Dataset: Salp and pteropod associated microorganisms

Name: Salp and pteropod associated microorganisms
Published: 2024-05-06
Keywords: Prochlorococcus, Synechococcus, salps, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:26.7425 E:-79.9875 S:26.7425 W:-79.9875

Western edge of the Gulf Stream

Temporal Extent: 2019-09-15

Project:

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Co-Principal Investigator:

Anne W. Thompson (Portland State University, PSU)

Contact:

Anne W. Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-05-06

Restricted:

Validated:

Current State:

Data not available

16S rRNA sequencing salp and pteropod microorganisms

Abstract:

Microbial mortality impacts the structure of food webs, carbon flow, and the interactions that create dynamic patterns of abundance across gradients in space and time in diverse ecosystems. In the oceans, estimates of microbial mortality by viruses, protists, and small zooplankton do not account fully for observations of loss, suggesting the existence of underappreciated mortality sources. We examined how ubiquitous mucous mesh feeders (i.e. gelatinous zooplankton) could contribute to microbial mortality in the open ocean. We coupled capture of live animals by blue-water diving to sequence-based approaches to measure the enrichment and selectivity of feeding by two coexisting mucous grazer taxa (pteropods and salps) on numerically dominant marine prokaryotes. We show that mucous mesh grazers consume a variety of marine prokaryotes and select between coexisting lineages and similar cell sizes. We show that Prochlorococcus may evade filtration more than other cells and that planktonic archaea are consumed by macrozooplanktonic grazers. Discovery of these feeding relationships identifies a new source of mortality for Earth's dominant marine microbes and alters our understanding of how top-down processes shape microbial community and function.

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Methods & Sampling

Collected from the western edge of the Gulf Stream (26°43′93″ N, 79° 59′15″ W) in September 2019, 5–8 km east of West Palm Beach, Florida. All samples were collected during daylight in the upper 15 m. Sampling was done by hand.

Jars with animals and jars with seawater were brought on the deck of a 10 m dive vessel for processing. Within 30 min of divers surfacing, samples were archived or processed as follows. Salps and pteropods were gently poured onto a metal sieve then rinsed with 0.2 μm filtered seawater. Each gut was then removed with dissecting scissors, avoiding as much of the gelatinous tissue as possible. Guts were placed into sterile bead-beating tubes with 0.55 and 0.25 mm sterile glass beads and stored on dry ice until archiving at −80°C in a shore-based laboratory. Salp faecal pellets were sampled from different salp specimens incubated in jars for approximately 1-h after collection. Faecal pellets were collected on a mesh sieve (500 μm), rinsed with 0.2 μm filtered seawater, then stored as above. Jars containing seawater collected near sampled animals were transported on blue ice to the shore-based laboratory. For flow cytometry samples, 2 ml of seawater was fixed at a final concentration of 0.125% TEM grade glutaraldehyde (Tousimis), incubated at room temperature for 10 min, then flash frozen in ethanol cooled with dry ice. Seawater DNA samples were taken by peristaltic pumping onto 0.2 μm membrane filters and were stored on dry ice until archiving at −80°C.

Data Processing Description

DNA was extracted with the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. Salp guts, salp fecal pellets, and pteropod tissues were ground with a sterile disposable pestle (Axygen, Tewksbury, USA) for 3 minutes prior to extraction. All samples, including seawater, were lysed by bead beating with 0.55 mm and 0.25 mm sterile glass beads at 30 Hz for 2 minutes after addition of lysis buffer, freeze-fractured 3 times, incubated with a final concentration of 2 mg/mL Proteinase K (VWR Chemicals, Solon, OH, USA) for 1 hour at 55 ˚C, and then incubated with a final concentration of 0.9 mg/mL RNase A for 10 minutes at 65˚C. To minimize amplification of eukaryotic host DNA, the primer pair 515F‐Y/806R was chosen to amplify the 16S rRNA V4 hypervariable region. Reactions were performed with 0.5-2 ng of DNA using the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). To overcome PCR inhibition in salp samples, bovine serum albumin (BSA) was added to the salp PCRs, see details below. The Agilent Bioanalyzer High Sensitivity Kit (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate PCRs from each sample were pooled, cleaned with magnetic beads, and paired-end sequenced (2 x 300 bp) with Illumina MiSeq v.3 (Illumina, San Diego, USA). Sequences were deposited in the Sequence Read Archive (SRA).

BCO-DMO Processing

* Merged biosample and SRA run file
* Removed no data columns from files
* Adjusted parameters to comply with database requirements (spaces, characters, etc)
* Converted date to ISO format
* Split lat/lon column into their own columns

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851412

Deployments

None available yet

Instruments

None available yet

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
bioproject_accession	NCBI Bioproject accession ID	unitless	BioProject
biosample_accession	NCBI Biosample accession ID	unitless	BioSample
message	NCBI message	unitless	no_bcodmo_term
sample_name	Submitter sample name	unitless	sample
sample_title	Sample accession title	unitless	sample_descrip
organism	Organism name by submitter	unitless	taxon
collection_date	Collection date of organism Format: %Y-%m-%d	unitless	date
depth	Sampling depth	feet	depth
env_broad_scale	Broad-scale environmental context	unitless	sample_descrip
env_local_scale	Local-scale environmental context	unitless	sample_descrip
env_medium	Material displaced by the entity at time of sampling	unitless	sample_descrip
geo_loc_name	Geographic location of the origin of the sample	unitless	region
sampling_lat	Latitude of sampling location, south is negative	decimal degrees	lat
sampling_lon	Longitude of sampling location, west is negative	decimal degrees	lon
sra_run_accession	NCBI SRA run accession ID	unitless	SRA_run
sra_study_accession	NCBI study accession ID	unitless	SRA_study
object_status	Status of object	unitless	no_bcodmo_term
library_ID	Unique identifier for the sequencing library (can be the sample name repeated).	unitless	sample
title	Library title	unitless	seq_descrip
library_strategy	Sequencing library strategy	unitless	seq_descrip
library_source	Source of sequencing library	unitless	seq_descrip
library_selection	Selection used for sequencing library	unitless	seq_descrip
library_layout	single or paired end sequencing reads	unitless	seq_descrip
platform	Sequencing platform manufacturer	unitless	instrument
instrument_model	Sequencer model	unitless	inst_model
design_description	Description explaining how this library was prepared and sequenced	unitless	seq_descrip
filetype	File type	unitless	datatype
filename	Forward reads file name	unitless	file_name
filename2	Reverse reads file name	unitless	file_name

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Dataset: Salp and pteropod associated microorganisms