Oligopeptides Represent a Preferred Source of Organic N Uptake: A Global Phenomenon?

Nitrogen dynamics and biological processes in soil amended with microalgae grown in abattoir digestate to recover nutrients

The use of microalgae for nutrient recovery from wastewater and subsequent conversion of the harvested biomass into fertilizers offers a sustainable approach towards creating a circular economy. Nonetheless, the process of drying the harvested microalgae represents an additional cost, and its impact on soil nutrient cycling compared to wet algal biomass is not thoroughly understood. To investigate this, a 56-day soil incubation experiment was conducted to compare the effects of wet and dried Scenedesmus sp. microalgae on soil chemistry, microbial biomass, CO2 respiration, and bacterial community diversity. The experiment also included control treatments with glucose, glucose + ammonium nitrate, and no fertilizer addition. The Illumina Mi-Seq platform was used to profile the bacterial community and in-silico analysis was performed to assess the functional genes involved in N and C cycling processes. The maximum CO2 respiration and microbial biomass carbon (MBC) concentration of dried microalgae treatment were 17% and 38% higher than those of paste microalgae treatment, respectively. NH4+ and NO3- released slowly and through decomposition of microalgae by soil microorganisms as compared to synthetic fertilizer control. The results indicate that heterotrophic nitrification may contribute to nitrate production for both microalgae amendments, as evidenced by low amoA gene abundance and a decrease in ammonium with an increase in nitrate concentration. Additionally, dissimilatory nitrate reduction to ammonium (DNRA) may be contributing to ammonium production in the wet microalgae amendment, as indicated by an increase in nrfA gene and ammonium concentration. This is a significant finding because DNRA leads to N retention in agricultural soils instead of N loss via nitrification and denitrification. Thus, further processing the microalgae through drying or dewetting may not be favorable for fertilizer production as the wet microalgae appeared to promote DNRA and N retention.

Development of a controlled release fertilizer by incorporating lauric acid into microalgal biomass: Dynamics on soil biological processes for efficient utilisation of waste resources

Utilisation of microalgae to extract nutrients from the effluent of anaerobic digestion of food waste is an emerging technology. A by-product of this process is the microalgal biomass which has potential to be used as an organic bio-fertilizer. However, microalgal biomass are rapidly mineralized when applied to soil which may result in N loss. One solution is to emulsify microalgal biomass with lauric acid (LA) to delay the release of mineral N. This study aimed to investigate whether combining LA with microalgae to develop a new fertilizer product with a controlled release function of mineral N when applied to soil, and any potential impacts the bacterial community structure and activity. The treatments were applied to soil emulsified with LA and were combined with either microalgae or urea at rates of 0%, 12.5%, 25% and 50% LA, untreated microalgae or urea and unamended control were incubated at 25 °C and 40% water holding capacity for 28 days. Quantification of soil chemistry (NH4+-N, NO3--N, pH and EC), microbial biomass carbon, CO2 production and bacterial diversity were characterised at 0, 1, 3, 7, 14 and 28 days. The NH4+-N and NO3--N concentration decreased with increasing rate of LA combined microalgae indicating that both N mineralization and nitrification were impacted. As a function of time, NH4+-N concentration increased up to 7 days for the microalgae at lower rates of LA, and then slowly decreased for 14 and 28 days, with an inverse relationship with soil NO3-N. Aligning with soil chemistry, an observed decrease in the predicted nitrification genes amoA·amoB and relative abundance of ammonia oxidizing bacteria (Nitrosomonadaceae) and nitrifying bacteria (Nitrospiraceae) with an increasing rate of LA with microalgae provides further support for possible inhibition of nitrification. The MBC and CO2 production was higher in the soil amended with increasing rates of LA combined microalgae and there was an increase in the relative abundance of fast-growing heterotrophs. Treating microalgae by emulsification with LA has the potential to control the release of N by increasing immobilization over nitrification and therefore it might be possible to engineer microalgae to match plant nutrient growth requirements whilst recovering waste from waste resources.

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-021-00793-9.

Can biostimulants be used to mitigate the effect of anthropogenic climate change on agriculture? It is time to respond

Anthropogenic climate change, namely climate alterations induced by human activities, is causing some issues to agricultural systems for their vulnerability to extreme events. Forecasts predict a global population increase in the near years that will exacerbate this situation, elevating the global demand for food. It will pose severe concerns in terms of natural resource usage and availability. Agriculture is one of the anthropogenic activities that will be more affected in the future. Climate extremes menace to affect the quantity and quality of crop production severely. Drought, water and soil salinity are considered among the most problematic factors that anthropogenic climate change will increase. This complex and worrying scenario requires the urgent implementation of sustainable measures which are capable of improving crop yield and quality, fostering the robustness and resilience of cropping systems. Among the more current methodology, the use of natural plant biostimulants (PBs) has been proposed to improve plant resistance to abiotic environmental stresses. The advantage of using these substances is due to their effectiveness in improving crop productivity and quality. Therefore, in this review, the most recent researches dealing with the use of natural PBs for improving plant resistance to drought and salinity, in an anthropogenic climate change scenario, have been reported and critically discussed.

Canadian permafrost stores large pools of ammonium and optically distinct dissolved organic matter

Permafrost degradation may lead to mobilization of carbon and nutrients and enhance microbial processing rates of previously frozen organic matter. Although the pool size and chemical composition of dissolved organic matter (DOM) are fundamental determinants of the carbon cycle in Arctic watersheds, its source within the seasonally thawing active layer and the underlying permafrost remains largely uncharacterized. Here, we used 25 soil cores that extended down into the permafrost from nine sites across Arctic Canada to quantify dissolved organic carbon (DOC) and nitrogen stocks, and to characterize DOM optical properties. Organic permafrost stores 5–7 times more DOC and ammonium than the active layer and mineral permafrost. Furthermore, the permafrost layers contain substantial low molecular weight DOM with low aromaticity suggesting high biodegradability. We conclude that soil organic matter stoichiometry and cryogenic processes determine permafrost DOM chemistry, and that thawing will mobilize large amounts of labile DOC and ammonium into Arctic watersheds.

Arctic warming leads to permafrost thaw and release of previously frozen organic matter and nutrients, but characterization of these pools is lacking. Here the authors use soil cores across Northern Canada to investigate dissolved organic matter and nitrogen stored in permafrost soils.

Long-term effects of copper exposure to agricultural soil function and microbial community structure at a controlled and experimental field site

The long-term effect of heavy metals on soil microbial communities and their function is relatively unknown and little work has been done in field settings. To address this gap, we revisited a field-based experiment, 12 years after the application of copper (Cu) to agricultural soils, with treatment concentrations ranging from 0 to 3310 mg Cu kg^-1 soil. We measured the long-term effects of Cu exposure to soils using multiple functionality assessments and environmental DNA-based community analyses. The assessment results revealed that soils that received moderate to high Cu doses had still not recovered functionality 12-years post exposure. However, plots that received doses of 200 mg kg^-1 Cu or less appeared to have a functionality index not dissimilar to control plots. Environmental DNA analyses of the microbial communities revealed a high level of beta diversity in low Cu treatment plots, whereas communities within high Cu treatment plots had similar community structures to one another (low beta diversity), indicating that specific Cu-tolerant or dormant taxa are selected for in high-Cu environments. Interestingly, high Cu plots had higher within-sample taxa counts (alpha diversity) compared with controls and low Cu plots. We hypothesise that taxa in high Cu plots activated dormancy mechanisms, such that their genetic signal remained present, whilst the functionality of the soil was reduced. Many species identified in high Cu plots are known to have associated dormancy mechanisms and survive in high stress environments. Understanding how these mechanisms collectively contribute to contaminant outcomes is of great importance for the goals of predicting and managing microbial communities and their function. As we found that Cu concentrations above 200 mg kg^-1 can cause significant functionality loss and a selective pressure on microbial communities, it is recommended that Cu concentrations above 200 mg kg^-1are avoided in agricultural soils.

Control of Bacterial Virulence through the Peptide Signature of the Habitat

To optimize fitness, pathogens selectively activate their virulence program upon host entry. Here, we report that the facultative intracellular bacterium Listeria monocytogenes exploits exogenous oligopeptides, a ubiquitous organic N source, to sense the environment and control the activity of its virulence transcriptional activator, PrfA. Using a genetic screen in adsorbent-treated (PrfA-inducing) medium, we found that PrfA is functionally regulated by the balance between activating and inhibitory nutritional peptides scavenged via the Opp transport system. Activating peptides provide essential cysteine precursor for the PrfA-inducing cofactor glutathione (GSH). Non-cysteine-containing peptides cause promiscuous PrfA inhibition. Biophysical and co-crystallization studies reveal that peptides inhibit PrfA through steric blockade of the GSH binding site, a regulation mechanism directly linking bacterial virulence and metabolism. L. monocytogenes mutant analysis in macrophages and our functional data support a model in which changes in the balance of antagonistic Opp-imported oligopeptides promote PrfA induction intracellularly and PrfA repression outside the host.

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Listeria PrfA virulence regulation is controlled by antagonistic nutritional peptides

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Opp-imported peptides regulate PrfA upstream of the activating cofactor GSH

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PrfA is activated by peptides that provide essential cysteine for GSH biosynthesis

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Blockade of PrfA’s GSH binding site by peptides inhibits virulence gene activation

Wide-spread limitation of soil organic nitrogen transformations by substrate availability and not by extracellular enzyme content

Proteins constitute the single largest soil organic nitrogen (SON) reservoir and its decomposition drives terrestrial N availability. Protein cleavage by extracellular enzymes is the rate limiting step in the soil organic N cycle and can be controlled by extracellular enzyme production or protein availability/stabilization in soil. Both controls can be affected by geology and land use, as well as be vulnerable to changes in soil temperature and moisture/O2. To explore major controls of soil gross protein depolymerization we sampled six soils from two soil parent materials (calcareous and silicate), where each soil type included three land uses (cropland, pasture and forest). Soil samples were subjected to three temperature treatments (5, 15, 25 °C at 60% water-holding capacity (WHC) and aerobic conditions) or three soil moisture/O2 treatments (30 and 60% WHC at 21% O2, 90% WHC at 1% O2, at 20 °C) in short-term experiments. Samples were incubated for one day in the temperature experiment and for one week in the moisture/O2 experiment. Gross protein depolymerization rates were measured by a novel 15N isotope pool dilution approach. The low temperature sensitivity of gross protein depolymerization, the lack of relationship with protease activity and strong effects of soil texture and pH demonstrate that this process is constrained by organo-mineral associations and not by soil enzyme content. This also became apparent from the inverse effects in calcareous and silicate soils caused by water saturation/O2 limitation. We highlight that the specific soil mineralogy influenced the response of gross depolymerization rates to water saturation/O2 limitation, causing (I) increasing gross depolymerization rates due to release of adsorbed proteins by reductive dissolution of Fe- and Mn-oxyhydroxides in calcareous soils and (II) decreasing gross depolymerization rates due to mobilization of coagulating and toxic Al3+ compounds in silicate soils.

Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce

Many studies on plant biostimulants and organic fertilizers have been focused on the ability of these products to increase crop productivity and ameliorate crop tolerance to abiotic stresses. However, little information is available on their effect on plant microbiota, whereas it is well known that microorganisms associated with plant play crucial roles on the health and productivity of their host. The aim of this study was to evaluate the effect of a vegetal-derived protein hydrolysate (PH), a vegetal-derived PH enriched with copper (Cu-PH), and a tropical plant extract enriched with micronutrients (PE) on shoot growth and the epiphytic bacterial population of lettuce plants and the ability of these products to enhance the growth of beneficial or harmful bacteria. The three plant-derived products enhanced shoot biomass of lettuce plants indicating a biostimulant effect of the products. Data obtained using culture-independent (Terminal Restriction Fragment Length Polymorphism and Next Generation Sequencing) and culture-dependent approaches indicated that foliar application of commercial products altered the composition of the microbial population and stimulated the growth of specific bacteria belonging to Pantoea, Pseudomonas, Acinetobacter, and Bacillus genus. Data presented in this work demonstrated that some of these strains exhibited potential plant growth-promoting properties and/or biocontrol activity against fungi and bacteria phytopathogens including Fusarium, Trichoderma, and Erwinia species. No indication of potential health risks associated to the enrichment of human or plant bacterial pathogens emerged by the analysis of the microbiota of treated and no-treated plants. Overall, the findings presented in this study indicate that the commercial organic-based products can enhance the growth of beneficial bacteria occurring in the plant microbiota and signals produced by these bacteria can act synergistically with the organic compounds to enhance plant growth and productivity.

Plant-microbe competition: does injection of isotopes of C and N into the rhizosphere effectively characterise plant use of soil N?

Despite considerable attention over the last 25 yr, the importance of early protein breakdown products to plant nitrogen (N) nutrition remains uncertain. We used rhizosphere injection of ¹⁵ N-, ¹³ C- and ¹⁴ C-labelled inorganic N and amino acid (l-alanine), with chase periods from 1 min to 24 h, to investigate the duration of competition for amino acid between roots (Triticum aestivum) and soil microorganisms. We further investigated how microbial modification of l-alanine influenced plant carbon (C) and N recovery. From recovery of C isotopes, intact alanine uptake was 0.2-1.3% of added. Soil microbes appeared to remove alanine from soil solution within 1 min and release enough NH₄⁺ to account for all plant ¹⁵ N recovery (over 24 h) within 5 min. Microbially generated inorganic or keto acid C accounted for < 25% of the lowest estimate of intact alanine uptake. Co-location of C and N labels appears a reasonable measure of intact uptake. Potential interference from microbially modified C is probably modest, but may increase with chase period. Similarly, competition for l-alanine is complete within a few minutes in soil, whereas NO₃^- added at the same rate is available for > 24 h, indicating that long chase periods bias outcomes and fail to accurately simulate soil processes.

Significant release and microbial utilization of amino sugars and D-amino acid enantiomers from microbial cell wall decomposition in soils

Amino sugars and D-amino acid enantiomers are major components of bacterial and fungal cell walls (i.e. peptidoglycan and chitin) and are often used as biomarkers of microbial residue turnover in soils. However, little is known about the in situ decomposition rates of microbial cell wall residues and how soil physicochemical properties affect this process. In this study, we investigated the in situ gross production and consumption rates of free amino sugars (glucosamine and muramic acid) and amino acids (meso-diaminopimelic acid, l-alanine, and d-alanine) by a novel isotope pool dilution assay using ¹⁵N-labeled amino compounds. Soils were obtained from six sites differing in land management (cropland, pasture, and forest) and bedrock (silicate and limestone) and incubated at three temperatures (5, 15, and 25 °C). Free glucosamine released during the decomposition of peptidoglycan and chitin contributed significantly to the extractable soil organic nitrogen pool. Gross production and consumption rates of glucosamine were higher than those of individual amino acids, i.e. L- and D-alanine. Muramic acid had a longer mean residence time (68 h compared to 2.7 h for glucosamine, L- and D-alanine) and made a negligible contribution to soil organic nitrogen fluxes, indicating that free muramic acid was not a major decomposition product of peptidoglycan in soils. Meso-diaminopimelic acid and D-alanine exhibited comparable gross production and consumption rates with L-alanine. These amino acids can be used as indicators to estimate the decomposition of peptidoglycan from bacterial cell wall residues. We found that chitin decomposition was greater in silicate soils, while peptidoglycan decomposition dominated in limestone soils. Glucosamine production rates were not correlated with soil total amino sugars, microbial community structure, or hydrolytic enzyme activities, but were highest in soils with low pH and high sand content, indicating that soil texture and soil pH may strongly influence the decomposition of amino sugar polymers. In contrast, mDAP, L- and D-alanine gross production and consumption rates were positively correlated with soil pH and clay content, due to greater depolymerization of peptidoglycan stem peptides in limestone soils. This isotope pool dilution approach strongly improves our understanding of the mechanisms and environmental controls on microbial cell wall decomposition in soils.

Nitrogen Fertilizer and Straw Applications Affect Uptake of 13C,15N-Glycine by Soil Microorganisms in Wheat Growth Stages

This study investigated the influence of nitrogen (N) fertilizer and straw on intact amino acid N uptake by soil microorganisms and the relationship between amino acid turnover and soil properties during the wheat growing season. A wheat pot experiment was carried out with three treatments: control (CK), N fertilizer (NF) and N fertilizer plus rice straw (NS). We used stable isotope compound-specific analysis to determine the uptake of 13C,15N-glycine by soil microorganisms. In the NF treatment, microbial 13C,15N-glycine uptake was lower compared with CK, suggesting that inorganic N was the preferred N source for soil microorganisms. However, The application of straw with N fertilizer (in NS treatment) increased microbial 13C,15N-glycine uptake even with the same amount of N fertilizer application. In this treatment, enzyme activities, soil microbial biomass C and microbial biomass N increased simultaneously because more C was available. Soil mineral N and plant N contents all decreased substantially. The increased uptake of intact 13C,15N-glycine in the NS treatment can be attributed to direct assimilation by soil microorganisms to satisfy the demand for N when inorganic N was consumed.

Complex N acquisition by soil diazotrophs: how the ability to release exoenzymes affects N fixation by terrestrial free-living diazotrophs

Terrestrial systems support a variety of free-living soil diazotrophs, which can fix nitrogen (N) outside of plant associations. However, owing to the metabolic costs associated with N fixation, free-living soil diazotrophs likely rely on soil N to satisfy the majority of cellular N demand and only fix atmospheric N under certain conditions. Culture-based studies and genomic data show that many free-living soil diazotrophs can access high-molecular weight organic soil N by releasing N-acquiring enzymes such as proteases and chitinases into the extracellular environment. Here, we formally propose a N acquisition strategy used by free-living diazotrophs that accounts for high-molecular weight N acquisition through exoenzyme release by these organisms. We call this the ‘LAH N-acquisition strategy' for the preferred order of N pools used once inorganic soil N is limiting: (1) low-molecular weight organic N, (2) atmospheric N and (3) high-molecular weight organic N. In this framework, free-living diazotrophs primarily use biological N fixation (BNF) as a short-term N acquisition strategy to offset the cellular N lost in exoenzyme excretion as low-molecular weight N becomes limiting. By accounting for exoenzyme release by free-living diazotrophs within a cost–benefit framework, investigation of the LAH N acquisition strategy will contribute to a process-level understanding of BNF in soil environments.

Environmental drivers of soil microbial community structure and function at the Avon River Critical Zone Observatory

The Critical Zone is defined as the thin, permeable layer from the tops of the trees to the bottom of the bedrock that sustains terrestrial life on Earth. The geometry and shape of the various weathering zones are known as the critical zone architecture. At the centre of the Critical Zone are soils and the microorganisms that inhabit them. In Western Australia, the million-year-old stable weathering history and more recent lateral erosion during the past hundreds of thousands of years have created a geomorphic setting where deep weathering zones are now exposed on the surface along the flanks of many lateritic hills. These old weathering zones provide diverse physical and chemical properties that influence near surface pedologic conditions and thus likely shape current surface microbiology. Here, we present data derived from a small lateritic hill on the UWA Farm Ridgefield. Spatial soil sampling revealed the contrasting distribution patterns of simple soil parameters such as pH (CaCl2) and electric conductivity. These are clearly linked with underlying changes of the critical zone architecture and show a strong contrast with low values of pH3.3 at the top of the hill to pH5.3 at the bottom. These parameters were identified as major drivers of microbial spatial variability in terms of bacterial and archaeal community composition but not abundance. In addition, we used sensitive (14)C labelling to assess turnover of three model organic nitrogen compounds - an important biogeochemical functional trait relating to nutrient availability. Though generally rapid and in the order of rates reported elsewhere (t½<5h), some points in the sampling area showed greatly reduced turnover rates (t½>10h). In conclusion, we have shown that the weathering and erosion history of ancient Western Australia affects the surface pedology and has consequences for microbial community structure and function.

Organic nitrogen storage in mineral soil: Implications for policy and management

Nitrogen is one of the most important ecosystem nutrients and often its availability limits net primary production as well as stabilization of soil organic matter. The long-term storage of nitrogen-containing organic matter in soils was classically attributed to chemical complexity of plant and microbial residues that retarded microbial degradation. Recent advances have revised this framework, with the understanding that persistent soil organic matter consists largely of chemically labile, microbially processed organic compounds. Chemical bonding to minerals and physical protection in aggregates are more important to long-term (i.e., centuries to millennia) preservation of these organic compounds that contain the bulk of soil nitrogen rather than molecular complexity, with the exception of nitrogen in pyrogenic organic matter. This review examines for the first time the factors and mechanisms at each stage of movement into long-term storage that influence the sequestration of organic nitrogen in the mineral soil of natural temperate ecosystems. Because the factors which govern persistence are different under this newly accepted paradigm we examine the policy and management implications that are altered, such as critical load considerations, nitrogen saturation and mitigation consequences. Finally, it emphasizes how essential it is for this important but underappreciated pool to be better quantified and incorporated into policy and management decisions, especially given the lack of evidence for many soils having a finite capacity to sequester nitrogen.

Freeze-thaw cycles have minimal effect on the mineralisation of low molecular weight, dissolved organic carbon in Arctic soils

Warmer winters in Arctic regions may melt insulating snow cover and subject soils to more freeze–thaw cycles. The effect of freeze–thaw cycles on the microbial use of low molecular weight, dissolved organic carbon (LMW-DOC) is poorly understood. In this study, soils from the Arctic heath tundra, Arctic meadow tundra and a temperate grassland were frozen to −7.5 °C and thawed once and three times. Subsequently, the mineralisation of 3 LMW-DOC substrates types (sugars, amino acids and peptides) was measured over an 8-day period and compared to controls which had not been frozen. This allowed the comparison of freeze–thaw effects between Arctic and temperate soil and between different substrates. The results showed that freeze–thaw cycles had no significant effect on C mineralisation in the Arctic tundra soils. In contrast, for the same intensity freeze–thaw cycles, a significant effect on C mineralisation was observed for all substrate types in the temperate soil although the response was substrate specific. Peptide and amino acid mineralisation were similarly affected by FT, whilst glucose had a different response. Further work is required to fully understand microbial use of LMW-DOC after freeze–thaw, yet these results suggest that relatively short freeze–thaw cycles have little effect on microbial use of LMW-DOC in Arctic tundra soils after thaw.

Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity

Globally only ≈50% of applied nitrogen (N) fertilizer is captured by crops, and the remainder can cause pollution via runoff and gaseous emissions. Synchronizing soil N supply and crop demand will address this problem, however current soil analysis methods provide little insight into delivery and acquisition of N forms by roots. We used microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure N fluxes in sugarcane cropping soils receiving different fertilizer regimes, and compare these with N uptake capacities of sugarcane roots. We show that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots' uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that (i) the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N, and (ii) organic N may contribute more to crop N supply than is currently assumed.

Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in western Siberia

Soil N availability is constrained by the breakdown of N-containing polymers such as proteins to oligopeptides and amino acids that can be taken up by plants and microorganisms. Excess N is released from microbial cells as ammonium (N mineralization), which in turn can serve as substrate for nitrification. According to stoichiometric theory, N mineralization and nitrification are expected to increase in relation to protein depolymerization with decreasing N limitation, and thus from higher to lower latitudes and from topsoils to subsoils. To test these hypotheses, we compared gross rates of protein depolymerization, N mineralization and nitrification (determined using 15N pool dilution assays) in organic topsoil, mineral topsoil, and mineral subsoil of seven ecosystems along a latitudinal transect in western Siberia, from tundra (67°N) to steppe (54°N). The investigated ecosystems differed strongly in N transformation rates, with highest protein depolymerization and N mineralization rates in middle and southern taiga. All N transformation rates decreased with soil depth following the decrease in organic matter content. Related to protein depolymerization, N mineralization and nitrification were significantly higher in mineral than in organic horizons, supporting a decrease in microbial N limitation with depth. In contrast, we did not find indications for a decrease in microbial N limitation from arctic to temperate ecosystems along the transect. Our findings thus challenge the perception of ubiquitous N limitation at high latitudes, but suggest a transition from N to C limitation of microorganisms with soil depth, even in high-latitude systems such as tundra and boreal forest.

KEY POINTS

We compared soil N dynamics of seven ecosystems along a latitudinal transectShifts in N dynamics suggest a decrease in microbial N limitation with depthWe found no decrease in microbial N limitation from arctic to temperate zones.

Nitrogen acquisition in Agave tequilana from degradation of endophytic bacteria

Plants form symbiotic associations with endophytic bacteria within tissues of leaves, stems, and roots. It is unclear whether or how plants obtain nitrogen from these endophytic bacteria. Here we present evidence showing nitrogen flow from endophytic bacteria to plants in a process that appears to involve oxidative degradation of bacteria. In our experiments we employed Agave tequilana and its seed-transmitted endophyte Bacillus tequilensis to elucidate organic nitrogen transfer from ¹⁵N-labeled bacteria to plants. Bacillus tequilensis cells grown in a minimal medium with ¹⁵NH₄Cl as the nitrogen source were watered onto plants growing in sand. We traced incorporation of ¹⁵N into tryptophan, deoxynucleosides and pheophytin derived from chlorophyll a. Probes for hydrogen peroxide show its presence during degradation of bacteria in plant tissues, supporting involvement of reactive oxygen in the degradation process. In another experiment to assess nitrogen absorbed as a result of endophytic colonization of plants we demonstrated that endophytic bacteria potentially transfer more nitrogen to plants and stimulate greater biomass in plants than heat-killed bacteria that do not colonize plants but instead degrade in the soil. Findings presented here support the hypothesis that some plants under nutrient limitation may degrade and obtain nitrogen from endophytic microbes.

Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial

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.

Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland

Turbic Cryosols (permafrost soils characterized by cryoturbation, i.e., by mixing of soil layers due to freezing and thawing) are widespread across the Arctic, and contain large amounts of poorly decomposed organic material buried in the subsoil. This cryoturbated organic matter exhibits retarded decomposition compared to organic material in the topsoil. Since soil organic matter (SOM) decomposition is known to be tightly linked to N availability, we investigated N transformation rates in different soil horizons of three tundra sites in north-eastern Siberia and Greenland. We measured gross rates of protein depolymerization, N mineralization (ammonification) and nitrification, as well as microbial uptake of amino acids and NH4+ using an array of 15N pool dilution approaches. We found that all sites and horizons were characterized by low N availability, as indicated by low N mineralization compared to protein depolymerization rates (with gross N mineralization accounting on average for 14% of gross protein depolymerization). The proportion of organic N mineralized was significantly higher at the Greenland than at the Siberian sites, suggesting differences in N limitation. The proportion of organic N mineralized, however, did not differ significantly between soil horizons, pointing to a similar N demand of the microbial community of each horizon. In contrast, absolute N transformation rates were significantly lower in cryoturbated than in organic horizons, with cryoturbated horizons reaching not more than 32% of the transformation rates in organic horizons. Our results thus indicate a deceleration of the entire N cycle in cryoturbated soil horizons, especially strongly reduced rates of protein depolymerization (16% of organic horizons) which is considered the rate-limiting step in soil N cycling.

Microbial utilisation of biochar-derived carbon

Whilst largely considered an inert material, biochar has been documented to contain a small yet significant fraction of microbially available labile organic carbon (C). Biochar addition to soil has also been reported to alter soil microbial community structure, and to both stimulate and retard the decomposition of native soil organic matter (SOM). We conducted a short-term incubation experiment using two (13)C-labelled biochars produced from wheat or eucalypt shoots, which were incorporated in an aridic arenosol to examine the fate of the labile fraction of biochar-C through the microbial community. This was achieved using compound specific isotopic analysis (CSIA) of phospholipid fatty acids (PLFAs). A proportion of the biologically-available fraction of both biochars was rapidly (within three days) utilised by gram positive bacteria. There was a sharp peak in CO2 evolution shortly after biochar addition, resulting from rapid turnover of labile C components in biochars and through positive priming of native SOM. Our results demonstrate that this CO2 evolution was at least partially microbially mediated, and that biochar application to soil can cause significant and rapid changes in the soil microbial community; likely due to addition of labile C and increases in soil pH.

How significant to plant N nutrition is the direct consumption of soil microbes by roots?

The high degree to which plant roots compete with soil microbes for organic forms of nitrogen (N) is becoming increasingly apparent. This has culminated in the finding that plants may consume soil microbes as a source of N, but the functional significance of this process remains unknown. We used (15) N- and (14) C-labelled cultures of soil bacteria to measure rates of acquisition of microbes by sterile wheat roots and plants growing in soil. We compared these rates with acquisition of (15) N delivered as nitrate, amino acid monomer (l-alanine) and short peptide (l-tetraalanine), and the rate of decomposition of [(14) C] microbes by indigenous soil microbiota. Acquisition of microbe (15) N by both sterile roots and roots growing in soil was one to two orders of magnitude slower than acquisition of all other forms of (15) N. Decomposition of microbes was fast enough to account for all (15) N recovered, but approximately equal recovery of microbe (14) C suggests that microbes entered roots intact. Uptake of soil microbes by wheat (Triticum aestivum) roots appears to take place in soil. If wheat is typical, the importance of this process to terrestrial N cycling is probably minor in comparison with fluxes of other forms of soil inorganic and organic N.