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Article ; Online: Where do the antibiotic resistance genes come from? A modulated analysis of sources and loads of resistances in Lake Maggiore.

Di Cesare, Andrea / Mammola, Stefano / Sabatino, Raffaella / Fontaneto, Diego / Eckert, Ester M / Rogora, Michela / Tonsi, Tiziana / Corno, Gianluca

FEMS microbiology ecology

2024 Volume 100, Issue 4

Abstract: Antibiotic resistance genes (ARGs) are abundant in aquatic ecosystems affected by human activities. Understanding the fate of ARGs across different ecosystems is essential because of the significant role aquatic environments play in the cycle of ... ...

Abstract	Antibiotic resistance genes (ARGs) are abundant in aquatic ecosystems affected by human activities. Understanding the fate of ARGs across different ecosystems is essential because of the significant role aquatic environments play in the cycle of antibiotic resistance. We quantified selected ARGs in Lake Maggiore, its main tributaries, and the effluent of the main wastewater treatment plant (WWTP) discharging directly into the lake. We linked their dynamics to the different anthropogenic impacts in each tributary's watershed. The dynamics of tetA in the lake were influenced by those of the rivers and the WWTP effluent, and by the concentration of N-NH4, related to anthropogenic pollution, while sul2 abundance in the lake was not influenced by any water inflow. The dynamics of the different ARGs varied across the different rivers. Rivers with watersheds characterized by high population density, touristic activities, and secondary industries released more ARGs, while ermB correlated with higher numbers of primary industries. This study suggests a limited contribution of treated wastewater in the spread of ARGs, indicating as prevalent origin other sources of pollution, calling for a reconsideration on what are considered the major sources of ARGs into the environment.
MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Lakes ; Ecosystem ; Drug Resistance, Microbial/genetics ; Rivers
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	283722-5
ISSN	1574-6941 ; 0168-6496
ISSN (online)	1574-6941
ISSN	0168-6496
DOI	10.1093/femsec/fiae025
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Article ; Online: Metabarcoding to monitor the crustacean zooplankton of a lake improves when using a reference DNA library from local samples

Giuseppe Garlasché / Giulia Borgomaneiro / Roberta Piscia / Marina Manca / Ester M. Eckert / Diego Fontaneto

Journal of Limnology, Vol 82, Iss

2023 Volume 1

Abstract: Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive ... ...

Abstract	Biodiversity surveys through morphology provide invaluable data to inform biological monitoring efforts, involving specialised taxonomic skills that are not always available. The revolution brought by the advent of metabarcoding associated to massive sequencing is currently seen as a potential advance, even if different approaches may often provide different results. Here we test if reliable results from metabarcoding can be obtained by i) basing the analyses on a detailed knowledge of the local diversity from morphology, ii) applying tools from DNA taxonomy to create a local reference library, ii) developing custom primers, taking as example the crustacean zooplankton of a subalpine lake in Northern Italy, Lake Maggiore. We support the idea that occurrences from metabarcoding can be reliable, especially with targeted primers, but we confirm that read numbers from massive sequencing could not be related to abundance of individuals in our analyses. Data from metabarcoding can thus be used to reliably monitor species occurrence in the lake, but not changes in abundance.
Keywords	Cladocera ; Copepoda ; DNA taxonomy ; Lake Maggiore ; metabarcoding ; zooplankton ; Geography. Anthropology. Recreation ; G ; Physical geography ; GB3-5030 ; Environmental sciences ; GE1-350
Subject code	333
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	PAGEPress Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment.

Eckert, Ester M / Anicic, Nikoleta / Fontaneto, Diego

Molecular ecology

2021 Volume 30, Issue 6, Page(s) 1545–1558

Abstract: The association with microbes in plants and animals is known to be beneficial for 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 ...

Abstract	The association with microbes in plants and animals is known to be beneficial for 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 pattern could be due to co-evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species-specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of "core" microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co-evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host-microbiome association to originate and persist.
MeSH term(s)	Animals ; Anthozoa ; Bacteria/genetics ; Fresh Water ; Microbiota/genetics ; Zooplankton/genetics
Language	English
Publishing date	2021-02-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15815
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Article: Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment

Eckert, Ester M / Anicic, Nikoleta / Fontaneto, Diego

Molecular ecology. 2021 Mar., v. 30, no. 6

2021

Abstract	The association with microbes in plants and animals is known to be beneficial for 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 pattern could be due to co‐evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species‐specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of “core” microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co‐evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host‐microbiome association to originate and persist.
Keywords	Cladocera ; Copepoda ; Rotifera ; coevolution ; ecology ; freshwater ; microbiome ; temperature ; zooplankton
Language	English
Dates of publication	2021-03
Size	p. 1545-1558.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.15815
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Article ; Online: Increased similarity of aquatic bacterial communities of different origin after antibiotic disturbance.

Eckert, Ester M / Galafassi, Silvia / Bastidas Navarro, Marcela / Di Cesare, Andrea / Corno, Gianluca

Environmental pollution (Barking, Essex : 1987)

2022 Volume 316, Issue Pt 2, Page(s) 120568

Abstract: 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 ... ...

Abstract	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 stability, meaning that previously rare taxa bloom when the community is disturbed. Since there might be a seed bank of similar, but not abundant, bacterial taxa in different waters, we tested whether a disturbance by an antibiotic cocktail would increase similarity in bacterial communities from different freshwater systems (a wastewater effluent and two lakes). In a continuous culture set-up in chemostats, we show that disturbance with antibiotics causes communities from different environments to become more similar. Once the antibiotic pressure is released the communities tend to become more dissimilar again. This shows that there is a similar shift in community composition even in waters from very different origins when they are disturbed by antibiotics, even at low concentrations. Antibiotics impact the bacterial communities at the cell and the community level, independently by the original degree of anthropogenic stress they are adapted to, altering the original phenotypes, genotypes, and the relations between bacteria.
MeSH term(s)	Anti-Bacterial Agents/toxicity ; Microbiota ; Bacteria/genetics ; Lakes/microbiology ; Waste Water
Chemical Substances	Anti-Bacterial Agents ; Waste Water
Language	English
Publishing date	2022-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2022.120568
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Article ; Online: PET particles raise microbiological concerns for human health while tyre wear microplastic particles potentially affect ecosystem services in waters.

Sathicq, Maria Belen / Sabatino, Raffaella / Di Cesare, Andrea / Eckert, Ester M / Fontaneto, Diego / Rogora, Michela / Corno, Gianluca

Journal of hazardous materials

2022 Volume 429, Page(s) 128397

Abstract: 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 ... ...

Abstract	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 pathobiome (the group of potential human pathogenic bacteria) of a freshwater microbial community exposed to contamination by the effluent of a urban wastewater treatment plant, for a period of 28 days. We could define the modulated impact of the two types of microplastic particles: while PET does not favour bacterial growth, it offers a refuge to several potential pathogens of allochthonous origin (from the treated sewage effluent), TWP act as an additional carbon source, promoting the development and the massive growth of a biofilm composed by fast-growing bacterial genera including species potentially harmful and competitive in abating biodiversity in surface waters. Our results demonstrate the different ecological role and impact on freshwater environments of TWP and PET particles, and the need to approach the study of this pollutant not as a whole, but considering the origin and the chemical composition of the different particles.
MeSH term(s)	Ecosystem ; Environmental Monitoring ; Humans ; Microbiota ; Microplastics/toxicity ; Plastics/toxicity ; Polyethylene Terephthalates ; Water Pollutants, Chemical/analysis ; Water Pollutants, Chemical/toxicity
Chemical Substances	Microplastics ; Plastics ; Polyethylene Terephthalates ; Water Pollutants, Chemical
Language	English
Publishing date	2022-01-31
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2022.128397
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: First Record of the Phylum Gnathostomulida in the Southern Ocean

Wolfgang Sterrer / Martin V. Sørensen / Matteo Cecchetto / Alejandro Martínez / Raffaella Sabatino / Ester M. Eckert / Diego Fontaneto / Stefano Schiaparelli

Diversity, Vol 14, Iss 382, p

2022 Volume 382

Abstract: 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 ... ...

Abstract	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 marine sediments collected with a Van Veen grab or by scuba diving in the area facing the Italian research station “Mario Zucchelli”.
Keywords	Antarctica ; Gnathostomulida ; Ross Sea ; Ross Sea Region Marine Protected Area ; species distribution ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Class 1 integron and related antimicrobial resistance gene dynamics along a complex freshwater system affected by different anthropogenic pressures.

Corno, Gianluca / Ghaly, Timothy / Sabatino, Raffaella / Eckert, Ester M / Galafassi, Silvia / Gillings, Michael R / Di Cesare, Andrea

Environmental pollution (Barking, Essex : 1987)

2022 Volume 316, Issue Pt 2, Page(s) 120601

Abstract: 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 ... ...

Abstract	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 factors potentially favoring their return to humans. The Class 1 integron is one of the most effective platforms for the dissemination of ARGs. In this study we investigated a freshwater system consisting of a lake-river-lake continuum, determining the abundance of class 1 integrons and their associated ARGs by a modulated metagenomic approach. Bacterial abundance and community composition were used to identify the potential carriers of class 1 integrons and their associated ARGs over a period of six months. Class 1 integrons and their ARG cargoes were significantly more abundant in riverine sampling sites receiving treated wastewater. Further, class 1 integrons carried ARGs ranked at the highest risk for human health (e.g., catB genes), in particular, genes encoding resistance to aminoglycosides. Genera of potential pathogens, such as Pseudomonas and Escherichia-Shigella, were correlated with class 1 integrons. The lake-river-lake system demonstrated a clear relationship between the integrase gene of class 1 integrons (intI1) and anthropogenic impact, but also a strong environmental filtering that favored the elimination of intI1 once the human derived stressors were reduced. Overall, the results of this study underline the role class 1 integrons as proxy of anthropogenic pollution and suggest this genetic platform as an important driver of aminoglycoside resistance genes, including high risk ARGs, of potential concern for human health.
MeSH term(s)	Humans ; Integrons/genetics ; Anti-Bacterial Agents/pharmacology ; Anthropogenic Effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Lakes
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	280652-6
ISSN	1873-6424 ; 0013-9327 ; 0269-7491
ISSN (online)	1873-6424
ISSN	0013-9327 ; 0269-7491
DOI	10.1016/j.envpol.2022.120601
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Article: PET particles raise microbiological concerns for human health while tyre wear microplastic particles potentially affect ecosystem services in waters

Sathicq, Maria Belen / Sabatino, Raffaella / Di Cesare, Andrea / Eckert, Ester M. / Fontaneto, Diego / Rogora, Michela / Corno, Gianluca

Journal of hazardous materials. 2022 May 05, v. 429

2022

Abstract	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 pathobiome (the group of potential human pathogenic bacteria) of a freshwater microbial community exposed to contamination by the effluent of a urban wastewater treatment plant, for a period of 28 days. We could define the modulated impact of the two types of microplastic particles: while PET does not favour bacterial growth, it offers a refuge to several potential pathogens of allochthonous origin (from the treated sewage effluent), TWP act as an additional carbon source, promoting the development and the massive growth of a biofilm composed by fast-growing bacterial genera including species potentially harmful and competitive in abating biodiversity in surface waters. Our results demonstrate the different ecological role and impact on freshwater environments of TWP and PET particles, and the need to approach the study of this pollutant not as a whole, but considering the origin and the chemical composition of the different particles.
Keywords	bacterial growth ; biodiversity ; biofilm ; carbon ; chemical composition ; ecosystems ; freshwater ; human health ; microbial communities ; microplastics ; polyethylene terephthalates ; sewage effluent ; sewage treatment ; tires ; wastewater treatment
Language	English
Dates of publication	2022-0505
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1491302-1
ISSN	1873-3336 ; 0304-3894
ISSN (online)	1873-3336
ISSN	0304-3894
DOI	10.1016/j.jhazmat.2022.128397
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Article ; Online: Bacterial epibionts of Daphnia: a potential route for the transfer of dissolved organic carbon in freshwater food webs.

Eckert, Ester M / Pernthaler, Jakob

The ISME journal

2014 Volume 8, Issue 9, Page(s) 1808–1819

Abstract: 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 ... ...

Abstract	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 carbon (DOC), as estimated via uptake of tritiated leucine: three times more tracer was consumed by microbes on a single Daphnia than in 1 ml of lake water. However, there was virtually no incorporation if daphnids were anaesthetised, suggesting that their filtration activity was essential for this process. Microbial DOC uptake could predominantly be assigned to microbes that were located on the filter combs of daphnids, where the passage of water would ensure a continuously high DOC supply. Most of these bacteria were Betaproteobacteria from the genus Limnohabitans. Specifically, we identified a monophyletic cluster harbouring Limnohabitans planktonicus that encompassed sequence types from D. galeata cultures, from the gut of Daphnia magna and from daphnids of Lake Zurich. Our results suggest that the epibiotic growth of bacteria related to Limnohabitans on Daphnia spp. may be a widespread and rather common phenomenon. Moreover, most of the observed DOC flux to Daphnia in fact does not seem to be associated with the crustacean biomass itself but with its epibiotic microflora. The unexplored physical association of daphnids with heterotrophic bacteria may have considerable implications for our understanding of carbon transfer in freshwater food webs, that is, a trophic 'shortcut' between microbial DOC uptake and predation by fish.
MeSH term(s)	Animals ; Bacteria/classification ; Bacteria/isolation & purification ; Bacteria/metabolism ; Carbon/metabolism ; Comamonadaceae/isolation & purification ; Comamonadaceae/metabolism ; Daphnia/microbiology ; Female ; Food Chain ; Lakes/microbiology ; Leucine/metabolism
Chemical Substances	Carbon (7440-44-0) ; Leucine (GMW67QNF9C)
Language	English
Publishing date	2014-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/ismej.2014.39
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