Measuring functional similarity of lncRNAs based on variable K-mer profiles of nucleotide sequences.

Long non-coding RNAs are a class of essential non-coding RNAs with a length of more than 200 nts. Recent studies have indicated that lncRNAs have various complex regulatory functions, which play great impacts on many fundamental biological processes. However, measuring the functional similarity between lncRNAs by traditional wet-experiments is time-consuming and labor intensive, computational-based approaches have been an effective choice to tackle this problem. Meanwhile, most sequences-based computation methods measure the functional similarity of lncRNAs with their fixed length vector representations, which could not capture the features on larger k-mers. Therefore, it is urgent to improve the predict performance of the potential regulatory functions of lncRNAs. In this study, we propose a novel approach called MFSLNC to comprehensively measure functional similarity of lncRNAs based on variable k-mer profiles of nucleotide sequences. MFSLNC employs the dictionary tree storage, which could comprehensively represent lncRNAs with long k-mers. The functional similarity between lncRNAs is evaluated by the Jaccard similarity. MFSLNC verified the similarity between two lncRNAs with the same mechanism, detecting homologous sequence pairs between human and mouse. Besides, MFSLNC is also applied to lncRNA-disease associations, combined with the association prediction model WKNKN. Moreover, we also proved that our method can more effectively calculate the similarity of lncRNAs by comparing with the classical methods based on the lncRNA-mRNA association data. The detected AUC value of prediction is 0.867, which achieves good performance in the comparison of similar models.

Predation risk-mediated indirect effects promote submerged plant growth: Implications for lake restoration.

Biological manipulation, involving fish stockings, is commonly used to counteract the deterioration of submerged vegetation in eutrophic lakes. Nevertheless, the non-consumptive effects (NCEs) of stocked carnivorous fish are often overlooked. Using a controlled experimental system, we investigated the NCEs of a native carnivorous fish, snakehead (Channa argus), on two key biological factors, herbivore-dominated grass carp (Ctenopharyngodon idella) and disturbance-dominated loach (Misgurnus anguillicaudatus), influencing submerged plants growth. Additionally, we conducted a meta-analysis on predation risk and primary productivity. The results reveal that predation risk induces oxidative stress damage and affects grass carp growth. Non-significant changes in cortisol and glucose may be linked to predation risk prediction. Simultaneously, predation risk reduces fish feeding and disturbance behavior, relieving pressure on submerged plants to be grazed and disturbed, thereby supporting plant development. The presence of submerged plants, in turn, enhances loach activity and influences water body characteristics through negative feedback. Furthermore, the meta-analysis results indicate the facilitative effect of predation risk on primary producers. Our findings contribute to the understanding of biological manipulation theory. We demonstrate that the predation risk associated with introducing carnivorous fish can promote the growth of submerged plants through behaviorally mediated indirect effects. This highlights the potential utility of predation risk in lake restoration efforts.

Decomposition of exotic versus native aquatic plant litter in a lake littoral zone: Stoichiometry and life form analyses.

The decomposition rates and stoichiometric characteristics of many aquatic plants remain unclear, and our understanding of material flow and nutrient cycles within freshwater ecosystems is limited. In this study, an in-situ experiment involving 23 aquatic plants (16 native and 7 exotic species) was carried out via the litter bag method for 63 days, during which time the mass loss and nutrient content (carbon (C), nitrogen (N), and phosphorus (P)) of plants were measured. Floating-leaved plants exhibited the highest decomposition rate (0.038 ± 0.002 day-1), followed by submerged plants and free-floating plants (0.029 ± 0.002 day-1), and emergent plants had the lowest decomposition rate (0.019 ± 0.001 day-1). Mass loss by aquatic plants correlated with stoichiometric characteristics; the decomposition rate increased with an increasing P content and with a decreasing C content, C:N ratio, and C:P ratio. Notably, the decomposition rate of submerged exotic plants (0.044 ± 0.002 day-1) significantly exceeded that of native plants (0.026 ± 0.004 day-1), while the decomposition rate of emergent exotic plants was 55 ± 4 % higher than that of native plants. The decomposition rates of floating-leaved and free-floating plants did not significantly differ between the native and exotic species. During decomposition, emergent plants displayed an increase in C content and a decrease in N content, contrary to patterns observed in other life forms. The P content decreased for submerged (128 ± 7 %), emergent (90 ± 5 %), floating-leaved (104 ± 6 %), and free-floating plants (32 ± 6 %). Exotic plants released more C and P but accumulated more N than did native plants. In conclusion, the decomposition of aquatic plants is closely linked to litter quality and influences nutrient cycling in freshwater ecosystems. Given these findings, the invasion of the littoral zone by submerged and emergent exotic plants deserves further attention.

Alien emergent aquatic plants develop better ciprofloxacin tolerance and metabolic capacity than one native submerged species.

Antibiotic pollution and biological invasion pose significant risks to freshwater biodiversity and ecosystem health. However, few studies have compared the ecological adaptability and ciprofloxacin (CIPR) degradation potential between alien and native macrophytes. We examined growth, physiological response, and CIPR accumulation, translocation and metabolic abilities of two alien plants (Eichhornia crassipes and Myriophyllum aquaticum) and one native submerged species (Vallisneria natans) exposed to CIPR at 0, 1 and 10 mg/L. We found that E. crassipes and M. aquaticum's growth were unaffected by CIPR while V. natans was significantly hindered under the 10 mg/L treatment. CIPR significantly decreased the maximal quantum yield of PSII, actual quantum yield of PSII and relative electron transfer rate in E. crassipes and V. natans but didn't impact these photosynthetic characteristics in M. aquaticum. All the plants can accumulate, translocate and metabolize CIPR. M. aquaticum and E. crassipes in the 10 mg/L treatment group showed greater CIPR accumulation potential than V. natans indicated by higher CIPR contents in their roots. The oxidative cleavage of the piperazine ring acts as a key pathway for these aquatic plants to metabolize CIPR and the metabolites mainly distributed in plant roots. M. aquaticum and E. crassipes showed a higher production of CIPR metabolites compared to V. natans, with M. aquaticum exhibiting the strongest CIPR metabolic ability, as indicated by the most extensive structural breakdown of CIPR and the largest number of potential metabolic pathways. Taken together, alien species outperformed the native species in ecological adaptability, CIPR accumulation and metabolic capacity. These findings may shed light on the successful invasion mechanisms of alien aquatic species under antibiotic pressure and highlight the potential ecological impacts of alien species, particularly M. aquaticum. Additionally, the interaction of antibiotic contamination and invasion might further challenge the native submerged macrophytes and pose greater risks to freshwater ecosystems.

Species-specific functional trait responses of canopy-forming and rosette-forming macrophytes to nitrogen loading: Implications for water-sediment interactions.

Globally intensified lake eutrophication, attributed to excessive anthropogenic nitrogen loading, emerges as a significant driver of submerged vegetation degradation. Consequently, the impact of nitrogen on the decline of submerged macrophytes has received increasing attention. However, a functional trait-based approach to exploring the response of submerged macrophytes to nitrogen loading and its environmental feedback mechanism was unclear. Our study utilized two different growth forms of submerged macrophytes (canopy-forming Myriophyllum spicatum, and rosette-forming Vallisneria natans) to established "submerged macrophytes-water-sediment" microcosms. We assessed the influence of nitrogen loading, across four targeted total nitrogen concentrations (original control, 2, 5, 10 mg/L), on plant traits, water parameters, sediment properties, enzyme activities, and microbial characteristics. Our findings revealed that high nitrogen (10 mg/L) adversely impacted the relative growth rate of fresh biomass and total chlorophyll content in canopy-forming M. spicatum, while the chlorophyll a/b and free amino acid content increased. On the contrary, the growth and photosynthetic traits of resource-conservative V. natans were not affected by nitrogen loading. Functional traits (growth, photosynthetic, and stoichiometric) of M. spicatum but not V. natans exhibited significant correlations with environmental variables. Nitrogen loading significantly increased the concentration of nitrogen components in overlying water and pore water. The presence of submerged macrophytes significantly reduced the ammonia nitrogen and total nitrogen both in overlying water and pore water, and decreased total organic carbon in pore water. Nitrogen loading significantly inhibited sediment extracellular enzyme activities, but the planting of submerged macrophytes mitigated their negative effects. Furthermore, rhizosphere bacterial interactions were less compact compared to bare control, while eukaryotic communities exhibited increased complexity and connectivity. Path modeling indicated that submerged macrophytes mitigated the direct effects of nitrogen loading on overlying water and amplified the indirect effects on pore water, while also attenuating the direct negative effects of pore water on extracellular enzymes. The findings indicated that the restoration of submerged vegetation can mitigate eutrophication resulting from increased nitrogen loading through species-specific changes in functional traits and direct or indirect feedback mechanisms in the water-sediment system.

Adaptive responses and transgenerational plasticity of a submerged plant to benthivorous fish disturbance.

Submerged macrophytes play a key role in the restoration of shallow eutrophic lakes. However, in some subtropical lakes, benthivorous fishes dominate the fish assemblages and influence the growth of submerged plants. A comprehensive understanding of the direct and indirect effects of benthivorous fishes on submerged plants is important. We conducted mesocosm experiments to examine the effects of three densities of benthivorous fish, Misgurnus anguillicaudatus, on the water properties, the growth, asexual reproduction, and the germination of turions of Potamogeton crispus L. Our results showed that fish disturbance increased TN, TP, PO4-P, NH4-N, and NO3-N of the water, raising the extinction coefficient K, Chl a, and the periphyton biomass. Benthivorous fish disturbance reduced the total biomass, root length, relative growth rate (RGR), and branching number while increasing the plant height of P. crispus. The P stoichiometric homeostasis coefficient (H P) (except turions) and H N was lower in plant tissues due to fish disturbance. Benthivorous fish disturbances promoted turions formation (e.g., increased turions total numbers and biomass) of P. crispus. Moreover, P. crispus exhibited transgenerational plasticity for benthivorous fish affecting turion emergence. The maximum final germination rate occurred only when fish density in the mother plant grow experiment matched that in the turion germination experiment. Turions generated by P. crispus disturbed by low-density fish exhibited increased germination rates. Our findings suggest that controlling benthivorous fish reduces its indirect and direct effects on submerged vegetation, facilitating the successful restoration of these plants.

NMR-based analysis of shear strength of weakly expansive clay in sodium chloride solution.

A series of direct shear and nuclear magnetic resonance (NMR) tests were performed on a compacted weakly expansive clay saturated by sodium chloride (NaCl) solutions with different concentrations to study the effect of NaCl solution on the shear strength and its mechanism. Results from the direct shear tests show that the shear strength decreases slightly with increasing the NaCl solution concentration when the concentration is less than 1.0 mol/L. The results of NMR tests show that the smaller transverse relaxation times (T2) of specimens saturated by NaCl solutions with concentrations of 0.5 and 1.0 mol/L are less than that of the specimen saturated by deionized water. This means that the amount of smaller pores in the specimens saturated by deionized water is greater than that in specimens by NaCl solutions. That is, the specimen saturated by deionized water is denser than those by NaCl solutions under the same vertical pressure, and thus the shear strength of weakly expensive clay decreases with increasing the NaCl solution concentration.

Effects of Eutrophication and Different Water Levels on Overwintering of Eichhornia crassipes at the Northern Margin of Its Distribution in China.

When exotic species are introduced into new areas, establishment is a vital step in their invasion process. Therefore, overwintering strategies determine whether an exotic species from low latitudes can successfully invade middle- and high-latitude areas. In this study, we investigated the effects of nutrient and water drawdown on overwintering in an exotic aquatic plant from the tropical zone, Eichhornia crassipes, at the northern margin of its distribution in China. The population density, size of individuals, and the size and nitrogen concentration of overwintering organs (stem base) of E. crassipes that grew in high-nutrition water were greater than those that grew in low-nutrient water before winter. The overwinter survival rate of E. crassipes was significantly affected by the water level and nutrient. The thick and dense floating mat of E. crassipes can increase the temperature of water bodies; therefore, the overwinter survival rate of E. crassipes was higher in constant-water-level and high-nutrient treatment. In contrast, due to the loss of heat preservation provided by the floating mats and the low nitrogen concentration in the stem base, all individuals of E. crassipes died in constant-water-level and low-nutrient treatment. In the water-drawdown treatments, the stem base of E. crassipes was directly exposed to low-temperature air; therefore, the overwinter survival rate of E. crassipes was lower. Our results reveal that eutrophication can not only improve the competitiveness of E. crassipes but can also improve the survival rate of overwintering plants in temperate regions. Our study also suggests that removing nutrients from the water and regulating the water level can limit the invasion of E. crassipes in temperate and subtropical regions.

Submerged Vegetation and Water Quality Degeneration From Serious Flooding in Liangzi Lake, China.

In shallow lake ecosystems, flooding is a key disturbance factor of aquatic vegetation. Aquatic plants, especially submerged plants, play key roles in water ecosystems. Liangzi Lake experienced severe flooding in July 2010, and the elevated water levels lasted for 3 months. In this study, 10 transects with 120 monitoring points were set up for monthly monitoring during the 3-year period, encompassing the period before and after the flooding (2009-2011). The numbers, biomass, and diversity of the submerged plants, as well as the physical and chemical characteristics of the lake water, were surveyed. There were 12 species belonging to 7 families and 7 genera in Liangzi Lake. Eleven of the submerged plant species were found in 2009, but, after the flood, that number decreased to five in 2011. The total biomass differed significantly over the three years (P < 0.05), with the largest biomass in 2009 and smallest in 2011. In 2009 and 2010, Potamogeton maackianus was the dominant species, but its dominant position weakened in 2011. After the flood, water transparency decreased, and the water depth, turbidity, total nitrogen, and total phosphorus increased. A redundancy analysis between the submerged plants and environmental factors found that the water transparency, turbidity, and water depth were the key environmental factors affecting the plants. These results suggest that the long-lasting severe flooding of Liangzi Lake in 2010 led to the degradation of both the submerged plant community and water quality.

Coverage of Native Plants Is Key Factor Influencing the Invasibility of Freshwater Ecosystems by Exotic Plants in China.

Understanding the biotic and abiotic factors that influence the susceptibility of a community to invasion is beneficial for the prediction and management of invasive species and the conservation of native biodiversity. However, the relationships between factors and invasibility of a community have not been fully confirmed, and the factors most associated with the susceptibility of a community to invasion have rarely been identified. In this study, we investigated the species richness patterns in aquatic exotic and native plants and the relationships of exotic species richness with habitat and water environment factors in 262 aquatic plant communities in China. A total of 11 exotic plant species were recorded in our field survey, and we found neither a negative nor a positive relationship between aquatic exotic and native plant species richness. The aquatic exotic plant species richness is negatively correlated with the relative coverage and biomass of native plants but positively correlated with the total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (COD) concentrations in the water. The native plant species richness, native species' relative coverage, and native species' biomass were positively related to each other, whereas the TP, TN, and COD were also positively related to each other. The native plant species richness, native species' relative coverage, and native species biomass were each negatively correlated with the TP, TN, and COD. In addition, biotic rather than abiotic predictors accounted for most of the variation in exotic plant richness. Our results suggest that improving the vegetation coverage and the biodiversity of native plants is the most effective approach for preventing alien plant invasions and minimizing their impacts on freshwater ecosystems.

Invasive plant Alternanthera philoxeroides suffers more severe herbivory pressure than native competitors in recipient communities.

Host-enemy interactions are vital mechanisms that explain the success or failure of invasive plants in new ranges. We surveyed the defoliation of invasive Alternanthera philoxeroides and co-occurring native plants on two islands during different seasons over three consecutive years and measured the leaf nitrogen content and the C/N ratio of each plant species. To evaluate the effects of herbivory on A. philoxeroides, an herbivore exclosure experiment was conducted. We found that the mean defoliation of A. philoxeroides was higher than that of native plants, regardless of whether the dominant species was A. philoxeroides or native plants. A. philoxeroides defoliation increased significantly as the months progressed, whereas the defoliation of the total population of native plants was constant. The leaf nitrogen content was positively correlated with defoliation, and it was highest in A. philoxeroides. Additionally, A. philoxeroides in the herbivore exclusion treatment showed an increase in shoot biomass and total shoot length. Our study revealed that native generalist herbivores prefer the invasive plant to the natives because of the higher leaf nitrogen content. These results support the biotic resistance hypothesis, suggesting that native herbivore species can limit the population spread of invasive plants.