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Microbial nitrogen use efficiency (NUE) reflects the allocation of microbially-acquired N between growth (anabolism) and the release of inorganic N to the environment (catabolism), and is central to understanding soil N cycling. However, the effects of N addition on microbial NUE are unclear. We determined microbial NUE in surface (0–10 cm) and subsurface (10–20 cm) soils in a temperate forest by the combined substrate-independent 18O-H2O tracer technique and 15N isotope pool dilution in a multi-level N addition experiment. We found that high N treatment (75 kg N ha−1 yr−1 as urea fertilizer) significantly decreased NUE in surface soil, but not in the subsurface soil. The decrease in NUE in surface soil was related to soil acidification, likely induced by N addition, and to reduced phosphorus availability, suggesting increased phosphorus limitation to microbial metabolism with N addition. Microbial NUE was inversely related to inorganic N flux (as NH4+) in both surface and subsurface soils and positively related to microbial biomass in surface soil. Our empirical evidence confirms that microbial NUE is a sensitive proxy and controlling branchpoint between soil microbial N immobilization and inorganic N cycling, which should be explicitly included in biogeochemical models to better predict soil N dynamics.

ABSTRACT Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to “Candidatus Nitrosocosmicus,” which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of “Ca. Nitrosocosmicus” was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, “Ca. Nitrosocosmicus” members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.IMPORTANCEAmmonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the “Ca. Nitrosocosmicus” clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that “Ca. Nitrosocosmicus” may be an important clade of AOA with potential AOA-plant interaction.

Abstract Foraminifera are single-celled protists which are important mediators of the marine carbon cycle. In our study, we explored the potential impact of polystyrene (PS) microplastic particles on two symbiont-bearing large benthic foraminifera species—Heterostegina depressa and Amphistegina lobifera—over a period of three weeks, employing three different approaches: investigating (1) stable isotope (SI) incorporation—via 13C- and 15N-labelled substrates—of the foraminifera to assess their metabolic activity, (2) photosynthetic efficiency of the symbiotic diatoms using imaging PAM fluorometry, and (3) microscopic enumeration of accumulation of PS microplastic particles inside the foraminiferal test. The active feeder A. lobifera incorporated significantly more PS particles inside the cytoplasm than the non-feeding H. depressa, the latter accumulating the beads on the test surface. Photosynthetic area of the symbionts tended to decrease in the presence of microplastic particles in both species, suggesting that the foraminiferal host cells started to digest their diatom symbionts. Compared to the control, the presence of microplastic particles lead to reduced SI uptake in A. lobifera, which indicates inhibition of inorganic carbon and nitrogen assimilation. Competition for particulate food uptake was demonstrated between algae and microplastic particles of similar size. Based on our results, both species seem to be sensitive to microplastic pollution, with non-feeding H. depressa being more strongly affected.

Abstract Background Ecoenzymatic stoichiometry models (EEST) are often used to evaluate microbial nutrient use efficiency, but the validity of these models under exogenous nitrogen (N) input has never been clarified. Here, we investigated the effects of long-term N addition (as urea) on microbial N use efficiency (NUE), compared EEST and 18O-labeling methods for determining NUE, and evaluated EEST’s theoretical assumption that the ratios of standard ecoenzymatic activities balance resource availability with microbial demand. Results We found that NUE estimated by EEST ranged from 0.94 to 0.98. In contrast, estimates of NUE by the 18O-labeling method ranged from 0.07 to 0.30. The large differences in NUE values estimated by the two methods may be because the sum of β-N-acetylglucosaminidase and leucine aminopeptidase activities in the EEST model was not limited to microbial N acquisition under exogenous N inputs, resulting in an overestimation of microbial NUE by EEST. In addition, the acquisition of carbon by N-acquiring enzymes also likely interferes with the evaluation of NUE by EEST. Conclusions Our results demonstrate that caution must be exercised when using EEST to evaluate NUE under exogenous N inputs that may skew standard enzyme assays.

Abstract Habitat loss and degradation are key drivers of the current biodiversity crisis. Most research focuses on the question of which traits allow species to persist in degraded habitats. We asked whether a species' trophic position or niche width influences the resilience of species in degraded habitats and to what extent habitat degradation affects trophic interactions between species. We used nitrogen isotope ratios (15N:14N, expressed as δ15N value) to quantify and compare trophic positions and niche widths of understory birds inhabiting old‐growth and young secondary forests in the Pacific lowlands of Costa Rica. We found that a species' trophic position rather than its trophic niche width determined its persistence in secondary forests. Species feeding at lower trophic levels in old‐growth forests were less likely to persist in secondary forests than those occupying a higher trophic position in old‐growth forests. This pattern is likely induced by the occurrence of relatively large‐bodied habitat specialists with a flexible and high‐trophic level diet in secondary forests. These habitat specialists likely caused generalist bird species to lower their trophic position relative to conspecifics in old‐growth forests. Regarding trophic niche widths, species in secondary forests tend to have larger niche widths than old‐growth forest species. However, as old‐growth forest specialists and generalists did not differ in their niche widths, no systematic effect of trophic niche width on species persistence after forest disturbance was found. This is the first study that shows a systematic effect of trophic position on the persistence of a wide range of bird species in a disturbed forest ecosystem. It therefore provides important insights into species' responses to habitat degradation and the conservation value of secondary forests. To improve habitat quality for old‐growth forest birds and facilitate avian seed dispersal, the creation of large contiguous forest patches should be prioritised when implementing reforestation measures.

Soil microorganisms play a key role in regulating soil organic carbon (SOC) accrual. Organic amendments with distinct stoichiometry may lead to imbalanced supply of carbon (C), nitrogen (N), and phosphorus (P) to the microbiome, causing changes in microbial community composition and their life strategies, as well as enzyme production. However, the response of soil microorganisms to these imbalances and whether their adaptive strategies are related to the fate of SOC pools remain largely unknown in low-fertility paddy soil. To address this uncertainty, soils were sampled from a 12-year experimental fertilisation trial under integrated application of mineral fertilizers and three types of organic materials (green manure, rice straw, and cattle manure). Stoichiometric imbalances between soil microbes and their available resources, enzyme activities, and microbial community composition, and their linkages with soil particulate (POC) and mineral-associated (MAOC) organic C were investigated. The results showed that despite equal C input, strongest increase in MAOC occurred with organic amendments causing the smallest microbial C:N imbalance and C:P imbalance, suggesting that alleviation in N and P limitation was inductive to the accrual of soil stable organic C fraction. Additional organic amendments with lower C: nutrient ratios shifted the microbial community towards the prevalence of r-strategists, with cattle manure addition supporting copiotrophic bacteria and green manure addition favouring copiotrophic fungi. Importantly, the relative abundances of Proteobacteria, Gemmatimonadetes, and Actinobacteria belonging to copiotrophs were negatively related to microbial C:N imbalance and C:P imbalance, but positively related to POC and MAOC, while Chloroflexi, Basidiomycota and Glomeromycota belonging to oligotrophs exhibited reversed relationships. In addition, greater MAOC accrual was associated with an increase in microbial biomass and a decrease in biomass-specific P-acquiring enzyme activity. Random forest analysis and partial least squares path model revealed that microbial C:N imbalance and C:P imbalance played an important but indirect role in shaping MAOC by concurrently regulating soil microbial biomass, community composition and enzyme production, whereas the POC pool was predominantly and directly controlled by the proportion of macroaggregates. These results provide empirical evidence for the stoichiometric control of microbial communities and their feedback to SOC pools, highlighting the role of low C:nutrient ratio organic amendments for long-term storage and the persistence of C in intensively managed paddy soils.

Microbial carbon and nitrogen use efficiencies (CUE and NUE) are central to our understanding of soil C and N cycling. Although both the 18O-labeling approach and ecoenzyme stoichiometry model have been widely used to estimate microbial CUE and NUE, comparisons of the two methods are scarce. Here, we investigated soil microbial CUE and NUE of 11 locations along a forest transect in eastern China using both the 18O-approach and ecoenzyme model. We found that microbial CUE-18O and NUE-18O estimated by the 18O-approach were positively related to each other and both decreased with soil acidification and phosphorus acquisition as measured by enzyme activity. However, CUEC:N and NUEN:C, estimated by C:N stoichiometry using the enzyme model were negatively related to each other and neither showed any relationship to soil acidification or phosphorus acquisition. Finally, CUEC:P and NUEN:P estimated according to C:P stoichiometry were positively related to each other and both increased with soil acidification and phosphorus acquisition efforts. We suggest that a reason for these differences is that the 18O-approach reflects the intracellular biochemical transformation of C, N, and P while the enzyme models reflect stoichiometric imbalances between external substrates and microbial biomass, i.e., different aspects of microbial metabolism. Moreover, differences between the C:N and C:P-based enzyme models resulted from P-limitation to soil microorganisms in this system. For these reasons, microbial element use efficiencies need to be clearly defined, i.e., as derived from growth-based or soil enzyme-based measurements, and caution must be made when comparing results obtained from different methods, and under different conditions of resource availability.

Foraminifera are protists primarily living in benthic marine and estuarine environments. We studied uptake of inorganic carbon (C) and nitrogen (N) of the photosymbiont-bearing benthic coral reef foraminifera Heterostegina depressa in the presence of heavy metals.Incubation experiments were accomplished with artificial seawater enriched with copper, iron, lead and zinc at two different concentration levels (10 and 100 fold enriched in contrast to the usual culture medium). Additionally, isotopically labelled 13C-sodium bicarbonate and 15N-ammonium chloride were added to trace their assimilation over time (1 d, 3 d, 5 d, 7 d). Pulse-amplified modulated fluorescence measurements were performed to measure the potential impacts of heavy metals on chlorophyll fluorescence of the photosymbiont. Increased levels of copper (430.5 μg Cu/l) exhibited the greatest toxicity, while for low levels no effect on the overall metabolism of the foraminifera and the fluorescence activity of the photosymbiont could be detected. Iron (III) increased the symbiont activity, independent of concentration applied (44.5 and 513.3 μg Fe/l), which indicates Fe-limitation of the algal symbiont. Lead enrichment showed no detectable effect even at high concentration. Low concentrations of zinc (35.1 μg Zn/l) promoted the metabolism of the foraminifera, while high concentrations (598.4 μg Zn/l) were toxic. At low levels, two metals (Fe and Zn) promoted symbiont activity, at high levels, iron still boosted photosynthesis, but Zn and Cu had a negative impact on the obligatory photosynthetic symbionts.

Free-flowing rivers are highly valuable to understand the taxonomic and functional community structure of organisms that inhabit fluvial ecosystems. We investigated patterns of macroinvertebrate community composition and food web structure using stable isotopes (δ13C and δ15N), including potential environmental drivers, over a free-flowing river continuum in the upper course of the Neretva River in Bosnia and Herzegovina. Results showed a high taxonomic diversity, a high percentage of EPT taxa (Ephemeroptera, Plecoptera, Trichoptera), and a slightly heterotrophic ecosystem (average allochthonous assimilation = 54%). The taxonomic composition differed prominently between a tributary located upstream and the mainstem. However, we also found notable species turnover between the upper (headwater and midsection) reaches and the downstream reaches of the mainstem. Macroinvertebrate abundance and the percentage of EPT peaked downstream while midsection reaches showed the highest taxonomic richness and diversity and allochthonous assimilation. Most of the functional metrics (maximum and average trophic position and isotopic richness and evenness) showed pronounced discontinuities in their spatial patterns, which did not follow the predictions of the River Continuum Concept. These results highlight the uniqueness of this section of the Neretva, where natural discontinuities structure macroinvertebrate communities in ways and by mechanisms not captured by smooth ecological concepts.

Abstract We studied metabolic activity of the symbiont-bearing large benthic foraminifer Heterostegina depressa under different light conditions. Besides the overall photosynthetic performance of the photosymbionts estimated by means of variable fluorescence, the isotope uptake (13C and 15N) of the specimens (= holobionts) was measured. Heterostegina depressa was either incubated in darkness over a period of 15 days or exposed to an 16:8 h light:dark cycle mimicking natural light conditions. We found photosynthetic performance to be highly related to light supply. The photosymbionts, however, survived prolonged darkness and could be reactivated after 15 days of darkness. The same pattern was found in the isotope uptake of the holobionts. Based on these results, we propose that 13C-carbonate and 15N-nitrate assimilation is mainly controlled by the photosymbionts, whereas 15N-ammonium and 13C-glucose utilization is regulated by both, the symbiont and the host cells.

Temperate forest soil warming (>14 years) increased soil phosphorus (P) losses and P sorption, reducing bioavailable P in soil solution and resulting in higher acid phosphatase activity but lower biotic phosphate immobilization and microbial biomass.

Trees can invest up to one-third of the carbon (C) fixed by photosynthesis into belowground allocation, including fine root exudation into the rhizosphere. It is still unclear how climate and soil warming affect tree root C exudation, in particular quantifying longer-term warming effects remains a challenge. In this study, using a C-free cuvette incubation method, in situ C exudation rates from tree fine roots of a mature spruce dominated temperate forest were measured in regular intervals during the 14th and 15th year of experimental soil warming (+ 4°C). In addition, a short-term temperature sensitivity experiment (up to + 10°C warming within 4 days) was conducted to determine the inherent temperature sensitivity of root exudation. Root exudation rates in the long-term warmed soil (17.9 μg C g–1 root biomass h–1) did not differ from those in untreated soil (16.2 μg C g–1 root biomass h–1). However, a clear increase (Q10 ∼5.0) during the short-term temperature sensitivity experiment suggested that fine root exudation can be affected by short-term changes in soil temperature. The absence of response in long-term warmed soils suggests a downregulation of C exudation from the individual fine roots in the warmed soils. The lack of any relationship between exudation rates and the seasonal temperature course, further suggests that plant phenology and plant C allocation dynamics have more influence on seasonal changes in fine root C exudation. Although exudation rates per g dry mass of fine roots were only marginally higher in the warmed soil, total fine root C exudation per m2 soil surface area increased by ∼30% from 0.33 to 0.43 Mg C ha–1 yr–1 because long-term soil warming has led to an increase in total fine root biomass. Mineralization of additional fine root exudates could have added to the sustained increase in soil CO2 efflux from the warmed forest soil at the experimental site.

IntroductionOrganic phosphorus (Po) compounds constitute an important pool in soil P cycling, but their decomposition dynamics are poorly understood. Further, it has never been directly tested whether low molecular weight Po compounds are taken up by soil microbes in an intact form, which reduces the dependence of their P acquisition on extracellular phosphatases.MethodsWe investigated the short-term fate (24 h) of five 33P-labelled Po compounds (teichoic acids, phospholipids, DNA, RNA and soluble organophosphates) and 33P-labelled inorganic P (Pi) in two soils.ResultsWe found indications that soil microbial breakdown of phosphodiesters was limited by the depolymerization step, and that direct microbial uptake of Po occurred to a substantial extent.DiscussionWe postulate a trade-off between direct Po uptake and complete extracellular Po mineralization. These findings have profound consequences for our understanding of microbial P cycling in soils.

Foraminifera are essential contributors to the marine carbon and nitrogen cycle. A small group of foraminifera hosts symbiotic microalgae and kleptoplasts and irradiance is a key variable influencing their metabolism. However, the majority of foraminifera is fully heterotrophic, and whether irradiance influences food ingestion patterns has remained an open question. We studied the food uptake of fully heterotrophic Cribroelphidium selseyense specimens exposed to varying light-dark cycles. Specimens obtained from the Baltic Sea were fed with lyophilised, isotopically labelled diatoms from the species of Phaeodactylum triconutum, to estimate the rate of food ingestion. We exposed the specimens to different light-dark cycles (0:24, 8:16, 16:8, 24:0 = light: dark) and irradiance intensities (0, 50, 100 and 200 µmol photons m−2 s−1) in this experiment. Differences in light-dark regime did not affect the food uptake rates of C. selseyense. Irradiance intensity, however, strongly affected food uptake, increasing with incubation time from day 1 to day 15. In parallel, the food uptake decreased with higher irradiance intensity. Therefore, we can conclude irradiance intensity and not the light-dark cycle affected food uptake of fully heterotrophic C. selseyense, leaving the mechanisms of how light intensity regulates food intake being unresolved yet.

Biotic processes drive rapid cyanate turnover and dominate cyanate consumption in soils, according to an extensive soil survey and stable isotope tracer experiments.

ABSTRACT Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH3) via nitrite (NO2−) to nitrate (NO3−) (15εNH4+→NO2- and 15εNO2-→NO3-). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH3 to NO3−. At high ammonium (NH4+) availability (1 mM) and pH between 6.5 and 8.5, its 15εNH4+→NO2- ranged from −33.1 to −27.1‰ based on substrate consumption (residual substrate isotopic composition) and −35.5 to −31.2‰ based on product formation (cumulative product isotopic composition), while the 15εNO2-→NO3- ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus Nitrospira, suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH4+ concentrations influenced the isotope effects in N. inopinata. The 15εNH4+→NO2- based on product formation was smaller at pH 6.5 (−31.2‰) compared to pH 7.5 (−35.5‰) and pH 8.5 (−34.9‰), while 15εNO2-→NO3- was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via 15εNH4+→NO2- and 15εNO2-→NO3- was smaller at 0.1 mM NH4+ compared to 0.5 to 1.0 mM NH4+. Environmental factors, such as pH and NH4+ availability, therefore need to be considered when using isotope effects in 15N isotope fractionation models of nitrification. IMPORTANCE Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of 15εNH4+→NO2- and 15εNO2-→NO3- in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH4+ concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.

Foraminifera are unicellular organisms and play a pivotal role in the marine material cycles. Past observations have shown that the species Elphidium excavatum is the most common foraminifera in the Baltic Sea. Feeding experiments showed that the food uptake and thus the turnover of organic matter are influenced by changes of physical parameters (e.g., temperature, salinity). Since many areas of the Baltic Sea are strongly affected by anthropogenic activity and are strongly contaminated by heavy elements from shipping in the past, this study examined the effect of heavy elements pollution on the food uptake of the most common foraminiferal species of the Baltic Sea, E. excavatum which was a subject of several previous studies. Therefore, Baltic Sea seawater was enriched with metals at various levels above normal seawater levels and the uptake of 13C- and 15N-labelled phytodetritus was measured by isotope ratio mass spectrometry. For each combination of metal type, concentration and time point 20 individuals of E. excavatum (three replicates) were fed with the green algae Dunaliella tertiolecta. The effect of dose parameters was measured in a two-way analysis of variance. Significant differences of food uptake were observable at different types and levels of heavy elements in sea water. Even a 557-fold increase in the Pb concentration did not affect food uptake, whereas strong negative effects were found for higher levels of Zn (144 and 1044-fold) and especially for Cu (5.6 and 24.3-fold). In summary it can be stated, that an increase in the heavy elements pollution in the Kiel Fjord will lead to a significant reduction in the turnover of organic matter by foraminifera such as E. excavatum.

Marine carbon and nitrogen processing through microorganisms’ metabolism is an important aspect of the global element cycles. For that purpose, we used foraminifera to analyze the element turnover with different algae food sources. In the Baltic Sea, benthic foraminifera are quite common and therefore it is important to understand their metabolism. Especially, Cribroelphidium selseyense, also occurring in the Baltic Sea, has often been used for laboratory feeding experiments to test their effect on carbon or nitrogen turnover. Therefore, foraminifera were collected from the Kiel Fjord and fed with six different algal species in two qualities (freeze-dried algae vs. fresh algae, all 13C- and 15N-labeled). Also, labeled dissolved inorganic C and N compounds and glucose were offered to the foraminifera to test direct assimilation of dissolved compounds (carbon and nitrogen) from the water column. Our experiments showed that after 15 days of incubation, there were highly significant differences in isotope labeling in foraminifera fed with fresh algae and dry algae, depending on algal species. Further, different algal species led to different 13C and 15N enrichment in the studied foraminifera, highlighting a feeding preference for one diatom species and an Eustigmatophyte. A significant carbon assimilation from HCO3– was observed after 7 days of incubation. The N assimilation from NH4+ was significantly higher than for NO3– as an inorganic N source. The uptake of glucose showed a lag phase, which was often observed during past experiments, where foraminifera were in a steady state and showed no food uptake at regular intervals. These results highlight the importance of food quality on the feeding behavior and metabolic pathways for further studies of foraminiferal nutrition and nutrient cycling.

The Bromeliaceae family has been used as a model to study adaptive radiation due to its terrestrial, epilithic, and epiphytic habits with wide morpho-physiological variation. Functional groups described by Pittendrigh in 1948 have been an integral part of ecophysiological studies. In the current study, we revisited the functional groups of epiphytic bromeliads using a 204 species trait database sampled throughout the Americas. Our objective was to define epiphytic functional groups within bromeliads based on unsupervised classification, including species from the dry to the wet end of the Neotropics. We performed a hierarchical cluster analysis with 16 functional traits and a discriminant analysis, to test for the separation between these groups. Herbarium records were used to map species distributions and to analyze the climate and ecosystems inhabited. The clustering supported five groups, C3 tank and CAM tank bromeliads with deep tanks, while the atmospheric group (according to Pittendrigh) was divided into nebulophytes, bromeliads with shallow tanks, and bromeliads with pseudobulbs. The two former groups showed distinct traits related to resource (water) acquisition, such as fog (nebulophytes) and dew (shallow tanks). We discuss how the functional traits relate to the ecosystems inhabited and the relevance of acknowledging the new functional groups.

The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2–), performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or εAMO, has been typically determined based on isotope kinetics during product formation (cumulative product, NO2–) alone, which may have overestimated εAMO due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH3/NH4+). Here, we analyzed 15N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, NH4+) and cumulative product (CP, NO2–) pools in pure cultures of the soil strain Nitrososphaera viennensis EN76 and in highly enriched cultures of the marine strain Nitrosopumilus adriaticus NF5, under non-limiting substrate conditions. We obtained εAMO values of 31.9–33.1‰ for both strains based on RS (δ15NH4+) and showed that estimates based on CP (δ15NO2–) give larger isotope fractionation factors by 6–8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was 15N-enriched (10.1‰), whereas nitrous oxide (N2O) was highly 15N depleted (−38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of NH4+ assimilation (biomass formation) and N2O production by AOA, our results nevertheless show that the discrepancy between εAMO estimates based on RS and CP might have derived from the incorporation of 15N-enriched residual NH4+ after AMO reaction into microbial biomass and that N2O production did not affect isotope fractionation estimates significantly.

Forest soils harbor diverse microbial communities responsible for the cycling of elements including carbon (C), nitrogen (N), and phosphorus (P). Conversely, anthropogenic N deposition can negatively feed back on soil microbes and reduce soil organic matter (SOM) decomposition. Mechanistically, this can include reductions of decomposer biomass, especially fungi, and decreases in activities of lignin-modifying enzyme (LMEs). Moreover, N inputs can lower resource C:N and thus decrease the C:N imbalance between microbial decomposers and their resources. As a result, microbially-mediated decomposition might slow down, resulting in larger SOM pools with consequences for ecosystem nutrition and climate regulation. Here, we studied the long-term impact of experimental N addition on soil microbes and microbially-mediated decomposition in two coniferous forests in Switzerland and Denmark. We measured microbial biomass C and N, phospholipid fatty acid (PLFA) biomarkers and potential enzyme activities related to C, N, and P acquisition along the topsoil profile (0–30 cm). In particular, we investigated shifts in microbial C:N homeostasis and relative C:N:P limitation. Contrary to prevailing theory, microbial biomass and community composition were remarkably resistant against two decades of 750 and 1,280 kg ha−1 of cumulative N inputs at the Swiss and Danish site, respectively. While N reduced fungal-specific PLFAs and lowered fungi-to-bacteria (F:B) ratios in some (mainly organic) horizons where soil organic carbon (SOC) has accumulated, it increased F:B ratios in other (mainly mineral) horizons where SOC has declined. We did not find a consistent reduction of LME activities in response to N. Rather, relationships between LME activities and SOC concentrations were largely unaffected by N addition. This questions prevalent theories of lignin decomposition and SOC storage under elevated N inputs. By using C:N stoichiometry, we further show that microbial communities responded in part non-homeostatically to decreasing resource C:N, in addition to a likely increase in their carbon use efficiency and a decrease in nitrogen use efficiency. While the expected increased allocation to C- and decreased allocation to N-acquiring enzymes was not found, microbial investment in P acquisition (acid phosphatase activity) increased in the nutrient-poor Podzol (but not in the nutrient-rich Gleysol). Enzyme vector analysis showed decreasing C but increasing P limitation of soil microbial communities at both sites. We conclude that simulated N deposition led to physiological adaptations of soil microbial communities across the topsoil profile in two independent experiments, with long-term implications for tree nutrition and SOC sequestration. However, we expect that microbial adaptations are not endless and may reach a tipping point when ecosystems experience nitrogen saturation.

Trait matching between interacting species may foster diversity. Thus, high epiphyte diversity in tropical forests may be partly due to the high diversity of trees and some degree of host specificity. However, possible trait matching between epiphyte and host is basically unexplored. Since the epiphytic habitat poses particular challenges to plants, their trait correlations should differ from terrestrial plants, but to what extent is unclear as epiphytes are underrepresented or missing in the large trait databases. We quantified 28 traits of 99 species of vascular epiphytes in a lowland forest in Panama that were related to plant size, leaf, stem, and root morphology; photosynthetic mode; and nutrient concentrations. We analyzed trait covariation, community weighted means, and functional diversity for assemblages on stems and in crowns of four tree species. We found intriguing differences between epiphytes and terrestrial plants regarding trait covariation in trait relations between plant maximal height, stem specific density, specific root length, and root tissue den-sity, i.e., stem and root economic spectra. Regarding host specificity, we found strong evidence for environmental filtering of epiphyte traits, but only in tree crowns. On stems, community weighted means differed in only one case, whereas > 2/3 of all traits differed in tree crowns. Although we were only partly able to interpret these differences in the light of tree trait differences, these findings mark an important step towards a functional understanding of epiphyte host specificity.

Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125–250 µm, 250–355 µm, >355 µm) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125–250 µm size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities.

The reasons why the range size of closely related species often varies significantly have intrigued scientists for many years. Among other hypotheses, species with high trait variation were suggested to occupy more diverse environments, have more continuity in their distributions, and consequently have larger range sizes. Here, using 34 tree species of lowlands tropical rainforest in southern Costa Rica, we explored whether inherent trait variability expressed at the local scale in functional traits is related to the species' total geographical range size. We formed 17 congeneric pairs of one narrow endemic and one widespread species, sampled 335 individuals and measured eight functional traits: leaf area, leaf thickness, leaf dry matter content, specific leaf area, leaf nitrogen content, leaf phosphorus content, leaf nitrogen to phosphorus ratio, and wood specific gravity. We tested whether there are significant differences in the locally expressed variation of individual traits or in multidimensional trait variance between the species in congeneric pairs and whether species' range size could hence be predicted from local trait variability. However, we could not find such differences between widely distributed and narrow range species. We discuss the possible reasons for these findings including the fact that higher trait variability of widespread species may result from successive local adaptations during range expansion and may hence often be an effect rather than the cause of larger ranges.

Tropical forests store large amounts of carbon in tree biomass, although the environmental controls on forest carbon stocks remain poorly resolved. Emerging airborne remote sensing techniques offer a powerful approach to understand how aboveground carbon density (ACD) varies across tropical landscapes. In this study, we evaluate the accuracy of the Carnegie Airborne Observatory (CAO) Light Detection and Ranging (LiDAR) system to detect top-of-canopy tree height (TCH) and ACD across the Osa Peninsula, Costa Rica. LiDAR and field-estimated TCH and ACD were highly correlated across a wide range of forest ages and types. Top-of-canopy height (TCH) reached 67 m, and ACD surpassed 225 Mg C ha-1, indicating both that airborne CAO LiDAR-based estimates of ACD are accurate in tall, high-biomass forests and that the Osa Peninsula harbors some of the most carbon-rich forests in the Neotropics. We also examined the relative influence of lithologic, topoedaphic and climatic factors on regional patterns in ACD, which are known to influence ACD by regulating forest productivity and turnover. Analyses revealed a spatially nested set of factors controlling ACD patterns, with geologic variation explaining up to 16% of the mapped ACD variation at the regional scale, while local variation in topographic slope explained an additional 18%. Lithologic and topoedaphic factors also explained more ACD variation at 30-m than at 100-m spatial resolution, suggesting that environmental filtering depends on the spatial scale of terrain variation. Our result indicate that patterns in ACD are partially controlled by spatial variation in geologic history and geomorphic processes underpinning topographic diversity across landscapes. ACD also exhibited spatial autocorrelation, which may reflect biological processes that influence ACD, such as the assembly of species or phenotypes across the landscape, but additional research is needed to resolve how abiotic and biotic factors contribute to ACD variation across high biomass, high diversity tropical landscapes.

Biochar production and subsequent soil incorporation could provide carbon farming solutions to global climate change and escalating food demand. There is evidence that biochar amendment causes fundamental changes in soil nutrient cycles, often resulting in marked increases in crop production, particularly in acidic and in infertile soils with low soil organic matter contents, although comparable outcomes in temperate soils are variable. We offer insight into the mechanisms underlying these findings by focusing attention on the soil nitrogen (N) cycle, specifically on hitherto unmeasured processes of organic N cycling in arable soils. We here investigated the impacts of biochar addition on soil organic and inorganic N pools and on gross transformation rates of both pools in a biochar field trial on arable land (Chernozem) in Traismauer, Lower Austria. We found that biochar increased total soil organic carbon but decreased the extractable organic C pool and soil nitrate. While gross rates of organic N transformation processes were reduced by 50-80%, gross N mineralization of organic N was not affected. In contrast, biochar promoted soil ammonia-oxidizer populations (bacterial and archaeal nitrifiers) and accelerated gross nitrification rates more than two-fold. Our findings indicate a de-coupling of the soil organic and inorganic N cycles, with a build-up of organic N, and deceleration of inorganic N release from this pool. The results therefore suggest that addition of inorganic fertilizer-N in combination with biochar could compensate for the reduction in organic N mineralization, with plants and microbes drawing on fertilizer-N for growth, in turn fuelling the belowground build-up of organic N. We conclude that combined addition of biochar with fertilizer-N may increase soil organic N in turn enhancing soil carbon sequestration and thereby could play a fundamental role in future soil management strategies.

A substantial portion of soil organic matter (SOM) is of microbial origin. The efficiency with which soil microorganisms can convert their substrate carbon (C) into biomass, compared to how much is lost as respiration, thus co-determines the carbon storage potential of soils. Despite increasing insight into soil microbial C cycling, empirical measurements of microbial C processing across biomes and across soil horizons remain sparse. The theory of ecological stoichiometry predicts that microbial carbon use efficiency (CUE), i.e. growth over uptake of organic C, strongly depends on the relative availability of C and nutrients, particularly N, as microorganisms will either respire excess C or conserve C while mineralising excess nutrients. Microbial CUE is thus expected to increase from high to low latitudes and from topsoil to subsoil as the soil C:N and the stoichiometric imbalance between SOM and the microbial biomass decrease. To test these hypotheses, we collected soil samples from the organic topsoil, mineral topsoil, and mineral subsoil of seven sites along a 1500-km latitudinal transect in Western Siberia. As a proxy for CUE, we measured the microbial substrate use efficiency (SUE) of added substrates by incubating soil samples with a mixture of 13C labelled sugars, amino sugars, amino acids, and organic acids and tracing 13C into microbial biomass and released CO2. In addition to soil and microbial C:N stoichiometry, we also determined the potential extracellular enzyme activities of cellobiohydrolase (CBH) and phenol oxidase (POX) and used the CBH:POX ratio as an indicator of SOM substrate quality. We found an overall decrease of SUE with latitude, corresponding to a decrease in mean annual temperature, in mineral soil horizons. SUE decreased with decreasing stoichiometric imbalance in the organic and mineral topsoil, while a relationship of SUE with soil C:N was only found in the mineral topsoil. However, contrary to our hypothesis, SUE did not increase with soil depth and mineral subsoils displayed lower average SUE than mineral topsoils. Both within individual horizons and across all horizons SUE was strongly correlated with CBH:POX ratio as well as with climate variables. Since enzyme activities likely reflect the chemical properties of SOM, our results indicate that SOM quality exerts a stronger control on SUE than SOM stoichiometry, particularly in subsoils were SOM has been turned over repeatedly and there is little variation in SOM elemental ratios.