Low-nutrient Environments Research Articles

Two antagonistic gene regulatory networks drive Arabidopsis root hair growth at low temperature linked to a low-nutrient environment.

Root hair (RH) cells can elongate to several hundred times their initial size, and are an ideal model system for investigating cell size control. Their development is influenced by both endogenous and external signals, which are combined to form an integrative response. Surprisingly, a low-temperature condition of 10°C causes increased RH growth in Arabidopsis and in several monocots, even when the development of the rest of the plant is halted. Previously, we demonstrated a strong correlation between RH growth response and a significant decrease in nutrient availability in the growth medium under low-temperature conditions. However, the molecular basis responsible for receiving and transmitting signals related to the availability of nutrients in the soil, and their relation to plant development, remain largely unknown. We have discovered two antagonic gene regulatory networks (GRNs) controlling RH early transcriptome responses to low temperature. One GNR enhances RH growth and it is commanded by the transcription factors (TFs) ROOT HAIR DEFECTIVE 6 (RHD6), HAIR DEFECTIVE 6-LIKE 2 and 4 (RSL2-RSL4) and a member of the homeodomain leucine zipper (HD-Zip I) group I 16 (AtHB16). On the other hand, a second GRN was identified as a negative regulator of RH growth at low temperature and it is composed by the trihelix TF GT2-LIKE1 (GTL1) and the associated DF1, a previously unidentified MYB-like TF (AT2G01060) and several members of HD-Zip I group (AtHB3, AtHB13, AtHB20, AtHB23). Functional analysis of both GRNs highlights a complex regulation of RH growth response to low temperature, and more importantly, these discoveries enhance our comprehension of how plants synchronize RH growth in response to variations in temperature at the cellular level.

Long-term survival of asexual Zymoseptoria tritici spores in the environment

BackgroundThe fungal phytopathogen Zymoseptoria tritici, causal agent of the economically damaging Septoria tritici blotch of wheat, is different from most foliar fungal pathogens in that its germination occurs slowly and apparently randomly after arrival on the leaf surface and is followed by a potentially prolonged period of epiphytic growth and even reproduction, during which no feeding structures are formed by the fungus. Thus, understanding the cues for germination and the mechanisms that underpin survival in low-nutrient environments could provide key new avenues for disease control.ResultsIn this work, we examine survival, culturability and virulence of spores following transfer from a high nutrient environment to water. We find that a sub-population of Z. tritici spores can survive and remain virulent for at least 7 weeks in water alone, during which time multicellular structures split to single cells. The fungus relies heavily on stored lipids; however, if cell suspensions in water are dried, the cells survive without lipid utilisation. Changes in gene expression in the first hours after suspension in water reflect adaptation to stress, while longer term starvation (7 days) induces changes particularly in primary metabolism and cytochrome P450 (CYP) gene expression. Importantly, we also found that Z. tritici spores are equally or better able to survive in soil as in water, and that rain-splash occurring 49 days after soil inoculation can transfer cells to wheat seedlings growing in inoculated soil and cause Septoria leaf blotch disease.ConclusionsZ. tritici blastospores can survive in water or soil for long periods, potentially spanning the intercrop period for UK winter wheat. They rely on internal lipid stores, with no external nutrition, and although a large proportion of spores do not survive for such an extended period, those that do remain as virulent as spores grown on rich media. Thus, Z. tritici has exceptional survival strategies, which are likely to be important in understanding its population genetics and in developing novel routes for Septoria leaf blotch control.

A Comparative Evaluation of the Antimicrobial Properties of 50% Grape Seed Extract, N-acetyl Cysteine and 5.25% Sodium Hypochlorite against Enterococcus faecalis (ATCC 19433) – An In vitro Study

Abstract Introduction: Endodontic infections are complex and polymicrobial, presenting significant challenges in dental treatment. Eliminating bacteria is the main objective of endodontic preparation, ensuring a tight seal to prevent reinfection. A commonly isolated bacterium, Enterococcus faecalis, is Gram positive and facultative anaerobic. It thrives in low-nutrient environments, forming resilient biofilms. Due to its tissue dissolving properties and broad-spectrum antimicrobial, sodium hypochlorite (NaOCl) is the most sought after irrigant, but its cytotoxicity is a concern. Alternatives such as grape seed extract (GSE) and N-acetyl cysteine (NAC) are being explored for their potential antimicrobial effects and biocompatibility. Materials and Methods: Forty single-rooted, non-carious premolars extracted for orthodontic reasons were selected. Teeth were cleaned, sectioned and prepared, ensuring apical patency. Specimens were autoclaved and contaminated with E. faecalis (ATCC 19433) for 30 days. Four groups (n = 10) were formed: Group I – GSE 50%, Group II – NAC 200 mg/ml, Group III – NaOCl 5.25% and Group IV – sodium chloride (0.9%). Manufacturer’s instructions were followed precisely to prep the solutions, and root canals were treated using the Reciproc R25 instrument. Samples were collected before (F1) and after (F2) instrumentation and irrigation. Colony-forming units (CFUs) were quantified and analysis was done using two-way analysis of variance and Tukey’s honestly significant difference post hoc tests, with significance set at P < 0.05. Results: NaOCl significantly reduced CFU counts, demonstrating superior antimicrobial efficacy compared to NAC and GSE (P < 0.01). In comparison to negative control and GSE (P < 0.01), NAC showed significant antimicrobial activity, but not significantly different from GSE (P > 0.05). GSE displayed potential antimicrobial properties but was less effective than NaOCl and NAC. Conclusion: NaOCl remains the most effective irrigant; however, NAC and GSE also demonstrated significant antimicrobial properties and could serve as adjuncts in endodontic therapy. Further research is needed to optimise their formulations and validate clinical applications.

Crystal structure of the 4-hydroxybutyryl-CoA synthetase (ADP-forming) from nitrosopumilus maritimus

The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle from ammonia-oxidizing Thaumarchaeota is currently considered the most energy-efficient aerobic carbon fixation pathway. The Nitrosopumilus maritimus 4-hydroxybutyryl-CoA synthetase (ADP-forming; Nmar_0206) represents one of several enzymes from this cycle that exhibit increased efficiency over crenarchaeal counterparts. This enzyme reduces energy requirements on the cell, reflecting thaumarchaeal success in adapting to low-nutrient environments. Here we show the structure of Nmar_0206 from Nitrosopumilus maritimus SCM1, which reveals a highly conserved interdomain linker loop between the CoA-binding and ATP-grasp domains. Phylogenetic analysis suggests the widespread prevalence of this loop and highlights both its underrepresentation within the PDB and structural importance within the (ATP-forming) acyl-CoA synthetase (ACD) superfamily. This linker is shown to have a possible influence on conserved interface interactions between domains, thereby influencing homodimer stability. These results provide a structural basis for the energy efficiency of this key enzyme in the modified 3HP/4HB cycle of Thaumarchaeota.

Microbial Community Structure in the Taklimakan Desert: The Importance of Nutrient Levels in Medium and Culture Methods.

Although the Taklimakan Desert lacks the necessary nutrients and conditions to support an extensive ecosystem, it is a treasure trove of extremophile resources with special structures and functions. We analyzed the bacterial communities using oligotrophic medium and velvet cloth replicate combined with an extended culture duration. We isolated numerous uncultured microorganisms and rare microorganisms belonging to genera not often isolated or recently described, such as Aliihoeflea, Halodurantibacterium, and Indioceanicola. A total of 669 strains were isolated from the soil of the Taklimakan Desert, which were classified into 5 phyla, 7 classes, 25 orders, 42 families, 83 genera, and 379 species. Among them, 148 strains were potential new species. Our data show that even when working with samples from extreme environments, simple approaches are still useful for cultivating stubborn microbes. Through comparing the isolation effects of different nutrient levels on microbial diversity and abundance, the results show that reducing the nutrient level of the medium was more conducive to improving the culturability of microorganisms in low-nutrient environments, while the high-nutrient medium was more suitable for the isolation of dominant fast-growing strains. This study helps to better reflect the diversity of microbial resources and lays a foundation for the further research and utilization of soil microbial resources in the Taklimakan Desert.

Gene expression in soft-shell clam (Mya arenaria) transmissible cancer reveals survival mechanisms during host infection and seawater transfer.

Transmissible cancers are unique instances in which cancer cells escape their original host and spread through a population as a clonal lineage, documented in Tasmanian Devils, dogs, and ten bivalve species. For a cancer to repeatedly transmit to new hosts, these lineages must evade strong barriers to transmission, notably the metastasis-like physical transfer to a new host body and rejection by that host's immune system. We quantified gene expression in a transmissible cancer lineage that has spread through the soft-shell clam (Mya arenaria) population to investigate potential drivers of its success as a transmissible cancer lineage, observing extensive differential expression of genes and gene pathways. We observed upregulation of genes involved with genotoxic stress response, ribosome biogenesis and RNA processing, and downregulation of genes involved in tumor suppression, cell adhesion, and immune response. We also observe evidence that widespread genome instability affects the cancer transcriptome via gene fusions, copy number variation, and transposable element insertions. Finally, we incubated cancer cells in seawater, the presumed host-to-host transmission vector, and observed conserved responses to halt metabolism, avoid apoptosis and survive the low-nutrient environment. Interestingly, many of these responses are also present in healthy clam cells, suggesting that bivalve hemocytes may have inherent seawater survival responses that may partially explain why transmissible cancers are so common in bivalves. Overall, this study reveals multiple mechanisms this lineage may have evolved to successfully spread through the soft-shell clam population as a contagious cancer, utilizing pathways known to be conserved in human cancers as well as pathways unique to long-lived transmissible cancers.

Impact of low nutrient environment on placental formation and metabolism: Novel insights from the MEM mouse model

Impact of low nutrient environment on placental formation and metabolism: Novel insights from the MEM mouse model

A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.

Low methyl nutrition microenvironment as a key regulator in modulating epigenetic regulation and switching energy metabolism to stimulate hepatocellular carcinoma stemness properties

The influence of changes in dietary habits, chemical treatments, variations in the activity of one-carbon enzyme gene modifications, and liver function impairment make hepatocellular carcinoma (HCC) patients prone to marginal methyl nutrient deficiency. Hepatocellular carcinoma has consistently ranked among the top five cancer incidence rates around the world, yet the issue of methyl nutrient deficiency still lacks systematic basic scientific assessment. This study aims to investigate whether the deficiency of methyl nutrients, specifically folate, choline, and betaine, induces the stem cell-like properties of hepatocellular carcinoma cells and promotes malignant progression, as well as to clarify the potential mechanisms involved. We found that human hepatocellular carcinoma cells (HepG2) cultured in a low methyl nutrient environment exhibited the following: (1) Methyl nutrient deficiency induced self-renewal cancer stem cell characteristics in hepatocellular carcinoma cells, forming tumor spheres on the seventh day, with a greater number and larger volume observed in environments with low folate and low choline. Upon isolating the tumor spheres and re-culturing, we found that the sphere cells induced by methyl nutrient deficiency (2) showed increased intracellular NADPH, accompanied by elevated lactate concentration in the microenvironment and changes in energy-related indicators of Warburg metabolism. At the same time, the expression of post-reprogramming related proteins Sirt1 and DNMT1 was altered. In summary, methyl nutrient deficiency may promote the malignant progression of hepatocellular carcinoma through both epigenetic modifications and energy conversion. National Science and Technology Council (NSTC112-2320-B-567-001). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Interactions between chaperone and energy storage networks during the evolution of Legionella pneumophila under heat shock.

Waterborne transmission of the bacterium Legionella pneumophila has emerged as a major cause of severe nosocomial infections of major public health impact. The major route of transmission involves the uptake of aerosolized bacteria, often from the contaminated hot water systems of large buildings. Public health regulations aimed at controlling the mesophilic pathogen are generally concerned with acute pasteurization and maintaining high temperatures at the heating systems and throughout the plumbing of hot water systems, but L. pneumophila is often able to survive these treatments due to both bacterium-intrinsic and environmental factors. Previous work has established an experimental evolution system to model the observations of increased heat resistance in repeatedly but unsuccessfully pasteurized L. pneumophila populations. Here, we show rapid fixation of novel alleles in lineages selected for resistance to heat shock and shifts in mutational profile related to increases in the temperature of selection. Gene-level and nucleotide-level parallelisms between independently-evolving lineages show the centrality of the DnaJ/DnaK chaperone system in the heat resistance of L. pneumophila. Inference of epistatic interactions through reverse genetics shows an unexpected interaction between DnaJ/DnaK and the polyhydroxybutyrate-accumulation energy storage mechanism used by the species to survive long-term starvation in low-nutrient environments.

Plant-associated bacteria and enzymes support Canavalia rosea growth in coastal hypersaline soils

Canavalia rosea is an extremophilic legume that grows in hypersaline and nutrient-deficient ecosystems. The extremophilic nature of C. rosea may be attributed to its ability to establish symbiotic associations with nutrient mineralizing and plant growth promoting (PGP) bacteria housed in the nodules. This study examined legume-microbe symbiosis and plant nutrition of C. rosea growing in subtropical coastal zone in KwaZulu-Natal province, South Africa. Canavalia rosea adult plants of the same age from Westbrook, Scottburgh and Durban were collected for plant biomass and plant nutrition and root nodules were used for bacterial extraction and identification. Rhizosphere soils sampled from the three localities were used for bacterial extraction and identification, extracellular enzyme assays and soil characteristics (pH, nutrient concentrations, total cation, and exchange acidity). Westbrook, Scottburgh and Durban soils were nutrient-deficient with varying total cations, acid saturation and a pH range of 7.3–7.6. Soil nutrient mineralizing extracellular enzyme activities varied across study sites. The culturable bacterial strains isolated from the sampled soils belonged to the Pseudomonas, Pantoea and Flavobacterium genera. Canavalia rosea root nodules were nodulated by Pseudomonas guariconensis, Pseudomonas fulva, Pseudomonas fluorescens, Pseudomonas chlororaphis and Pseudomonas chlororaphis subsp. aurantiaca. Plants growing in Westbrook soils had a significantly higher total plant biomass compared to Scottburgh and Durban plants. Plant P concentration did not vary significantly between sites while plant N and C concentrations varied significantly. Plant-associated and soil bacteria with phosphorus (P) solubilising, nitrogen (N) cycling, and N fixing functions and associated enzymes seem to facilitate the mobilization of nutrients enabling C. rosea to thrive in hypersaline and low-nutrient environments.

Nitrogen and phosphorus availability alters tree‐grass competition intensity in savannas

Abstract Plant essential macronutrients like nitrogen (N) and phosphorus (P) can limit savanna tree growth and are important determinants of savanna vegetation dynamics, along with rainfall, fire and herbivory. How nitrogen and phosphorus shape tree‐grass competition and their coexistence remain unclear, hindering our ability to predict how savannas may respond to altered nutrient cycling. Here, we evaluate (1) if trees and grasses respond differently to N versus P availability, or (2) if grasses are more competitive in low nutrient environments while trees are more competitive in high nutrient environments. To do this, we grew saplings of 6 tree and 1 grass species from the Kruger National Park, South Africa, for 16 weeks under fully factorial nutrient and competition treatments (with/without competitors, low/high rate of N supply and low/high rate of P supply) under a watering regime designed to mimic wet season rainfall in a mesic savanna. Trees and grasses foraged most aggressively for nitrogen and allocated biomass differently depending on nitrogen availability. Overall, tree growth decreased in competition with grass, even in high nutrient environments where they grew faster. Grasses were always better below‐ground competitors, utilising aggressive nutrient foraging strategies, including high root phosphatase activity in response to nitrogen and large root biomass allocation. Synthesis. In low nutrient environments (e.g. on nutrient‐poor sandy soils), nutrients may limit tree growth. Nutrient rich environments enable tree growth, but grasses continue to compete effectively with trees. Understanding what this means for ecosystem responses to nutrient availability is not trivial, especially in the context of fire and herbivory. However, it is clear that soil nutrients likely affect tree and grass growth and competition in savannas, which suggests that future changes in nutrient cycling, such as N deposition, may have important effects on savanna vegetation.

Paleoecological and paleobiogeographic implications of a seagrass-indicating foralgal skeletal assemblage: Retracing the Burdigalian Quilon Limestone (Kerala Basin, SW India)

Seagrasses are marine angiosperms documented in shallow-marine, soft bottom settings across the Cenozoic. They proliferated globally after their divergence from other alismatid monocots in the late Cretaceous followed by an adaptation to the marine environment. Detailed evaluation of seagrasses in the geological archives is of utmost importance to understand their responses to climatic and environmental alterations in the deep time perspective. Here we examine the lower Miocene Quilon Limestone from the Kerala Basin (southwest India) that encompasses a Pseudotaberina-Halimeda floatstone signalling a robust photozoan foralgal skeletal assemblage. This is characterized by the dominant soritid foraminifer Pseudotaberina and the calcareous green alga Halimeda, in association with other foraminifera and representatives from various biotic groups that indicate a tropical seagrass paleoenvironment. Abundant soritids together with various bryopsidalean Halimeda species indicate light and temperature as the major ecological drivers regulating the Quilon Limestone seagrass paleocommunity during the early Miocene (Burdigalian). The spatio-temporal distribution patterns of Halimeda also indicate temperature as the most prominent ecological constraint determining its dispersal and evolution at multiple latitudes. A well illuminated substrate is envisaged to support the development and calcification of the Halimeda thalli. Abundance of K-strategist foraminifera with minor occurrence of suspension-feeding bryozoans and some gastropods, bivalves indicate a low-nutrient environment.

Community structure and species composition of typical Quercus variabilis natural secondary forest at the northern foothills of the Qinling Mountains, China

We investigated species composition and community structure of a typical Quercus variabilis natural secondary forest in the northern foothills of the Qinling Mountains, within the dynamic monitoring plot of deciduous broad-leaved forest at the Louguantai experimental forest farm in Zhouzhi County, Shaanxi Province. The results showed that there were 3162 individual woody plants with diameter at breast height ≥1 cm in the plot, which were belonged to 42 species, 36 genera, and 25 families. The community genus's areal type was dominated by the temperate component, which accounted for 44.4%, and followed by the tropical component. The community was dominated by several tree species. The top three species with respect to importance value were Q. variabilis, Pinus tabuliformis, and Quercus aliena, with the sum of their importance value being 64.7%. The average DBH of all woody plants was 7.58 cm. The distribution of all individuals and dominant species in the tree layer was approximately normal, with more medium-size individuals. The community structure was stable. The community was poorly renewed, with a trend of population decline. Biodiversity indices varied considerably among different plots, being lower than those of subtropical broad-leaved evergreen forests. There was a significant correlation between community species distribution and environmental factors. Soil and topography explained 42.4% of the variation in community distribution. Altitude and soil alkali hydrolysable nitrogen had a significant effect on community distribution. Altitude, soil total phosphorus, and organic matter content significantly affected the species diversity of Q. variabilis communities. The stronger adaptability of Q. variabilis populations allowed them to become dominant in low-nutrient environments, which limited species diversity in the community.

Comparing Vegetation and Substrate Performances on Nutrient Removal and Biomass Establishment Using a Natural Swimming Pool Experiment

Natural swimming pools (NSPs) rely on the interaction of bog vegetation, bacteria, and substrate to maintain water quality. Nitrogen (N) and phosphorus (P) levels in NSPs are critical because of their involvement in eutrophication. We conducted a 15-week greenhouse study to address the significant literature gap regarding nutrient removal capabilities of substrates and vegetation in the low-nutrient environment of NSPs. We used mass balance analyses to compare the performances of four substrates [river gravel (control), recycled glass, expanded clay, expanded shale] and two plant species [blue flag iris (Iris versicolor) and lizard’s tail (Saururus cernuus)] under two flow conditions: free water surface and subsurface flow. At the end of the experiment, except for the recycled glass group, all other substrate groups reduced water nitrate (NO3) levels to less than 30 mg⋅L−1, the standard of the 2011 Forschungsgesellschaft Landschaftsentwicklung Landschaftsbau (FLL) guidelines. However, only the expanded clay group closely approached the P standard (≤0.01 mg⋅L−1). Expanded clay and expanded shale demonstrated potential as substrates for NSP bogs. The final aboveground biomass dry weight was strongly negatively correlated with the final NO3 and P water concentrations. However, direct plant uptake proved insufficient to remove all nutrient inputs, especially for P. Except for the recycled glass group (34%), a significant portion of N (79%–90%) from total N added was removed by aboveground biomass. However, P uptake by biomass was substantially lower (18%–37%). With acceptable vigor and biomass accumulation, blue flag iris may be a suitable species for vegetated NSPs, whereas lizard’s tail is not because of uncertain establishment. Compared with controlling N, managing P for FLL standards in NSPs will be more challenging. Our work begins to fill the essential gap in the NSP literature regarding nutrient removal capabilities of substrates and vegetation. Future work should continue to study alternative substrates and plant species for P removal, particularly in field conditions and over longer periods.

Impact of dust deposition on the growth of marine autotrophic and heterotrophic microorganisms: Evidence from the South China Sea

Aeolian dust can provide nutrients for the ocean and affect the growth of phytoplankton. However, the impacts of dust deposition on autotrophic and heterotrophic microorganisms have rarely been studied. In this study, we conducted two microcosm experiments in the low-nutrient and low-chlorophyll environment of the South China Sea and found that dust did not stimulate the abundance of autotrophic and heterotrophic microorganisms. Our results show that dust contains most of the unreacted iron-bearing minerals, and thus provides limited bioavailable iron and nitrogen for bacterioplankton and phytoplankton growth. These results elucidate the overlooked impacts of the properties of the iron-bearing minerals in aeolian dust on microbial communities, which may play an important role in marine ecosystems and climate change.

The exception to the rule? TORC1 triggers growth under low nutrient environments

Eukaryotic cells' proliferation and growth are controlled by the target of rapamycin kinase (TOR). TOR usually activates in favorable energy and nutritional circumstances. This is challenged by recent research, suggesting that plant cells optimized for nutrient absorption in low nutritional conditions may activate the TOR pathway in a polarized manner.

Selection for oligotrophy among bacteria inhabiting host microbiomes.

Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.

Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature.

In the current study, metabolic genes and networks that influence the persistence of pathogenic Escherichia coli O104:H4 strain C227/11Φcu in agricultural soil microenvironments at low temperature were investigated. The strain was incubated in alluvial loam (AL) and total RNA was prepared from samples at time point 0, and after 1 and 4 weeks. Differential transcriptomic analysis was performed by RNA sequencing analysis and values obtained at weeks 1 and 4 were compared to those of time point 0. We found differential expression of more than 1500 genes for either time point comparison. The two lists of differentially expressed genes were then subjected to gene set enrichment of Gene Ontology terms. In total, 17 GO gene sets and 3 Pfam domains were found to be enriched after 1 week. After 4 weeks, 17 GO gene sets and 7 Pfam domains were statistically enriched. Especially stress response genes and genes of the primary metabolism were particularly affected at both time points. Genes and gene sets for uptake of carbohydrates, amino acids were strongly upregulated, indicating adjustment to a low nutrient environment. The results of this transcriptome analysis show that persistence of C227/11Φcu in soils is associated with a complex interplay of metabolic networks.

Effects of ammonia nitrogen and organic carbon availability on microbial community structure and ecological interactions in a full-scale partial nitritation and anammox (PN/A) system

Nutrient availability significantly impacts microbial biosynthesis, cell growth, and cell cycle progression. In this study, a full-scale plug-flow partial nitritation/anammox (PN/A) system was used to investigate variations in the microbial community structure in both immobilized carriers and flocs, as well as a gradual decrease in nutrient availability from upstream to downstream. We found that reduced ammonia nitrogen (from 150.4 to 30.6 mg/L) and organic carbon (from 415.7 to 342.8 mg/L) availability significantly lowered microbial diversity and altered microbial communities in biofilms other than flocs from upstream to downstream. The abundance of all anammox bacteria increased by 1.97 times, from 3.25×1010 to 6.40×1010 copies per gram of wet sludge, in the biofilm core microbiome. Furthermore, from upstream to downstream, taxa with lower ribosomal RNA operon copy numbers were consistently enriched in both biofilm and floc communities, indicating that slow-growing microorganisms are more likely to be enriched in low-nutrient environments. Rare taxa with a relative abundance of less than 0.1% exhibited unique metabolic functions, including amino acid, carbohydrate, cofactor, and vitamin metabolisms, which was inferred by PICRUST2 and persisted across the nutrient gradient in both the biofilm and floc communities. Despite their low abundance, they may play important roles in mediating the stability and function of the PN/A system. Overall, the results demonstrate the impact of a naturally formed ammonia nitrogen and organic carbon gradient in a full-scale plug-flow PN/A installation on nutrient availability and its effects on microbial diversity, community composition, and microbial interactions, which expands our fundamental understanding of this energy-efficient and promising biotechnology for treating high-strength ammonium wastewater.