Ester M Eckert

Ester M Eckert
Italian National Research Council | CNR · CNR-IRSA

Doctor of Philosophy

About

75
Publications
14,621
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1,814
Citations
Citations since 2017
62 Research Items
1716 Citations
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20172018201920202021202220230100200300400
20172018201920202021202220230100200300400
20172018201920202021202220230100200300400
Additional affiliations
January 2011 - December 2013
University of Zurich

Publications

Publications (75)
Article
The impact of Fenton oxidation (FO) and Air stripping (AS) pre-treatments on the bacterial community of a biological activated sludge (B-AS) process for the co-treatment of mature landfill leachate (MLL) and urban wastewater (UWW) was assessed. In this work high-throughput sequencing was used to identify changes in the composition of the bacterial...
Article
Stochastic or deterministic processes control the bacterial community assembly in waters and their understanding is a fundamental question to correctly manage aquatic environments exposed to the release of antibiotics from anthropogenic sources. It has been suggested that microdiversity (i.e. the rare biosphere) convers freshwater communities with...
Article
The risk for human health posed by polluted aquatic environments, and especially those carrying antibiotic resistance genes (ARGs) of clinical interest, is still debated. This is because of our limited knowledge of the dynamics of antimicrobial resistance in the environment, the selection mechanisms underlying the spread of ARGs, and the ecological...
Article
Full-text available
The holobiont concept places emphasis on the strict relationship between a host and its associated microbiome, with several studies supporting a strong effect of the quality of the microbiome on the host fitness. The generalities of the holobiont have been questioned for several invertebrates, including zooplankton. Here we assess the role of host...
Article
Seas and oceans are a global reservoir of antibiotic resistance genes (ARGs). Only a few studies investigated the dynamics of ARGs along the water column of the Black Sea, a unique environment, with a peculiar geology, biology and history of anthropogenic pollution. In this study, we analyzed metagenomic data from two sampling campaigns (2013 and 2...
Article
We investigated the performance of a heterogeneous Fenton-like reaction (ZVI-Fenton, i.e., ZVI + H2O2, where ZVI = zero-valent iron) towards the removal of potentially pathogenic bacteria in wastewater (WW). The effectiveness of the process was investigated towards live bacteria (measured by flow cytometry) as well as potentially pathogenic bacteri...
Chapter
The temporal dynamics of coastal planktic communities can be disclosed through DNA metabarcoding on the filters of reverse-osmosis desalination plants. Here, we describe the steps that are necessary to process the filters in order to create the subsamples used for DNA extraction and the bioinformatic pipeline to perform the first exploratory analys...
Article
Full-text available
We report for the first time the occurrence of at least two species of the phylum Gnathostomulida in the Southern Ocean, along the shores of the Ross Sea in Antarctica. At least one species for each of the orders of the phylum (Filospermoidea and Bursovaginoidea) was found using both morphological inspection and DNA metabarcoding of the shallow mar...
Article
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This study shows that Escherichia coli can be temporarily enriched in zooplankton under natural conditions and that these bacteria can belong to different phylogroups and sequence types (STs), including environmental, clinical, and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically, the two is...
Article
Although abundant and chemically peculiar, tyre wear microplastic particles (TWP) and their impact on the microbial communities in water are largely understudied. We tested in laboratory based semi-continuous cultures the impact of TWP and of polyethylene terephthalate (PET) derived particles (following a gradient of relative abundance) on the path...
Preprint
Full-text available
This study shows that Escherichia coli can be temporarily enriched in zooplankton in natural conditions and that these bacteria can belong to different phylogroups and sequence types including environmental as well as clinical and animal isolates. We isolated 10 E. coli strains and sequenced the genomes of two of them. Phylogenetically the two isol...
Article
Wastewater treatment plants (WWTPs) are among the main hotspots of antibiotic resistance genes (ARGs) in the environment. Previously, we demonstrated that by increasing anthropogenic pollution the antibiotic resistome persisted in the microbial community of rivers and lakes, independently by changes in community composition. In this study we reanal...
Article
Full-text available
Aquatic organisms rely on microbial symbionts for coping with various challenges they encounter during stress and for defending themselves against predators, pathogens and para- sites. Microbial symbionts are also often indispensable for the host’s development or life cycle com- pletion. Many aquatic ecosystems are currently under pressure due to d...
Article
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Transparent Exopolymer Particles (TEP) play an important role in the organic carbon cycle of many aquatic systems but the production and distribution of TEP have been studied mainly in the marine environment, neglecting the large oligotrophic lakes. We selected Lake Maggiore, one of the most important freshwater reserve in Northern Italy, to study...
Article
Microplastic Particles (MPs) are ubiquitous pollutants widely found in aquatic ecosystems. Although MPs are mostly retained in wastewater treatment plants (WWTPs), a high number of MPs reaches the open waters potentially contributing to the spread of pathogenic bacteria and antibiotic resistance genes in the environment. Nowadays, a limited number...
Article
Aim The long history of isolation of the Antarctic continent, coupled with the harsh ecological conditions of freezing temperatures, could affect the patterns of genetic diversity in the organisms living there. We aim (a) to test whether such pattern can be seen in a mitochondrial marker of bdelloid rotifers, a group of microscopic aquatic and limn...
Article
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De novo OTU picking from large metabarcoding read datasets is at the same time a current and a complex task, and several methods coexist to perform it. We present here the outcome of a collective project developed within Working Group on « Data Analysis and Storage » in DNAqua.net. Our aim has been to organize a thorough comparison of OTU compositi...
Article
The association with microbes in plants and animals is known to be beneficial for the host’s survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the patter...
Article
One of the main requirements of any sound biological monitoring is the availability of long term and, possibly, temporal data with a high resolution. This is often difficult to be achieved, especially in Antarctica, due to a variety of logistic constraints, which make continuous sampling and monitoring activities generally unfeasible. Here we focus...
Article
Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are worldwide considered as emerging contaminants of large interest, and a primary threat to human health. It is becoming clear that the environment plays a central role in the transmission, spread, and evolution of antibiotic resistance. Although marine systems have been la...
Article
Full-text available
The diffusion of antibiotic resistance determinants in different environments, e.g., soil and water, has become a public concern for global health and food safety and many efforts are currently devoted to clarify this complex ecological and evolutionary issue. Horizontal gene transfer (HGT) has an important role in the spread of antibiotic resistan...
Article
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Picocyanobacteria of the genus Synechococcus are major contributors to global primary production and nutrient cycles due to their oxygenic photoautotrophy, their abundance, and the extensive distribution made possible by their wide-ranging biochemical capabilities. The recent recovery and isolation of strains from the deep euxinic waters of the Bla...
Article
The efficiency of a new Advanced Oxidation Process (AOP), namely the photo Fenton like process UV-C/H2O2/IDS-Cu, in removing determinants of antibiotic resistance and pathogenic bacteria was compared to a consolidated AOP (namely UV-C/H2O2) in a secondary treated municipal WasteWater (WW). A reductionist experimental laboratory-based approach was a...
Article
Microorganisms in coastal sediments are fundamental for ecosystem functioning, and regulate processes relevant in global biogeochemical cycles. Still, our understanding of the effects anthropogenic perturbation and pollution can have on microbial communities in marine sediments is limited. We surveyed the microbial diversity, and the occurrence and...
Article
Full-text available
Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofau...
Article
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Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data wit...
Article
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Natural water bodies contain physically interconnected habitats suitable for microbes, such as different water layers and substrates for biofilms. Yet, little is known on the extent to which microbial communities are shared between such habitats and whether differences and similarities are consistent between sites. Here we explicitly tested hypothe...
Article
Lakes are exposed to anthropogenic pollution including the release of allochthonous bacteria into their waters. Antibiotic resistance genes (ARGs) stabilize in bacterial communities of temperate lakes, and these environments act as long-term reservoirs of ARGs. Still, it is not clear if the stabilization of the ARGs is caused by a periodical introd...
Article
Superstition has it that tossing coins into wells or fountains brings good luck, thereby causing a potential accumulation of microbially contaminated metal particles in the water. Here, we characterized the microbiota and the resistance profile in biofilm on such coins and their surrounding sediments. The study site was a tidal marine lake within a...
Article
Full-text available
The beta lactamase gene blaCTX-M, responsible of the resistance to cephalosporins, has been detected in microbes from hospitals to open waters. We studied the seasonality and stability of blaCTX-M in Lake Maggiore over 3 years and the role of potential inputs of allochthonous bacteria and/or antibiotic pollution in promoting its occurrence. blaCTX-...
Article
Full-text available
Transparent exopolymer particles (TEP) are mainly acidic polysaccharides directly or indirectly formed by phytoplankton and bacteria. These particles are often colonized by picoplankton and considered a hot spot for microbial activity. Recent studies suggested an important role of Synechococcus in TEP production found in lakes and prompted us to fu...
Article
We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water...
Chapter
The Lanzarote and Chinijo Islands UNESCO Global Geopark hosts one of the most extensive and diverse volcanic anchialine ecosystems in the world, consisting of water bodies with marine origin that penetrated inland through coastal crevicular systems. Marine infiltration is facilitated by the low rainfall and the permeability of the coastal terrains....
Article
Treated wastewater discharged into the environment acts as a disturbance of the natural microbial communities in terms of taxonomic composition and of functional gene pool, including antibiotic resistance genes. We tested whether stochastic and heterogeneous site-specific trajectories or generalities, potentially driven by deterministic processes,...
Article
Full-text available
The Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000 m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells...
Article
Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with pot...
Article
Full-text available
The spread of antibiotic-resistant bacteria is a threatening risk for human health at a global scale. Improved knowledge on the cycle of antibiotic resistance spread between human and the environment is a major requirement for the management of the current crisis. Compared to the well-studied cycle in clinical settings much less is known about the...
Article
The identification of biological diversity through DNA barcoding and metabarcoding of the organisms living in the field has the potential to revolutionise the way biological surveys and monitoring are performed. Yet, we still do not know if the current representativeness of the reference database of DNA sequence data is sufficient to allow such app...
Article
The massive use of antimicrobials in animal farming is considered as the greatest contributor to the phenomenon of antimicrobial resistant bacteria (ARB) presence in food of animal origin. Nevertheless, sewage from treated animals may impact on vegetables grown on fertilized fields, but it is largely unknown whether and to what extent ARB are trans...
Article
Antibiotic resistance is a rising threat for human health. Although in clinical settings and terrestrial environments the rise of antibiotic resistant bacteria is well documented, their dissemination and spread in the marine environment, covering almost two‐thirds of the Earth's surface, is still poorly understood. In this study, the presence and a...
Article
Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plan...
Article
Macroalgal competition can indirectly influence the health of corals and their response to changing environmental conditions by altering their associated bacterial community. However, the effect of macroalgae on the composition of epilithic microbial biofilms, an important determinant of coral recruitment, is poorly known. In the back-reefs of Moor...
Article
Full-text available
Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here t...
Chapter
Aquatic microbial community can be defined as an assemblage of co-occurring, and potentially interacting, microbes, present in a defined habitat in space and time. Despite the small size, microorganisms are key elements for the ecological dynamics of the biosphere. They are not only the most diffused life forms; they are also characterized by an in...
Article
Plastic pollution is a major global concern with several million microplastic particles entering every day freshwater ecosystems via wastewater discharge. Microplastic particles stimulate biofilm formation (plastisphere) throughout the water column and have the potential to affect microbial community structure if they accumulate in pelagic waters,...
Article
Full-text available
Sediment resuspension represents a key process in all natural aquatic systems, owing to its role in nutrient cycling and transport of potential contaminants. Although suspended solids are generally accepted as an important quality parameter, current monitoring programs cover quantitative aspects only. Established methodologies do not provide inform...
Article
Full-text available
Planktonic cyanobacteria belonging to the genus Synechococcus are ubiquitously distributed in marine and fresh waters, substantially contributing to total carbon fixation on a global scale. While their ecological relevance is acknowledged, increasing resolution in molecular techniques allows disentangling cyanobacteria's role at the micro-scale, wh...
Article
Peracetic acid (PAA) is an organic compound used efficiently as disinfectant in wastewater treatments. Yet, at low doses it may cause selection; thus, the effect of low doses of PAA on Enterococcus faecium as a proxy of human-related microbial waste was evaluated. Bacteria were treated with increasing doses of PAA (from 0 to 25 mg L⁻¹ min) and incu...
Technical Report
Full-text available
The report includes and examines the list of taxonomists from IAMC (Institute for Coastal Marine Environment), IGG (Institute of Geosciences and Earth Resources), ISE (Institute of Ecosystem Study), and ISMAR (Institute of Marine Sciences), who responded to the Taxonomy Census 2016, their scientific publications and the number of taxa described new...
Article
Full-text available
Type II Toxin-Antitoxin systems (TAs), known for their presence in virulent and antibiotic resistant bacterial strains, were recently identified in Salmonella enterica isolates. However, the relationships between the presence of TAs (ccdAB and vapBC) and the epidemiological and genetic features of different non-typhoidal Salmonella serovars are lar...
Article
The impact of human activities on the spread and on the persistence of antibiotic resistances in the environment is still far from being understood. The natural background of resistances is influenced by human activities, and the wastewater treatment plants (WWTPs) are among the main sources of the release of antibiotic resistance into the environm...
Article
Full-text available
The annually recurrent spring phytoplankton blooms in freshwater lakes initiate pronounced successions of planktonic ciliate species. Although there is considerable knowledge on the taxonomic diversity of these ciliates, their species-specific interactions with other microorganisms are still not well understood. Here we present the succession patte...
Article
Full-text available
Antibiotic resistant bacteria are found in most environments, especially in highly anthropized waters. A direct correlation between human activities (e.g., pollution) and spread and persistence of antibiotic resistant bacteria (ARB) and resistance genes (ARGs) within the resident bacterial communities appears more and more obvious. Furthermore, the...
Article
The fate of antibiotic resistance genes (ARGs) in environmental microbial communities is of primary concern as prodromal of a potential transfer to pathogenic bacteria. Although of diverse origin, the persistence of ARGs in aquatic environments is highly influenced by anthropic activities, allowing potential control actions in well-studied environm...
Article
Full-text available
The amount of information that is available on 16S rRNA sequences for prokaryotes thanks to high-throughput sequencing could allow a better understanding of diversity. Nevertheless, the application of predetermined threshold in genetic distances to identify units of diversity (Operative Taxonomic Units, OTUs) may provide biased results. Here we tes...
Article
Full-text available
The identification of interacting species and elucidation of their mode of interaction may be crucial to understand ecosystem-level processes. We analysed the activity and identity of bacterial epibionts in cultures of Daphnia galeata and of natural daphnid populations. Epibiotic bacteria incorporated considerable amounts of dissolved organic carbo...
Article
Full-text available
The interest for microorganisms inhabiting the hypolimnion and for their role in biogeochemical cycles of lakes is considerable, but knowledge is far from complete. The presence of chemolithoautotrophic Bacteria and mesophilic Archaea ( e.g ., Thaumarchaeota) assimilating inorganic carbon in the deep hypolimnion of lakes has been ascertained. We me...
Article
The rise of grazing resistant planktonic bacteria in freshwater lakes during vernal phytoplankton blooms is favoured by predation of heterotrophic nanoflagellates (HNF). The spring period is also characterized by increased availability of organic carbon species that are in parts derived from cellular debris generated during bacterivory or viral lys...
Article
The vernal successions of phytoplankton, heterotrophic nanoflagellates (HNF) and viruses in temperate lakes result in alternating dominance of top-down and bottom-up factors on the bacterial community. This may lead to asynchronous blooms of bacteria with different life strategies and affect the channelling of particular components of the dissolved...

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Projects (2)
Project
The 4th International Symposium on Anchialine Ecosystems aims at gathering scientists and students from throughout the world who dedicate their studies to any aspect concerning anchialine environments. Our multidisciplinary gathering will integrate fields of Biology, Systematics and Evolution, Biogeography, Geomicrobiology, Ecology, Geology, Hydrology, Paleontology, and Archeology
Project
This is a 3 years project funded by Italian Ministry of Foreign Affair (MAE) in the context of bilateral cooperation Italy-China. The full title of the project is “Efficiency of different disinfection processes in the removal of antibiotic resistance determinants in experimental pilot systems and full-scale WWTPs” and the main objective is the investigation of different disinfection systems in the removal of antibiotic determinants (i.e. antibiotic resistant bacteria, ARB; and antibiotic resistance genes, ARGs) from wastewater in settings with high human impact. Accordingly, conventional (chlorination, UV radiation and peracetic acid) and new (advanced oxidation processes) disinfection treatment methods will be evaluated at lab, pilot and full scale. The Italian research team includes (i) dr. Gianluca Corno (coordinator), Andrea Di Cesare, Cristiana Callieri and Ester Eckert from Institute of Ecosystem Study, Italian National Research Council (CNR) - Verbania, (ii) prof. Luigi Rizzo from Department of Civil Engineering, University of Salerno, (iii) dr.Gianmarco Luna and Grazia Quero from Institute Marine Sciences, CNR - Venice. The Chinese research team includes prof. Ying Yang (coordinator), Shichun Zou and Baowei Chen from School of Marine Sciences, Sun Yat-sen University Guangzhou.