Article
Biochemistry & Molecular Biology
Francois Keck, Jeanine Brantschen, Florian Altermatt
Summary: The current advances of environmental DNA (eDNA) have brought significant changes to ecological monitoring and understanding of biological diversity. The challenging nature of eDNA data has revolutionized the analysis of biological monitoring information, and machine learning algorithms show promise in capturing complex relationships between environmental pressures and biological communities. In this study, we explored the potential of using machine learning techniques to analyze a large eDNA dataset and demonstrated that a model trained on eDNA performs similarly to a model trained on traditional data. This proof-of-concept illustrates the potential of combining eDNA and machine learning approaches to complement or even replace traditional environmental monitoring.
Review
Biochemistry & Molecular Biology
Tristan Cordier, Laura Alonso-Saez, Laure Apotheloz-Perret-Gentil, Eva Aylagas, David A. Bohan, Agnes Bouchez, Anthony Chariton, Simon Creer, Larissa Fruehe, Francois Keck, Nigel Keeley, Olivier Laroche, Florian Leese, Xavier Pochon, Thorsten Stoeck, Jan Pawlowski, Anders Lanzen
Summary: A decade after the integration of high-throughput sequencing technologies into environmental science, genomics-based monitoring of anthropogenic impacts on biodiversity and ecosystems still faces challenges in implementation by regulatory frameworks. Technical limitations, conceptual issues, and diverse implementation strategies may contribute to the perception that routine application of this methodology is premature. Reviewing recent implementations, the strengths and limitations of four general implementation strategies for environmental genomics monitoring are discussed, with emphasis on the potential of integrating meiofauna and microorganisms into biomonitoring.
Review
Environmental Sciences
Lilian Dayana Cruz, Diego Mauricio Lopez, Rubiel Vargas-Canas, Apolinar Figueroa, Juan Carlos Corrales
Summary: This scoping review provides an overview of different approaches in computer-assisted bioindication with freshwater macroinvertebrates (FwM). The review identifies two areas of applying computational technologies in bioindication studies with FwM: evaluating water quality through samples already classified by human experts, and the automatic classification of FwM. The review also discusses critical factors affecting strategy selection in these studies and establishes the relationship between the strategies and algorithms employed in a timeline for automatic classification. Overall, this study helps enhance confidence in computational technologies in FwM studies and extends their use in bioassessment tasks.
Article
Biochemistry & Molecular Biology
Verena Dully, Thomas A. Wilding, Timo Muehlhaus, Thorsten Stoeck
Summary: Environmental DNA metabarcoding is a powerful tool for biomonitoring, and the random forest (RF) machine learning algorithm can accurately classify unknown samples. This study found that extreme to moderate rarefaction was sufficient to achieve prediction performance similar to full datasets, and the most important criterion for accuracy is the ability of training data to characterize classes effectively. This information can be used to inform future sampling designs for eDNA biomonitoring to reduce costs and computation time.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Ecology
Da-Yeong Lee, Dae-Seong Lee, YoonKyung Cha, Joong-Hyuk Min, Young-Seuk Park
Summary: This study reviews data-based research using models to predict the biological elements of freshwater ecosystems over the last three decades. It evaluates the ability of current models to predict changes in freshwater organisms and suggests future research directions.
ECOLOGICAL INFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Anders Lanzen, Inaki Mendibil, Angel Borja, Laura Alonso-Saez
Summary: Routine monitoring of benthic biodiversity is crucial for managing and understanding the impact of human activities on various types of ecosystems. Metabarcoding of environmental DNA shows promise in overcoming the challenges of traditional monitoring, particularly for microorganisms. Two different methods, Random Forests and Threshold Indicator Taxa Analysis, are used to predict impacts in estuaries and coastal areas, showing strong correlation to reference values and potential for predicting specific types of pressure. Further evaluation and improvement are needed to apply these methods in new regions or habitats.
Article
Biology
Joanne E. Littlefair, Jose S. Hleap, Vince Palace, Michael D. Rennie, Michael J. Paterson, Melania E. Cristescu
Summary: The spatial connectivity in aquatic ecosystems has a significant impact on the structure, function, and dynamics of aquatic communities. Environmental DNA can be used to conduct high-throughput, spatially integrated biodiversity surveys in these ecosystems.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Environmental Sciences
Tan Chen, Chunqiao Song, Chenyu Fan, Xin Gao, Kai Liu, Zhen Li, Jian Cheng, Pengfei Zhan
Summary: This study simulated the impact of environmental variables on fish catches in China's Poyang Lake using remote sensing techniques and machine learning algorithms. The findings showed that hydrometeorological conditions, water quality, and water ecological variables all have significant influences on fish catches. The integration of multiple variables can further improve the accuracy of fish catch simulation.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Computer Science, Information Systems
Mutsumi Kimura, Hiroki Yamanaka, Yasuhiko Nakashima
Summary: In this study, machine learning is applied to environmental DNA metabarcoding, and three coding methods are proposed. Among them, the two-bit coding method shows the highest accuracy. The results indicate that machine learning has significant applications in environmental DNA metabarcoding.
Article
Environmental Sciences
Thiri Shwesin Aung
Summary: The impacts of armed conflict on the environment are complex to investigate, but satellite data and machine learning algorithms have proven useful in studying the direct and indirect effects of war on ecosystems. The Rohingya conflict has been described as one of the worst humanitarian crises and man-made disasters of the 21st Century. Despite ongoing agreements to repatriate refugees, research on damage quantification and suitability of human resettlement is lacking.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Ecology
Qianqian Wu, Jinxin Zhou, Tatsuya Komoto, Toshiyuki Ishikawa, Naoshige Goto, Masayuki K. Sakata, Daisuke Kitazawa, Toshifumi Minamoto
Summary: This study demonstrates the impact of climate-driven changes on the distribution of environmental DNA (eDNA) of two species in Lake Biwa, Japan, and provides insights into the species-environment relationship under existing and future environments. The results highlight the different responses of species to climate change and emphasize the importance of special attention to vulnerable species in the face of climate change. Furthermore, the study emphasizes the potential application of interdisciplinary methodologies for improved species conservation.
Article
Biodiversity Conservation
Chloe Victoria Robinson, Teresita M. Porter, Victoria Carley Maitland, Michael T. G. Wright, Mehrdad Hajibabaei
Summary: This study used DNA metabarcoding to identify macroinvertebrates and diatoms from different habitat samples, and obtained a different perspective of ecological conditions through a more comprehensive taxonomic assessment. The results showed that sites with 'good' condition had higher beta diversity, directed connectance, and modularity, indicating higher resilience compared to 'fair' condition sites. DNA metabarcoding data detected 29 site condition indicator species consistent with known bioindicators and expected relative tolerances, and identified 11 keystone taxa through trophic network analysis.
ECOLOGICAL INDICATORS
(2022)
Article
Biodiversity Conservation
Zelong Zhao, Hongjun Li, Yi Sun, Aibin Zhan, Wenlu Lan, Sau Pinn Woo, Aileen Tan Shau-Hwai, Jingfeng Fan
Summary: This study investigated the benthic microbial community composition in a typical subtropical coast area in Southern China using metabarcoding and physicochemical analysis. The results showed that stochastic processes were the dominant ecological driver in shaping the community assembly of both bacteria and fungi. Environmental factors explained a considerable portion of variation in bacterial communities, while spatial factors were more influential in structuring fungal communities. Furthermore, a random forest model based on bacterial communities was able to predict the concentrations of heavy metals. These findings provide new insights into the factors influencing coastal ecosystems and support the integration of biological information into routine ecological monitoring.
ECOLOGICAL INDICATORS
(2022)
Article
Environmental Sciences
Shan Zhang, Jindong Zhao, Meng Yao
Summary: Using environmental DNA (eDNA) sampling from 109 water sites in Beijing, China, we detected 126 vertebrate species including fish, birds, mammals, and reptiles. The eDNA approach showed higher detection probabilities for aquatic species compared to terrestrial and arboreal species, and higher detection probabilities for lentic sites compared to lotic sites. The detection probabilities were also correlated with the size of lentic waterbodies. These findings demonstrate the potential of eDNA metabarcoding for efficient monitoring of urban vertebrate biodiversity.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Environmental Sciences
Fatemeh Kardel, Shadi Karbalaei Hassan, Hamideh Rashid, Reza Dehbandi, Philip K. Hopke, Sajjad Abbasi
Summary: The magnetic properties of root, bark and leaf of Avicenna marina and sediment in the northern Persian Gulf were determined to assess pollution. The study found that the sources of particles on leaf surfaces can be distinguished by SIRM values and heavy metal content. However, factors such as wind direction, particle size and crown density affect the use of SIRM for biomonitoring. The significant correlation between SIRM and leaf elemental contents indicates that the deposited particles on leaves mainly come from geological sources. The magnetic properties of sediments and mangrove roots are suitable indicators of pollution in aquatic environments.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Rong-Gui Zhu, Chang-Gui Pan, Feng-Jiao Peng, Chao-Yang Zhou, Jun-Jie Hu, Kefu Yu
Summary: This comprehensive survey investigated the occurrence, bioaccumulation, and trophic magnification of parabens and their metabolite 4-HB in a marine food web. Results showed that parabens were the predominant pollutants in marine organisms, with significant bioaccumulation from sediments. The estimated trophic magnification factor indicated biomagnification for MeP and trophic dilution for 4-HB. Overall, the risks for humans consuming marine organisms were found to be low.
Article
Engineering, Environmental
Andres F. Torres-Franco, Deborah Leroy-Freitas, Cristina Martinez-Fraile, Elisa Rodriguez, Pedro A. Garcia-Encina, Raul Munoz
Summary: Anaerobic and microalgae-based technologies have emerged as sustainable alternatives for municipal wastewater treatment. However, the presence of viruses in the treated wastewater is a major concern for reuse applications. This study assessed the ability of these technologies to reduce viruses during secondary wastewater treatment. The results showed that all technologies were effective in reducing the concentration of viruses, with microalgae-based treatment exhibiting the highest potential for reducing the disinfection requirements of treated wastewater.
Article
Engineering, Environmental
Young Gwang Kim, Sae Yun Kwon, Spencer J. Washburn, Scott C. Brooks, Ji Won Yoon, Lucien Besnard
Summary: The study uses Hg isotope ratios to identify the sources and exposure pathways of mercury in bivalves, finding that dissolved Hg phases in the water column are the primary source and exposure pathway to bivalves. This provides new insights into using bivalves as bioindicators for sediment quality monitoring.
Article
Engineering, Environmental
Hui Geng, Ying Xu, Rui Liu, Dianhai Yang, Xiaohu Dai
Summary: This study investigates the effect of cation exchange resin (CER) on the sequential recovery of hydrogen and methane from anaerobic digestion (AD) and the corresponding mechanisms. The results show that CER can simultaneously enhance the production of hydrogen and methane by promoting the solubilisation, hydrolysis, and acidification of organic matter. Additionally, CER facilitates effective contact between bacteria and organic particulates and reduces the energy barrier for mass transfer during methane production. The study also reveals changes in the microbial community structure and metagenomics during the AD process.
Article
Engineering, Environmental
Xiaojing Lin, Zhan Jin, Shunfeng Jiang, Zhiquan Wang, Suqing Wu, Ke Bei, Min Zhao, Xiangyong Zheng
Summary: Dehumidification combined with addition of absorbent resin supplement (ARS) was used to achieve rapid evaporation of non-pretreated urine, resulting in high water evaporation efficiency and nutrient recovery.
Article
Engineering, Environmental
Yangli Che, Chaoran Lin, Shen Li, Jiao Liu, Longhai Zhu, Shilei Yu, Nan Wang, Haoshuai Li, Mutai Bao, Yang Zhou, Tonghao Si, Rui Bao
Summary: Hydrodynamic processes play a crucial role in the transmission of sediments, microbial assembly, and organic carbon redistribution in the ocean. Through experiments and analysis, we found that hydrodynamics shape the assembly of microbial communities and control the redistribution of different sourced organic carbon, thereby influencing microbial-mediated biogeochemical transformation.
Article
Engineering, Environmental
Chao Chen, Yu Yang, Nigel J. D. Graham, Zhenyu Li, Xingtao Yang, Zhining Wang, Nadia Farhat, Johannes S. Vrouwenvelder, Li -an Hou
Summary: The fouling of seawater reverse osmosis membranes is a persistent challenge in desalination. This study monitored the operational performance of a desalination plant for 7 years and the fouling development in different areas of membrane modules. The findings showed that operational performance declined over time and fouling mainly occurred at the feed side of the modules, with the highest microbial diversity. Keystone species like Chloroflexi and Planctomycetes played an important role in maintaining community structure and biofilm maturation. Polysaccharides, soluble microbial products, marine humic acid-like substances, and inorganic substances contributed to fouling. Overall, biofouling had a significant impact on membrane fouling after 7 years of operation.
Article
Engineering, Environmental
Dan Li, Jieyi Sun, Yibo Fu, Wentao Hong, Heli Wang, Qian Yang, Junhong Wu, Sen Yang, Jianhui Xu, Yunfei Zhang, Yirong Deng, Yin Zhong, Ping'an Peng
Summary: Sulfidation-oxidation treatment of magnetite (Fe3O4) enhances the production of dark center dot OH, which can efficiently degrade dissolved organic matter (DOM) and accelerate carbon cycling.
Article
Engineering, Environmental
Cheng Yu, Kaijun Wang, Kaiyuan Zhang, Ruiyang Liu, Pingping Zheng
Summary: This study implemented a microaerobic-aerobic configuration in a full-scale municipal wastewater treatment facility and investigated the effects on sludge characteristics, pollutant removal, microbial community, and granulation mechanisms. The results showed successful transition from flocculent-activated sludge to well-defined AGS after two months of operation. The primary pathways for pollutant removal were simultaneous nitrification, denitrification, and phosphorus removal. Moreover, the incorporation of internal separators induced shifts in the flow pattern, which promoted granulation.
Article
Engineering, Environmental
Zhe Zhang, Shaoyang Hu, Guangrong Sun, Wei Wang
Summary: Halogenated aromatic disinfection byproducts (DBPs), such as halogenated phenols, have garnered widespread attention due to their high toxicity and prevalence. This study reports on the analysis, occurrence, and cytotoxicity of a group of emerging halogenated aromatic DBPs, known as halogenated polyhydroxyphenols (HPPs), in drinking water.
Article
Engineering, Environmental
Shengyue Chen, Jinliang Huang, Peng Wang, Xi Tang, Zhenyu Zhang
Summary: Accurate prediction of river water quality is crucial for sustainable water management. This study introduces wavelet analysis and transfer learning techniques to assist LSTM modeling, proposing a newly coupled modeling approach that improves short-term prediction of river water quality.
Article
Engineering, Environmental
Bang Du, Xinmin Zhan, Piet N. L. Lens, Yifeng Zhang, Guangxue Wu
Summary: Efficient anaerobic digestion relies on the cooperation of different microorganisms with different metabolic pathways. This study investigated the effects of different operational modes and the addition of powdered activated carbon (PAC) on ethanol metabolic pathways. The results showed that the SBR mode and the presence of CO2 facilitated ethanol metabolism towards propionate production, while the CFR mode with extended solids retention time enriched Geobacter. Adjusting operational modes and PAC addition can modulate anaerobic ethanol metabolism and enrich Geobacter.
Article
Engineering, Environmental
Wanfa Wang, Si-Liang Li, Jun Zhong, Yuanbi Yi, Fujun Yue, Zenglei Han, Qixin Wu, Ding He, Cong-Qiang Liu
Summary: This study compares the carbon biogeochemical processes in karst and non-karst regions within large thermal stratified river-reservoir systems. The results demonstrate that karst reservoirs have a reduced potential for carbon emissions and highlight the importance of considering geologic settings to improve accuracy in regional and global CO2 emission estimates.
Article
Engineering, Environmental
Chunxia Jiang, Zelong Zhao, Dong Zhu, Xiong Pan, Yuyi Yang
Summary: This study analyzed the occurrence and distribution of antibiotic resistance genes (ARGs) in different environmental media of the Yangtze River using metagenomics. Core resistome dominated by multidrug resistance genes was found in all samples, while rare resistome dominated by various resistance genes was more prevalent in plasmids. Specific bacteria were identified as hosts for both core and rare resistomes, with high clinical concern ARGs found in the rare resistome. Particle-associated environment provided the most ideal conditions for resistome hosts. This study provided insights into the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.
Article
Engineering, Environmental
Yu Zhang, Yongtao He, Linchun Jia, Lei Xu, Zheng Wang, Yueling He, Ling Xiong, Xumeng Lin, Hong Chen, Gang Xue
Summary: By synergizing organic carbon source, thiosulfate, and zero-valent iron, efficient mixotrophic denitrification of oligotrophic secondary effluent can be achieved. Thiosulfate plays a vital role in promoting TN removal efficiency, while corrosion of Fe0 releases OH- to neutralize H+ from thiosulfate-driven denitrification, creating a suitable environment for denitrification. The coordination of thiosulfate and Fe0 maintains the dominance of Thiobacillus for denitrification.