Marc Besseling

Utrecht University

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Jaap S. Sinninghe Damsté

Utrecht University

Ellen C. Hopmans

Royal Netherlands Institute for Sea Research

Laura Villanueva

Royal Netherlands Institute for Sea Research

Stefan Schouten

Royal Netherlands Institute for Sea Research

Nicole J. Bale

Royal Netherlands Institute for Sea Research

Corina P. D. Brussaard

Royal Netherlands Institute for Sea Research

Tracy A. Villareal

The University of Texas at Austin

Denise J C Dorhout

Royal Netherlands Institute for Sea Research

Harry J. Witte

Royal Netherlands Institute for Sea Research

Alejandro Abdala Asbun

Royal Netherlands Institute for Sea Research

Cooperative Institutions

Royal Netherlands Institute for Sea Research

Utrecht University

Centre National de la Recherche Scientifique

Sorbonne Université

Laboratoire d'Océanographie Microbienne

Observatoire Océanologique de Banyuls-sur-Mer

University of Massachusetts Amherst

University of Cologne

National Oceanography Centre

Université Paris Cité

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Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results

Frontiers in Genetics (2020)

Alejandro Abdala Asbun Marc Besseling Sergio Balzano Judith van Bleijswijk Harry J. Witte

Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene, or even only parts of a single gene rather than the entire genome, the number of reads needed per sample to assess the microbial community structure is lower than that required for metagenome sequencing. This makes marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel , a scalable, flexible, and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in BIOM and text format and representative sequences. Cascabel is a highly versatile software that allows users to customize several steps of the pipeline, such as selecting from a set of OTU clustering methods or performing ASV analysis. In addition, we designed Cascabel to run in any linux/unix computing environment from desktop computers to computing servers making use of parallel processing if possible. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL .

Amplicon

Amplicon sequencing

10.3389/fgene.2020.489357

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Citations (37)

Intact polar lipid composition and bottom water and surface sediment characteristics during R/V Pelagia cruise PASOM to the Arabian Sea in 2009

Marc Besseling Ellen C. Hopmans Jaap S. Sinninghe Damsté Laura Villanueva

10.1594/pangaea.891253

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Citations (0)

(Table 2) Abundance of the detected intact polar lipids (IPL) in surface and subsurface sediments during R/V Pelagia cruise PASOM in January 2009

Marc Besseling Ellen C. Hopmans Jaap S. Sinninghe Damsté Laura Villanueva

Table (database)

10.1594/pangaea.891252

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Citations (0)

Organic Geochemistry (2019)

Marc Besseling Ellen C. Hopmans Michel Koenen Marcel T. J. van der Meer Sanne Vreugdenhil

Thaumarchaeota are one of the most abundant groups of Archaea in the marine water column. Their membrane consists of isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) which are applied in the widely used TEX86 proxy to reconstruct past sea surface temperatures (SSTs). However, in some specific marine systems, such as the Mediterranean Sea, core-top TEX86-derived temperatures do not seem to reflect annual mean SSTs. This has been attributed to contributions of deep-water dwelling Thaumarchaeota. Here, we investigate the potential causes of this bias by studying both the archaeal diversity as well as the intact polar lipid (IPL) GDGT composition in the Mediterranean water column by a combined 16S rRNA gene amplicon sequencing and a lipidomic approach on suspended particulate matter (SPM) at different water depths. The archaeal distribution showed a dominance of archaea other than Thaumarchaeota, i.e. Marine Euryarchaeota group II and III in the upper epipelagic waters (0–100 m deep), while Thaumarchaeota (Marine group I; MGI) dominated the subsurface and the deeper waters. This shift in the archaeal community composition coincided with a decrease in IPL GDGT-0 and increase of IPL crenarchaeol. The ratio of GDGT-2/GDGT-3 increased with water depth, but values were lower than observed in deep marine waters of some other regions. The increase of the GDGT-2/GDGT-3 ratio coincided with the high relative abundance of deep-water MGI, which may be linked to the high temperature and salinity found in specific water masses of the Mediterranean Sea. We conclude that these particularities of the Mediterranean Sea are responsible for the overestimated SST based on TEX86.

Thaumarchaeota

Dominance (genetics)

Mesopelagic zone

10.1016/j.orggeochem.2019.06.008

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Citations (54)

Developing molecular tools to estimate the biological sources of long chain diols : “Towards the improvement of a paleotemperature reconstruction proxy based on long chain diols”

Marc Besseling

Proxy (statistics)

Long chain

Chain (unit)

Source

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Citations (0)

Cascabel: a flexible, scalable and easy to use amplicon sequence data analysis pipeline

F1000Research (2019)

Alejandro Abdala Asbun Marc Besseling Sergio Balzano Harry J. Witte Judith van Bleijswijk

Open peer review

Sequence (biology)

Amplicon

10.7490/f1000research.1117286.1

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Citations (7)

Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

Marc Besseling Ellen C. Hopmans Jaap S. Sinninghe Damsté Laura Villanueva

Abstract. Benthic Archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter but the distribution and abundance of these archaeal groups is still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN superphylum. Members of the MCG were diverse with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, 2 and 3 with dihexose IPL-types, as well as GDGT-0 with a cyclopentanetetraol molecule and a hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.

Thaumarchaeota

Oxygen minimum zone

Crenarchaeota

Euryarchaeota

Dominance (genetics)

10.5194/bg-2017-289

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Citations (5)

Cascabel: a flexible, scalable and easy-to-use amplicon sequence data analysis pipeline

bioRxiv (Cold Spring Harbor Laboratory) (2019)

Alejandro Abdala Asbun Marc Besseling Sergio Balzano Judith van Bleijswijk Harry J. Witte

ABSTRACT Marker gene sequencing of the rRNA operon (16S, 18S, ITS) or cytochrome c oxidase I (CO1) is a popular means to assess microbial communities of the environment, microbiomes associated with plants and animals, as well as communities of multicellular organisms via environmental DNA sequencing. Since this technique is based on sequencing a single gene rather than the entire genome, the number of reads needed per sample is lower than that required for metagenome sequencing, making marker gene sequencing affordable to nearly any laboratory. Despite the relative ease and cost-efficiency of data generation, analyzing the resulting sequence data requires computational skills that may go beyond the standard repertoire of a current molecular biologist/ecologist. We have developed Cascabel , a flexible and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational steps. Cascabel takes the raw data as input and delivers a table of operational taxonomic units (OTUs) and a representative sequence tree. Our pipeline allows customizing the analyses by offering several choices for most of the steps, for example different OTU generating methods. The pipeline can make use of multiple computing nodes and scales from personal computers to computing servers. The analyses and results are fully reproducible and documented in an HTML and optional pdf report. Cascabel is freely available at Github: https://github.com/AlejandroAb/CASCABEL and licensed under GNU GPLv3.

Amplicon sequencing

Amplicon

Sequence (biology)

10.1101/809384

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Citations (9)

(Table 1) Bottom water temperature and oxygen concentration, oxygen penetration depth, and pore water composition in surface sediments during R/V Pelagia cruise PASOM in January 2009

Marc Besseling Ellen C. Hopmans Jaap S. Sinninghe Damsté Laura Villanueva

Table (database)

Penetration (warfare)

10.1594/pangaea.891250

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