Nitrogen-poor Environments Research Articles

Tree species-specific wood traits control diazotrophic community composition in deadwood

Deadwood is a nitrogen (N) poor environment and its decomposition rate is limited by low N bioavailability. Diazotrophs reduce such N limitations as they are capable of fixing N2 which employs the functional gene nifH. The present study investigates the diazotrophic community composition in deadwood logs of 13 different tree species in temperate forests. Directly after sampling, deadwood was incubated with water (total fraction) or bromodeoxyuridine (BrdU), and latter labeled the metabolically active fraction. Nucleic acid extracts from both fractions were used to assess the nifH gene-based diversity by amplicon sequencing. The active fraction was a subset of the total fraction, which differed in abundance and with a lower richness. Wood traits such as phosphorous, molybdenum, magnesium, glucose concentration, and C:N ratio were positive factors of richness and community composition of the active fraction. Bradyrhizobium and Methylocapsa dominated the total fraction, while the active fraction was mainly governed by Frankia and Treponema regardless of tree species studied, suggesting that they are well adapted to C sources and nutrient-poor conditions in deadwood. The great diazotrophic diversity (50 genera) in the active fraction indicates an enormous potential for biological N fixation during deadwood decay.

Fertilisation with potato starch wastewater effect on the growth of Scots pine (Pinus sylvestris L.) forest in Poland

Fertilisation is often used to increase plant productivity in agriculture but has also been used in forestry. In our study, Scots pine forest growing in a nitrogen-poor environment was fertilised with NPK post-production wastewater from a potato starch factory. Our research aimed to investigate the dependence of tree growth on different NPK concentrations. Cell characteristics such as cell wall thickness (CWT), lumen diameter (LD) and tree-ring features such as ring width (RW), total number of cells in annual growth (nTotal), earlywood (EW) and latewood (LW) were investigated. Twenty-six years of regular fertilisation of the forest with different doses of wastewater rich in NPK elements have affected the anatomical structure of Scots pine trees. It is presumed that the reduction in CWT and LD on the fertilised site was due to deficiencies in plant water conductivity, which may have occurred due to physiological drought. The influence of nitrogen on unfertilised site from the wastewater area could contribute to the CWT thickening. The results confirm that the use of NPK in excessive doses is detrimental to trees' conductive system.

Lipopeptides as rhizosphere public goods for microbial cooperation.

Here, we provide new insights into the possible fate of cyclic lipopeptides as prominent specialized metabolites from beneficial bacilli and pseudomonads once released in the soil. Our data illustrate how the B. velezensis lipopeptidome may be enzymatically remodeled by Streptomyces as important members of the soil bacterial community. The enzymatic arsenal of S. venezuelae enables an unsuspected extensive degradation of these compounds, allowing the bacterium to feed on these exogenous products via a mechanism going beyond linearization, which was previously reported as a detoxification strategy. As soils are carbon-rich and nitrogen-poor environments, we propose a new role for cyclic lipopeptides in interspecies interactions, which is to fuel the nitrogen metabolism of a part of the rhizosphere microbial community. Streptomyces and other actinomycetes, producing numerous peptidases and displaying several traits of beneficial bacteria, should be at the front line to directly benefit from these metabolites as "public goods" for microbial cooperation.

Exuviae Recycling Can Enhance Queen Oviposition and Colony Growth in Subterranean Termites (Blattodea: Rhinotermitidae: Coptotermes).

Wood-feeding termites have a nitrogen-poor diet and have therefore evolved nitrogen conservation strategies. However, termite workers molt periodically, and throughout the lifetime of a colony, millions of exuviae, a nitrogen-rich resource, are produced by the colony. In Coptotermes Wasmann, workers foraging at remote feeding sites must return to the central part of the nest to molt, where the queen, king, eggs, and larvae are located. It was hypothesized that this molting-site fidelity is an efficient way to recycle nitrogen for reproduction and colony growth, as nestmates involved in exuviae consumption can directly transfer such resources to individuals engaged in reproduction (the queen) or growth (larvae). This study investigates whether incipient colonies of C. gestroi (Wasmann) can gain additional biomass when they are fed supplementary exuviae. Incipient colonies were reared in nitrogen-poor or nitrogen-rich conditions, and 0, 1, 5, or 10 exuviae were added to 3-month-old colonies. After 6.5 months, colonies reared in nitrogen-poor environments gained significantly more biomass when exuviae were added than colonies with no added exuviae. However, the addition of exuviae had no effect on colony growth for colonies reared in nitrogen-rich environments. In a second experiment, queens from colonies in which exuviae were effectively removed laid fewer eggs than queens from colonies in which exuviae were not removed. Therefore, consumption of exuviae from molting individuals by nestmates is an important part of the nitrogen recycling strategy in Coptotermes colonies, as it facilitates queen oviposition and colony growth, especially when such colonies have limited access to nitrogen-rich soils.

Combined effect of acute salt and nitrogen stress on the physiology of lichen symbiotic partners

Nitrogen pollution and excessive salinity are commonly regarded as one of the major environmental concerns in recent decades in many urban environments. Although in urban areas lichens are exposed to both salt and nitrogen stress, no studies have been conducted to date on the simultaneous impact and interaction of these factors on lichen physiology. The aim was to determine the effect of various combinations of NaCl and NH4NO3 doses on the physiology of epigeic lichen Cladonia rei. We also aimed to compare the response of lichens collected from polluted and unpolluted sites to verify whether lichens exposed to different levels of environmental stress in their native environment will react differently. The combined salt-nitrogen treatment caused significant disturbances in the integrity of cell membranes and chlorophyll fluorescence parameters. The most detrimental effect concerned the loss of cell membrane integrity, which suggests that this parameter can serve as a relevant indicator of acute salt-nitrogen stress incidents. Salt stress decreased the photosynthetic efficiency 1 h after exposure, but after 72 h, the FV/FM returned to the level characteristic of healthy lichens in experimental groups without and with small doses of ammonium nitrate. In contrast, recovery was not possible in combination with high nitrogen doses. This indicates that exposure to short-term salt stress in a nitrogen-poor environment only causes a temporary reduction in photosynthetic efficiency, but in urban eutrophic environments may have more serious consequences. The weakened physiological condition of the mycobiont manifested by an increased level of cell membrane damage and a persistent decrease in the photosynthetic efficiency of the photobiont in lichens growing along the roads may indicate an excess of nitrogen in the environment, enhanced by the effect of salt. Lichens collected from a heavy-metal-polluted habitat responded more strongly than those from an unpolluted habitat suggesting that in lichens previously affected by certain harmful factors, exposure to another stress factor may lead to greater disturbances. This is of particular importance for lichens inhabiting the vicinity of roads, since they are also under the influence of other pollutants emitted by road traffic.

Enhanced leaf turnover and nitrogen recycling sustain CO2 fertilization effect on tree-ring growth.

Whether increased photosynthates under elevated atmospheric CO2 could translate into sustained biomass accumulation in forest trees remains uncertain. Here we demonstrate how tree radial growth is closely linked to litterfall dynamics, which enhances nitrogen recycling to support a sustained effect of CO2 fertilization on tree-ring growth. Our ten-year observations in two alpine treeline forests indicated that annual (or seasonal) stem radial increments generally had a positive relationship with the previous year's (or season's) litterfall and its associated nitrogen return and resorption. Annual tree-ring width, annual litterfall and annual nitrogen return and resorption all showed an increasing trend during 2007-2017, and most of the variations were explained by elevated atmospheric CO2 rather than climate change. Similar patterns were found in the longer time series of tree-ring width index from 1986-2017. The regional representativeness of our observed patterns was confirmed by the literature data of six other tree species at 11 treeline sites over the Tibetan Plateau. Enhanced nitrogen recycling through increased litterfall under elevated atmospheric CO2 supports a general increasing trend of tree-ring growth in recent decades, especially in cold and nitrogen-poor environments.

Lotus japonicus HAR1 regulates root morphology locally and systemically under a moderate nitrate condition in the absence of rhizobia.

The local and long-distance signaling pathways mediated by the leucine-rich repeat receptor kinase HAR1 suppress root branching and promote primary root length in response to nitrate supply. The root morphology of higher plants changes plastically to effectively absorb nutrients and water from the soil. In particular, legumes develop root organ nodules, in which symbiotic rhizobia fix atmospheric nitrogen in nitrogen-poor environments. The number of nodules formed in roots is negatively regulated by a long-distance signaling pathway that travels through shoots called autoregulation of nodulation (AON). In the model plant Lotus japonicus, defects in AON genes, such as aleucine-rich repeat receptor kinase HYPERNODULATION ABERRANT ROOT FORMATION 1 (HAR1), an orthologue of CLAVATA1, and the F-box protein TOO MUCH LOVE (TML), induce the formation of an excess number of nodules. The loss-of-function mutant of HAR1 exhibits a short and bushy root phenotype in the absence of rhizobia. We show that the har1 mutant exhibits high nitrate sensitivity during root development. The uninfected har1 mutant significantly increased lateral root number and reduced primary root length in the presence of 3mM nitrate, compared with the wild-type and tml mutant. Grafting experiments indicated that local and long-distance signaling pathways via root- and shoot-acting HAR1 additively regulated root morphology under the moderate nitrate concentrations. These findings allow us topropose that HAR1-mediated signaling pathways control the root system architecture by suppressing lateral root branching and promoting primary root elongation in response to nitrate availability.

Plant biology: Nectar bacteria grow by germinating and bursting pollen

Microbial residents of floral nectar must survive in a carbohydrate-rich yet seemingly nitrogen-poor environment. A new study shows that Acinetobacter spp., common nectar-inhabiting bacteria, differentially induce the pollen commonly found in nectar to germinate and burst, releasing nutrients for microbial growth.

A Major Facilitator Superfamily Peptide Transporter From Fusarium oxysporum Influences Bioethanol Production From Lignocellulosic Material.

Fusarium oxysporum is a leading microbial agent in the emerging consolidated bioprocessing (CBP) industry owing to its capability to infiltrate the plant’s lignin barrier and degrade complex carbohydrates to value-added chemicals such as bioethanol in a single step. Membrane transport of nutrients is a key factor in successful microbial colonization of host tissue. This study assessed the impact of a peptide transporter on F. oxysporum’s ability to convert lignocellulosic straw to ethanol. We characterized a novel F. oxysporum peptide transporter (FoPTR2) of the dipeptide/tripeptide transporter (PTR) class. FoPTR2 represents a novel transporter with high homology to the Trichoderma sp. peptide transporters ThPTR2 and TrEST-AO793. Its expression level was highly activated in nitrogen-poor environments, which is a characteristic of PTR class peptide transporters. Overexpression and post-translational gene silencing of the FoPTR2 in F. oxysporum affected the peptide transport capacity and ethanol yielded from a both a wheat straw/bran mix and glucose. Thus, we conclude that it FoPTR2 plays a role in the nutrient acquisition system of F. oxysporum which serves to not only enhance fungal fitness but also CBP efficacy.

Down-regulation of Cdk1 activity in G1 coordinates the G1/S gene expression programme with genome replication.

Cell division is regulated by cyclin-dependent kinases (Cdks) and requires the periodic activation and inactivation of transcription factors that generate waves of gene expression in different cell-cycle phases. In fission yeast, the MCB-binding transcription factor (MBF) is activated at the end of G1 and regulates the expression of a set of genes that encode for proteins involved in the G1/S transition and DNA replication. Here, we review the importance of controlling MBF by Cdk activity at the onset of S phase. Furthermore, we emphasize that MBF regulation by Cdk is particularly critical under conditions in which G1 is extended, such as in nitrogen-poor environments, where down-regulation of Cdk activity in G1 is crucial to generate a proper wave of MBF-dependent transcription at the end of G1, which is critical to promote a successful S phase.

Framework for community functioning: synthesis of stress gradient and resource partitioning concepts.

To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richness in stressful nitrogen-poor environments. Thus, diatom guild abundance patterns were determined primarily by biotic and/or environmental impacts and, with the exception of the low profile guild, were insensitive to spatial effects. This framework identifies major sources of variability in diatom guild abundance with implications for the understanding of biodiversity-ecosystem functioning.

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes

Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.

Diazotrophic methanotrophs in peatlands: the missing link?

Commentary A recent publication in Plant and Soil (Leppanen et al. 2015) reports on the effect of peat moss species and water table on the N2 fixation rate in boreal peatlands and forests. The lack of CH4-stimulated N2 fixation led the authors to conclude that methanotrophs do not contribute significantly to the N-supply of the mosses. This is in contrast to other studies in peatlands which suggest that methanotrophs may be responsible for the “unaccounted” N-input. The importance of peatlands in the global carbon cycle, combined with the crucial role of N not only in ombotrophic peatlands but also in thawing permafrost warrants a synthesis of these controversies. Evidence for and against diazotrophic N-provision by aerobic methanotrophs in peatlands Ombrotrophic peatlands are nitrogen poor environments, relying solely on atmospheric N deposition. Yet, there is an imbalance in atmospheric N deposition and N accumulation in Sphagnum mosses, with N accumulation by far exceeding N-deposition

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that knowledge of the selective environment and the regulatory mechanisms important for growth and survival in that environment greatly increase the predictability of adaptive evolution.

Cells in cells: morphogenetic and metabolic strategies conditioning rice infection by the blast fungus Magnaporthe oryzae

The rice blast fungus Magnaporthe oryzae is a global food security threat due to its destruction of cultivated rice. Of the world's rice harvest, 10-30 % is lost each year to this pathogen, and changing climates are likely to favor its spread into new areas. Insights into how the fungus might be contained could come from the wealth of molecular and cellular studies that have been undertaken in order to shed light on the biological underpinnings of blast disease, aspects of which we review herein. Infection begins when a three-celled spore lands on the surface of a leaf, germinates, and develops the specialized infection structure called the appressorium. The mature appressorium develops a high internal turgor that acts on a thin penetration peg, forcing it through the rice cuticle and into the underlying epidermal cells. Primary then invasive hyphae (IH) elaborate from the peg and grow asymptomatically from one living rice cell to another for the first few days of infection before host cells begin to die and characteristic necrotic lesions form on the surface of the leaf, from which spores are produced to continue the life cycle. To gain new insights into the biology of rice blast disease, we argue that, conceptually, the infection process can be viewed as two discrete phases occurring in markedly different environments and requiring distinct biochemical pathways and morphogenetic regulation: outside the host cell, where the appressorium develops in a nutrient-free environment, and inside the host cell, where filamentous growth occurs in a glucose-rich, nitrogen-poor environment, at least from the perspective of the fungus. Here, we review the physiological and metabolic changes that occur in M. oryzae as it transitions from the surface to the interior of the host, thus enabling us to draw lessons about the strategies that allow M. oryzae cells to thrive in rice cells.

Genome Sequence of Klebsiella oxytoca SA2, an Endophytic Nitrogen-Fixing Bacterium Isolated from the Pioneer Grass Psammochloa villosa

Klebsiella oxytoca strain SA2 is an endophytic nitrogen-fixing bacterium isolated from the pioneer grass Psammochloa villosa, which grows in the moving sand dunes of Ordos Plateau, China. The SA2 genome sequence provides the genetic background for understanding its endophytic lifestyle and survival in association with grass in nitrogen-poor environments.

A Unique Pool of Compatible Solutes on Rhodopirellula baltica, Member of the Deep-Branching Phylum Planctomycetes

The intracellular accumulation of small organic solutes was described in the marine bacterium Rhodopirellula baltica, which belongs to the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. Sucrose, α-glutamate, trehalose and mannosylglucosylglycerate (MGG) are the main solutes involved in the osmoadaptation of R. baltica. The ratio and total intracellular organic solutes varied significantly in response to an increase in salinity, temperature and nitrogen content. R. baltica displayed an initial response to both osmotic and thermal stresses that includes α-glutamate accumulation. This trend was followed by a rather unique and complex osmoadaptation mechanism characterized by a dual response to sub-optimal and supra-optimal salinities. A reduction in the salinity to sub-optimal conditions led primarily to the accumulation of trehalose. In contrast, R. baltica responded to salt stress mostly by increasing the intracellular levels of sucrose. The switch between the accumulation of trehalose and sucrose was by far the most significant effect caused by increasing the salt levels of the medium. Additionally, MGG accumulation was found to be salt- as well as nitrogen-dependent. MGG accumulation was regulated by nitrogen levels replacing α-glutamate as a K+ counterion in nitrogen-poor environments. This is the first report of the accumulation of compatible solutes in the phylum Planctomycetes and of the MGG accumulation in a mesophilic organism.

Progress on nitrogen regulation gene expression of plant pathogenic fungi under nitrogen starvation

It has been confirmed that the occurrence of plant disease is caused by the effector molecules secreted by plant pathogens. The regulation effector gene expression is an important aspect in understanding of the infection process. The nutritional status of cells has been postulated to be a vital role for effector gene expression. Studies have indicated that the induction of the same effecter genes during growth in vitro as those during growth in planta under nitrogen-starved conditions. This showed that the nitrogen poor environment existed in the early time of plant evolution. This paper describes the system in the pathogenesis of several fungal pathogens and nitrogen in the process of gene expression effects from the results of several species by comparing and contrasting the function of nitrogen regulatory genes, as well as by studying plants in vivo and in vitro gene under nitrogen limitation inductive effect in order to reveal the effectiveness of nitrogen in the development process of host plant disease is an important factor.

Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH(3), while others, notably in plants, transport the positively charged NH(4)(+). On the basis of the structural data for AmtB from Escherichia coli , we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH(4)(+) is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH(3), while the excess proton is cotransported through a highly conserved hydrogen-bonded His168-His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown.

Native defects in hybrid C/BN nanostructures by density functional theory calculations

First-principles calculations of substitutional defects and vacancies are performed for zigzag-edged hybrid C/BN nanosheets and nanotubes which recently have been proposed to exhibit half-metallic properties. The formation energies show that defects form preferentially at the interfaces between graphene and BN domains rather than in the middle of these domains, and that substitutional defects dominate over vacancies. Chemical control can be used to favor localization of defects at C-B interfaces (nitrogen-rich environment) or C-N interfaces (nitrogen-poor environment). Although large defect concentrations have been considered here (10${}^{6}$ cm${}^{\ensuremath{-}1}$), half-metallic properties can subsist when defects are localized at the C-B interface and for negatively charged defects localized at the C-N interface; hence the promising magnetic properties theoretically predicted for these zigzag-edged nanointerfaces might not be destroyed by point defects if these are conveniently engineered during synthesis.