Article
Biology
Matt Lloyd Jones, Damian William Rivett, Alberto Pascual-Garcia, Thomas Bell
Summary: This study found that naturally occurring microbial communities with well-growing combinations of bacteria can drive invasion resistance, mirroring results seen in artificial communities grown in the lab. The results suggest that productivity is a key factor underpinning invasion resistance in naturally-occurring microbial communities.
Article
Environmental Sciences
Pinja Nakki, Eeva Eronen-Rasimus, Hermanni Kaartokallio, Harri Kankaanpaa, Outi Setala, Emil Vahtera, Maiju Lehtiniemi
Summary: Biodegradable plastic alternatives have potential impacts on marine ecosystems, especially in terms of sorption of polycyclic aromatic hydrocarbons (PAHs) and plastic bacterial biofilms. Certain biodegradable plastics may harbor bioplastic-degrading bacterial communities, and the capacity for PAH sorption varies between polymer types.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Infectious Diseases
Lamprini Karygianni, Pune N. Paque, Thomas Attin, Thomas Thurnheer
Summary: Biofilm virulence relies on the bacterial cell surrounding the biofilm matrix, targeting nucleic acids or proteins can efficiently control biofilm formation. The study found that using proteinase K significantly reduced the quantity of Candida albicans and decreased biofilm thickness, while DNase I had no significant effect on total bacterial growth. Targeting biofilm proteins with proteinase K shows promise as an adjunctive tool for biofilm control.
Article
Engineering, Environmental
Mohd Hafizuddin Muhamad, Siti Rozaimah Sheikh Abdullah, Hassimi Abu Hasan, Siti Nur Hatika Abu Bakar, Setyo Budi Kurniawan, Nur 'Izzati Ismail
Summary: The study found that the hybrid treatment system of MM-SBBR is highly effective in removing PCP from wastewater, with a diverse presence of PCP resistant bacteria enriching in the reactor, contributing to the enhanced removal of PCP.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Article
Environmental Sciences
Kun Guo, Naicheng Wu, Wei Li, Annette Baattrup-Pedersen, Tenna Riis
Summary: Stream biofilms are complex aggregates of diverse organism groups that are essential for global carbon and nitrogen cycles. The study found that specific phyla dominated the prokaryotic and eukaryotic communities at most sites, with diversity peaking in July and January. Hydrological and physicochemical variables were significant factors in explaining community composition, but a large portion of variation remained unexplained, likely due to unmeasured factors such as light intensity and biological interactions. A multitrophic level perspective is suggested for future biofilm studies to capture the complexity of trophic and non-trophic interactions.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biodiversity Conservation
M. Laporte, C. S. Berger, E. Garcia-Machado, G. Cote, O. Morissette, L. Bernatchez
Summary: The study found that the use of environmental DNA (eDNA) metabarcoding can accurately assess the composition and spatial distribution of freshwater fish communities. In a transplant experiment in the St. Lawrence River, the eDNA of brown trout was detected at five locations up to 5,000 meters from the cage, but only one sampling location downstream from the cage showed a significant impact on community composition. Cluster analysis confirmed the impact of the brown trout eDNA on community composition, separating this location from others. No evidence of transport effect of brown trout eDNA on fish community composition was observed in other sampling locations.
ECOLOGICAL INDICATORS
(2022)
Article
Environmental Sciences
Zebing Zhu, Lili Shan, Xinyun Zhang, Fengping Hu, Dan Zhong, Yixing Yuan, Jie Zhang
Summary: The study investigated the formation of multi-species biofilms in simulated DWDS and found that community-intrinsic properties could affect the formation of multi-species biofilms. The resistance of multi-species biofilms to chlorine was influenced by specific bacteria, with some promoting growth and others inhibiting it. The study concluded that community-intrinsic properties were maintained at low disinfectant concentrations but weakened at higher concentrations, affecting the resistance of microbial communities to disinfectants.
Review
Oceanography
Stefan Thiele, Anna Vader, Stuart Thomson, Karoline Saubrekka, Elzbieta Petelenz, Hilde Rief Armo, Oliver Mueller, Lasse Olsen, Gunnar Bratbak, Lise Ovreas
Summary: Climate change in the Arctic affects marine ecosystems, especially phytoplankton bloom dynamics, which in turn impact bacterial and archaeal communities. This study compared the composition of these communities from the Barents Sea to the Arctic Ocean north of Svalbard over three summers using 16S rRNA gene sequencing. The results showed variations in the dominant taxa in surface waters between years, potentially due to different phytoplankton bloom stages and carbon source availability. Deep water communities were consistently dominated by specific taxa. Changes in phytoplankton blooms can influence bacterial and archaeal communities and marine carbon cycling in surface waters.
PROGRESS IN OCEANOGRAPHY
(2023)
Article
Ecology
Rita L. Grunberg
Summary: The study investigated the concordance of community similarity patterns among parasites, fish hosts, and environmental factors. It found concordance in community composition patterns between parasites and fish hosts, but not in community abundance patterns. Additionally, concordance was observed between fish communities and the physical river environment.
FRESHWATER BIOLOGY
(2021)
Article
Environmental Sciences
Theodor Sperlea, Jan Philip Schenk, Hagen Dressler, Daniela Beisser, Georges Hattab, Jens Boenigk, Dominik Heider
Summary: Microbes play a vital role in element cycling and ecosystem functioning, yet there are still many unanswered questions about their role in ecology. This study analyzes the relationship between lake microbiomes and the land cover surrounding the lakes using machine learning methods. The results show that the microbial community of the lakes is significantly correlated with herbaceous and open spaces, but the correlation with land cover categories is generally lower than with physico-chemical parameters. The integration of land cover and physico-chemical bioindicators provides insights into the environmental drivers of the lake microbial community composition and allows for the study of the ecosystem's structure from the standpoint of the microbiome.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Stefan Thiele, Anna Vader, Stuart Thomson, Karoline Saubrekka, Elzbieta Petelenz, Oliver Mueller, Gunnar Bratbak, Lise ovreas
Summary: In this study, the bacterial and archaeal community in the Barents Sea and Arctic Ocean were investigated using 16S rRNA metabarcoding, revealing a seasonal shift from carbon cycling in spring and summer to nitrogen cycling in winter. These findings provide important baseline data for studying the effects of climate change on these processes.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Engineering, Environmental
Charlotte J. Beloe, Mark Anthony Browne, Emma L. Johnston
Summary: Pathogens and polymers can both cause diseases, and researchers are increasingly studying the potential of polymers to transfer pathogenic bacteria and cause disease in new environments. By integrating frameworks from ecology and epidemiology, the researchers reviewed 111 papers and found a lack of evidence for polymers as preferential vectors for bacterial colonization and disease transmission. There is a need for structured surveys and experiments to better understand the risks and impacts of pathogens on polymers.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Ecology
Neal D. Mundahl, Erik D. Mundahl
Summary: The study revealed that agriculture-dominated karst areas had significant negative impacts on stream habitats and biota, with over half of the sites showing degradation. Wide riparian buffers and avoidance of groundwater influence have allowed for some recovery in certain stream reaches, but more buffers and soil conservation practices are needed to protect additional stream segments and biota. New stream buffer laws have resulted in establishment of vegetated buffers at all study sites, potentially leading to improved habitat and biotic communities in the future.
ECOLOGICAL PROCESSES
(2022)
Editorial Material
Biodiversity Conservation
Daniel C. Carvalho, Cecilia G. Leal
Summary: The paper by Coutant et al. (2022) is an important advancement in understanding the species distribution patterns and drivers of biodiversity in the Neotropical realm, particularly in the Amazon. By quantifying the contribution of environmental and anthropogenic factors, the study provides valuable insights for future monitoring programs and identifies priority areas for conservation.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Microbiology
Nicholas A. Lesniak, Alyxandria M. Schubert, Kaitlin J. Flynn, Jhansi L. Leslie, Hamide Sinani, Ingrid L. Bergin, Vincent B. Young, Patrick D. Schloss
Summary: Clostridioides difficile colonization can lead to a range of infection severities, from mild diarrhea to life-threatening conditions. While factors such as patient age, blood cell count, and C. difficile characteristics have been associated with disease severity, the role of specific gut bacteria in influencing severity is unclear. This study demonstrates that different gut bacterial communities can contribute to variations in Clostridioides difficile infection outcomes. Certain bacterial groups were associated with more severe outcomes, while others were associated with milder outcomes. Incorporating gut bacterial community data into severity models may aid in identifying at-risk patients and improving interventions.
Article
Biochemistry & Molecular Biology
Lorenzo Pin, Alexander Eiler, Stefano Fazi, Nikolai Friberg
Summary: Microbial communities play a crucial role in river ecosystems, but biomonitoring tools relying on prokaryotes are still lacking. This study compared the efficacy of metabarcoding and CARD-FISH techniques in detecting changes in microbial community structure in rivers. Metabarcoding showed higher accuracy in differentiating regions and river systems compared to CARD-FISH, making it a faster and more reliable option for large-scale bio-assessment.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Engineering, Environmental
M. Sagova-Mareckova, J. Boenigk, A. Bouchez, K. Cermakova, T. Chonova, T. Cordier, U. Eisendle, T. Elersek, S. Fazi, T. Fleituch, L. Fruhe, M. Gajdosova, N. Graupner, A. Haegerbaeumer, A. -M. Kelly, J. Kopecky, F. Leese, P. Noges, S. Orlic, K. Panksep, J. Pawlowski, A. Petrusek, J. J. Piggott, J. C. S. Rusch, R. Salis, J. Schenk, K. Simek, A. Stovicek, D. A. Strand, M. I. Vasquez, T. Vralstad, S. Zlatkovic, M. Zupancic, T. Stoeck
Summary: The importance and potential of utilizing microbes as bioindicators in water quality monitoring are discussed in this review. Molecular methods have revealed microbial diversity and new metabolic pathways, which can improve our understanding of environmental processes, serving as a solid foundation for novel monitoring programs. Microbial community dynamics are highlighted as a missing link essential for comprehending rapid changes in aquatic ecosystem structure and function, suggesting they should be addressed in future environmental monitoring of freshwater ecosystems.
Article
Environmental Sciences
Rita Masciale, Stefano Amalfitano, Eleonora Frollini, Stefano Ghergo, Marco Melita, Daniele Parrone, Elisabetta Preziosi, Michele Vurro, Annamaria Zoppini, Giuseppe Passarella
Summary: This study in the Apulia region of Italy analyzes the natural background levels of geochemical parameters in groundwater, finding that certain inorganic compounds exceed national standards, likely due to salt contamination along the coast, agricultural practices, or natural reasons. By excluding monitoring sites impacted by evident anthropic activities, the NBL values were determined, which were higher than the legal limits.
Article
Microbiology
Sarah Zecchin, Simona Crognale, Patrizia Zaccheo, Stefano Fazi, Stefano Amalfitano, Barbara Casentini, Matteo Callegari, Raffaella Zanchi, Gian Attilio Sacchi, Simona Rossetti, Lucia Cavalca
Summary: Arsenic mobilization in groundwater systems is influenced by diverse microorganisms and physicochemical factors, with diverse microbial communities found in the Po Plain. The oxidation state of arsenic is a key driver in shaping these communities, with the oxidation rate linearly correlated to As(III) concentration. These findings provide valuable insights for biotechnology-based arsenic bioremediation efforts.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Environmental Sciences
Ana Rotter, Michele Barbier, Francesco Bertoni, Atle M. Bones, M. Leonor Cancela, Jens Carlsson, Maria F. Carvalho, Marta Ceglowska, Jeronimo Chirivella-Martorell, Meltem Conk Dalay, Mercedes Cueto, Thanos Dailianis, Irem Deniz, Ana R. Diaz-Marrero, Dragana Drakulovic, Arita Dubnika, Christine Edwards, Hjoerleifur Einarsson, Aysegul Erdogan, Orhan Tufan Eroldogan, David Ezra, Stefano Fazi, Richard J. FitzGerald, Laura M. Gargan, Susana P. Gaudencio, Marija Gligora Udovic, Nadica Ivosevic DeNardis, Rosa Jonsdottir, Marija Katarzyte, Katja Klun, Jonne Kotta, Leila Ktari, Zrinka Ljubesic, Lada Lukic Bilela, Manolis Mandalakis, Alexia Massa-Gallucci, Inga Matijosyte, Hanna Mazur-Marzec, Mohamed Mehiri, Soren Laurentius Nielsen, Lucie Novoveska, Donata Overlinge, Giuseppe Perale, Praveen Ramasamy, Celine Rebours, Thorsten Reinsch, Fernando Reyes, Baruch Rinkevich, Johan Robbens, Eric Roettinger, Vita Rudovica, Jerica Sabotid, Ivo Safarik, Siret Talve, Deniz Tasdemir, Xenia Theodotou Schneider, Olivier P. Thomas, Anna Torunska-Sitarz, Giovanna Cristina Varese, Marlen Vasquez
Summary: Coastal countries have traditionally relied on marine resources for various needs, while modern societies have increased demands for diverse products leading to the emergence of blue biotechnology. This field offers opportunities for commercial interests in pharmaceuticals, cosmetics, food, and related industries. Exploration of marine resources and their potential applications in various sectors are highlighted, along with the importance of legislation, funding, communication, and stakeholder engagement in the development of marine biotechnology.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Environmental Sciences
Maria Papale, Carmen Rizzo, Gabriella Caruso, Stefano Amalfitano, Giovanna Maimone, Stefano Miserocchi, Rosabruna La Ferla, Paul Eric Aspholm, Franco Decembrini, Filippo Azzaro, Antonella Conte, Marco Graziano, Alessandro Ciro Rappazzo, Angelina Lo Giudice, Maurizio Azzaro
Summary: This study investigated the structural and functional traits of microbial communities in the Arctic Pasvik River during the ice-melting season, revealing how seasonal ice melting impacts microbial community composition and activity levels. The results provide evidence on the adaptability and response of riverine microbial communities to seasonal ice melting in glacial-fed aquatic ecosystems.
Article
Biology
Stefano Fazi, Stefano Amalfitano, Stefania Venturi, Nic Pacini, Eusebi Vazquez, Lydia A. Olaka, Franco Tassi, Simona Crognale, Peter Herzsprung, Oliver J. Lechtenfeld, Jacopo Cabassi, Francesco Capecchiacci, Simona Rossetti, Michail M. Yakimov, Orlando Vaselli, David M. Harper, Andrea Butturini
Summary: An extraordinarily high biogenic methane concentration was detected in surface waters of Lake Sonachi, Kenya. Gas chromatography and microbiome profiling revealed that these high concentrations are associated with cyanobacterial blooms and provide insights into methanogenesis in meromictic soda lakes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Analytical
Carmela Maria Montone, Benedetta Giannelli Moneta, Sara Elsa Aita, Federico Aulenta, Chiara Cavaliere, Andrea Cerrato, Stefano Fazi, Aldo Lagana, Valerio Paolini, Francesco Petracchini, Susy Piovesana, Anna Laura Capriotti
Summary: An untargeted approach using UHPLC-HRMS/MS was employed to analyze contaminants in surface water, with optimized SPE conditions for 30 target compounds. River water samples near Rome were analyzed, resulting in identification of 241 compounds, mainly pharmaceuticals, by matching tandem mass spectra with mass spectral library.
MICROCHEMICAL JOURNAL
(2022)
Review
Environmental Sciences
J. Pawlowski, K. Bruce, K. Panksep, F. Aguirre, S. Amalfitano, L. Apotheloz-Perret-Gentil, T. Baussant, A. Bouchez, L. Carugati, K. Cermakova, T. Cordier, C. Corinaldesi, F. O. Costa, R. Danovaro, A. Dell'Anno, S. Duarte, U. Eisendle, B. J. D. Ferrari, F. Frontalini, L. Fruehe, A. Haegerbaeumer, V Kisand, A. Krolicka, A. Lanzen, F. Leese, F. Lejzerowicz, E. Lyautey, I Macek, M. Sagova-Mareckova, J. K. Pearman, X. Pochon, T. Stoeck, R. Vivien, A. Weigand, S. Fazi
Summary: Environmental DNA (eDNA) metabarcoding is transforming aquatic biomonitoring by sequencing DNA/RNA to identify entire communities within a targeted group. Most studies have focused on water eDNA and macroinvertebrate samples, but eDNA metabarcoding has also been applied to soft sediment samples, especially for microbial or meiofaunal communities. Compared to traditional methods, eDNA metabarcoding offers advantages for assessing sediment environmental quality. However, there is a need for standardization to improve robustness and comparability. This review focuses on sampling, preservation, and DNA extraction protocols for sediment eDNA metabarcoding, aiming to identify best practices and promote harmonization for future benthic monitoring.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Microbiology
Maria Papale, Carmen Rizzo, Stefania Giannarelli, Gabriella Caruso, Stefano Amalfitano, Paul Eric Aspholm, Giovanna Maimone, Stefano Miserocchi, Alessandro Ciro Rappazzo, Angelina Lo Giudice, Maurizio Azzaro
Summary: This study aims to study the riverine benthic microbial community in the Paasvik River and evaluate its ecological role in relation to contamination levels. The results show that bacterial diversity in the river sediments is influenced by micro-niche conditions, with differences in the abundance of taxa involved in the C, Fe, and N cycles, as well as organic pollutant and toxic compound degradation.
Article
Biology
Stefania Venturi, Simona Crognale, Francesco Di Benedetto, Giordano Montegrossi, Barbara Casentini, Stefano Amalfitano, Tommaso Baroni, Simona Rossetti, Franco Tassi, Francesco Capecchiacci, Orlando Vaselli, Stefano Fazi
Summary: This study provides a comprehensive characterization of an active hydrothermal travertine system, revealing the influence of both abiotic and biotic processes on mineralization and mineral fabric formation. The results show that microbial activity plays a role in shaping mineralogical features and driving calcite redissolution processes, while also indirectly participating in mineral deposition.
Article
Environmental Sciences
Marco Melita, Stefano Amalfitano, Elisabetta Preziosi, Stefano Ghergo, Eleonora Frollini, Daniele Parrone, Annamaria Zoppini
Summary: Groundwater, as an important freshwater resource, is home to specialized microbial communities that play fundamental roles in ecosystem services. This study aimed to investigate the relationship between groundwater hydrogeochemical properties and microbial community traits in a volcanic unconfined aquifer, moderately influenced by human activities. The results revealed distinct oxidizing and reducing groundwater conditions, which had significant effects on microbial metabolic potential and functional diversity.
Article
Environmental Sciences
Francesca Di Pippo, Simona Crognale, Caterina Levantesi, Luca Vitanza, Maria Sighicelli, Loris Pietrelli, Stefania Di Vito, Stefano Amalfitano, Simona Rossetti
Summary: This study provides new insights into microbial diversity and biofilm structure on plastic microspheres in lake waters. The presence of eukaryotic core members and their relationship with biofilm-forming bacteria on plastic microspheres were investigated for the first time. The study also suggests that plastic microspheres may serve as potential vectors for the dispersal of harmful organisms and antibiotic resistance genes.
ENVIRONMENTAL POLLUTION
(2022)
