DOI: 10.5061/dryad.wm37pvmnv
title: The ProkaBioDen database, a global database of benthic prokaryotic biomasses and densities in the marine realm

description: Benthic prokaryotes include Bacteria and Archaea and dominate densities of
 marine benthos. They play major roles in element cycles and heterotrophic,
 chemoautotrophic, and phototrophic carbon production. To understand how
 anthropogenic disturbances and climate change might affect these
 processes, better estimates of prokaryotic biomasses and densities are
 required. Hence, I developed the ProkaBioDen database, the largest
 open-access database of benthic prokaryotic biomasses and densities in
 marine surface sediments. In total, the database comprises
 1,089 georeferenced benthic prokaryotic biomass and
 1,875 density records extracted from 85 and 112 studies,
 respectively. I identified all references applying the procedures for
 systematic reviews and meta analyses and report prokaryotic biomasses as
 g C cm-3 sediment, g C g-1 sediment,
 and g C m-2. Density records are presented as cell
 cm-3 sediment, cell g-1 sediment/ sulfide/ vent
 precipitate, and cell m-2. This database should serve as
 reference to close sampling gaps in the future.
description: In March and June 2020, I
 compiled the “ProkaBio” part of the “ProkaBioDen database” applying the
 principles of “Preferred Reporting Items for Systematic Reviews and
 Meta-Analyses” (PRISMA). In the so-called “Identification” step, I
 identified 1,553 peer-reviewed articles in the <em>Web of
 Science</em> by using the key words “microb* biomass benth*”,
 “benthic prokaryotic biomass”, “benth* bacteria* biomass marin*”, and
 “Archaea biomass marin*”. Additionally, I found 138 publications in other
 sources, such as PANGAEA® Data Publisher (https://www.pangaea.de/) and
 peer-reviewed publications known to the author. After removing duplicate
 publications, I screened all titles and abstracts of 1,299 studies
 (“Screening” step) and excluded 967 studies that did not report
 prokaryotic biomasses. In step 3, the so-called “Eligibility” step, I
 excluded in total 249 studies because they did not present prokaryotic
 biomasses in the marine sediment surface in standardizable units, i.e., in
 g C cm<sup>-3</sup> wet sediment, g C
 g<sup>-1</sup> wet sediment, g C
 g<sup>-1</sup> dry sediment, or g C
 m<sup>-2</sup>. Furthermore, several studies lacked detailed
 geographical information about sampling stations or did not present
 primary research. Additional reasons for study exclusion were presenting
 prokaryotic biomasses for specific taxa instead of for all prokaryotes,
 being inaccessible, or introducing modelling, simulation, or experimental
 studies. In the final step, I included 85 studies from which I extracted
 1,098 georeferenced benthic prokaryotic biomass records. In March and June 2020, I established
 the “ProkaDen” part of the database that consists of records of
 prokaryotic density as well as of density of Bacteria and of Archaea.
 Following the PRISMA approach, I searched the <em>Web of
 Science</em> using the key words “marin* microb* abundance benth*”,
 “‘benthic bacteria’ abundance marin*”, “prokaryotic abundance marin*”,
 “prokaryotic density marin*”, “Archaea density abundance marin*”, “Archaea
 density marin*”, “Archaea abundance marin* benth*”, “Crenarchaea density
 abundance marin*”, “Crenarchaea density marin*”, “Crenarchaea abundance
 marin* benth*”, “Euryarchaea density abundance marin*”, and “Euryarchaea
 abundance marin* benth*” and found 1,204 peer-reviewed articles. I was
 aware of 171 additional studies that I included in the dataset which
 contained 1,104 studies after removing duplicates. In step 2 of the PRISMA
 approach (“Screening” step), I excluded 752 studies because they did not
 report benthic prokaryotic densities. In the “Eligibility” step, I
 furthermore omitted 239 studies because they did not present surface
 sediment prokaryotic densities or densities of a reduced number of
 prokaryotic taxa instead of reporting densities of all prokaryotes. I also
 removed studies that showed prokaryotic densities in poor-quality figures
 impeding data extraction and studies that listed densities which could not
 be converted to the common density units cell cm<sup>-3</sup>
 dry sediment, cell cm<sup>-3</sup> wet sediment, cell
 g<sup>-1</sup> dry sediment, cell g<sup>-1</sup>
 dry sulfide, cell g<sup>-1</sup> vent precipitate, cell
 g<sup>-1</sup> wet sediment, or cell
 m<sup>-2</sup>. I also excluded studies that reported
 experimental or culture studies and publications that I could not access.
 In the last step, I included 112 studies in the global benthic prokaryotic
 density database from which I extracted 1,875 georeferenced benthic
 prokaryotic density records.