Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Review of biological algal fertilizer technology: Alleviating salinization, sequestering carbon, and improving crop productivity

Periphyton-based biofertilizer have a high potential for soil remediation, particularly for controlling soil salinization. This global environmental problem leads to low soil utilization and insufficient crop yields. Efficient and sustainable methods of managing saline soils are needed to reduce salinization and improve soil fertility and crop quality. Traditional methods such as physical mulching and chemical amendments, while improving soil conditions, exhibit limited effectiveness and may damage soil structure. This study aims to evaluate the feasibility of algae-based fertilizers in remediating saline-alkali soils and improving crop performance. The review delves into the and application prospects of algae-based fertilizers, highlighting their potential from both sustainable development and economic perspectives. It further advocates integrating other emerging technologies with the production and application of algae-based fertilizers to address the increasingly severe challenges posed by degraded soil resources and environmental instability. The review found that algal fertilizers are more environmentally friendly than traditional chemical fertilizers but are not inferior in function. This approach offers more efficient and sustainable solutions for managing saline-alkaline soils and effectively achieves sustainable agricultural production. Furthermore, it is necessary to conduct experimental research and monitoring evaluations of algal fertilizers to formulate scientific and rational fertilization plans to meet the increasingly serious challenges facing soil resources and unstable environments. The findings of this study will provide theoretical and technical support for using algae biofertilizers for soil remediation, improving crop quality and sequestering carbon.

Water periods impact the structure and metabolic potential of the nitrogen-cycling microbial communities in rivers of arid and semi-arid regions

This study examined the influence of water periods on river nitrogen cycling by analysing nitrogen functional genes and bacterial communities in the Qingshui River, an upstream tributary of the Yellow River in China. Nitrate nitrogen predominated as inorganic nitrogen during the low-flow seasons, whereas salinity was highest during the high-flow seasons. Overall, the functional gene abundance increased with decreasing water volume, and nitrogen concentrations were determined by various specific gene groups. The relative abundance of bacteria carrying these genes varied significantly across water periods. The abundance of Pseudomona, Hydrogenophaga (carrying narGHI and nirB genes), and Flavobacterium (carrying nirK, norBC, and nosZ genes) significantly increased during the low-flow seasons. Nitrogen transformation bacteria exhibited both symbiotic and mutualistic relationships. Microbial network nodes and sizes decreased with decreasing water volume, whereas modularity increased. Additionally, the water period affected the functional microbial community structure by influencing specific environmental factors. Among them, SO42- primarily determined the denitrification, dissimilatory nitrate reduction to ammonium, and assimilatory nitrate reduction to ammonium communities, whereas NO2--N and Mg2+ were the main driving factors for the nitrogen-fixing and nitrifying communities, respectively. These findings have substantial implications for better understanding the reduction in river nitrogen loads in arid and semi-arid regions during different water periods.

Migration, transformation of arsenic, and pollution controlling strategies in paddy soil-rice system: A comprehensive review

Arsenic pollution in paddy fields has become a public concern by seriously threatening rice growth, food security and human health. In this review, we delve into the biogeochemical behaviors of arsenic in paddy soil-rice system, systemically revealing the complexity of its migration and transformation processes, including the release of arsenic from soil to porewater, uptake and translocation of arsenic by rice plants, as well as transformation of arsenic species mediated by microorganism. Especially, microbial processes like reduction, oxidation and methylation of arsenic, and the coupling of arsenic with carbon, iron, sulfur, nitrogen cycling through microbes and related mechanisms were highlighted. Environmental factors like pH, redox potential, organic matter, minerals, nutrient elements, microorganisms and periphyton significantly influence these processes through different pathways, which are discussed in this review. Furthermore, the current progress in remediation strategies, including agricultural interventions, passivation, phytoremediation and microbial remediation is explored, and their potential and limitations are analyzed to address the gaps. This review offers comprehensive perspectives on the complicated behaviors of arsenic and influence factors in paddy soil-rice system, and provides a scientific basis for developing effective arsenic pollution control strategies.

Bacterial biofilm-mediated environmental remediation: Navigating strategies to attain Sustainable Development Goals

Bacterial biofilm is a structured bacterial community enclosed within a three-dimensional polymeric matrix, governed by complex signaling pathways, including two-component systems, quorum sensing, and c-di-GMP, which regulate its development and resistance in challenging environments. The genetic configurations within biofilm empower bacteria to exhibit significant pollutant remediation abilities, offering a promising strategy to tackle diverse ecological challenges and expedite progress toward Sustainable Development Goals (SDGs). Biofilm-based technologies offer advantages such as high treatment efficiency, cost-effectiveness, and sustainability compared to conventional methods. They significantly contribute to agricultural improvement, soil fertility, nutrient cycling, and carbon sequestration, thereby supporting SDG 1 (No poverty), SDG 2 (Zero hunger), SDG 13 (Climate action), and SDG 15 (Life on land). In addition, biofilm facilitates the degradation of organic-inorganic pollutants from contaminated environments, aligning with SDG 6 (Clean water and sanitation) and SDG 14 (Life below water). Bacterial biofilm also has potential applications in industrial innovation, aligning SDG 7 (Affordable and clean energy), SDG 8 (Decent work and economic growth), and SDG 9 (Industry, innovation, and infrastructure). Besides, bacterial biofilm prevents several diseases, aligning with SDG 3 (Good health and well-being). Thus, bacterial biofilm-mediated remediation provides advanced opportunities for addressing environmental issues and progressing toward achieving the SDGs. This review explores the potential of bacterial biofilms in addressing soil pollution, wastewater, air quality improvement, and biodiversity conservation, emphasizing their critical role in promoting sustainable development.

Intensified river salinization alters nitrogen-cycling microbial communities in arid and semi-arid regions of China

Freshwater salinization is receiving increasing global attention due to its profound influence on nitrogen cycling in aquatic ecosystems and the accessibility of water resources. However, a comprehensive understanding of the changes in river salinization and the impacts of salinity on nitrogen cycling in arid and semi-arid regions of China is currently lacking. A meta-analysis was first conducted based on previous investigations and found an intensification in river salinization that altered hydrochemical characteristics. To further analyze the impact of salinity on nitrogen metabolism processes, we evaluated rivers with long-term salinity gradients based on in situ observations. The genes and enzymes that were inhibited generally by salinity, especially those involved in nitrogen fixation and nitrification, showed low abundances in three salinity levels. The abundance of genes and enzymes with denitrification and dissimilatory nitrate reduction to ammonium functions still maintained a high proportion, especially for denitrification genes/enzymes that were enriched under medium salinity. Denitrifying bacteria exhibited various relationships with salinity, while dissimilatory nitrate reduction to ammonium bacterium (such as Hydrogenophaga and Curvibacter carrying nirB) were more inhibited by salinity, indicating that diverse denitrifying bacteria could be used to regulate nitrogen concentration. Most genera exhibited symbiotic and mutual relationships, and the highest proportion of significant positive correlations of abundant genera was found under medium salinity. This study emphasizes the role of river salinity on environment characteristics and nitrogen transformation rules, and our results are useful for improving the availability of river water resources in arid and semi-arid regions.

Recovery mechanism of a microalgal species, Chlorella sp. from toxicity of doxylamine: Physiological and biochemical changes, and transcriptomics

Ubiquitous distribution of pharmaceutical contaminants in environment has caused unexpected adverse effects on ecological organisms; however, how microorganisms recover from their toxicities remains largely unknown. In this study, we comprehensively investigated the effect of a representative pollutant, doxylamine (DOX) on a freshwater microalgal species, Chlorella sp. by analyzing the growth patterns, biochemical changes (total chlorophyll, carotenoid, carbohydrate, protein, and antioxidant enzymes), and transcriptomics. We found toxicity of DOX on Chlorella sp. was mainly caused by disrupting synthesis of ribosomes in nucleolus, and r/t RNA binding and processing. Intriguingly, additional bicarbonate enhanced the toxicity of DOX with decreasing the half-maximum effective concentrations from 15.34 mg L-1 to 4.63 mg L-1, which can be caused by inhibiting fatty acid oxidation and amino acid metabolism. Microalgal cells can recover from this stress via upregulating antioxidant enzymatic activities to neutralize oxidative stresses, and photosynthetic pathways and nitrogen metabolism to supply more energies and cellular signaling molecules. This study extended our understanding on how microalgae can recover from chemical toxicity, and also emphasized the effect of environmental factors on the toxicity of these contaminants on aquatic microorganisms.

Seasonal impact of constructed wetlands on nitrogen and phosphorus in sediments of flood control lakes with pollution assessment

The primary drivers of eutrophication in lakes following the reduction of external nutrient inputs are the release of N and P from sediments. Constructed wetlands play a pivotal role in ameliorating N, P, and other biogenic element levels. However, the presence of large vegetation in these wetlands also substantially contributes to nutrient accumulation in sediments, a phenomenon influenced by seasonal variations. In this study, a typical constructed wetland was selected as the research site. The research aimed to analyze the forms of N and P in sediments during both summer and winter. Simultaneously, a comprehensive pollution assessment and analysis were conducted within the study area. The findings indicate that elevated summer temperatures, together with the presence of wetland vegetation, promote the release of N through the nitrification process. Additionally, seasonal variations exert a significant impact on the distribution of P storage. Furthermore, the role of constructed wetlands in the absorption and release of N and P is primarily controlled by the influence of organic matter on nitrate-nitrogen, nitrite-nitrogen, and available phosphorus, and is also subject to seasonal fluctuations. In summary, under the comprehensive influence of constructed wetlands, vegetation types, and seasons, sediments within the lake generally exhibit a state of mild or moderate pollution. Therefore, targeted measures should be adopted to optimally adjust vegetation types, and human intervention is necessary, involving timely sediment harvesting during the summer to reduce N and P loads, and enhancing sediment adsorption and retention capacity for N and P during the winter.

Indole-3-acetic acid improves periphyton's resistance to ultraviolet-B: From physiological-biochemical properties and bacteria community to livestock-polluted water purification

Livestock-polluted water is a pressing water environmental issue in plateau pastoral regions, necessitating the adoption of eco-friendly solutions. Despite periphyton being a promising alternative, its efficacy is limited by the prevalence of intense ultraviolet radiation, particularly ultraviolet-B (UVB), in these regions. Therefore, this study employs molecular tools and small-scale trials to explore the crucial role of indole-3-acetic acid (IAA) in modulating periphyton characteristics and mediating nutrient removal from livestock-polluted water under UVB exposure. The results revealed that IAA augments periphyton's resilience to UVB stress through several pathways, including increasing periphyton's biomass, producing more extracellular polymeric substances (EPS), and enhancing antioxidant enzyme activities and photosynthetic activity of periphyton. Moreover, IAA addition increased periphyton's bacterial diversity, reshaped bacterial community structure, enhanced community stability, and elevated the R2 value of neutral processes in bacterial assembly from 0.257 to 0.651 under UVB. Practically, an IAA concentration of 50 mg/L was recommended. Small-scale trials confirmed the effectiveness of IAA in assisting UVB-stressed periphyton to remove nitrogen and phosphorus from livestock-polluted water, without the risk of nitrogen accumulation. These findings offer valuable insights into the protection of aquatic ecosystems in plateau pastoral regions based on periphyton property in an eco-friendly manner.

Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms

The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.

Epidermal microorganisms contributed to the toxic mechanism of nZVI and TCEP in earthworms by robbing metal elements and nutrients

Disrupting effects of pollutants on symbiotic microbiota have been regarded as an important mechanism of host toxicity, with most current research focusing on the intestinal microbiota. In fact, the epidermal microbiota, which participates in the nutrient exchange between hosts and environments, could play a crucial role in host toxicity via community changes. To compare the contributions of intestinal and epidermal symbiotic microorganisms to host toxicity, this study designed single and combined scenarios of soil contamination [nano zero-valent iron (nZVI) and tris (2-chloroethyl) phosphate (TCEP)], and revealed the coupling mechanisms between intestinal/epidermal symbiotic bacterial communities and earthworm toxicological endpoints. Microbiome analysis showed that 15% of intestinal microbes were highly correlated with host endpoints, compared to 45% of epidermal microbes showing a similar correlation. Functional comparisons revealed that key species on the epidermis were mainly heterotrophic microbes with genetic abilities to utilize metal elements and carbohydrate nutrients. Further verifications demonstrated that when facing the co-contamination of nZVI and TCEP, certain symbiotic microorganisms became dominant and consumed zinc, copper, and manganese along with saccharides and amino acids, which may be responsible for the nutritional deficiencies in the host earthworms. The findings can enrich the understanding of the coupling relationship between symbiotic microorganisms and host toxicity, highlighting the importance of epidermal microorganisms in host resistance to environmental pollution.

The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes

The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

Invasive Spartina alterniflora accelerates the increase in microbial nitrogen fixation over nitrogen removal in coastal wetlands of China

Salt marsh plants play a vital role in mediating nitrogen (N) biogeochemical cycle in estuarine and coastal ecosystems. However, the effects of invasive Spartina alterniflora on N fixation and removal, as well as how these two processes balance to determine the N budget, remain unclear. Here, simultaneous quantifications of N fixation and removal via 15N tracing experiment with native Phragmites australis, invasive S. alterniflora, and bare flats as well as corresponding functional gene abundance by qPCR were carried out to explore the response of N dynamics to S. alterniflora invasion. Our results showed that N fixation and removal rates ranged from 0.77 ± 0.08 to 16.12 ± 1.13 nmol/(g·h) and from 1.42 ± 0.14 to 16.35 ± 1.10 nmol/(g·h), respectively, and invasive S. alterniflora generally facilitated the two processes rates. Based on the difference between N removal and fixation rates, net N2 fluxes were estimated in the range of -0.39 ± 0.14 to 8.24 ± 2.23 nmol/(g·h). Estimated net N2 fluxes in S. alterniflora stands were lower than those in bare flats and P. australis stands, indicating that the increase in N removal caused by S. alterniflora invasion may be more than offset by N fixation process. Random forest analysis revealed that functional microorganisms were the most important factor associated with the corresponding N transformation process. Overall, our results highlight the importance of N fixation in evaluating N budget of estuarine and coastal wetlands, providing valuable insights into the ecological effect of S. alterniflora invasion.

Efficient aerobic denitrification without nitrite accumulation by Pseudomonas mendocina HITSZ-D1 isolated from sewage sludge

A highly efficient aerobic denitrifying microbe was isolated from sewage sludge by using a denitrifier enrichment strategy based on decreasing carbon content. The microbe was identified as Pseudomonas mendocina HITSZ-D1 (hereafter, D1). Investigation of the conditions under which D1 grew and denitrified revealed that it performed good growth and nitrate removal performance under a wide range of conditions. In particular, D1 rapidly removed all types of inorganic nitrogen without accumulation of the intermediate products nitrite and nitrous oxide. Overall, D1 showed a total nitrogen removal efficiency >96% at a C/N ratio of 8. The biotransformation modes and fates of three typical types of inorganic nitrogen were also assessed. Moreover, D1 had significantly higher denitrification efficiency and enzyme activities than other aerobic denitrifying microbes (Paracoccus denitrificans, Pseudomonas aeruginosa, and Pseudomonas putida). These results suggest that D1 has great potential for treating wastewater containing high concentrations of nitrogen.