Bacterial community driven nitrogen cycling in coastal sediments of intertidal transition zone

Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments

Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.

Environmental drivers of the resistome across the Baltic Sea

BACKGROUND

Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

RESULTS

We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

CONCLUSIONS

We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.

Distribution of potentially toxic elements in sediments of the municipal river channel (Balu), Dhaka, Bangladesh: Ecological and health risks assessment

The concern of potential toxic elements (PTEs) contamination in the river ecosystem is growing due to anthropological activity. The contents of seven PTEs in sediments from the Balu River channel were analyzed using atomic absorption spectroscopy (AAS) and an environmental risk model. Several PTEs were found in the sediment at high levels, including zinc (Zn), copper (Cu), arsenic (As), lead (Pb), cadmium (Cd), nickel (Ni), and mercury (Hg), that might pose a risk to human and ecological health. The highest mean concentration of PTEs in sediment followed in decreasing order Zn (1365.21 mg/kg) > Cu (149.34 mg/kg) > Pb (46.34 mg/kg) > Ni (34.78 mg/kg) > As (6.31 mg/kg) > Cd (2.34 mg/kg) > Hg (1.03 mg/kg). In addition, most of these PTEs were significantly correlated (p < 0.05) among the sites and exceeded the safety guideline value. The geo-accumulation index (Igeo), contamination factor (CF), and pollution load index (PLI) showed high levels of PTEs contamination and moderately polluted to highly polluted levels of these elements. At the BL3, BL4, and BL6 sites within the study site, the ecological risk (PERI) score was extremely high, and the PERI values range found was from 75.39 to 355.72. Every PTE had a slightly greater concentration during the dry season than the wet season. Interestingly, PTE accumulation from sediment indicated non-carcinogenic risk (HQdermal) in human health, whereas most of the sites showed carcinogenic risk (CRdermal) to human health (adult and child) due to Cd and Ni accumulation. Multivariate statistical analysis (MVSA) indicated the most likely anthropological sources were the untreated wastes discharged in the river sampling area. People who come into contact with polluted sediments are constantly exposed to Ni and Cd pollution, which increases the risk of cancer and non-cancerous diseases. So, continuous PTE monitoring is advised by this study to assess ecological and human health risks.

Paddy-upland rotation combined with manure application: An optimal strategy for enhancing soil multifunctionality

Promoting soil multifunctionality is pivotal for maintaining agricultural productivity and sustainable agriculture, especially with the increasing global population and food demand. The effectiveness of different agricultural practices in enhancing soil multifunctionality and how the combination can maximize soil multifunctionality remains unknown. This study aimed to investigate the different impacts of rotation (paddy-upland rotation and dryland rotation) combined with fertilization (chemical fertilizer and manure) on soil multifunctionality, microbial community structure, and microbial networks. A two-year field experiment was conducted at the Fengqiu National Agro-Ecosystem Observation and Research Station in Henan Province, China, comparing the differences between rice-wheat rotation (paddy-upland rotation) and maize-wheat rotation (dryland rotation) combined with chemical fertilizer and pig manure. This finding revealed that paddy-upland rotation combined with manure application had the optimal effect in enhancing soil multifunctionality with a 216.25 % enhancement while contributing to a yield increase of 222.71 %. Notably, paddy-upland rotation and fertilization significantly promoted the soil bacterial network complexity and robustness, and these network properties were crucial factors in predicting soil multifunctionality. This study provides a new insight for developing a comprehensive strategy combining paddy-upland rotation with manure application in the future, which can help us to better improve soil health and agricultural sustainability.

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.

Hypoxia exerts greater impacts on shallow groundwater nitrogen cycling than seawater mixture in coastal zone

There is no doubt that hypoxia and seawater mixture are profoundly affecting the global nitrogen (N) cycle. However, their mechanisms for altering N cycling patterns in shallow coastal groundwater are largely unknown. Here, we examined shallow groundwater N transformation characteristics (dissolved inorganic N and related chemical properties) in the coastal area of east and west Shenzhen City. Results showed that common hypoxic conditions exist in this study area. Ions/Cl- ratios indicated varying levels of saltwater mixture and sulfide formation across this study area. Dissolved oxygen (DO) affects the N cycle process by controlling the conditions of nitrification and the formation of sulfides. Salinity affects nitrification and denitrification processes by physiological effects, while sulfide impacts nitrification, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) processes through its own toxicity mechanism and the provision of electron donors for DNRA organisms. Redundancy analysis (RDA) results indicate that the influence magnitude is in the following order: DO > sulfide > salinity. Seawater mixture weakened the nitrification and denitrification of groundwater by changing salinity, while hypoxia and its controlled sulfide formation not only weaken nitrification and denitrification but also stimulated the DNRA process and promotes N regeneration. In this study area, hypoxia is considered to exert greater impacts on N cycling in the coastal shallow groundwater than seawater mixture. These findings greatly improve our understanding of the consequences of hypoxia and seawater mixture on coastal groundwater N cycling.

Biogeographic effects shape soil bacterial communities across intertidal zones on island beaches through regulating soil properties

Island coastal zones are often mistakenly perceived as "ecological desert". Actually, they harbour unique communities of organisms. The biodiversity on islands is primarily influenced by the effects of area and isolation (distance from the mainland), which mainly focused on plants and animals, encompassing studies of entire islands. However, the application of area and isolation effects to soil microorganisms on island beaches across the intertidal zones remains largely unexplored. We hypothesized that island area and isolation shape soil bacterial communities by regulating soil properties on island beaches, due to the fact that local soil properties might be strongly influenced by land-use, which may vary among islands of different sizes and isolations. To test this hypothesis, we conducted a study on 108 plots spanning 4 intertidal zones on 9 representative island beaches within Zhoushan Archipelago, eastern China. We employed one-way ANOVA and Tukey's honestly significant difference (HSD) test to assess the differences in diversity, composition of soil bacterial communities and soil properties among intertidal zones. Redundancy analysis and structural equation modelling (SEM) were used to examine the direct and indirect impacts of beach area and isolation on soil bacterial communities. Our findings revealed that the area and isolation did not significantly influence soil bacterial diversity and the relative abundance of dominant soil bacterial phyla. However, soil nitrogen (soil N), phosphorus (soil P), organic carbon (SOC), available potassium content (soil AK), and electrical conductivity (soil EC) showed significant increases with the area and isolation. As the tidal gradient increased on beaches, soil bacterial OTU richness, Chao 1, and relative abundance of Planctomycetota and Crenarchaeota decreased, while relative abundance of other soil bacterial phyla increased. We found that influences of island area and isolation shape soil bacterial communities on beaches by regulating soil properties, particularly soil moisture, salinity, and nutrients, all of which are also influenced by area and isolation. Island with larger areas and in lower intertidal zones, characterized by higher soil water content (SWC), soil EC, and soil AK, exhibited greater soil bacterial diversity and fewer dominant soil bacterial phyla. Conversely, in the higher intertidal zones with vegetation containing higher soil N and SOC, lower soil bacterial diversity and more dominant soil bacterial phyla were observed. These findings have the potential to enhance our new understanding of how island biogeography in interpreting island biome patterns.

Novel adaptive activated sludge process leverages flow fluctuations for simultaneous nitrification and denitrification in rural sewage treatment

The fluctuating characteristics of rural sewage flow pose a significant challenge for wastewater treatment plants, leading to poor effluent quality. This study establishes a novel adaptive activated sludge (AAS) process specifically designed to address this challenge. By dynamically adjusting to fluctuating water flow in situ, the AAS maintains system stability and promotes efficient pollutant removal. The core strategy of AAS leverages the inherent dissolved oxygen (DO) variations caused by flow fluctuations to establish an alternating anoxic-aerobic environment within the system. This alternating operation mode fosters the growth of aerobic denitrifiers, enabling the simultaneous nitrification and denitrification (SND) process. Over a 284-day operational period, the AAS achieved consistently high removal efficiencies, reaching 94 % for COD and 62.8 % for TN. Metagenomics sequencing revealed HN-AD bacteria as the dominant population, with the characteristic nap gene exhibiting a high relative abundance of 0.008 %, 0.010 %, 0.014 %, and 0.015 % in the anaerobic, anoxic, dynamic, and oxic zones, respectively. Overall, the AAS process demonstrates efficient pollutant removal and low-carbon treatment of rural sewage by transforming the disadvantage of flow fluctuation into an advantage for robust DO regulation. Thus, AAS offers a promising model for SND in rural sewage treatment.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.