Application of the Biological Toxicity Effect Ratio (BER) Method for Advancing Water Quality Criteria Derivation.

Water quality criteria (WQC) serve as a scientific foundation for pollutant risk assessment and control in aquatic ecosystems. The development of regionally differentiated WQC tailored to specific regional characteristics has become an emerging trend. However, the current WQC is constrained by a lack of regional species toxicity data. To address these limitations, this study proposes the biological toxicity effect ratio (BER) method, which indirectly reflects the toxicity sensitivity of the overall aquatic ecosystem through the toxicity information on a limited number of species, enabling rapid WQC prediction. Using the established WQC in China and the USA as a case study, we combined mathematical derivation and data validation to evaluate the BER method. Among various species-taxon groups of freshwater organisms, planktonic crustaceans demonstrated the highest predictive accuracy. Our analysis further revealed that species toxicity sensitivity and regional variability jointly influence the prediction accuracy. Regardless of the evaluation indexes, planktonic crustaceans emerged as the most suitable species-taxon group for the BER method. Additionally, the BER method is particularly applicable to pollutants with conserved mechanisms across species. This study systematically explores the feasibility of using the BER method and offers new insights for deriving regionally differentiated WQC.

CnnPOGTP: a novel CNN-based predictor for identifying the optimal growth temperatures of prokaryotes using only genomic k-mers distribution.

SUMMARY: Temperature is very important for the growth of microorganisms. Appropriate temperature conditions can improve the possibility for isolation of currently uncultured microorganisms. The development of metagenomic binning technology had dramatically increased the availability of genomic information of prokaryotes, providing convenience to infer the optimal growth temperature (OGT). Here, we proposed CnnPOGTP, a predictor for OGTs of prokaryotes based on deep learning method using only k-mers distribution derived from genomic sequence. This method was annotation free, and the predicted OGT could be obtained by simply providing the genome sequence to the CnnPOGTP website. AVAILABILITY AND IMPLEMENTATION: http://www.orgene.net/CnnPOGTP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Investigation of the transport and metabolic patterns of oil-displacing bacterium FY-07-G in the microcosm model using X-CT technology.

AIMS: Microbial enhanced oil recovery (MEOR) is dedicated to enhancing oil recovery by harnessing microbial metabolic activities and their byproducts within reservoir rocks and fluids. Therefore, the investigation of microbial mobility and their extensive distribution within crude oil is of paramount importance in MEOR. While microscale models have been valuable for studying bacterial strain behavior in reservoirs, they are typically limited to 2D representations of porous media, making them inadequate for simulating actual reservoir conditions. Consequently, there is a critical need for 3D models and dependable visualization methods to observe bacterial transport and metabolism within these complex reservoir environments. METHODS AND RESULTS: Bacterial cellulose (bc) is a water-insoluble polysaccharide produced by bacteria that exhibits biocompatibility and biodegradability. It holds significant potential for applications in the field of MEOR as an effective means for selective plugging and spill prevention during oil displacement processes. Conditionally cellulose-producing strain, FY-07-G, with green fluorescent labeling, was engineered for enhanced oil recovery. 3D micro-visualization model was constructed to directly observe the metabolic activities of the target bacterial strain within porous media and to assess the plugging interactions between cellulose and the medium. Additionally, X-ray computed tomography (X-CT) technology was employed for a comprehensive analysis of the transport patterns of the target strain in oil reservoirs with varying permeabilities. The results indicated that FY-07-G, as a microorganism employing biopolymer-based plugging principles to enhance oil recovery, selectively targets and seals regions characterized by lower permeability and smaller pore spaces. CONCLUSIONS: This work provided valuable insights into the transport and metabolic behavior of MEOR strains and tackled the limitation of 2D models in faithfully replicating oil reservoir conditions, offering essential theoretical guidance and insights for the further application of oil-displacing bacterial strains in MEOR processes.

Wastewater treatment and reuse situations and influential factors in major Asian countries.

As Asia is the most populous continent in the world, the contradiction between water supply and demand is increasing. Wastewater treatment and reclaimed water use are important means to solve the contradiction between supply and demand and realize the sustainability of the water management system. Based on the data collected from 48 typical countries and regions in Asia, this study evaluates the possible influential factors on wastewater treatment and reclaimed water use such as Gross Domestic Product (GDP) level, water resource availability, water withdrawn and water stress. It is identified that per capita GDP and water stress are important factors affecting wastewater treatment and reclaimed water use. Although reclaimed water use in most Asian countries is still at the early stage, the development of wastewater treatment is conducive to the development of reclaimed water. The results of this study are believed to be useful in improving water management and sustainability levels in Asian countries.

Profound regional disparities shaping the ecological risk in surface waters: A case study on cadmium across China.

The scientific advancement of water quality criteria (WQC) stands as one of the paramount challenges in ensuring the security of aquatic ecosystem. The region-dependent species distribution and water quality characteristics would impact the toxicity of pollutant, which would further affect the derivation of WQC across regions. Presently, however, numerous countries adhere to singular WQC values. The "One-size-fits-all" WQC value for a given pollutant may lead to either "over-protection" or "under-protection" of organisms in specific region. In this study, we used cadmium(Cd) pollution in surface waters of China as a case study to shed light on this issue. This study evaluated critical water quality parameters and species distribution characteristics to modify WQC for Cd across distinct regions, thus unveiling the geographical variations in ecological risk for Cd throughout China. Notably, regional disparities in ecological risk emerged a substantial correlation with water hardness, while species-related distinctions magnified these regional variations. After considering the aforementioned factors, the variation in long-term WQC among different areas reached 84-fold, while the divergence in risk quotient extended to 280-fold. This study delineated zones of both heightened and diminished ecological susceptibility of Cd, thereby establishing a foundation for regionally differentiated management strategies.

[Analysis of Regional Differences in Cadmium Ecological Risk in Surface Waters of the Yangtze River Basin].

This study primarily focused on the regional disparities in both water quality criteria and ecological risks attributed to cadmium presence within the surface waters of the Yangtze River Basin. In the initial phase, the long-term water quality criteria for cadmium were recalibrated in accordance with the guidelines outlined in China's "Water Quality Criteria for Freshwater Aquatic Organisms-Cadmium," accounting for the prevalent hardness distribution within the Yangtze River Basin's surface water. Subsequently, a more refined revision was undertaken considering the specific characteristics of the species residing within the Yangtze River Basin. This undertaking led to a comprehensive interpretation of the regional variations in both the distribution of long-term water quality criteria values and the risk quotient distribution of cadmium throughout the Yangtze River Basin. The incorporation of hardness and species-specific attributes resulted in a revised range of long-term water quality criteria for cadmium across different urban locales within the Yangtze River Basin. Notably, the recalibrated values ranged from 0.08 µg·L-1 as the lowest threshold to 0.75 µg·L-1 as the upper limit, signifying a tenfold differentiation. Correspondingly, the urban average annual risk quotient associated with cadmium exposure demonstrated a variation from 0.035 to 1.12, marking a significant 32-fold discrepancy between the lowest and highest values. It is essential to highlight that regions of paramount importance, such as the confluence area connecting the upper and middle stretches of the Yangtze River Basin and the intricate Dongting Lake system, exhibited noteworthy ecological risks attributed to cadmium presence. Consequently, further in-depth investigations into these critical regions are imperative for a comprehensive understanding of the associated risks.

HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background.

The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming. We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of homologous enzymes which took non-hydrocarbons as substrates to HMDB. The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data. HMDB is freely available at http://www.orgene.net/HMDB/.

A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements.

Background: Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods: To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results: A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions: We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.

A novel co-cultivation strategy to generate low-crystallinity bacterial cellulose and increase nisin yields.

In this study, a co-culturing Enterobacter sp. and Lactococcus lactis strategy was developed to alter bacterial cellulose (BC) properties and increase nisin yields. We generated high nisin yields (6260 IU/mL) by altering inoculum ratios and inoculation times in a novel co-culture system. Critically, these were 85% higher than L. lactis monocultures. By monitoring fermentation broth pH and lactic acid yields, the pH was higher and lactic acid yields lower during co-culture conditions when compared with L. lactis monocultures, suggesting that co-culturing was more suitable for L. lactis nisin production. We also determined BC film yields and properties (BC, BC-N, and BC-N after nisin release). BC yields produced by co-culturing were not very different from Enterobacter sp. monocultures, but crystallinity was significantly altered. Collectively, our co-culture system adequately and economically modified BC fibers by interfering with self-assembly and crystallization processes during BC synthesis, with significantly improved nisin yields.

Highly efficient production of bacterial cellulose from corn stover total hydrolysate by Enterobacter sp. FY-07.

Bacterial cellulose (BC) has a huge global market due to its excellent properties and wide range of applications. However, due to high production costs, low productivity, and unsatisfactory scale-up production, industrialisation has been slow. Herein, stabilization of strain, optimisation of culture conditions, and a cheap carbon source were combined to achieve highly efficient, low-cost, large-scale BC production in 20 L containers. Optimisation of culture conditions increased both BC productivity and sugar conversion ratio significantly, from 2.08 g/L/day and 9.78% to 17.13 g/L/day and 70.31%, respectively. Furthermore, BC productivity and sugar conversion ratio reached 13.96 g/L/day and 85.50% using corn stover total hydrolysate as carbon source. The low-cost, facile, and highly efficient process can generate large quantities of BC, and could promote industrialisation of BC production.