Large-Scale Distribution and Activity of Prokaryotes in Deep-Sea Surface Sediments of the Mediterranean Sea and the Adjacent Atlantic Ocean

The deep-sea represents a substantial portion of the biosphere and has a major influence on carbon cycling and global biogeochemistry. Benthic deep-sea prokaryotes have crucial roles in this ecosystem, with their recycling of organic matter from the photic zone. Despite this, little is known about the large-scale distribution of prokaryotes in the surface deep-sea sediments. To assess the influence of environmental and trophic variables on the large-scale distribution of prokaryotes, we investigated the prokaryotic assemblage composition (Bacteria to Archaea and Euryarchaeota to Crenarchaeota ratio) and activity in the surface deep-sea sediments of the Mediterranean Sea and the adjacent North Atlantic Ocean. Prokaryotic abundance and biomass did not vary significantly across the Mediterranean Sea; however, there were depth-related trends in all areas. The abundance of prokaryotes was positively correlated with the sedimentary concentration of protein, an indicator of the quality and bioavailability of organic matter. Moving eastwards, the Bacteria contribution to the total prokaryotes decreased, which appears to be linked to the more oligotrophic conditions of the Eastern Mediterranean basins. Despite the increased importance of Archaea, the contributions of Crenarchaeota Marine Group I to the total pool was relatively constant across the investigated stations, with the exception of Matapan-Vavilov Deep, in which Euryarchaeota Marine Group II dominated. Overall, our data suggest that deeper areas of the Mediterranean Sea share more similar communities with each other than with shallower sites. Freshness and quality of sedimentary organic matter were identified through Generalized Additive Model analysis as the major factors for describing the variation in the prokaryotic community structure and activity in the surface deep-sea sediments. Longitude was also important in explaining the observed variability, which suggests that the overlying water masses might have a critical role in shaping the benthic communities.

• Publication year

  2013

• Venue

  PLoS ONE

• Publication date

  2013-08-28

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0072996PMID 24039667PMCID 3755984
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• R: A language and environment for statistical computing.

  2014cited by this paper
• Dark inorganic carbon fixation sustains the functioning of benthic deep‐sea ecosystems

  2013cited by this paper
• Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean

  2013cited by this paper
• Links between viruses and prokaryotes throughout the water column along a North Atlantic latitudinal transect

  2012cited by this paper
• Factors influencing prokaryotic community structure composition in sub-surface coastal sediments

  2012cited by this paper
• Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

  2012cited by this paper
• Global distribution of microbial abundance and biomass in subseafloor sediment

  2012cited by this paper
• The dark portion of the Mediterranean Sea is a bioreactor of organic matter cycling

  2012influential reference
• Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

  2011cited by this paper
• Microbial diversity and stratification of South Pacific abyssal marine sediments.

  2011cited by this paper
• Reliability of CARD-FISH Procedure for Enumeration of Archaea in Deep-Sea Surficial Sediments

  2011influential reference
• Genomic Library Screening for Viruses from the Human Dental Plaque Revealed Pathogen-Specific Lytic Phage Sequences

  2011cited by this paper
• Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes

  2011cited by this paper
• DOC dynamics in the meso and bathypelagic layers of the Mediterranean Sea

  2010cited by this paper
• Organic matter in sediments of canyons and open slopes of the Portuguese, Catalan, Southern Adriatic and Cretan Sea margins

  2010influential reference
• Spatial patterns of bacterial abundance, activity and community composition in relation to water masses in the eastern Mediterranean Sea

  2010cited by this paper
• Sediment-associated microdiversity within the Marine Group I Crenarchaeota.

  2010cited by this paper
• Prokaryotic abundance and heterotrophic metabolism in the deep Mediterranean Sea

  2010cited by this paper
• Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

  2010cited by this paper
• Global ecological patterns in uncultured Archaea

  2010cited by this paper
• Phylogenetic diversity of sediment bacteria from the deep Northeastern Pacific Ocean: a comparison with the deep Eastern Mediterranean Sea.

  2010cited by this paper
• Spatial distribution of Bacteria and Archaea and amoA gene copy numbers throughout the water column of the Eastern Mediterranean Sea

  2009cited by this paper
• Distribution and activity of Bacteria and Archaea in the different water masses of the Tyrrhenian Sea

  2009cited by this paper
• Climate, carbon cycling, and deep-ocean ecosystems

  2009cited by this paper
• Quantity and bioavailability of sediment organic matter as signatures of benthic trophic status

  2009cited by this paper
• Methods for the Study of Deep-Sea Sediments, Their Functioning and Biodiversity

  2009cited by this paper
• Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

  2009cited by this paper
• Major viral impact on the functioning of benthic deep-sea ecosystems

  2008cited by this paper
• Significant contribution of Archaea to extant biomass in marine subsurface sediments

  2008cited by this paper
• Factors influencing benthic bacterial abundance, biomass, and activity on the northern continental margin and deep basin of the Gulf of Mexico

  2008cited by this paper
• Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic

  2008cited by this paper
• Biogeochemistry: Who lives in the sea floor?

  2008cited by this paper
• Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

  2008cited by this paper
• Feast and famine — microbial life in the deep-sea bed

  2007cited by this paper
• Microbial structuring of marine ecosystems

  2007cited by this paper
• Ocean Data View

  2007cited by this paper
• Contribution of Crenarchaeota and Euryarchaeota to the prokaryotic plankton in the coastal northwestern Black Sea

  2007cited by this paper
• Annually reoccurring bacterial communities are predictable from ocean conditions

  2006cited by this paper
• Flushing submarine canyons

  2006cited by this paper
• Global bathymetric patterns of standing stock and body size in the deep-sea benthos

  2006cited by this paper
• Distribution and activity of Bacteria and Archaea in the deep water masses of the North Atlantic

  2006cited by this paper
• Generalized Additive Models

  2006cited by this paper
• Prokaryotic respiration and production in the meso‐ and bathypelagic realm of the eastern and western North Atlantic basin

  2006cited by this paper
• Synoptic determination of living/dead and active/dormant bacterial fractions in marine sediments.

  2006cited by this paper
• Predation on prokaryotes in the water column and its ecological implications

  2005cited by this paper
• Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

  2005cited by this paper
• Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria

  2005cited by this paper
• Isolation of an autotrophic ammonia-oxidizing marine archaeon

  2005cited by this paper
• Particle flux and food supply to a seamount cold-water coral community (Galicia Bank, NW Spain)

  2004cited by this paper
• Combining Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization and Microautoradiography To Detect Substrate Utilization by Bacteria and Archaea in the Deep Ocean

  2004cited by this paper
• Application of a rapid direct viable count method to deep-sea sediment bacteria.

  2004cited by this paper
• Distributions of Microbial Activities in Deep Subseafloor Sediments

  2004cited by this paper
• An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments.

  2004cited by this paper
• Mesozooplankton community respiration and its relation to particle flux in the oligotrophic eastern Mediterranean

  2004cited by this paper
• Biodiversity, Community Structural Shifts, and Biogeography of Prokaryotes within Antarctic Continental Shelf Sediment

  2003cited by this paper
• Evolution of dynamics in the eastern Mediterranean affecting water mass structures and properties in the Ionian and Adriatic Seas

  2003cited by this paper
• Induction of Sucrose Utilization Genes from Bifidobacterium lactis by Sucrose and Raffinose

  2003cited by this paper
• Higher Abundance of Bacteria than of Viruses in Deep Mediterranean Sediments

  2002cited by this paper
• Respiration in the open ocean

  2002cited by this paper
• Bacterial numbers and growth in surficial deep-sea sediments and phytodetritus in the NE Atlantic: Relationships with particulate organic carbon and total nitrogen

  2002cited by this paper
• Primary production, carbon export and nutrients availability in western and eastern Mediterranean Sea in early summer 1996 (MINOS cruise)

  2002cited by this paper
• Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria

  2002cited by this paper
• Meiofauna and macrofauna community structure in relation to sediment composition at the Iberian margin compared to the Goban Spur (NE Atlantic)

  2002cited by this paper
• Horizontal and vertical complexity of attached and free‐living bacteria of the eastern Mediterranean Sea, determined by 16S rDNA and 16S rRNA fingerprints

  2001cited by this paper
• Archaeal dominance in the mesopelagic zone of the Pacific Ocean

  2001influential reference
• Dominance of bacterial metabolism in oligotrophic relative to eutrophic waters

  2001cited by this paper
• Microbial diversity, producer–decomposer interactions and ecosystem processes: a theoretical model

  2001cited by this paper
• Quantitative Molecular Analysis of the Microbial Community in Marine Arctic Sediments (Svalbard)

  2001cited by this paper
• Measuring Bacterial Production in Deep-Sea Sediments using 3H-Thymidine Incorporation: Ecological Significance

  2001cited by this paper
• Bacterioplankton distribution and production in deep Pacific waters: Large–scale geographic variations and possible coupling with sinking particle fluxes

  2000cited by this paper
• A Few Cosmopolitan Phylotypes Dominate Planktonic Archaeal Assemblages in Widely Different Oceanic Provinces

  2000cited by this paper
• Bacteria in the cold deep-sea benthic boundary layer and sediment-water interface of the NE Atlantic.

  2000cited by this paper
• Depth‐related cell‐specific bacterial leucine incorporation rates on particles and its biogeochemical significance in the Northwest Mediterranean

  2000cited by this paper
• Variability of the large scale general circulation of the Mediterranean Sea from observations and modelling: a review

  2000cited by this paper
• Bacterial activity in sediments of the deep Arabian Sea in relation to vertical flux

  2000cited by this paper
• Population Structure and Phylogenetic Characterization of Marine Benthic Archaea in Deep-Sea Sediments

  1999cited by this paper
• The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set.

  1999influential reference
• Visualization and Enumeration of Marine Planktonic Archaea and Bacteria by Using Polyribonucleotide Probes and Fluorescent In Situ Hybridization

  1999cited by this paper
• Benthic oxygen uptake, hydrolytic potentials and microbial biomass at the Arctic continental slope

  1998cited by this paper
• Abundance, vertical distribution, and community structure of benthic prokaryotes from permanently cold marine sediments (Svalbard, Arctic Ocean)

  1998cited by this paper
• Seasonal and Spatial Variability of Bacterial and Archaeal Assemblages in the Coastal Waters near Anvers Island, Antarctica

  1998cited by this paper
• Microbial Community Composition of Wadden Sea Sediments as Revealed by Fluorescence In Situ Hybridization

  1998cited by this paper
• Small benthic size classes along the N.W. European Continental Margin: spatial and temporal variability in activity and biomass

  1998cited by this paper
• A consumer's guide to phytoplankton primary productivity models

  1997cited by this paper
• Biomass distribution in marine planktonic communities

  1997cited by this paper
• Microbial food webs and the export of biogenic carbon in oceans

  1995cited by this paper
• A three-year time series of elemental and biochemical composition of organic matter in subtidal sandy sediments of the Ligurian Sea (northwestern Mediterranean)

  1995cited by this paper
• Fluorescently labelled, rRNA‐targeted oligonucleotide probes in the study of microbial ecology

  1995cited by this paper
• Deep bacterial biosphere in Pacific Ocean sediments

  1994cited by this paper
• Deep-sea food chains and the global carbon cycle

  1993cited by this paper
• The Early Diagenesis of Organic Matter: Bacterial Activity

  1993cited by this paper
• Bacterioplankton Roles in Cycling of Organic Matter: The Microbial Food Web

  1992cited by this paper
• parB: an auxin-regulated gene encoding glutathione S-transferase.

  1992cited by this paper
• Primary Productivity and Biogeochemical Cycles in the Sea

  1992cited by this paper
• Natural Bacterial Assemblages in Deep-Sea Sediments: Towards a Global View

  1992cited by this paper
• Archaea in coastal marine environments.

  1992cited by this paper
• Beyond BACI: Experimental designs for detecting human environmental impacts on temporal variations in natural populations

  1991cited by this paper
• Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations

  1990influential reference
• 2 Direct Methods and Biomass Estimation

  1990cited by this paper
• Phytodetritus on the Deep-Sea Floor in a Central Oceanic Region of the Northeast Atlantic

  1989cited by this paper

• The chemosynthetic biofilm microbiome of deep-sea hydrothermal vents across space and time

  2025cites this paper
• Metagenomic probing toward an atlas of the taxonomic and metabolic foundations of the global ocean genome

  2024cites this paper
• Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology

  2023cites this paper
• Diversity, activity and abundance of benthic microbes in the Southeastern Mediterranean Sea.

  2022cites this paper
• Bacterial Communities and Culturable Petroleum Hydrocarbon Degrading Bacteria in Marine Sediments in the Northeastern South China Sea

  2022cites this paper
• Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

  2021influential citation
• Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean—Atlantic Gradient

  2021cites this paper
• Dynamic prokaryotic communities in the dark western Mediterranean Sea

  2021cites this paper
• P Fluxes and Prokaryotic Cycling at Benthic Boundary Layer in the Deep Southeastern Mediterranean Sea

  2021cites this paper
• Effect of tectonic processes on biosphere–geosphere feedbacks across a convergent margin

  2021cites this paper
• Patterns in extracellular enzyme activity and microbial diversity in deep-sea Mediterranean sediments

  2020cites this paper
• Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean

  2019cites this paper
• Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay

  2019cites this paper
• The Effect of Historic Shipwrecks on Sediment Microbiomes in the Northern Gulf of Mexico

  2019cites this paper
• Plate tectonics drive deep biosphere microbial community structure

  2019cites this paper
• Environmental Drivers Controlling Bacterial and Archaeal Abundance in the Sediments of a Mediterranean Lagoon Ecosystem

  2018cites this paper
• Bioturbation as a key driver behind the dominance of Bacteria over Archaea in near-surface sediment

  2017cites this paper
• Exploring the Relationship between Macrofaunal Biodiversity and Ecosystem Functioning in the Deep Sea

  2017influential citation
• Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

  2016cites this paper
• Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

  2016cites this paper
• Deep-sea ecosystem : a world of positive biodiversity – ecosystem functioning 1 relationships ? 2 3

  2016cites this paper
• Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field

  2016influential citation
• Spatial homogeneity of bacterial and archaeal communities in the deep eastern Mediterranean Sea surface sediments.

  2016cites this paper
• New perspectives in benthic deep-sea microbial ecology

  2015cites this paper
• Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

  2015cites this paper
• Diversity of marine microbes in a changing Mediterranean Sea

  2015influential citation
• Effect of wastewater disposal on the bacterial and archaeal community of sea sediment in an industrial area in China.

  2014cites this paper
• Large Spatial Scale Variability in Bathyal Macrobenthos Abundance, Biomass, α- and β-Diversity along the Mediterranean Continental Margin

  2014cites this paper
• Microbial community composition and diversity in Caspian Sea sediments

  2014cites this paper