Article
Multidisciplinary Sciences
Guillaume Patoine, Nico Eisenhauer, Simone Cesarz, Helen R. P. Phillips, Xiaofeng Xu, Lihua Zhang, Carlos A. Guerra
Summary: Soil microorganisms play a crucial role in maintaining soil functions and services, but our understanding of their spatial-temporal dynamics is still limited. This study analyzes the temporal trends in soil microbial biomass carbon and identifies the main drivers of change, revealing the areas sensitive to environmental factors. The research finds that global soil microbial biomass carbon has decreased by approximately 3.4% over the past 20 years, with increasing temperatures being the main driver of decline in the northern regions.
NATURE COMMUNICATIONS
(2022)
Article
Environmental Sciences
Ronghua Qin, Xumeng Lin, Zhenpeng Chen, Chengyuan Su, Fenghua Zhu, Wenjing Yang, Zhuxin Chen, Pingping Lu
Summary: The study revealed that different aromatic carboxylic acids have impacts on the performance and microbial communities of anaerobic granular sludge, with benzoic acid showing the highest efficiency in COD removal. The addition of aromatic carboxylic acids led to an increase in functional groups in the anaerobic granular sludge and affected the decay of LB-EPS.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Environmental Sciences
Anna Christine Trego, Simon Mills, Gavin Collins
Summary: Anaerobic digestion is recognized as a sustainable method for waste management, producing methane-rich biogas. Different specialized granules, including anaerobic and aerobic granules, have opened up new opportunities in wastewater treatment and resource recovery biotechnology. Each type of granule has unique characteristics, biochemical processes, and microbial community compositions.
CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY
(2021)
Article
Ecology
Qingjuan Meng, Pengfei Li, Jianhua Qu, Ying Liu, Yifan Wang, Zhaobo Chen, Ying Zhang
Summary: This study successfully degraded TCE using a UASB reactor, with the anaerobic sludge containing a variety of bacteria including acid-forming bacteria, anaerobic dechlorinating bacteria, and methanogenic bacteria.
Article
Engineering, Environmental
Jennifer Ekholm, Frank Persson, Mark de Blois, Oskar Modin, Mario Pronk, Mark C. M. van Loosdrecht, Carolina Suarez, David J. I. Gustavsson, Britt-Marie Wilen
Summary: This study assessed the implementation of AGS process in Nordic countries and found rapid changes in microbial community composition during start-up and factors affecting granulation. The results showed that immigration from influent wastewater had a minor impact on microbial community after granules formation, while seasonal environmental factors were identified as important for AGS performance.
ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY
(2022)
Article
Environmental Sciences
Simon Mills, Thi Phi Yen Nguyen, Umer Zeeshan Ijaz, Piet N. L. Lens
Summary: In this study, the effects of long-term bioreactor (un)stability on resistance to shock loads were evaluated. The results showed that the reactor with stable operation performed better in terms of resistance to a sudden increase in organic loading rate, despite having lower microbial community diversity. The operation history of a reactor plays a crucial role in determining its ability to withstand environmental perturbations.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Biotechnology & Applied Microbiology
Lei Lei, Jin-chi Yao, Yong-di Liu, Wei Li
Summary: The study explored an efficient strategy for cultivating salt-tolerant aerobic granular sludge (SAGS) by seeding anaerobic granular sludge in a SBR, which showed high removal efficiency of COD, NH4+-N, and total nitrogen at 3% salinity. Bacterial community analysis identified dominant AOB and denitrifiers as Nitrosomonas and Defluviimonas, respectively, with low abundance of Nitrospira. qPCR results revealed decreased abundance of nirS and nirK under high salinity, explaining the lower TN removal efficiency and NO2--N accumulation.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2021)
Article
Environmental Sciences
Yutian Zuo, Wenzhi Zeng, Jiesheng Huang
Summary: Carbon nanomaterials (CNMs) have effects on soil microbial communities, causing reduced microbial biomass carbon (MBC) and increased soil Shannon index. Different types of CNMs have different impacts on soil microbes, with MWCNTs having less toxicity and being more suitable as crop growth promoters.
LAND DEGRADATION & DEVELOPMENT
(2023)
Article
Environmental Sciences
Shutao Chen, Tingting Zhang, Jun Wang
Summary: The study investigated the impact of warming and straw application on soil microbial biomass C, N and C/N in a winter wheat-soybean rotation cropland. It found that warming significantly increased microbial biomass C and C/N over the crop-growing seasons, while straw application did not have a significant effect. Soil microbial biomass C, N, and C/N were affected by different soil moisture conditions, with warming-associated water losses playing a key role in influencing them. The results suggest that soil microorganisms in agroecosystems may accumulate more C under future warmer climate conditions.
WATER AIR AND SOIL POLLUTION
(2021)
Article
Engineering, Environmental
Chen Wang, Wei Wei, Yu-Ting Zhang, Xiaohu Dai, Bing-Jie Ni
Summary: The inhibitory effect of different sizes of polystyrene microplastics (PS-MPs) on an anaerobic granular sludge (AGS) wastewater treatment system was investigated. The results showed that larger PS-MPs had a stronger inhibitory effect on methane production and organic carbon degradation by AGS, as well as causing damage to AGS granules and reduction in acidogens and methanogens populations.
Article
Ecology
Alfred Burian, Daisy Pinn, Ignacio Peralta-Maraver, Michael Sweet, Quentin Mauvisseau, Ozge Eyice, Mark Bulling, Till Roethig, Pavel Kratina
Summary: Experimental manipulation of protozoan predation pressure in activated sludge communities had strong and positive effects on bacterial diversity components, with responses leveling off at higher predation pressure levels. While predator intensity positively impacted taxa richness, predator diversity had mixed effects on bacterial diversity. Reduction in top-down control by predators negatively affected taxa associated with treatment efficiency, particularly nitrogen removal. The study highlights distinct mechanisms linking protozoan predation with bacterial diversity and community composition in activated sludge communities.
Article
Engineering, Environmental
Xiao Yang, Hui Liu, Yihu Xu, Ling Liu, Yunpeng Zhu, Keyang Jiang, Zheyun Zhang, Guoning Chen, Zhiwei Wang
Summary: The study found that a low concentration of UF resin had minimal impact on AnGS activity, while high concentrations decreased methane production and COD removal while increasing SCFA production. Additionally, high concentrations of UF resin inhibited EPS production, leading to the fragmentation of AnGS and decreased cell viability.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2022)
Article
Energy & Fuels
Yufang Wei, Hongbing Zhao, Xuejiao Qi, Tianxue Yang, Junping Zhang, Wangmi Chen, Mingxiao Li, Beidou Xi
Summary: The magnetite nanoparticle-anaerobic granular sludge complex (Fe-AnGS) was used in microbial electrolysis cells (MEC) to enhance the direct interspecies electron transfer (DIET) pathway for biogas production. Fe-AnGS improved magnetization and conductivity, and enriched specific electrogenic microorganisms. It also increased the gene expression for carbon dioxide reduction and enhanced methane production. Inoculation of Fe-AnGS in MEC established and enhanced the DIET pathway for methane production.
Article
Food Science & Technology
Bao-Hong Lee, Cheng-Hao Huang, Tsung-Yu Liu, Jung-Shiang Liou, Chih-Yao Hou, Wei-Hsuan Hsu
Summary: The flavor of coffee is affected by the fermentation process, which is influenced by factors such as temperature, oxygen concentration, and microbial diversity. This study examined the microbial diversity in coffee beans undergoing anaerobic fermentation at different temperatures and durations. The results showed that Acetobacter dominated at higher temperatures, while Leuconostoc and Gluconobacter were dominant at lower temperatures. This study provides valuable insights into the microbial diversity involved in the anaerobic fermentation of coffee beans and its potential impact on coffee quality.
Article
Environmental Sciences
Georgia Gatidou, Charis G. Samanides, Michalis S. Fountoulakis, Ioannis Vyrides
Summary: In this study, the treatment of undiluted real bilge water using a membraneless single chamber Microbial Electrolysis Cell (MEC) with Anaerobic Granular Sludge (AGS) was examined for the first time. It was found that the undiluted bilge water had a higher impact on acetoclastic methanogens compared to hydrogenotrophic methanogens. However, dilution of bilge water allowed for its biodegradation. The coupling of MEC with AGS showed promising performance for bilge water treatment.
Article
Engineering, Environmental
Alma Siggins, Florence Abram, Mark G. Healy
JOURNAL OF HAZARDOUS MATERIALS
(2020)
Article
Biochemical Research Methods
Bernardino Machado-Moreira, Silvia Monteiro, Ricardo Santos, Antonio Martinez-Murcia, Andreja Rajkovic, Nada Smigic, Karl G. Richards, Florence Abram, Catherine M. Burgess
JOURNAL OF MICROBIOLOGICAL METHODS
(2020)
Article
Soil Science
Fabiana S. Paula, Enrico Tatti, Camilla Thorn, Florence Abram, Jude Wilson, Vincent O'Flaherty
SOIL BIOLOGY & BIOCHEMISTRY
(2020)
Article
Engineering, Environmental
Alma Siggins, Camilla Thorn, Mark G. Healy, Florence Abram
Summary: This study investigated the potential for environmental micro-organisms to establish a TCE-dechlorinating biofilm on biochar, using a packed column system containing herbal pomace and spruce biochar. The results showed that biochar was capable of supporting a dechlorinating biofilm to promote bioremediation of TCE, with TCE removal rates greater than 99.7% observed.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Microbiology
Anna Christine Trego, Paul G. McAteer, Corine Nzeteu, Therese Mahony, Florence Abram, Umer Zeeshan Ijaz, Vincent O'Flaherty
Summary: The study utilized null-model approaches to investigate community assembly mechanisms in the built environment, focusing on biological wastewater treatment. Significant differences in diversity were observed between floating and settled granules, with both stochastic and deterministic processes playing important roles in community assembly. Homogeneous selection was identified as the primary mechanism, with dispersal processes also contributing. The analysis highlighted changes in microbial community composition during process disturbances, emphasizing the importance of certain groups for process stability.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Bernardino Machado-Moreira, Brijesh K. Tiwari, Karl G. Richards, Florence Abram, Catherine M. Burgess
Summary: This study evaluated the disinfecting ability of plasma activated water (PAW) on alfalfa and mung bean seeds, showing that PAW can effectively reduce pathogenic microorganisms while not affecting the germination and growth rate of the sprouts. Additionally, combining PAW treatment with ultrasound can enhance antimicrobial activity, presenting potential for improving produce safety.
Article
Food Science & Technology
Bernardino Machado-Moreira, Karl Richards, Florence Abram, Fiona Brennan, Michael Gaffney, Catherine M. Burgess
Summary: This study found that both E. coli and L. innocua strains can persist on lettuce plants for up to 28 days after contamination, and in water for up to 28 days. This highlights the importance of ensuring high quality irrigation water to prevent multiple plant contamination events.
Article
Green & Sustainable Science & Technology
Corine Orline Nzeteu, Fabiana Coelho, Anna Christine Trego, Florence Abram, Javier Ramiro-Garcia, Lara Paulo, Vincent O'Flaherty
Summary: The efficient production of caproic acid can be achieved by manipulating the inoculum and adjusting the concentration and ratio of lactic acid and butyric acid. A threshold concentration of lactic acid to butyric acid was found, above or below which the selectivity for caproic acid is reduced.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Biochemical Research Methods
Kevin McDonnell, Florence Abram, Enda Howley
Summary: This study focuses on using machine learning models to identify amino acids in mass spectrometry spectra and proposes a new encoding module. By evaluating the proposed model in real and artificial data with different noise and missing peptide peaks, it is found that the model performs best among others. The study also discusses the inclusion of additional features and the issue with using AUC as a metric in the encoding modules.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Environmental Sciences
Parvin Hasani Zadeh, Fernando G. Fermoso, Gavin Collins, Antonio Serrano, Simon Mills, Florence Abram
Summary: Harnessing microbial capabilities for metal recovery from secondary waste sources is an eco-friendly and sustainable approach. Soluble microbial products (SMP) and extracellular polymeric substances (EPS) are important for remediation and recovery of metals. Microorganisms can regulate the content and composition of EPS and SMP in response to metal stress to increase their capacity for metal binding. Investigating the metal binding affinity of these compounds under metal stress conditions is crucial for selective metal recovery applications.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Soil Science
Matthias Waibel, Kevin McDonnell, Maria Tuohy, Sally Shirran, Sylvia Synowsky, Barry Thornton, Eric Paterson, Fiona Brennan, Florence Abram
Summary: Soil organic matter (SOM) is complex and important for providing nutrients to plants. Understanding SOM utilisation processes can improve fertiliser management for plant growth and reduce environmental losses. Metaproteomics can characterise protein profiles and provide insights into SOM microbial decomposition mechanisms. This study applied different extraction methods to recover SOM with different characteristics in two soil types and analysed peptide identification using liquid chromatography and tandem mass spectrometry. The results showed contrasting protein and humic substance content in different extracts, and diverse peptide hits associated with Proteobacteria and derived taxa. This work suggests areas for optimisation in chromatography and mass spectrometry to characterise SOM-associated metaproteomes.
EUROPEAN JOURNAL OF SOIL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Kevin McDonnell, Enda Howley, Florence Abram
Summary: Proteins are crucial for living cells and proteomics, the study of their expression, has diverse applications. Peptide identification is typically done by matching mass spectra to a protein database, but de novo methods can also be used. This study critically analyzes the use of artificial data for training and evaluating de novo peptide identification algorithms.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Kevin McDonnell, Enda Howley, Florence Abram
Summary: Proteomics is a technique used to study system-wide protein expression, which has wide ranging applications and impacts every area of biology. De novo peptide sequencing, a popular method, is improving with the integration of machine learning. This research evaluates two algorithms for de novo peptide sequencing and explores the characteristics of tandem mass spectra. The study highlights the challenges of missing cleavage sites and noise, and provides recommendations for algorithm improvements.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Food Science & Technology
Lauren Russell, Paul Whyte, Annetta Zintl, Stephen V. Gordon, Bryan Markey, Theo de Waal, Stephen Nolan, Vincent O'Flaherty, Florence Abram, Karl Richards, Owen Fenton, Declan Bolton
Summary: This study examined the survival of various bacteria in sandy and clay loam soils when applied in bovine slurry or digestate, finding that soil texture and application material did not significantly affect survival rates for most bacteria.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2022)
Article
Agricultural Engineering
Paul G. McAteer, Anna Christine Trego, Camilla Thorn, Therese Mahony, Florence Abram, Vincent O'Flaherty
BIORESOURCE TECHNOLOGY
(2020)