Mesopelagic zone ecology and biogeochemistry – a synthesis

Robinson, Carol; Steinberg, Deborah K.; Anderson, Thomas R.; Arı́stegui, Javier; Carlson, Craig A.; Frost, Jessica R.; Ghiglione, Jean François; Hernández‐León, Santiago; Jackson, George A.; Koppelmann, Rolf; Quéguiner, Bernard; Ragueneau, Olivier; Rassoulzadegan, Fereidoun; Robison, Bruce H.; Tamburini, Christian; Tanaka, Tsuneo; Wishner, Karen F.; Zhang, Jing

doi:10.1016/j.dsr2.2010.02.018

Cited by 272 publications

(215 citation statements)

References 195 publications

(246 reference statements)

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“…The deep-scattering layer is a mid-water (200-1,000 m) mass of small fishes, cephalopods, crustaceans and zooplankton that provides a rich source and variety of prey items [28][29][30] . It should be possible for C. rupestris to feed there at a relatively high trophic level (and some data are consistent with this 31 ; Supplementary Fig.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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W hile longitudinal and latitudinal habitat transitions have been proposed to define marine communities and promote intraspecific differentiation 1-3 , little is known about the importance of transitions along ocean depth gradients 4,5 , although substantial changes in species assemblages with depth have been recorded (for example, ref. 6 ), and relatively narrow depth ranges may distinguish closely related species (for example, refs 7,8 ). Understanding the relevant mechanisms will contribute significantly to our understanding of eco-evolutionary processes and the origin of marine biodiversity. We chose the roundnose grenadier (Coryphaenoides rupestris) as a model system because it is a widespread species that can inhabit a comparatively broad range of depths 9 from ~180 m to 2,600 m. It is a batch spawner, producing up to 69,000 pelagic eggs per female 10 . It has a spawning season peaking in autumn 11 (recent observations were in September at 1,500 m; ref. 12 ), preys on fish, cephalopods and invertebrates in both benthic and pelagic habitats 13 , and shows minor genetic differentiation across its geographic range [14][15][16] .Adaptation to habitat can occur among populations within a species, and if disruptive selection is associated with assortative mating has the potential to promote incipient speciation through ecological processes in sympatry 17 . When environmental change exposes new habitats and niche potential, adaptive radiations may rapidly generate a new lineage of species 18,19 . To the extent that differential selection can retain polymorphisms within or among populations, this may facilitate the process of adaptive radiation. Here, we focus on one of the key habitat transitions in the oceans-between the photic mesopelagic region and the aphotic regions below (together with the more contiguous changes associated with increasing depth). There is the potential for species (such as the roundnose grenadier), whose habitat range extends across this boundary or along the depth gradient, to experience differential selective pressures. We tested hypotheses about adaptation to these deep-sea habitats using genome sequence data together with data on the ecology and life history of the subject species. We found that juvenile fish of this species are found primarily in relatively shallow depths (near the transition between the mesopelagic and bathypelagic zones) and then migrate as they mature to different depths, and this is strongly associated with their genotype at a set of functional loci. In particular, all adults below ~1,800 m share the same homozygous genotype at each locus. There is evidence for strong selection maintaining this difference, but no clear evidence for differentiation driven by assortative mating. Results and discussionWe produced an annotated reference genome for C. rupestris with a total length of 0.829 gigabase pairs, a mean depth of 104× and an N50 of 159,738 (see Supplementary Methods for details). We used this draft genome to map 60 additional genomes sequenced to a mean depth ...

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Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Genomics of habitat choice and adaptive evolution in a deep-sea fish

et al. 2018

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“…This results in high bacterial growth at depth as a result of the decomposition of organic carbon in sinking particulate matter, yielding very low oxygen concentrations [19]. While species from many taxa (including copepods, euphausiids, cnidarians, ctenophores, fish and squid) live entirely or part of the time (during diel or ontogenetic vertical migrations) within the most pronounced OMZs [20,21], many organisms are stressed or die under hypoxic conditions [22], and overall abundance and species diversity are reduced. OMZs have dramatic effects on the spatial distribution patterns of animals in the water column, and zones of enhanced biological and biogeochemical activity exist at the OMZ's upper and lower boundaries [23,24].…”

Section: Introductionmentioning

confidence: 99%

Vampire squid: detritivores in the oxygen minimum zone

Hoving

Robison

2012

Proc. R. Soc. B.

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Vampire squid (Vampyroteuthis infernalis) are considered phylogenetic relics with cephalopod features of both octopods and squids. They lack feeding tentacles, but in addition to their eight arms, they have two retractile filaments, the exact functions of which have puzzled scientists for years. We present the results of investigations on the feeding ecology and behaviour of Vampyroteuthis, which include extensive in situ, deep-sea video recordings from MBARI's remotely operated vehicles (ROVs), laboratory feeding experiments, diet studies and morphological examinations of the retractile filaments, the arm suckers and cirri. Vampire squid were found to feed on detrital matter of various sizes, from small particles to larger marine aggregates. Ingested items included the remains of gelatinous zooplankton, discarded larvacean houses, crustacean remains, diatoms and faecal pellets. Both ROV observations and laboratory experiments led to the conclusion that vampire squid use their retractile filaments for the capture of food, supporting the hypothesis that the filaments are homologous to cephalopod arms. Vampyroteuthis' feeding behaviour is unlike any other cephalopod, and reveals a unique adaptation that allows these animals to spend most of their life at depths where oxygen concentrations are very low, but where predators are few and typical cephalopod food is scarce.

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Section: Introductionmentioning

confidence: 99%

“…The mesopelagic (200-1000 m) and bathypelagic (1000-4000 m) zones contain 470% of marine microbial biomass (Arıstegui et al, 2009) and these organisms have vital roles in global cycling of carbon, nitrogen and other biogeochemical processes (Nagata et al, 2010;Robinson et al, 2010). In addition to microorganisms necessarily being adapted to cold and increased pressure there, the deep sea also contains more recalcitrant forms of carbon than at the surface (Arıstegui et al, 2009;Nagata et al, 2010;Robinson et al, 2010). Cultivated isolates have revealed some microbial adaptations associated with life at depth, including increased intergenic spacer regions, rRNA gene indels and higher abundances of membrane polyunsaturated fatty acids and surface-adhesion/ motility genes (Simonato et al, 2006;Lauro and Bartlett, 2008;Wang et al, 2008;Nagata et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

et al. 2014

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Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.

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Mesopelagic zone ecology and biogeochemistry – a synthesis

Cited by 272 publications

References 195 publications

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Genomics of habitat choice and adaptive evolution in a deep-sea fish

Vampire squid: detritivores in the oxygen minimum zone

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

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