Unraveling the ecological mechanisms of bacterial succession in epiphytic biofilms on Vallisneria natans and Hydrilla verticillata during bioremediation of phenanthrene and pyrene polluted wetland

Effects of BDE-47 injection on vertical redox zonation and microbial community assemblage in capped sediment columns

Polybrominated diphenyl ethers (PBDEs) are of significant interest in ecological risk assessment and bioremediation in sediments. However, their impact on microbial diversity and activity in capped lake sediments remains unclear, despite the widespread use of capping in lake management. In this study, two series of sediment columns were established to examine vertical redox zonation at 2-cm intervals from 2 to 16 cm and evaluate the impact of artificially injected PBDEs on microbial communities during a 60-day capping period. Variations in redox indicators, including nitrate, sulfate, total dissolved iron, and total dissolved manganese in porewater, showed that the capping layer (1 cm, d = 75 μm) increased the redox potential of subsurface sediments. BDE-47 was primarily concentrated in the injection layer (4-6 cm), but over time, it exhibited upward migration (0.4-0.7 cm) and a broader distribution range (0.5-1.0 cm), with no consistent decrease in the total BDE-47 mass. Microbial α-diversity declined, whereas microbial network analysis revealed increased connectivity and enhanced cooperation within communities in the BDE group. Notably, negative correlations between microbial taxa and iron exclusively in the BDE group, suggesting that BDE-47 counteracted capping-induced iron reduction. In contrast, sulfate showed an opposite trend with iron between the BDE and noBDE groups. Methanolinea [Euryarchaeota] and certain co-metabolizing dechlorinating bacteria, such as Flavobacterium dominated in the capping layer, were correlated to BDE-47. These findings provide the first evidence of redox-regulated natural attenuation of PBDEs in capped lake sediments, shedding light on their environmental impact and guiding sediment management strategies.

Host selection and nutrient status jointly drive algal and bacterial interactions in epiphytic biofilms of submerged macrophytes: Structural and functional insights

Epiphytic biofilms play a crucial role in aquatic biogeochemical cycles but are simultaneously influenced by host selection and eutrophication. However, the compositional structure and interaction mechanisms of these factors on algal and bacterial communities remain poorly understood. In this study, we employed Confocal Laser Scanning Microscopy (CLSM), Scanning Electron Microscopy (SEM), and high-throughput sequencing to investigate the physicochemical properties, algal and bacterial diversity, and community structure of epiphytic biofilms on two submerged macrophytes - Vallisneria natans (VN) and Hydrilla verticillata (HV) - across three urban shallow lakes with varying trophic levels in the Yangtze River Basin. Our results revealed distinct algal and bacterial communities influenced by both host plants and lake nutrient conditions, with unique core species identified in VN, HV, and the surrounding water. Host-environment effects index (HEEI = 1.79) indicated that bacterial communities were predominantly shaped by host selection, exhibiting lower diversity in HV (1.66 ± 0.92) and VN (2.31 ± 1.12) biofilms compared to surrounding waters (3.80 ± 0.47). In contrast, algal communities were primarily regulated by environmental factors (HEEI = 0.43), with higher diversity in less eutrophic lakes. Algal-bacterial co-occurrence network analysis revealed greater network complexity in VN biofilms than that in HV, with predominantly synergistic interactions facilitating carbon and nitrogen cycling. Eutrophication increased biofilm thickness, nutrient content, and extracellular polymeric substance (EPS) production but reduced microbial diversity and altered community interaction patterns. This study advances our understanding of epiphytic biofilms and offers insights into optimizing host-microbe interactions for improving lake restoration strategies.

A baroduric immobilized composite material promoting remediation of oil-polluted sediment at typical deep-sea condition: The performances and potential mechanisms

Contriving immobilized bioreagent is of great significance to enhance bioremediation of marine oil pollution. However, there remains a notable scarcity of correlational study conducted at deep sea condition. Herein, we first developed a baroduric microsphere encasing biotic and chemical materials to remediate oil-contaminated sediments at deep-sea microcosm. Total oil degradation efficiency of microsphere-treated group reached 71% within a month, representing an approximate 35% increase compared to natural remediation. Absorption and biodegradation by microsphere provided a comparable contribution to oil elimination. Together with scanning electron microscope observation, the physical mechanism was that the reticulate structure of microsphere surface facilitating oil adsorption and bacteria attachment. Via metabarcoding analysis for meta and metabolically-active microbes, we demonstrated the primary working center was located at the microsphere. Proteobacteria, Firmicutes, Bacteroidota and Desulfobacterota were the key activated bacteria. More importantly, we revealed the ecological mechanisms were associated with the following aspects: 1) the addition of microsphere significantly improved the metabolic activity of bacteria (particularly including several oil-degrading taxa); 2) the microspheres enhanced ecological stability and microbial functional diversification during bioremediation; 3) expressing activity of pathways involving oil component degradation, biosurfactant production, biofilm architecture, biogeochemical and energy cycling all were observed to be up-regulated in microsphere-treated samples. Altogether, our results provide important theoretical guidance and data support on application of immobilization technology in removing in-situ oil pollution of deep-sea sediment.

Spatiotemporal distributions, co-occurrence networks, and assembly mechanisms of the bacterial community in sediments of the Yangtze River: comprehensive insights into abundant and rare taxa

Sediments are key reservoirs for rare bacterial biospheres that provide broad ecological services and resilience in riverine ecosystems. Compared with planktons, there is a lack of knowledge regarding the ecological differences between abundant and rare taxa in benthic bacteria along a large river. Here, we offer comprehensive insights into the spatiotemporal distributions, co-occurrence networks, and assembly processes of three divided categories namely always rare taxa (ART), conditionally rare taxa (CRT), and conditionally rare and abundant taxa (CRAT) in sediments covering a distance of 4,300 km in the Yangtze River. Our study demonstrated that ART/CRT contributed greatly to the higher Chao-1 index, Shannon-Wiener index, and phylogenetic alpha diversity of benthic bacteria in autumn than in spring. ART showed high overall beta diversity, and CRT/CRAT exhibited more significant distance-decay patterns than ART in both seasons, mainly corresponding to macroscopic landform types. CRT predominated the nonrandom co-occurrence network, with 97% of the keystone species mostly affiliated with Acidobacteriota flourishing in the lower-reach plain. Two selection processes had the greatest influences on the assembly of CRT (74.7-77.6%), whereas CRAT were driven primarily by dispersal limitation (74.9-86.8%) and ART were driven by heterogeneous selection (33.9-48.5%) and undominated stochasticity (32.7-36.5%). Natural factors such as river flow and channel slope exhibited more significant correlations with community variation than nutrients in all three groups, and total organic carbon mediated the balance among the distinct assembly processes of the ART and CRT in both seasons. Taken together, these results provide an improved ecological understanding of the discrepancy in biogeographic patterns between abundant and rare bacterial taxa in the sediments of Asia's largest river.

Temporal dynamics of the diazotrophic community during corpse decomposition

Corpse decomposition affects soil organisms through the formation of "cadaver decomposition islands." Soil diazotrophic microbes possess essential ecological functions on nitrogen input and nutrient cycling in the terrestrial ecosystem. However, our knowledge about how soil diazotrophic communities respond to corpse decomposition is lacking. In this study, we focused on the succession patterns and biological interaction of nitrogen-fixing microorganisms during animal (Ochotona curzoniae) corpse decomposition in terrestrial ecosystems by targeting nifH gene with high-throughput sequencing. Our results revealed that corpse decomposition of pikas reduced the α diversity and significantly impacted the β diversity of diazotrophic community across different decomposition stages. The divergent succession of diazotrophic community occurred under corpse pressure. Furthermore, the relative importance of stochasticity to the community assembly was improved by corpse decomposition, while the importance decreased over decomposition time. Cadaver decay also simplified the diazotrophic networks and weakened the biological interactions among diazotrophic populations. Notably, NH4-N was the most important factor affecting diazotrophic community, followed by time and total carbon. This work emphasized that corpse decomposition perhaps influences the process of biological nitrogen fixation by altering soil diazotrophic communities, which is of great significance for understanding the terrestrial ecosystems' nitrogen cycle functions. KEY POINTS: • Corpse decomposition reduced the α diversity of diazotrophic community. • Corpse decomposition improved the stochasticity of diazotrophic community assembly. • Corpse decomposition weakened the interactions among diazotrophic populations.

The response of structure and nitrogen removal function of the biofilm on submerged macrophytes to high ammonium in constructed wetlands

The ammonium exceedance discharge from sewage treatment plants has a great risk to the stable operation of subsequent constructed wetlands (CWs). The effects of high ammonium shocks on submerged macrophytes and epiphytic biofilms on the leaves of submerged macrophytes in CWs were rarely mentioned in previous studies. In this paper, the 16S rRNA sequencing method was used to investigate the variation of the microbial communities in biofilms on the leaves of Vallisneria natans plants while the growth characteristics of V. natans plants were measured at different initial ammonium concentrations. The results demonstrated that the total chlorophyll and soluble sugar synthesis of V. natans plants decreased by 51.45% and 57.16%, respectively, and malondialdehyde content increased threefold after 8 days if the initial NH4+-N concentration was more than 5 mg/L. Algal density, bacterial quantity, dissolved oxygen, and pH increased with high ammonium shocks. The average removal efficiencies of total nitrogen and NH4+-N reached 73.26% and 83.94%, respectively. The heat map and relative abundance analysis represented that the relative abundances of phyla Proteobacteria, Cyanobacteria, and Bacteroidetes increased. The numbers of autotrophic nitrifiers and heterotrophic nitrification aerobic denitrification (HNAD) bacteria expanded in biofilms. In particular, HNAD bacteria of Flavobacterium, Hydrogenophaga, Acidovorax, Acinetobacter, Pseudomonas, Aeromonas, and Azospira had higher abundances than autotrophic nitrifiers because there were organic matters secreted from declining leaves of V. natans plants. The analysis of the nitrogen metabolic pathway showed aerobic denitrification was the main nitrogen removal pathway. Thus, the nitrification and denitrification bacterial communities increased in epiphytic biofilms on submerged macrophytes in constructed wetlands while submerged macrophytes declined under ammonium shock loading.

Fate and removal of fluoroquinolone antibiotics in mesocosmic wetlands: Impact on wetland performance, resistance genes and microbial communities

The fate of fluoroquinolone antibiotics norfloxacin and ofloxacin were investigated in mesocosmic wetlands, along with their effects on nutrients removal, antibiotic resistance genes (ARGs) and epiphytic microbial communities on Hydrilla verticillate using bionic plants as control groups. Approximately 99% of norfloxacin and ofloxacin were removed from overlaying water, and H. verticillate inhibited fluoroquinolones accumulation in surface sediments compared to bionic plants. Partial least squares path modeling showed that antibiotics significantly inhibited the nutrient removal capacity (0.55) but had no direct effect on plant physiology. Ofloxacin impaired wetland performance more strongly than norfloxacin and more impacted the primary microbial phyla, whereas substrates played the most decisive role on microbial diversities. High antibiotics concentration shifted the most dominant phyla from Proteobacteria to Bacteroidetes and inhibited the Xenobiotics biodegradation function, contributing to the aggravation in wetland performance. Dechloromonas and Pseudomonas were regarded as the key microorganisms for antibiotics degradation. Co-occurrence network analysis excavated that microorganisms degrade antibiotics mainly through co-metabolism, and more complexity and facilitation/reciprocity between microbes attached to submerged plants compared to bionic plants. Furthermore, environmental factors influenced ARGs mainly by altering the community dynamics of differential bacteria. This study offers new insights into antibiotic removal and regulation of ARGs accumulation in wetlands with submerged macrophyte.

Degradation of pyrene by Xanthobacteraceae bacterium strain S3 isolated from the rhizosphere sediment of Vallisneria natans: active conditions, metabolite identification, and proposed pathways

Polycyclic aromatic hydrocarbons (PAHs) were typical environmental contaminants that accumulated continuously in sediment. Microbial degradation is the main way of PAH degradation in the natural environment. Therefore, expanding the available pool of microbial resources and investigating the molecular degrading mechanisms of PAHs are critical to the efficient control of PAH-polluted sites. Here, a strain (identified as Xanthobacteraceae bacterium) with the ability to degrade pyrene was screened from the rhizosphere sediment of Vallisneria natans. Response surface analysis showed that the strain could degrade pyrene at pH 5-7, NaCl addition 0-1.5%, and temperature 25-40 °C, and the maximum pyrene degradation (~ 95.4%) was obtained under the optimum conditions (pH 7.0, temperature 28.5 °C, and NaCl-free addition) after 72 h. Also, it was observed that the effect of temperature on the degradation ratio was the most significant. Furthermore, eighteen metabolites were identified by mass spectrometry, among which (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid, 7-(carboxymethyl)-8-formyl-1-naphthyl acetic acid, phthalic acid, naphthalene-1,2-diol, and phenol were the main metabolites. And the degradation pathway of pyrene was proposed, suggesting that pyrene undergoes initial ortho-cleavage under the catalysis of metapyrocatechase to form (2Z)-2-hydroxy-3-(4-oxo-4H-phenalen-3-yl) prop-2-enoic acid. Subsequently, this intermediate was progressively oxidized and degraded to phthalic acid or phenol, which could enter the tricarboxylic acid cycle. Furthermore, the pyrene biodegradation by the strain followed the first-order kinetic model and the degradation rate changed from fast to slow, with the rate remaining mostly slow in the later stages. The slow biodegradation rate was probably caused by a significant amount of phenol accumulation in the initial stage of degradation, which resulted in a decrease in bacterial activity or death.

Submerged macrophyte promoted nitrogen removal function of biofilms in constructed wetland

Biofilm is one of the important factors affecting nitrogen removal in constructed wetlands (CWs). However, the impact of submerged macrophyte on nitrogen conversion of biofilms on leaf of submerged macrophyte and matrix remains poorly understood. In this study, the CWs with Vallisneria natans and with artificial plant were established to investigate the effects of submerged macrophyte on nitrogen conversion and the composition of nitrogen-converting bacteria in leaf and matrix biofilms under high ammonium nitrogen (NH4+-N) loading. The 16S rRNA sequencing method was employed to explore the changes in bacterial communities in biofilms in CWs. The results showed that average removal rates of total nitrogen and NH4+-N in CW with V. natans reached 71.38% and 82.08%, respectively, representing increases of 24.19% and 28.79% compared with the control with artificial plant. Scanning electron microscope images indicated that high NH4+-N damaged the leaf cells of V. natans, leading to the cellular content release and subsequent increases of aqueous total organic carbon. However, the specific surface area and carrier function of V. natans were unaffected within 25 days. As a natural source of organic matters, submerged macrophyte provided organic matters for bacterial growth in biofilms. Bacterial composition analysis revealed the predominance of phylum Proteobacteria in CW with V. natans. The numbers of nitrifiers and denitrifiers in leaf biofilms reached 1.66 × 105 cells/g and 1.05 × 107 cells/g, as well as 2.79 × 105 cells/g and 7.41 × 107 cells/g in matrix biofilms, respectively. Submerged macrophyte significantly increased the population of nitrogen-converting bacteria and enhanced the expressions of nitrification genes (amoA and hao) and denitrification genes (napA, nirS and nosZ) in both leaf and matrix biofilms. Therefore, our study emphasized the influence of submerged macrophyte on biofilm functions and provided a scientific basis for nitrogen removal of biofilms in CWs.

Linking ecological niches to bacterial community structure and assembly in polluted urban aquatic ecosystems

Introduction

Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited.

Methods

In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach.

Results

Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes.

Discussion

Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.

Driving forces and recovery potential of the macrophyte decline in East Taihu Lake

Macrophytes are of key importance to the structure and ecological services of shallow lakes and are sensitive to anthropogenic and natural perturbations. Ongoing eutrophication and hydrological regime change affect macrophytes through changes in water transparency and water level, which lead to a dramatic decrease in bottom light availability. Here an integrated dataset (2005-2021) of multiple environmental factors is used to demonstrate the driving forces and recovery potential of the macrophyte decline in East Taihu Lake by using a critical indicator, which is the ratio of the Secchi disk depth to the water depth (SD/WD). The macrophyte distribution area showed a remarkable decrease from 136.1 ± 9.7 km² (2005-2014) to 66.1 ± 6.5 km² (2015-2021). The macrophyte coverage in the lake and in the buffer zone decreased by 51.4% and 82.8%, respectively. The structural equation model and correlation analysis showed that the distribution and coverage of macrophytes decreased with the decrease in the SD/WD over time. Moreover, an extensive hydrological regime change, which caused a sharp decrease in SD and an increase in the water level, is likely to be the driving force that brought about the decline of macrophytes in this lake. The proposed recovery potential model shows that the SD/WD has been low in recent years (2015-2021), and that this SD/WD cannot ensure the growth of submerged macrophytes and is unlikely to ensure the growth of floating-leaved macrophytes, especially in the buffer zone. The approach developed in the present study provides a basis for the assessment of macrophyte recovery potential and the management of ecosystems in shallow lakes that suffer from macrophyte loss.

Diversity and interaction of bacterial and microeukaryotic communities in sediments planted with different submerged macrophytes: Responses to decabromodiphenyl ether

Although various persistent organic pollutants (POPs) can affect microbial communities and functions in aquatic ecosystems, little is known about how bacteria and microeukaryotes respond to the POPs in sediments planted with different submerged macrophytes. Here, a 60-day microcosm experiment was carried out to investigate the changes in the diversity and interaction of bacterial and microeukaryotic communities in sediments collected from Taihu lake, either with decabromodiphenyl ether (BDE-209) own or combined with two common submerged macrophyte species (Vallisneria natans and Hydrilla verticillate). The results showed that BDE-209 significantly decreased the bacterial α-diversity but increased the microeukaryotic one. In sediments planted with submerged macrophytes, the negative effect of BDE-209 on bacterial diversity was weakened, and its positive effect on microeukaryotic one was strengthened. Co-occurrence network analysis revealed that the negative relationship was dominant in bacterial and microeukaryotic communities, while the cooperative relationship between microbial species was increased in planted sediments. Among nine keystone species, one belonging to bacterial family Thermoanaerobaculaceae was enriched by BDE-209, and others were inhibited. Notably, such inhibition was weakened, and the stimulation was enhanced in planted sediments. Together, these observations indicate that the responses of bacteria and microeukaryotes to BDE-209 are different, and their communities under BDE-209 contamination are more stable in sediments planted with submerged macrophytes. Moreover, the effects of plant species on the microbial responses to BDE-209 need to be explored by more specific field studies in the future.