the extent and magnitude of microbial nitrate production (via nitrification) and consumption (via denitrification). We find that NO₃^- accumulates far above bottom seawater concentrations (~ 21 μM) throughout the sediment column (up to ~ 50 μM) down to the oceanic basement as deep as 90 m b.s.f. (below sea floor), reflecting the predominance of aerobic nitrification/remineralization within the deep marine sediments. Large changes in the δ¹⁵N and δ¹⁸O of nitrate, however, reveal variable influence of nitrate respiration across the three sites. We use an inverse porewater diffusion–reaction model, constrained by the N and O isotope systematics of nitrification and denitrification and the porewater NO₃^- isotopic composition, to estimate rates of nitrification and denitrification throughout the sediment column. Results indicate variability of reaction rates across and within the three boreholes that are generally consistent with the differential distribution of dissolved oxygen at this site, though not necessarily with the canonical view of how redox thresholds separate nitrate regeneration from dissimilative consumption spatially. That is, we provide stable isotopic evidence for expanded zones of co-occurring nitrification and denitrification. The isotope biogeochemical modeling also yielded estimates for the δ¹⁵N and δ¹⁸O of newly produced nitrate (δ¹⁵N_NTR (NTR, referring to nitrification) and δ¹⁸O_NTR), as well as the isotope effect for denitrification (¹⁵ϵ_DNF) (DNF, referring to denitrification), parameters with high relevance to global ocean models of N cycling. Estimated values of δ¹⁵N_NTR were generally lower than previously reported δ¹⁵N values for sinking particulate organic nitrogen in this region. We suggest that these values may be, in part, related to sedimentary N₂ fixation and remineralization of the newly fixed organic N. Values of δ¹⁸O_NTR generally ranged between −2.8 and 0.0 ‰, consistent with recent estimates based on lab cultures of nitrifying bacteria. Notably, some δ¹⁸O_NTR values were elevated, suggesting incorporation of ¹⁸O-enriched dissolved oxygen during nitrification, and possibly indicating a tight coupling of NH₄⁺ and NO₂^− oxidation in this metabolically sluggish environment. Our findings indicate that the production of organic matter by in situ autotrophy (e.g., nitrification, nitrogen fixation) supplies a large fraction of the biomass and organic substrate for heterotrophy in these sediments, supplementing the small organic-matter pool derived from the overlying euphotic zone. This work sheds new light on an active nitrogen cycle operating, despite exceedingly low carbon inputs, in the deep sedimentary biosphere

Micro-aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south-Alpine Lake Lugano (Switzerland)

We measured seasonal variations in the vertical distribution of methane concentration, methane oxidation rates, and lipid biomarkers in the northern basin of Lake Lugano. Methane consumption below the oxic–anoxic interface co-occurred with concentration maxima of 13C-depleted C16 fatty acid biomarkers (with d13C values as low as 270%) in the anoxic water column, as well as characteristic d13CCH4 profiles. We argue that the conspicuous methane concentration gradients are primarily driven by (micro-)aerobic methane oxidation (MOx) below the chemocline. We measured a strong MOx potential throughout the anoxic water column, while MOx rates at in situ O2 concentration . 10 nmol L21 were undetectable. Similarly, we found MOx-related biomarkers and gene sequences encoding the particulate methane monooxygenase in the anoxic, but not the oxic, water. The mechanism of (episodic) oxygen supply sustaining the MOx community in anoxic waters is still uncertain. Our results indicate that a bacterial methanotrophic community is responsible for the methane consumption in Lake Lugano, without detectable contribution from archaeal methanotrophs. Bacterial populations that accumulated both at the suboxic–anoxic interface and in the deeper anoxic hypolimnion, where maximum potential MOx rates were observed throughout the year (1.5–2.5 mmol L21 d21) were mainly related to Methylobacter sp. Close relatives are found in lacustrine environments throughout the world, and their potential to thrive under micro- and anoxic conditions in Lake Lugano may imply that micro-aerobic methane oxidation is important in methane cycling and competition for methane and oxygen in stratified lakes worldwide

Differential N2O dynamics in two oxygen-deficient lake basins revealed by stable isotope and isotopomer distributions

Lakes are a nitrous oxide (N2O) source to the atmosphere, but the biogeochemical controls and microbial pathways of N2O production are not well understood. To trace microbial N2O production (denitrification, nitrifier denitrification, and nitrification) and consumption (denitrification) in two basins of Lake Lugano, we measured the concentrations and N and O isotope compositions of N2O, as well as the intramolecular 15N distribution, i.e., site preference (SP). Our results revealed differential N2O dynamics in the two lake basins, with N2O concentrations between 12 nmol L−1 and > 900 nmol L−1 in the holomictic South Basin, and significantly lower concentrations in the meromictic North Basin (<13 nmol L−1). In the South Basin, the isotope signatures reflected a complex combination of N2O production by nitrifying bacteria through hydroxylamine (NH2OH) oxidation, N2O production through incomplete denitrification, and N2O reduction to N2, all occurring in close vicinity within the redox transition zone (RTZ). In the North Basin, in contrast, the N2O isotopomer signatures suggested that nitrifier denitrification was the main N2O source. The pronounced decrease in N2O concentrations to undetectable levels within the RTZ, in tandem with an increase in δ15N-N2O, δ18O-N2O, and SP indicated quantitative N2O consumption by microbial denitrification. In the northern basin this was primarily sulfide-dependent. The apparent N and O isotope enrichment factors associated with net N2O consumption were 15ε ≈ 3.2‰ and 18ε ≈ 8.6‰, respectively. The according 18O to 15N enrichment ratio (18ε: 15ε ≈ 2.5) is consistent with previous reports for microbial N2O reduction, underscoring its robust nature across environments