Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime

Sousa, António G G; Tomasino, Maria Paola; Duarte, Pedro; Fernández‐Méndez, Mar; Assmy, Philipp; Ribeiro, Hugo; Surkont, Jarosław; Leite, Ricardo B.; Pereira-Leal, José B.; Torgo, Luı́s; Magalhães, Catarina

doi:10.1007/s00248-018-01314-2

Cited by 29 publications

(47 citation statements)

References 125 publications

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“…DNA was extracted from 0.5 g (w.w.) of each homogenized soil sample, using the PowerSoil™ DNA isolation kit (MoBio, Carlsbad, CA, USA), according to the manufacturer's instructions. The 16S rRNA gene was amplified with the prokaryotic primer pair 515F-Y (5 -GTGYCAGCMGCCGCGGTAA-3 ) [31] and 926R (5 -CCGYCAATTYMTTTRAGTTT-3 ) [32] in order to be paired-end sequenced on an Illumina MiSeq platform using V3 Chemistry (Illumina), according to Sousa and co-workers [33]. Sequencing was carried out by LGC Genomics (LGC Genomics GmbH, Berlin, Germany).…”

Section: Dna Extraction and 16s Rrna Gene Amplification And Sequencingmentioning

confidence: 99%

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica

et al. 2020

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Bacterial natural products (NPs) are still a major source of new drug leads. Polyketides (PKs) and non-ribosomal peptides (NRP) are two pharmaceutically important families of NPs and recent studies have revealed Antarctica to harbor endemic polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, likely to be involved in the production of novel metabolites. Despite this, the diversity of secondary metabolites genes in Antarctica is still poorly explored. In this study, a computational bioprospection approach was employed to study the diversity and identity of PKS and NRPS genes to one of the most biodiverse areas in maritime Antarctica-Maxwell Bay. Amplicon sequencing of soil samples targeting ketosynthase (KS) and adenylation (AD) domains of PKS and NRPS genes, respectively, revealed abundant and unexplored chemical diversity in this peninsula. About 20% of AD domain sequences were only distantly related to characterized biosynthetic genes. Several PKS and NRPS genes were found to be closely associated to recently described metabolites including those from uncultured and candidate phyla. The combination of new approaches in computational biology and new culture-dependent and -independent strategies is thus critical for the recovery of the potential novel chemistry encoded in Antarctica microorganisms. target the highly conserved ketosynthase (KS) and adenylation (AD) domains of PKS and NRPS genes, respectively. A growing number of studies have employed the PCR-based sequence tag approach to uncover PKS and NRPS gene diversity across different environmental microbiomes [7][8][9].Extreme environments, such as Antarctica, have the potential to reveal novel molecules since they are still a poorly explored source of chemical scaffolds and novel chemical diversity [10,11]. As such, metabarcoding approaches to study PKS and NRPS diversity in Antarctic ecosystems represent a simple and effective strategy to understand the biosynthetic potential of a large number of sampling sites [7]. A couple of such studies have been carried out very recently in Antarctica [12,13] revealing that soils at different Antarctica locations harbor multiple endemic PKS and NRPS genes, likely to be involved in the synthesis of new chemical diversity. In Antarctic soils, the percentage of yet-uncultured genera is expected to be much higher [14] than the 82% described for general soils [15]. A considerable fraction of such uncultured bacteria corresponds to members of the NP-rich Actinobacteria [16,17] and Cyanobacteria [18,19] phyla.King George Island is one of the largest ice-free and biodiverse areas in maritime Antarctica [20]. It harbors a high density of scientific stations, particularly in Maxwell Bay [21], where most of terrestrial biology research takes place. Although bacterial diversity studies have been conducted in this area [22,23], the diversity of bacterial biosynthetic genes has not been a target of study. Here, we perform a detailed study on soil samples from Maxwell Bay, with the main goal of assessing the...

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Section: Dna Extraction and 16s Rrna Gene Amplification And Sequencingmentioning

confidence: 99%

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica

et al. 2020

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“…Picosized cells have also been proposed to thrive as the Arctic Ocean freshens, this being one of the possible consequences of global warming (Li et al, 2009). More recently, cultureindependent approaches, e.g., the sequencing techniques based on the extraction and amplification of environmental DNA, have enabled the acquisition of more complete picture of Arctic microbial eukaryotic communities from sea ice and SW (Eddie et al, 2010;Bachy et al, 2011;Piwosz et al, 2013;de Sousa et al, 2018). However, active microbial eukaryotes dwelling in MPs, and differences in their community assembly processes compared with SW, have been rarely studied, especially using culture independent methods such as high throughput sequencing (Kilias et al, 2014b;Hardge et al, 2017;de Sousa et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Contrasting Community Composition of Active Microbial Eukaryotes in Melt Ponds and Sea Water of the Arctic Ocean Revealed by High Throughput Sequencing

Kong

Yang

et al. 2020

Front. Microbiol.

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Melt ponds (MPs), form as the result of thawing of snow and sea ice in the summer, have lower albedo than the sea ice and are thus partly responsible for the polar amplification of global warming. Knowing the community composition of MP organisms is key to understanding their roles in the biogeochemical cycles of nutrients and elements. However, the community composition of MP microbial eukaryotes has rarely been studied. In the present study, we assessed the microbial eukaryote biodiversity, community composition, and assembly processes in MPs and surface sea water (SW) using high throughput sequencing of 18S rRNA of size-fractionated samples. Alpha diversity estimates were lower in the MPs than SW across all size fractions. The community composition of MPs was significantly different from that of SW. The MP communities were dominated by members from Chrysophyceae, the ciliate classes Litostomatea and Spirotrichea, and the cercozoan groups Filosa-Thecofilosea. One open MP community was similar to SW communities, which was probably due to the advanced stage of development of the MP enabling the exchange of species between it and adjacent SW. High portions of shared species between MPs and SW may indicate the vigorous exchange of species between these two major types of environments in the Arctic Ocean. SW microbial eukaryote communities are mainly controlled by dispersal limitation whereas those of MP are mainly controlled by ecological drift.

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“…More and more investigations are focusing on the description of co-occurrence patterns and linkages within microbes through network analysis (Cavicchioli 2015). Networks of prokaryotes are intimately linked to ecosystem functioning and play a crucial role in maintaining biodiversity in polar areas (de Sousa et al 2019;Grzymski et al 2012). In addition, co-occurrence patterns of prokaryotes, based on next-generation sequencing data, have been shown to be able to predict positive and negative interactions between planktonic bacteria and environmental variables (Mo et al 2018).…”

Section: Hotspotsmentioning

confidence: 99%

Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

Liu

Zhao

McMinn

et al. 2020

Mar Life Sci Technol

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Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles. Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity, revealing a huge, previously underestimated phylogenetic diversity with many new lineages. This technology has now become the most important tool to understand the ecological significance of this huge and novel diversity in polar oceans. In particular, high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments. Here, a brief overview of polar microbial eukaryote diversity, as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene, is presented. Using these 'omic' approaches, further attention still needs to be focused on differences between specific locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.

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Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime

Cited by 29 publications

References 125 publications

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica

Diversity of Bacterial Biosynthetic Genes in Maritime Antarctica

Contrasting Community Composition of Active Microbial Eukaryotes in Melt Ponds and Sea Water of the Arctic Ocean Revealed by High Throughput Sequencing

Planktonic microbial eukaryotes in polar surface waters: recent advances in high-throughput sequencing

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