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Article ; Online: Shared and contrasting associations in the dynamic nano‐ and picoplankton communities of two close but contrasting sites from the Bay of Biscay

Garate, Leire / Alonso‐Sáez, Laura / Revilla, Marta / Logares, Ramiro / Lanzén, Anders

Environmental Microbiology. 2022 Dec., v. 24, no. 12 p.6052-6070

2022

Abstract: Pico‐ and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic ... ...

Abstract	Pico‐ and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterization of these is critical for understanding and predicting ecosystem functioning under anthropogenic pressures. We used environmental DNA metabarcoding across a 6‐year time series to explore the structure and seasonality of pico‐ and nanoplankton communities in two sites of the Bay of Biscay, one coastal and one offshore, and construct association networks to reveal potential keystone and connector taxa. Temporal trends in alpha diversity were similar between the two sites, and concurrent communities more similar than within the same site at different times. However, we found differences between the network topologies of the two sites, with both shared and site‐specific keystones and connectors. For example, Micromonas, with lower abundance in the offshore site is a keystone here, indicating a stronger effect of associations such as resource competition. This study provides an example of how time series and association network analysis can reveal how similar communities may function differently despite being geographically close.
Keywords	Archaea ; DNA barcoding ; ecosystems ; environmental DNA ; microbiology ; plankton ; species diversity ; time series analysis ; Bay of Biscay
Language	English
Dates of publication	2022-12
Size	p. 6052-6070.
Publishing place	John Wiley & Sons, Inc.
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16153
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Shared and contrasting associations in the dynamic nano- and picoplankton communities of two close but contrasting sites from the Bay of Biscay.

Garate, Leire / Alonso-Sáez, Laura / Revilla, Marta / Logares, Ramiro / Lanzén, Anders

Environmental microbiology

2022 Volume 24, Issue 12, Page(s) 6052–6070

Abstract: Pico- and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic ... ...

Abstract	Pico- and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterization of these is critical for understanding and predicting ecosystem functioning under anthropogenic pressures. We used environmental DNA metabarcoding across a 6-year time series to explore the structure and seasonality of pico- and nanoplankton communities in two sites of the Bay of Biscay, one coastal and one offshore, and construct association networks to reveal potential keystone and connector taxa. Temporal trends in alpha diversity were similar between the two sites, and concurrent communities more similar than within the same site at different times. However, we found differences between the network topologies of the two sites, with both shared and site-specific keystones and connectors. For example, Micromonas, with lower abundance in the offshore site is a keystone here, indicating a stronger effect of associations such as resource competition. This study provides an example of how time series and association network analysis can reveal how similar communities may function differently despite being geographically close.
MeSH term(s)	Ecosystem ; Bays ; Plankton/genetics ; Archaea/genetics ; Eukaryota/genetics
Language	English
Publishing date	2022-08-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.16153
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Identifying Lethal Dependencies with HUGE Predictive Power.

Gimeno, Marian / San José-Enériz, Edurne / Rubio, Angel / Garate, Leire / Miranda, Estíbaliz / Castilla, Carlos / Agirre, Xabier / Prosper, Felipe / Carazo, Fernando

Cancers

2022 Volume 14, Issue 13

Abstract: Recent functional genomic screens—such as CRISPR-Cas9 or RNAi screening—have fostered a new wave of targeted treatments based on the concept of synthetic lethality. These approaches identified LEthal Dependencies (LEDs) by estimating the effect of ... ...

Abstract	Recent functional genomic screens—such as CRISPR-Cas9 or RNAi screening—have fostered a new wave of targeted treatments based on the concept of synthetic lethality. These approaches identified LEthal Dependencies (LEDs) by estimating the effect of genetic events on cell viability. The multiple-hypothesis problem is related to a large number of gene knockouts limiting the statistical power of these studies. Here, we show that predictions of LEDs from functional screens can be dramatically improved by incorporating the “HUb effect in Genetic Essentiality” (HUGE) of gene alterations. We analyze three recent genome-wide loss-of-function screens—Project Score, CERES score and DEMETER score—identifying LEDs with 75 times larger statistical power than using state-of-the-art methods. Using acute myeloid leukemia, breast cancer, lung adenocarcinoma and colon adenocarcinoma as disease models, we validate that our predictions are enriched in a recent harmonized knowledge base of clinical interpretations of somatic genomic variants in cancer (AUROC > 0.87). Our approach is effective even in tumors with large genetic heterogeneity such as acute myeloid leukemia, where we identified LEDs not recalled by previous pipelines, including FLT3-mutant genotypes sensitive to FLT3 inhibitors. Interestingly, in-vitro validations confirm lethal dependencies of either NRAS or PTPN11 depending on the NRAS mutational status. HUGE will hopefully help discover novel genetic dependencies amenable for precision-targeted therapies in cancer. All the graphs showing lethal dependencies for the 19 tumor types analyzed can be visualized in an interactive tool.
Language	English
Publishing date	2022-07-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers14133251
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Molecular phylogenies confirm the presence of two cryptic

Uriz, Maria J / Garate, Leire / Agell, Gemma

PeerJ

2017 Volume 5, Page(s) e2958

Abstract: Background: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. : Methods: Hemimycale columella: Results: ... ...

Abstract	Background: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Methods: Hemimycale columella Results: The several phylogenetic reconstructions retrieved both Conclusions: A new family (Hemimycalidae) including the genus
Language	English
Publishing date	2017-03-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.2958
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Redescription and establishment of a holotype and three paratypes for the species

Uriz, Maria J / Garate, Leire / Agell, Gemma

PeerJ

2017 Volume 5, Page(s) e3426

Abstract: Background: In a recent paper, we described a new sponge species named : Results: The present work fulfills the requirements of the ICZN by designating a holotype, three paratypes and the type locality for the new ... ...

Abstract	Background: In a recent paper, we described a new sponge species named Results: The present work fulfills the requirements of the ICZN by designating a holotype, three paratypes and the type locality for the new species
Language	English
Publishing date	2017-06-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3426
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Contrasting biological features in morphologically cryptic Mediterranean sponges.

Garate, Leire / Blanquer, Andrea / Uriz, Maria J

PeerJ

2017 Volume 5, Page(s) e3490

Abstract: Sponges are key organisms in the marine benthos where they play essential roles in ecological processes such as creating new niches, competition for resources, and organic matter recycling. Despite the increasing number of taxonomical studies, many ... ...

Abstract	Sponges are key organisms in the marine benthos where they play essential roles in ecological processes such as creating new niches, competition for resources, and organic matter recycling. Despite the increasing number of taxonomical studies, many sponge species remain hidden, whether unnoticed or cryptic. The occurrence of cryptic species may confound ecological studies by underestimating biodiversity. In this study, we monitored photographically growth, fusions, fissions, and survival of two morphologically cryptic species
Language	English
Publishing date	2017-06-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.3490
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identifying Lethal Dependencies with HUGE Predictive Power

Marian Gimeno / Edurne San José-Enériz / Angel Rubio / Leire Garate / Estíbaliz Miranda / Carlos Castilla / Xabier Agirre / Felipe Prosper / Fernando Carazo

Cancers, Vol 14, Iss 3251, p

2022 Volume 3251

Abstract: Recent functional genomic screens—such as CRISPR -Cas9 or RNAi screening—have fostered a new wave of targeted treatments based on the concept of synthetic lethality. These approaches identified LEthal Dependencies (LEDs) by estimating the effect of ... ...

Abstract	Recent functional genomic screens—such as CRISPR -Cas9 or RNAi screening—have fostered a new wave of targeted treatments based on the concept of synthetic lethality. These approaches identified LEthal Dependencies (LEDs) by estimating the effect of genetic events on cell viability. The multiple-hypothesis problem is related to a large number of gene knockouts limiting the statistical power of these studies. Here, we show that predictions of LEDs from functional screens can be dramatically improved by incorporating the “HUb effect in Genetic Essentiality” (HUGE) of gene alterations. We analyze three recent genome-wide loss-of-function screens—Project Score, CERES score and DEMETER score—identifying LEDs with 75 times larger statistical power than using state-of-the-art methods. Using acute myeloid leukemia, breast cancer, lung adenocarcinoma and colon adenocarcinoma as disease models, we validate that our predictions are enriched in a recent harmonized knowledge base of clinical interpretations of somatic genomic variants in cancer (AUROC > 0.87). Our approach is effective even in tumors with large genetic heterogeneity such as acute myeloid leukemia, where we identified LEDs not recalled by previous pipelines, including FLT3 -mutant genotypes sensitive to FLT3 inhibitors. Interestingly, in-vitro validations confirm lethal dependencies of either NRAS or PTPN11 depending on the NRAS mutational status. HUGE will hopefully help discover novel genetic dependencies amenable for precision-targeted therapies in cancer. All the graphs showing lethal dependencies for the 19 tumor types analyzed can be visualized in an interactive tool.
Keywords	CRISPR -Cas9 screening ; precision medicine ; synthetic lethality ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
Subject code	006
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Redescription and establishment of a holotype and three paratypes for the species Hemimycale mediterranea sp. nov.

Maria J. Uriz / Leire Garate / Gemma Agell

PeerJ, Vol 5, p e

2017 Volume 3426

Abstract: ... Garate & Agell, 2017. However, we failed to designate a holotype and a type locality, as required ...

Abstract	Background In a recent paper, we described a new sponge species named Hemimycale mediterranea Uriz, Garate & Agell, 2017. However, we failed to designate a holotype and a type locality, as required by the International Commission on Zoological Nomenclature (ICZN). Although the validity of the previous conclusions remains unchanged, the species name cannot be considered available according to ICZN regulations until a holotype is designated. Results The present work fulfills the requirements of the ICZN by designating a holotype, three paratypes and the type locality for the new species Hemimycale mediterranea and has been registered in ZooBank.
Keywords	Hemimycale mediterranea ; Holotype ; Paratypes ; Nomenclature ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Contrasting biological features in morphologically cryptic Mediterranean sponges

Leire Garate / Andrea Blanquer / Maria J. Uriz

PeerJ, Vol 5, p e

2017 Volume 3490

Abstract: ... Hemimycale mediterranea Uriz, Garate & Agell, 2017 and H. columella (Bowerbank, 1874). Additionally ...

Abstract	Sponges are key organisms in the marine benthos where they play essential roles in ecological processes such as creating new niches, competition for resources, and organic matter recycling. Despite the increasing number of taxonomical studies, many sponge species remain hidden, whether unnoticed or cryptic. The occurrence of cryptic species may confound ecological studies by underestimating biodiversity. In this study, we monitored photographically growth, fusions, fissions, and survival of two morphologically cryptic species Hemimycale mediterranea Uriz, Garate & Agell, 2017 and H. columella (Bowerbank, 1874). Additionally, we characterized the main environmental factors of the corresponding species habitats, trying to ascertain whether some abiotic factors were correlated with the distribution of these species. Sponge monitoring was performed monthly. Seawater samples were collected the same monitoring days in the vicinity of the target sponges. Results showed contrasting growth and survival patterns for each species: H. mediterranea totally disappeared after larval release while 64% of individuals of H. columella survived the entire two years we monitored. The species also differed in the number of fissions and fusions. These events were evenly distributed throughout the year in the H. mediterranea population but concentrated in cold months in H. columella. No measured environmental factor correlated with H. mediterranea growth rates, while temperature and dissolved organic nitrogen were negatively correlated with H. columella growth rates. The strong differences in depth distribution, survival, growth, fusions, and fissions found between these two cryptic species, highlights the importance of untangling cryptic species before ecological studies are performed in particular when these species share geographical distribution.
Keywords	Sponges ; Survival ; Life span ; Growth ; Fusions ; Fissions ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	590 ; 580
Language	English
Publishing date	2017-06-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae

Maria J. Uriz / Leire Garate / Gemma Agell

PeerJ, Vol 5, p e

Poecilosclerida)

2017 Volume 2958

Abstract: Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, ... ...

Abstract	Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean Hemimycale also suggest that Hemimycale ...
Keywords	Biodiversity ; Molecular taxonomy ; Morphological taxonomy ; Cryptic species ; Marine sponges ; Phylogeny ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	590 ; 580
Language	English
Publishing date	2017-03-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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