Nutrient-limited Environments Research Articles

Comparative Genomics Reveals Species-Specific Genes and Symbiotic Adaptations in Tricholoma matsutake.

Tricholoma matsutake, a highly valued ectomycorrhizal fungus, requires a symbiotic relationship with pine trees for growth, complicating its cultivation. This study presents a comprehensive comparative genomic analysis of Tricholoma species, with a focus on T. matsutake. Genomic data from 19 assemblies representing 13 species were analyzed to identify genus-, species-, and strain-specific genes, revealing significant evolutionary adaptations. Notably, T. matsutake exhibits a higher proportion of repetitive elements compared to other species, with retrotransposons like LTR Gypsy dominating its genome. Phylogenomic analyses showed that T. matsutake forms a monophyletic group closely related to T. bakamatsutake. Gene family expansion and contraction analyses highlighted the unique evolutionary pressures on T. matsutake, particularly the loss of tryptophan-related metabolic pathways and the gain of genes related to iron ion homeostasis, which may be crucial for its adaptation to nutrient-limited environments. Additionally, the reduction in secreted proteins and carbohydrate-active enzymes reflects the host-dependent lifestyle of T. matsutake and related species. These findings enhance our understanding of the genetic and evolutionary mechanisms underlying the complex symbiotic relationships of T. matsutake, offering potential avenues for optimizing its cultivation and commercial value.

Exploring the Siderophore Portfolio for Mass Spectrometry-Based Diagnosis of Scedosporiosis and Lomentosporiosis.

Scedosporium apiospermum and Lomentospora prolificans secrete siderophores (iron scavengers) during hyphal proliferation. Siderophores are virulence factors and potential clinical biomarkers of invasive scedosporiosis and lomentosporiosis. Both strains secreted a uniform spectrum of siderophores, including coprogen B (CopB), N α-methyl-coprogen B, dimethyl-coprogen, and ferricrocin, with N α-methyl-coprogen B being the fastest secreted and most abundant coprogen. Under iron and zinc restriction, reflecting a nutrient-limited host environment, L. prolificans secreted 45 times more CopB than did S. apiospermum, presumably contributing to its higher virulence. This robust mobilization of CopB was further enhanced by zinc surplus. Additionally, two novel cyclic peptides, Scedocyclin A and B, were characterized inScedosporium boydii using the de novo sequencing tool CycloBranch. Utilizing matrix-assisted laser desorption/ionization, the portfolio of coprogens detected had limits of detection and quantitation of 4.9 and 14.6 fmol/spot in complex matrices, respectively, making them strong candidates for the next-generation, routine diagnosis of invasive scedosporiosis and lomentosporiosis through the Biotyper siderotyping.

Calorie Restriction Decreases Competitive Fitness in Saccharomyces cerevisiae Following Heat Stress.

Experiments exposing Saccharomyces cerevisiae to glucose limitation (calorie restriction) are widely used to determine impacts on cell health as a model for aging. Using growth on plates and in liquid culture, we demonstrated that calorie restriction reduces fitness in subsequent nutrient-limited environments. Yeast grown in a calorie-restricted environment took longer to emerge from the lag phase, had an extended doubling time and had a lower percentage of culturability. Cells grown under moderate calorie restriction were able to withstand a gradual heat stress in a similar manner to cells grown without calorie restriction but fared less well with a sudden heat shock. Yeast grown under extreme calorie restriction were less fit when exposed to gradual heating or heat shock. Using RNAseq analysis, we provide novel insight into the mechanisms underlying this response, showing that in the absence of calorie restriction, genes whose products are involved in energy metabolism (glycolysis/gluconeogenesis and the citrate cycle) are predominantly overexpressed when yeasts were exposed to gradual heating, whereas this was not the case when they were exposed to shock. We show that both the culture history and the current environment must be considered when assaying physiological responses, and this has wider implications when developing strategies for the propagation, preservation or destruction of microbial cells.

Induction and comparative resuscitation of viable but nonculturable state on Vibrio parahaemolyticus serotypes O3:K6 and O1:K25.

Vibrio parahaemolyticus, an important food-borne pathogens found to be associated with seafoods and marine environs. It has been a topic of debate for many decades that most pathogens are known to enter a viable but nonculturable (VBNC) state under cold temperature and nutrient limited conditions. The present study examined the time required for the induction of VBNC state and the revival strategies of both the endemic O3:K6 and O1:K25 sporadic strains of V. parahaemolyticus. The results revealed that V. parahaemolyticus survived even after 55 days of incubation in nutrient starved media such as phosphate buffered saline (PBS) and Coastal Water (CW) and could be recovered by temperature upshift method, and compared the resuscitation using Dulbecco's Modified Eagle Medium (DMEM), sheep blood serum, chitin flakes with live Artemia salina, and the results suggests that chitin plays a significant role in regulating the VBNC state. It was also confirmed by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscope (SEM) analysis that VBNC cells can alter their morphology to coccoid forms in order to survive in most extreme nutrient limited environment. Further data on the promoting factors and the exact mechanism that resuscitate VBNC V. parahaemolyticus in cold natural environments and frozen foods are needed to perform a robust risk assessment.

Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances

BackgroundIsolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances.ResultsThe two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the ‘rare biosphere’, at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions.ConclusionsOur findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities’ response in the face of future environmental changes.

Microbes produce biofilms to support their communities in nutrient-limited environments.

Microbes produce biofilms to support their communities in nutrient-limited environments.

Picocyanobacterial-bacterial interactions sustain cyanobacterial blooms in nutrient-limited aquatic environments

Cyanobacterial blooms (CBs) and concomitant water quality issues in oligotrophic/mesotrophic waters have been recently reported, challenging the conventional understanding that CBs are primarily caused by eutrophication. To elucidate the underlying mechanism of CBs in nutrition-deficient waters, the changes in Chlorophyll a (Chl-a), cyanobacterial-bacterial community composition, and certain microbial function in Qingcaosha Reservoir, the global largest tidal estuary storage reservoir, were analyzed systematically and comprehensively after its pilot run (2011–2019) in this study. Although the water quality was improved and stabilized, more frequent occurrences of bloom level of Chl-a (>20 μg L−1) in warm seasons were observed during recent years. The meteorological changes (CO2, sunshine duration, radiation, precipitation, evaporation, and relative humidity), water quality variations (pH, total organic carbon content, dissolved oxygen, and turbidity), accumulated sediments as an endogenous source, as well as unique estuarine conditions collectively facilitated picocyanobacterial-bacterial coexistence and community functional changes in this reservoir. A stable and tight co-occurrence pattern was established between dominant cyanobacteria (Synechococcus, Cyanobium, Planktothrix, Chroococcidiopsis, and Prochlorothrix) and certain heterotrophic bacteria (Proteobacteria, Actinobacteria, and Bacteroidetes), which contributed to the remineralization of organic matter for cyanobacteria utilization. The relative abundance of chemoorganoheterotrophs and bacteria related to nitrogen transformation (Paracoccus, Rhodoplanes, Nitrosomonas, and Zoogloea) increased, promoting the emergence of CBs in nutrient-limited conditions through enhanced nutrient recycling. In environments with limited nutrients, the interaction between photosynthetic autotrophic microorganisms and heterotrophic bacteria appears to be non-competitive. Instead, they adopt complementary roles within their ecological niche over long-term succession, mutually benefiting from this association. This long-term study confirmed that enhanced nutrient cycling, facilitated by cyanobacterial-bacterial symbiosis following long-term succession, could promote CBs in oligotrophic aquatic environments devoid of external nutrient inputs. This study advances understanding of the mechanisms that trigger and sustain CBs under nutritional constraints, contributing to developing more effective mitigation strategies, ensuring water safety, and maintaining ecological balance.

Dissolved organic carbon spurs bacterial-algal competition and phosphorus-paucity adaptation: Boosting Microcystis' phosphorus uptake capacity

Dissolved organic carbon (DOC) can alter the availability of background nutrients by affecting the proliferation of heterotrophic bacteria, which exerts a notable influence on algal growth and metabolism. However, the mechanism of how allochthonous DOC (aDOC) precipitates shifts in bacterial-algal interactions and modulates the occurrence of cyanobacteria blooms remains inadequately elucidated. Therefore, this study investigated the relationship between bacteria and algae under aDOC stimulation. We found that excess aDOC triggered the breakdown and reestablishment of the equilibrium between Microcystis and heterotrophic bacteria. The rapid proliferation of heterotrophic bacteria led to a dramatic decrease in soluble phosphorus and thereby resulted in the inhibition of the Microcystis growth. When the available DOC was depleted, the rapid death of heterotrophic bacteria released large amounts of dissolved phosphorus, which provided sufficient nutrients for the recovery of Microcystis. Notably, Microcystis rejuvenated and showed higher cell density compared to the carbon-absent group. This phenomenon can be ascribed that Microcystis regulated the compositions of extracellular polymeric substances (EPS) and the expression of relevant proteins to adapt to a nutrient-limited environment. Using time of flight secondary ion mass spectrometry (TOF-SIM) and proteomic analysis, we observed an enhancement of the signal of organic matter and metal ions associated with P complexation in EPS. Moreover, Microcystis upregulated proteins related to organic phosphorus transformation to increase the availability of phosphorus in various forms. In summary, this study emphasized the role of DOC in algal blooms, revealing the underestimated enhancement of Microcystis nutrient utilization through DOC-induced heterotrophic competition and providing valuable insights into eutrophication management and control.

Combined functional genomic and metabolomic approaches identify new genes required for growth in human urine by multidrug-resistant Escherichia coli ST131.

Uropathogenic Escherichia coli (UPEC) cause ~80% of all urinary tract infections (UTIs), with increasing rates of antibiotic resistance presenting an urgent threat to effective treatment. To cause infection, UPEC must grow efficiently in human urine (HU), necessitating a need to understand mechanisms that promote its adaptation and survival in this nutrient-limited environment. Here, we used a combination of functional genomic and metabolomic techniques and identified roles for the metabolism of small peptides, amino acids, nucleotides, and L-lactate, as well as the stringent response pathway, lipopolysaccharide biosynthesis, and fluoride resistance, for UPEC growth in HU. We further demonstrated that pathways involving nucleotide metabolism and the stringent response are required for UPEC colonization of the mouse bladder. The UPEC genes and metabolic pathways identified in this study represent targets for the development of innovative therapeutics to prevent UPEC growth during human UTI, an urgent need given the rapidly rising rates of global antibiotic resistance.

Abstract B051: Investigating lipid homeostasis in pancreatic ductal adenocarcinoma under tumor-like stress

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a 5-year survival rate of only 10%. One hallmark of PDAC’s tumor microenvironment is dense desmoplasia, due to abnormal accumulation of extracellular matrix and proliferative fibroblasts. During tumorigenesis, pancreatic stellate cells (PSCs) obtain myofibroblast-like signatures and contribute to the fibrotic environment of PDAC. Desmoplasia-induced hypovascularity severely limits oxygen and nutrient delivery. Our laboratory revealed that hypoxia is prominent even at the pancreatic intraepithelial neoplasia (PanIN) stage, a dominant precursor lesion of PDAC. Hypoxia inhibits oxygen-dependent metabolic processes. For example, unsaturated lipid biosynthesis relies on oxygen to maintain desaturase enzymatic activities. Hypoxia also stimulates lipid uptake. Previous studies demonstrated that RAS-transformed cells preferentially import unsaturated lysophosphatidylcholines (LPCs) from culture media. However, in a nutrient-limited fibrotic environment, the potential source of lipids is unclear. Interestingly, a lipidomic study of a PSC secretome displayed a significant amount of LPCs, suggesting that PSCs are the potential lipid source in the PDAC microenvironment. Our data indicate that exogenous unsaturated lipids sustain PDAC cell viability under hypoxia and nutrient deficiency. Moreover, we find PDAC cell survival under tumor-like stress is enhanced in PSC conditioned medium, but not in delipidated conditioned medium. Strikingly, we show that cancer-associated fibroblasts do not experience hypoxic stress as much as adjacent malignant epithelium cells in vivo, suggesting cancer-associated fibroblasts provide unsaturated (and other) lipids to PDAC cells. Based on our lipidomic mass spectra of PSC conditioned medium, we determined that LPCs are actively utilized by PDAC cells for phosphatidylcholine and triglyceride regeneration. By inhibiting LPC to PC conversion with the drug TSI-01, which targets LPCAT (acyltransferase), unsaturated LPC no longer sustains cancer cell survival and ER stress is reactivated. In this study, we demonstrated metabolic crosstalk between fibroblasts and PDAC cells under stress conditions. Our findings revealed a novel metabolic inhibitor to disrupt the metabolic crosstalk between PSC and pancreatic cancer cells which might benefit developing combinatorial therapy of PDAC. Citation Format: Xu Han, Michelle Burrows, Laura Kim, Clementina Mesaros, John Tobias, Brian Keith, Celeste Simon. Investigating lipid homeostasis in pancreatic ductal adenocarcinoma under tumor-like stress [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B051.

Chattonella marina blooms in a trophic gradient system: Interaction with environmental drivers

For coastal eutrophication, lots of studies focused on the influence from environmental factors, especially nitrogen and phosphorus, on algae blooms. The interaction between algae and environmental factors has been often ignored. Using Chattonella marina, a dominant species in marine algal blooms, we established a trophic gradient system that simulated C. marina blooms at three trophic levels: eutrophic, mesotrophic, and oligotrophic, and examined the life history patterns of C. marina and the interactions with environmental factors. Increased trophic levels influenced the growth potential of C. marina, while its unique cyst reproduction allowed it to thrive in nutrient-limited environments. Adequate nutrients caused changes in dissolved oxygen (DO) and pH led by C. marina, with the carbonate system playing a crucial role in regulating pH under nutrient-limited conditions. Limiting the growth of C. marina in areas with low nutrient by manipulating reactive silicate (SiO32−) availability may prove effective. Nitrate (NO3−) was the preferred nutrient for C. marina when its concentration exceeded that of ammonium (NH4+). Phosphorus played a crucial role in the growth and proliferation of C. marina, especially when other nutrients were scarce. The findings of this study may provide valuable insights into the effective management and prevention of algae blooms.

Genome streamlining and clonal erosion in nutrient-limited environments: a test using genome-size variable populations.

Some selection-based theories propose that genome streamlining, favoring smaller genome sizes, is advantageous in nutritionally limited environments, particularly under P-limitation. To test this prediction, we conducted several experimental evolution trials on clonal populations of a facultatively asexual rotifer that exhibits intraspecific variation in genome size. Most trials showed a rapid decline in clonal diversity, which was accelerated in populations that were initially non-adapted. Populations consisting of three rotifer clones often became monoclonal within a few weeks, while populations starting with 120 clones eroded to ten multi-locus genotypes, of which only five were abundant in higher numbers. While P-limitation affected population growth during the experiments, it did not affect the outcome of clonal competition or the speed at which clonal diversity was lost. Common garden transplant experiments revealed that the evolved populations were better adapted to the experimental conditions than the ancestral controls. However, contrary to expectations, the evolved populations did not show an overrepresentation of small genomes. Intermediate genomes were also frequently abundant, although very large genomes were rare. Our findings suggest that fitness is more influenced by genotypic differences among clones than by differences in GS, and indicate that such differences might hinder genome streamlining during early adaptation to a new environment.

Nutrient condition modulates the antibiotic tolerance of Pseudomonas aeruginosa

The variation in nutrient content across diverse environments has a significant impact on the survival and metabolism of microorganisms. In this study, we examined the influence of nutrients on the antibiotic tolerance of the PAO1 strain of Pseudomonas aeruginosa. Our findings indicate that under nutrient-rich conditions, this strain exhibited relatively high tolerance to ceftazidime, chloramphenicol, and tetracycline, but not aminoglycosides and fluoroquinolones. Transcriptome analysis revealed that genes associated with antibiotic tolerance were expressed more efficiently in nutrient-rich media, including ribosomal protein genes and multidrug efflux pump genes, which conferred higher tetracycline tolerance to the strain. Furthermore, the genes responsible for translation, biosynthesis, and oxidative phosphorylation were suppressed when nutrients were limited, resulting in decreased metabolic activity and lower sensitivity to ciprofloxacin. Artificial interference with ATP synthesis utilizing arsenate confirmed that the curtailment of energy provision bolstered the observed tolerance to ciprofloxacin. In general, our results indicate that this strain of P. aeruginosa tends to activate its intrinsic resistance mechanisms in nutrient-rich environments, thereby enhancing resistance to certain antibiotics. Conversely, in nutrient-limited environments, the strain is more likely to enter a dormant state, which enables it to tolerate antibiotics to which it would otherwise be sensitive. These findings further suggest that antibiotics released in environments with varying eutrophication levels may have divergent effects on the development of bacterial antibiotic resistance.

Genome Sequencing Provides Novel Insights into Mudflat Burrowing Adaptations in Eel Goby Taenioides sp. (Teleost: Amblyopinae).

Amblyopinae is one of the lineage of bony fish that preserves amphibious traits living in tidal mudflat habitats. In contrast to other active amphibious fish, Amblyopinae species adopt a seemly more passive lifestyle by living in deep burrows of mudflat to circumvent the typical negative effects associated with terrestriality. However, little is known about the genetic origin of these mudflat deep-burrowing adaptations in Amblyopinae. Here we sequenced the first genome of Amblyopinae species, Taenioides sp., to elucidate their mudflat deep-burrowing adaptations. Our results revealed an assembled genome size of 774.06 Mb with 23 pseudochromosomes anchored, which predicted 22,399 protein-coding genes. Phylogenetic analyses indicated that Taenioides sp. diverged from the active amphibious fish of mudskipper approximately 28.3 Ma ago. In addition, 185 and 977 putative gene families were identified to be under expansion, contraction and 172 genes were undergone positive selection in Taenioides sp., respectively. Enrichment categories of top candidate genes under significant expansion and selection were mainly associated with hematopoiesis or angiogenesis, DNA repairs and the immune response, possibly suggesting their involvement in the adaptation to the hypoxia and diverse pathogens typically observed in mudflat burrowing environments. Some carbohydrate/lipid metabolism, and insulin signaling genes were also remarkably alterated, illustrating physiological remolding associated with nutrient-limited subterranean environments. Interestingly, several genes related to visual perception (e.g., crystallins) have undergone apparent gene losses, pointing to their role in the small vestigial eyes development in Taenioides sp. Our work provide valuable resources for understanding the molecular mechanisms underlying mudflat deep-burrowing adaptations in Amblyopinae, as well as in other tidal burrowing teleosts.

Mixotrophic lifestyle of the ichthyotoxic haptophyte, Prymnesium parvum, offered different sources of phosphorus

Many harmful algae are mixoplanktonic, i.e. they combine phototrophy and phagotrophy, and this ability may explain their ecological success, especially when environmental conditions are not optimal for autotrophic growth. In this study, laboratory experiments were conducted with the mixotrophic and ichthyotoxic haptophyte Prymnesium parvum (strain CCAP 946/6) to test the effects of phosphorus (P) sufficiency and deficiency on its growth rate, phagotrophic and lytic activities. P-deficient P. parvum cultures were grown without or with addition of P in the form of inorganic phosphorus (nutrients) and/or living algal prey (i.e. the cryptophyte Teleaulax amphioxeia). The ingestion rate of P. parvum and prey mortality rate were calculated using flow cytometry measurements based on pigment-derived-fluorescence to distinguish between prey, predators and digesting predators. The first aim of the study was to develop a method taking into account the rate of digestion, allowing the calculation of ingestion rates over a two-week period. Growth rates of P. parvum were higher in the treatments with live prey, irrespective of the concentration of inorganic P, and maximum growth rates were found when both inorganic and organic P in form of prey were added (0.79 ± 0.07 d-1). In addition, the mortality rate of T. amphioxeia induced by lytic compounds was 0.2 ± 0.02 d-1 in the P-deficient treatment, while no mortality was observed under P-sufficiency in the present experiments. This study also revealed the mortality due to cell lysis exceeded that of prey ingestion. Therefore, additional experiments were conducted with lysed prey cells. When grown with debris from prey cells, the mean growth rate of P. parvum was similar to monocultures without additions of prey debris (0.30 ± 0.1 vs. 0.38 ± 0.03 d-1), suggesting that P. parvum is able to grow on prey debris, but not as fast as with live prey. These results provide the first quantitative evidence over two weeks of experiment that ingestion of organic P in the form of living prey and/or debris of prey plays an important role in P. parvum growth and may explain its ecological success in a nutrient-limited environments.

Phosphoproteome Profiling of Klebsiella pneumoniae under Zinc-Limited and Zinc-Replete Conditions.

The bacterial pathogen Klebsiella pneumoniae causes nosocomial infections with the acquisition of multidrug resistance, impeding treatment options. This study investigated the effect of zinc limitation on the phosphoproteome of K. pneumoniae using quantitative mass spectrometry. New insight is provided into cellular signaling methods used by the pathogen to respond to nutrient-limited environments.

Rapid Recovery of Buoyancy in Eutrophic Environments Indicates That Cyanobacterial Blooms Cannot Be Effectively Controlled by Simply Collapsing Gas Vesicles Alone

Many aquatic ecosystems are seriously threatened by cyanobacteria blooms; gas vesicles enable cyanobacteria to form harmful cyanobacterial blooms rapidly. Many lake managers try to control cyanobacterial blooms by collapsing gas vesicle, but it is still unclear whether gas vesicle recovery will cause this method to fail. Through the culture experiments of three cyanobacteria, it was found that all cyanobacteria with collapsed gas vesicles can rapidly regain buoyancy in a few days under nutrient-sufficient environments, and average gas vesicle content was even 9% higher than initially. In contrast, buoyancy recovery of all cyanobacteria under nutrient-limited environments was significantly worse. After culture experiments, the average gas vesicle content of all cyanobacteria in phosphorus-limited environments only reach 49% of the initial value. The gas vesicle content of two non-nitrogen-fixing cyanobacteria in nitrogen-limited environments only reached 38% of initial value. The buoyancy of cyanobacteria in different tropic levels was similar to the gas vesicle content. These results indicate that collapsing gas vesicles can only control cyanobacterial blooms in the short-term. To control cyanobacterial blooms in the long-term, in deep lakes, lake managers should discharge gas vesicles’ collapsed cyanobacteria into deep water. In shallow lakes, the disruption of gas vesicles must be combined with nutrient control measures to effectively control cyanobacteria blooms.

Soil bacteria, archaea, and enzymatic activity of natural and rewetted peatlands display varying patterns in response to water levels

Peatland restoration is an efficient approach to enhance soil carbon sequestration and mitigate climate change. However, successful restoration outcomes require an in-depth comprehension of the underlying soil ecological processes following restoration. To gain a processed perspective on the distinctions between natural and rewetted peatlands, this study compared the soil properties, enzymatic activities, and bacterial and archaeal community structures under uniform water level gradients. The results confirmed our hypothesis that the ecological processes between rewetted and natural peatlands vary significantly. Although the rewetted peatland exhibited different soil properties compared to the natural peatland, increasing water levels resulted in a shift in soil physicochemical properties and hydrolase activities toward those of the natural peatland. This highlights the importance of maintaining a high water level for successful peatland restoration. However, enzymatic activities in the rewetted and natural peatlands exhibited opposite trends with increased water levels, with the natural peatland exhibiting lower polyphenol oxidase activity (-56.7%), higher archaeal diversity (7.3%) and lower bacterial diversity (-2.1%). As the water level increased, ecological processes in the natural peatland shifted from bacteria-dominated faster processes to archaea-dominated slower processes, while no such trends were observed in the rewetted peatland. The study suggest that the lower pH and more restrictive nutrient conditions in the natural peatland, which were altered by rice cultivation with fertilization and vegetation deterioration in the rewetted peatland, may contribute to the biological differences between the two peatland types. These differences may hinder the restoration process after rewetting. Therefore, to enhance the effectiveness of peatland restoration, particularly in the context of rich fens, it is necessary to consider measures that can promote the development of a nutrient-limited and acidic environment aside from rewetting.

Nutrient Limitation Mimics Artemisinin Tolerance in Malaria.

Mounting evidence demonstrates that nutritional environment can alter pathogen drug sensitivity. While the rich media used for in vitro culture contains supraphysiological nutrient concentrations, pathogens encounter a relatively restrictive environment in vivo. We assessed the effect of nutrient limitation on the protozoan parasite that causes malaria and demonstrated that short-term growth under physiologically relevant mild nutrient stress (or "metabolic priming") triggers increased tolerance of a potent antimalarial drug. We observed beneficial effects using both short-term survival assays and longer-term proliferation studies, where metabolic priming increases parasite survival to a level previously defined as resistant (>1% survival). We performed these assessments by either decreasing single nutrients that have distinct roles in metabolism or using a media formulation that simulates the human plasma environment. We determined that priming-induced tolerance was restricted to parasites that had newly invaded the host red blood cell, but the effect was not dependent on genetic background. The molecular mechanisms of this intrinsic effect mimic aspects of genetic tolerance, including translational repression and protein export. This finding suggests that regardless of the impact on survival rates, environmental stress could stimulate changes that ultimately directly contribute to drug tolerance. Because metabolic stress is likely to occur more frequently in vivo compared to the stable in vitro environment, priming-induced drug tolerance has ramifications for how in vitro results translate to in vivo studies. Improving our understanding of how pathogens adjust their metabolism to impact survival of current and future drugs is an important avenue of research to slow the evolution of resistance. IMPORTANCE There is a dire need for effective treatments against microbial pathogens. Yet, the continuing emergence of drug resistance necessitates a deeper knowledge of how pathogens respond to treatments. We have long appreciated the contribution of genetic evolution to drug resistance, but transient metabolic changes that arise in response to environmental factors are less recognized. Here, we demonstrate that short-term growth of malaria parasites in a nutrient-limiting environment triggers cellular changes that lead to better survival of drug treatment. We found that these strategies are similar to those employed by drug-tolerant parasites, which suggests that starvation "primes" parasites to survive and potentially evolve resistance. Since the environment of the human host is relatively nutrient restrictive compared to growth conditions in standard laboratory culture, this discovery highlights the important connections among nutrient levels, protective cellular pathways, and resistance evolution.

DXP Synthase Function in a Bacterial Metabolic Adaptation and Implications for Antibacterial Strategies.

Pathogenic bacteria possess a remarkable ability to adapt to fluctuating host environments and cause infection. Disturbing bacterial central metabolism through inhibition of 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) has the potential to hinder bacterial adaptation, representing a new antibacterial strategy. DXPS functions at a critical metabolic branchpoint to produce the metabolite DXP, a precursor to pyridoxal-5-phosphate (PLP), thiamin diphosphate (ThDP) and isoprenoids presumed essential for metabolic adaptation in nutrient-limited host environments. However, specific roles of DXPS in bacterial adaptations that rely on vitamins or isoprenoids have not been studied. Here we investigate DXPS function in an adaptation of uropathogenic E. coli (UPEC) to d-serine (d-Ser), a bacteriostatic host metabolite that is present at high concentrations in the urinary tract. UPEC adapt to d-Ser by producing a PLP-dependent deaminase, DsdA, that converts d-Ser to pyruvate, pointing to a role for DXPS-dependent PLP synthesis in this adaptation. Using a DXPS-selective probe, butyl acetylphosphonate (BAP), and leveraging the toxic effects of d-Ser, we reveal a link between DXPS activity and d-Ser catabolism. We find that UPEC are sensitized to d-Ser and produce sustained higher levels of DsdA to catabolize d-Ser in the presence of BAP. In addition, BAP activity in the presence of d-Ser is suppressed by β-alanine, the product of aspartate decarboxylase PanD targeted by d-Ser. This BAP-dependent sensitivity to d-Ser marks a metabolic vulnerability that can be exploited to design combination therapies. As a starting point, we show that combining inhibitors of DXPS and CoA biosynthesis displays synergy against UPEC grown in urine where there is increased dependence on the TCA cycle and gluconeogenesis from amino acids. Thus, this study provides the first evidence for a DXPS-dependent metabolic adaptation in a bacterial pathogen and demonstrates how this might be leveraged for development of antibacterial strategies against clinically relevant pathogens.