18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York

Ingala, Melissa R.; Werner, Irena E.; Fitzgerald, Allison M.; Naro‐Maciel, Eugênia

doi:10.3897/mbmg.5.69691

Cited by 4 publications

(4 citation statements)

References 44 publications

(65 reference statements)

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“…Indeed, even though the microbial eukaryote diversity is more studied now especially with the use of metabarcoding, their study through other approaches such as metagenomics and single cell genomics is less developed especially due the complexity of their genomes (e.g., large intergenic regions, introns, repetitive DNA) making them very difficult to analyse. However, this imbalance will hopefully tend to diminish with the high number of ongoing projects targeting this group (e.g., the PELAGICS project covering 70 European lakes and targeting both bacteria and eukaryotes) and the advance in the analysis of eukaryotic genomics data (Bailet et al, 2019; Cahoon et al, 2018; Delmont et al, 2022; Ingala et al, 2021; Matsuoka et al, 2019; Meredith et al, 2021; Valentin et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

Biderre‐Petit

Charvy

Bronner

et al. 2022

Molecular Ecology Resources

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Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high‐throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater –omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG‐RAST repositories) covering all sequence‐based ‐omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta‐analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).

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Section: Discussionmentioning

confidence: 99%

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

Biderre‐Petit

Charvy

Bronner

et al. 2022

Molecular Ecology Resources

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“…1, Table 1), were quantified using a Qubit Fluorometer according to manufacturer instructions (Thermo Scientific, USA) and then sent to MRDNA (www. mrdnalab.com, Molecular Research LP, Shallowater, TX, USA) for purification, PCR amplification, sequencing, and analysis using standard and previously described procedures (Dowd et al 2008;Ingala et al 2021). First, preliminary runs were conducted and examined, and once deemed successful for satisfactory amplification of organisms of interest (e.g.…”

Section: Dna Sequencingmentioning

confidence: 99%

“…The uniquely tagged PCR products were pooled together in equal proportions based on DNA concentrations and electrophoresis band characteristics, and purified using Ampure XP beads (Agencourt Bioscience, USA) with a ratio of beads to PCR products of 0.75× following Illumina guidelines. They were then ligated to Illumina adapters using the Illumina TruSeq protocol, and sequenced on an Illumina MiSeq platform using a paired-end 2 × 300bp procedure (Dowd et al 2008;Naro-Maciel et al 2020;Ingala et al 2021).…”

Section: Dna Sequencingmentioning

confidence: 99%

“…Both seawater and ARMS samples were examined using 18S rDNA, a promising genetic marker offering advantages of broad amplification across eukaryotic kingdoms, a rapidly growing reference database, and wide use (Taberlet et al 2018). In this work the V1-V3 segment, with demonstrated utility for uncovering a broad range of aquatic taxa (Ingala et al 2021), was sequenced. Our analysis of preliminary data showed that V1-V3 captured groups of interest, including corals and algae, while also contributing information about a less frequently sequenced 18S gene region.…”

Section: Introductionmentioning

confidence: 99%

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18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific

Reid¹,

Servis²,

Timmers³

et al. 2022

MBMG

Self Cite

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To address the global biodiversity crisis, standardized data that are rapidly obtainable through minimally invasive means are needed for documenting change and informing conservation within threatened and diverse systems, such as coral reefs. In this data paper, we describe 18S rRNA gene amplicon data (V1–V3 region) generated from samples collected to begin characterizing coral reef eukaryotic community composition at the Palmyra Atoll National Wildlife Refuge in the Central Pacific Ocean. Sixteen samples were obtained across four sample types: sediments from two sieved fractions (100–500 μm, n = 3; 500 μm-2 mm, n = 3) and sessile material scrapings (n = 3) from Autonomous Reef Monitoring Structures (ARMS) sampled in 2015, as well as seawater from 2012 (n = 7). After filtering and contaminant removal, 3,861 Amplicon Sequence Variants (ASVs) were produced from 1,062,238 reads. The rarefaction curves demonstrated adequate sampling depth, and communities grouped by sample type. The dominant orders across samples were polychaete worms (Eunicida), demosponges (Poecilosclerida), and bryozoans (Cheilostomatida). The ten most common orders in terms of relative abundance comprised ~60% of all sequences and 23% of ASVs, and included reef-building crustose coralline algae (CCA; Corallinophycidae) and stony corals (Scleractinia), two taxa associated with healthy reefs. Highlighting the need for further study, ~21% of the ASVs were identified as uncultured, incertae sedis, or not assigned to phylum or order. This data paper presents the first 18S rDNA survey at Palmyra Atoll and serves as a baseline for biodiversity assessment, monitoring, and conservation of this remote and pristine ecosystem.

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Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream

Cohen,

Johnke,

Abed-Rabbo

et al. 2024

FEMS Microbiology Ecology

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Wastewater pollution of water resources takes a heavy toll on humans and on the environment. In highly polluted water bodies, self-purification is impaired, as the capacity of the riverine microbes to regenerate the ecosystem is overwhelmed. To date, information on the composition, dynamics, and functions of the microbial communities in highly sewage-impacted rivers is limited in particular in arid and semi-arid environments. In this year-long study of the highly sewage-impacted Al-Nar/Kidron stream in the Barr al-Khalil/Judean Desert east of Jerusalem we show, using 16S and 18S rRNA gene-based community analysis and targeted QPCR, that both the bacterial and micro-eukaryotic communities, while abundant, exhibited low stability and diversity. Organic compounds hydrolyzers, and nitrogen and phosphorus recyclers were lacking, pointing at a reduced potential for regeneration. Furthermore, facultative bacterial predators were almost absent, and the obligate predators Bdellovibrio-and-like-organisms were found at very low abundance. Finally, the micro-eukaryotic predatory community differed from those of other freshwater environments. The lack of essential biochemical functions may explain the stream's inability to self-purify while the very low levels of bacterial predators and the disturbed assemblages of micro-eukaryote predators present in Al-Nar/Kidron may contribute to community instability and disfunction.

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18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York

Cited by 4 publications

References 44 publications

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific

Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream

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18S rRNA amplicon sequence data (V1–V3) of the Bronx river estuary, New York

Cited by 4 publications

References 44 publications

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes

﻿18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific

Unbalanced predatory communities and a lack of microbial degraders characterize the microbiota of a highly sewage-polluted Eastern-Mediterranean stream

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18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific