How elevated nitrogen load affects bacterial community structure and nitrogen cycling services in coastal water

Harnessing plant-microbe interactions: strategies for enhancing resilience and nutrient acquisition for sustainable agriculture

The rhizosphere, a biologically active zone where plant roots interface with soil, plays a crucial role in enhancing plant health, resilience, and stress tolerance. As a key component in achieving Sustainable Development Goal 2, the rhizosphere is increasingly recognized for its potential to promote sustainable agricultural productivity. Engineering the rhizosphere microbiome is emerging as an innovative strategy to foster plant growth, improve stress adaptation, and restore soil health while mitigating the detrimental effects of conventional farming practices. This review synthesizes recent advancements in omics technologies, sequencing tools, and synthetic microbial communities (SynComs), which have provided insights into the complex interactions between plants and microbes. We examine the role of root exudates, composed of organic acids, amino acids, sugars, and secondary metabolites, as biochemical cues that shape beneficial microbial communities in the rhizosphere. The review further explores how advanced omics techniques like metagenomics and metabolomics are employed to elucidate the mechanisms by which root exudates influence microbial communities and plant health. Tailored SynComs have shown promising potential in enhancing plant resilience against both abiotic stresses (e.g., drought and salinity) and biotic challenges (e.g., pathogens and pests). Integration of these microbiomes with optimized root exudate profiles has been shown to improve nutrient cycling, suppress diseases, and alleviate environmental stresses, thus contributing to more sustainable agricultural practices. By leveraging multi-disciplinary approaches and optimizing root exudate profiles, ecological engineering of plant-microbiome interactions presents a sustainable pathway for boosting crop productivity. This approach also aids in managing soil-borne diseases, reducing chemical input dependency, and aligning with Sustainable Development Goals aimed at global food security and ecological sustainability. The ongoing research into rhizosphere microbiome engineering offers significant promise for ensuring long-term agricultural productivity while preserving soil and plant health for future generations.

Impacts of aquaculture on nitrogen cycling and microbial community dynamics in coastal tidal flats

The expansion of aquaculture areas has encroached upon vast areas of coastal wetlands and introduced excessive nitrogen inputs, disrupting microbial communities and contributing to various environmental issues. However, investigations on how aquaculture affects microbial communities and nitrogen metabolism mechanisms in coastal tidal flats remain scarce. Hence, we explored the composition, diversity, and assembly processes of nitrogen-cycling (N-cycling) microbial communities in tidal flats in Jiangsu using metagenomic assembly methods. Our study further delved into the seasonal variations of these microbial characteristics to better explore the effects of seasonal changes in aquaculture areas on microbial community. Nitrogen metabolism-related processes and functional genes were identified through the KEGG and NCyc databases. The results revealed significant seasonal variation in the relative abundance and composition of microbial communities. Higher diversity was observed in winter, while the co-occurrence network of microbial communities was more complex in summer. Pseudomonadota emerged as the most abundant phylum in the N-cycling community. Furthermore, pH and NO3-N were identified as the primary factors influencing bacterial community composition, whereas NO2-N was more strongly associated with the N-cycling community. Regarding the nitrogen metabolism processes, nitrogen mineralization and nitrification were predominant in the tidal flat regions. NO2-N and NO3-N exhibited significant effects on several N-cycling functional genes (e.g., nirB, hao, and narG). Finally, neutral and null modeling analyses indicated that bacterial communities were predominantly shaped by stochastic processes, whereas N-cycling communities were largely driven by deterministic processes. These findings highlighted the significant role that aquaculture pollution plays in shaping the N-cycling communities in tidal flats. This underscored the importance of understanding microbial community dynamics and nitrogen metabolism in tidal flats to improve environmental management in coastal aquaculture areas.

Dielectrophoresis for Isolating Low-Abundance Bacteria Obscured by Impurities in Environmental Samples

Bacterial communities associated with living organisms play critical roles in maintaining health and ecological balance. While dominant bacteria have been widely studied, understanding the role of low-abundance bacteria has become increasingly important due to their unique roles, such as regulating bacterial community dynamics and supporting host-specific functions. However, detecting these bacteria remains challenging, as impurities in environmental samples mask signals and compromise the accuracy of analyses. This study explored the use of dielectrophoresis (DEP) as a practical approach to isolate low-abundance bacteria obscured by impurities, comparing its utility to conventional centrifugation methods. Using two shrimp species, Neocaridina denticulata and Penaeus japonicus, DEP effectively isolated bacterial fractions while reducing impurities, enabling the detection of bacteria undetected in centrifuged samples. These newly detected bacteria were potentially linked to diverse ecological and host-specific functions, such as nutrient cycling and immune modulation, highlighting DEP as a highly potential approach to support the study of host-microbial interactions. Overall, we believe that DEP offers a practical solution for detecting overlooked bacteria in conventional methods and exploring their diversity and functional roles, with potential contributions to aquaculture and environmental biotechnology.

Microbiota succession, species interactions, and metabolic functions during autotrophic biofloc formation in zero-water-exchange shrimp farming without organic carbon supplements

Autotrophic bioflocs (ABF) exhibits lower energy consumption, more environment-friendly and cost-effective than heterotrophic bioflocs depending on organic carbon supplements. Whereas ABF has not been widely applied to aquaculture production. Here, ABF successfully performed to control ammonia and nitrite under harmless levels even when carbon-to-nitrogen ratio reduced to 2.0, during 12-week shrimp farming in commercial scale. ABF was mainly dominated by bacteria of Proteobacteria, Bacteroidota, Chloroflexi and eukaryotes of Bacillariophyta, Rotifera, Ciliophora. A notable shift occurred in ABF with the significant decreases of Proteobacteria and Rotifera replaced by Bacteroidota, Chloroflexi, and Bacillariophyta after four weeks. Nitrogen metabolism was synergistically executed by bacteria and microalgae, especially the positive interaction between Nitrospira and Halamphora for ABF nitrification establishment. Metagenomics confirmed the complete functional genes of key bacteria related to the cycling of carbon, nitrogen, and phosphorus by ABF. This study may promote the development application of ABF in low-carbon shrimp aquaculture.

Living in a multi-stressor world: nitrate pollution and thermal stress interact to affect amphibian larvae

The interaction of widespread stressors such as nitrate pollution and increasing temperatures associated with climate change is likely to affect aquatic ectotherms such as amphibians. The metamorphic and physiological traits of amphibian larvae during the critical onset of metamorphosis are particularly susceptible to these stressors. We used a crossed experimental design subjecting Rana temporaria larvae to four constant rearing temperatures (18, 22, 26, 28°C) crossed with three environmentally relevant nitrate concentrations (0, 50, 100 mg l-1) to investigate the interactive and individual effects of these stressors on metamorphic (i.e. growth and development) and physiological traits (i.e. metabolism and heat tolerance) at the onset of metamorphosis. Larvae exposed to elevated nitrate concentrations and thermal stress displayed increased metabolic rates but decreased developmental rate, highlighting interactive effects of these stressors. However, nitrate pollution alone had no effect on either metamorphic or physiological traits, suggesting that detoxification processes were sufficient to maintain homeostasis but not in combination with increased rearing temperatures. Furthermore, larvae exposed to nitrate displayed diminished abilities to exhibit temperature-induced plasticity in metamorphosis timing and heat tolerance, as well as reduced acclimation capacity in heat tolerance and an increased thermal sensitivity of metabolic rate to higher temperatures. These results highlight the importance of considering the exposure to multiple stressors when investigating how natural populations respond to global change.

Impact of tidal fluctuations on bacterial community structure in Wuyuan Bay: A comparative analysis of waters inside and outside the tidal barrage

The tidal barrage at Wuyuan Bay effectively mitigated the odor from the tidal flat during ebb tide, however, its effect on bacterial community structure in waters are still unclear. In this study, high-throughput sequencing was used to analyze the structure of the microbial community in waters inside and outside the tidal barrage during flood and ebb tides. Results showed bacterial diversity was higher in water outside the barrage during flood tide. The dominated species at phylum and genus levels were various in waters inside and outside the tidal barrage during flood and ebb tides. The water inside during ebb tide (E1) were dominated by two cyanobacterial genera, Cyanobium_PCC-6307 (42.90%) and Synechococcus_CC9902 (12.56%). The microbial function, such as porphyrin and chlorophyll metabolism and photosynthesis, were increased in E1. Norank_f__Nitriliruptoraceae was identified as differential microorganism in waters inside the barrage. Inorganic nitrogen and nonionic ammonia were significantly high in E1, and were negatively correlated with norank_f__Nitriliruptoraceae. These results suggest tidal barrage blocks water exchange, resulting in the accumulation of nutrients in Wuyuan Bay. Consequently, the environment became favorable for the growth of cyanobacteria, leading to the dominance of algae in the water inside the barrage and posing the risk of cyanobacterial bloom. Higher Nitriliruptoraceae inside the barrage might be a cue for the change of water quality.

Exploring the environmental influences and community assembly processes of bacterioplankton in a subtropical coastal system: Insights from the Beibu Gulf in China

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes.

Role of nanofertilization in plant nutrition under abiotic stress conditions

Plants require nutrients for growth, which they obtain from the soil via the root system. Fertilizers offer the essential nutrients (nitrogen, phosphorus, and potassium, as well as critical secondary elements) required by plants. Soil productivity falls with each crop until nutrients are provided. A wide range of so-called fertilizer products, such as organic fertilizers, argon mineral fertilizers, and mineral fertilizers, can assist farmers in adjusting fertilization methods based on the environment and agricultural conditions (inhibitors, restricted materials, growth mediums, plant bio-stimulants, etc.). Agricultural land is reduced by erosion, pollution, careless irrigation, and fertilization. On the other hand, more agricultural production is needed to meet the demands of expanding industries and the nutritional needs of a growing population. Nano fertilizers have recently started to be manufactured to obtain the highest yield and its quality per unit area. Previous researchers found that nano fertilizers could improve plant nutrient uptake efficiency, lower soil toxicity, mitigate the potential negative effects of excessive chemical fertilizer use, and reduce the frequency of fertilization. To maximize crop yields and optimize nutrient use while reducing the overuse of chemical fertilizers, nano fertilizersNFs are crucial in agriculture. The key component of these fertilizers is that they contain one or more macro- and micronutrients that can be applied regularly in minute doses while not damaging the environment. However, they have a minimal effect on plant growth and agricultural yields when employed in high numbers, like synthetic fertilizers. This article explains the features, relevance and classification of nano-fertilizers, their use in plant development, their advantages and disadvantages, and the results achieved in this field.

Microbial community analysis of membrane bioreactor incorporated with biofilm carriers and activated carbon for nitrification of urine

The integration of powdered activated carbon and biofilm carriers in a membrane bioreactor (MBR) presents a promising approach to address the challenge of long hydraulic retention time (HRT) for nitrification of hydrolysed urine. This study investigated the effect of the incorporation in the MBR on microbial dynamics, focusing on dominant nitrifying bacteria. The results showed that significant shifts in microbial compositions were observed with the feed transition to full-strength urine and across different sludge growth forms. Remarkably, the nitrite-oxidizing bacteria Nitrospira were highly enriched in the suspended sludge. Simultaneously, ammonia-oxidizing bacteria, Nitrosococcaceae thrived in the attached biomass, showing a significant seven-fold increase in relative abundance compared to its suspended counterpart. Consequently, the incorporated MBR displayed 36% higher nitrification rate and 40% HRT reduction compared to the conventional MBR. This study provides valuable insights on the potential development of household or building scale on-site nutrient recovery from urine to fertiliser.

Microplastics perturb nitrogen removal, microbial community and metabolism mechanism in biofilm system

Microplastics (MPs) are a significant component of global pollution and cause widespread concern, particularly in wastewater treatment plants. While understanding the impact of MPs on nutrient removal and potential metabolism in biofilm systems is limited. This work investigated the impact of polystyrene (PS) and polyethylene terephthalate (PET) on the performance of biofilm systems. The results revealed that at concentrations of 100 and 1000 μg/L, both PS and PET had almost no effect on the removal of ammonia nitrogen, phosphorus, and chemical oxygen demand, but reduced the removal of total nitrogen by 7.40-16.6%. PS and PET caused cell and membrane damage, as evidenced by increases in reactive oxygen species and lactate dehydrogenase to 136-355% and 144-207% of the control group. Besides, metagenomic analysis demonstrated both PS and PET changed the microbial structure and caused functional differences. Some important genes in nitrite oxidation (e.g. nxrA), denitrification (e.g. narB, nirABD, norB, and nosZ), and electron production process (e.g. mqo, sdh, and mdh) were restrained, meanwhile, species contribution to nitrogen-conversion genes was altered, therefore disturbing nitrogen-conversion metabolism. This work contributes to evaluating the potential risks of biofilm systems exposed to PS and PET, maintaining high nitrogen removal and system stability.