scholarly journals Deep-sea sponge grounds as nutrient sinks: denitrification is common in boreo-Arctic sponges

2020 ◽  
Vol 17 (5) ◽  
pp. 1231-1245 ◽  
Author(s):  
Christine Rooks ◽  
James Kar-Hei Fang ◽  
Pål Tore Mørkved ◽  
Rui Zhao ◽  
Hans Tore Rapp ◽  
...  
Keyword(s):  
Deep Sea ◽  
Cold Water ◽  
Marine Ecosystem ◽  
Sponge Species ◽  
Lag Phase ◽  
Sponge Tissue ◽  
Ammonium Oxidation ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Nutrient Sinks

Abstract. Sponges are commonly known as general nutrient providers for the marine ecosystem, recycling organic matter into various forms of bioavailable nutrients such as ammonium and nitrate. In this study we challenge this view. We show that nutrient removal through microbial denitrification is a common feature in six cold-water sponge species from boreal and Arctic sponge grounds. Denitrification rates were quantified by incubating sponge tissue sections with 15NO3--amended oxygen-saturated seawater, mimicking conditions in pumping sponges, and de-oxygenated seawater, mimicking non-pumping sponges. It was not possible to detect any rates of anaerobic ammonium oxidation (anammox) using incubations with 15NH4+. Denitrification rates of the different sponge species ranged from below detection to 97 nmol N cm−3 sponge d−1 under oxic conditions, and from 24 to 279 nmol N cm−3 sponge d−1 under anoxic conditions. A positive relationship between the highest potential rates of denitrification (in the absence of oxygen) and the species-specific abundances of nirS and nirK genes encoding nitrite reductase, a key enzyme for denitrification, suggests that the denitrifying community in these sponge species is active and prepared for denitrification. The lack of a lag phase in the linear accumulation of the 15N-labelled N2 gas in any of our tissue incubations is another indicator for an active community of denitrifiers in the investigated sponge species. Low rates for coupled nitrification–denitrification indicate that also under oxic conditions, the nitrate used to fuel denitrification rates was derived rather from the ambient seawater than from sponge nitrification. The lack of nifH genes encoding nitrogenase, the key enzyme for nitrogen fixation, shows that the nitrogen cycle is not closed in the sponge grounds. The denitrified nitrogen, no matter its origin, is then no longer available as a nutrient for the marine ecosystem. These results suggest a high potential denitrification capacity of deep-sea sponge grounds based on typical sponge biomass on boreal and Arctic sponge grounds, with areal denitrification rates of 0.6 mmol N m−2 d−1 assuming non-pumping sponges and still 0.3 mmol N m−2 d−1 assuming pumping sponges. This is well within the range of denitrification rates of continental shelf sediments. Anthropogenic impact and global change processes affecting the sponge redox state may thus lead to deep-sea sponge grounds changing their role in marine ecosystem from being mainly nutrient sources to becoming mainly nutrient sinks.

scholarly journals Deep-sea sponge grounds as nutrient sinks: High denitrification rates in boreo-arctic sponges

2019 ◽  
Author(s):  
Christine Rooks ◽  
James Kar-Hei Fang ◽  
Pål Tore Mørkved ◽  
Rui Zhao ◽  
Hans Tore Rapp ◽  
...  
Keyword(s):  
Organic Matter ◽  
Deep Sea ◽  
Marine Ecosystem ◽  
Coastal Sediments ◽  
Sponge Species ◽  
Sponge Tissue ◽  
Ammonium Oxidation ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Nutrient Sinks

Abstract. Sponges are commonly known as general nutrient providers for the marine ecosystem, recycling organic matter into various forms of bio-available nutrients such as ammonium and nitrate. In this study we challenge this view. We show that nutrient removal through microbial denitrification is a common feature in six cold-water sponge species from boreal and Arctic sponge grounds. Denitrification rates were quantified by incubating sponge tissue sections with 15NO3- – amended oxygen saturated seawater, mimicking conditions in pumping sponges, and de-oxygenated seawater, mimicking non-pumping sponges. Rates of anaerobic ammonium oxidation (anammox) using incubations with 15NH4+ could not be detected. Denitrification rates of the different sponge species ranged from 0 to 114 nmol N cm-3 sponge day-1 under oxic conditions, and from 47 to 342 nmol N cm-3 sponge day-1 under anoxic conditions. An exponential relationship between the highest potential rates of denitrification (in the absence of oxygen) and the species-specific abundances of nirS and nirK genes encoding nitrite reductase, a key enzyme for denitrification, suggests that the denitrifying community in these sponge species is both prepared and optimized for denitrification. The lack of a lag phase in the linear accumulation of the 15N labelled N2 gas in any of our tissue incubations is another indicator for an active community of denitrifiers in the investigated sponge species. High rates for coupled nitrification-denitrification (up to 89 % of nitrate reduction in the presence of oxygen) shows that under these conditions, the NO3- reduced in denitrification was primarily derived from nitrification within the sponge, directly coupling organic matter degradation and nitrification to denitrification in sponge tissues. Under anoxic condition when nitrification was not possible, nitrate to fuel the much higher denitrification rates had to be retrieved directly from the seawater. The lack of nifH genes encoding nitrogenase, the key enzyme for nitrogen fixation, shows that the nitrogen cycle is not closed in the sponge grounds. The denitrified nitrogen, no matter of its origin, is then no longer available as a nutrient for the marine ecosystem. Considering average sponge biomasses on typical boreal and Arctic sponge grounds, our sponge denitrification rates reveal areal denitrification rates of 0.8 mmol N m-2 day-1 assuming non-pumping sponges and still 0.3 mmol N m-2 day-1 assuming pumping sponges. This is well within the range of denitrification rates of continental shelf sediments. For the most densely populated boreal sponge grounds we calculated denitrification rates of up to 2 mmol N m-2 day-1, which is comparable to rates in coastal sediments. Increased future impact of sponge grounds by anthropogenic stressors reducing sponge pumping activity and further stimulating sponge anaerobic processes may thus lead to that deep-sea sponge grounds change their role in the marine ecosystem from nutrient sources to nutrient sinks.

scholarly journals A Deep-Sea Sponge Loop? Sponges Transfer Dissolved and Particulate Organic Carbon and Nitrogen to Associated Fauna

2021 ◽  
Vol 8 ◽  
Author(s):  
Martijn C. Bart ◽  
Meggie Hudspith ◽  
Hans Tore Rapp ◽  
Piet F. M. Verdonschot ◽  
Jasper M. de Goeij
Keyword(s):  
Organic Matter ◽  
Coral Reefs ◽  
Shallow Water ◽  
Deep Sea ◽  
Cold Water ◽  
Trophic Levels ◽  
Sponge Species ◽  
Sponge Tissue ◽  
Associated Fauna ◽  
Brittle Stars

Cold-water coral reefs and sponge grounds are deep-sea biological hotspots, equivalent to shallow-water tropical coral reefs. In tropical ecosystems, biodiversity and productivity are maintained through efficient recycling pathways, such as the sponge loop. In this pathway, encrusting sponges recycle dissolved organic matter (DOM) into particulate detritus. Subsequently, the sponge-produced detritus serves as a food source for other organisms on the reef. Alternatively, the DOM stored in massive sponges was recently hypothesized to be transferred to higher trophic levels through predation of these sponges, instead of detritus production. However, for deep-sea sponges, the existence of all prerequisite, consecutive steps of the sponge loop have not yet been established. Here, we tested whether cold-water deep-sea sponges, similar to their tropical shallow-water counterparts, take up DOM and transfer assimilated DOM to associated fauna via either detritus production or predation. We traced the fate of 13carbon (C)- and 15nitrogen (N)-enriched DOM and particulate organic matter (POM) in time using a pulse-chase approach. During the 24-h pulse, the uptake of 13C/15N-enriched DOM and POM by two deep-sea sponge species, the massive species Geodia barretti and the encrusting species Hymedesmia sp., was assessed. During the subsequent 9-day chase in label-free seawater, we investigated the transfer of the consumed food by sponges into brittle stars via two possible scenarios: (1) the production and subsequent consumption of detrital waste or (2) direct feeding on sponge tissue. We found that particulate detritus released by both sponge species contained C from the previously consumed tracer DOM and POM, and, after 9-day exposure to the labeled sponges and detritus, enrichment of 13C and 15N was also detected in the tissue of the brittle stars. These results therefore provide the first evidence of all consecutive steps of a sponge loop pathway via deep-sea sponges. We cannot distinguish at present whether the deep-sea sponge loop is acting through a detrital or predatory pathway, but conclude that both scenarios are feasible. We conclude that sponges could play an important role in the recycling of DOM in the many deep-sea ecosystems where they are abundant, although in situ measurements are needed to confirm this hypothesis.

scholarly journals Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes

2020 ◽  
Vol 6 (16) ◽  
pp. eaaz4354 ◽  
Author(s):  
Zihao Zhao ◽  
Federico Baltar ◽  
Gerhard J. Herndl
Keyword(s):  
Organic Matter ◽  
Deep Sea ◽  
Organic Molecules ◽  
Extracellular Enzymes ◽  
Surrounding Medium ◽  
Hydrolytic Enzymes ◽  
Diffusion Limited ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Heterotrophic Prokaryotes

Heterotrophic prokaryotes express extracellular hydrolytic enzymes to cleave large organic molecules before taking up the hydrolyzed products. According to foraging theory, extracellular enzymes should be cell associated in dilute systems such as deep sea habitats, but secreted into the surrounding medium in diffusion-limited systems. However, extracellular enzymes in the deep sea are found mainly dissolved in ambient water rather than cell associated. In order to resolve this paradox, we conducted a global survey of peptidases and carbohydrate-active enzymes (CAZymes), two key enzyme groups initiating organic matter assimilation, in an integrated metagenomics, metatranscriptomics, and metaproteomics approach. The abundance, percentage, and diversity of genes encoding secretory processes, i.e., dissolved enzymes, consistently increased from epipelagic to bathypelagic waters, indicating that organic matter cleavage, and hence prokaryotic metabolism, is mediated mainly by particle-associated prokaryotes releasing their extracellular enzymes into diffusion-limited particles in the bathypelagic realm.

scholarly journals Isolating an active and inactive CACTA transposon from lettuce color mutants and characterizing their family

2021 ◽  
Author(s):  
Csanad Gurdon ◽  
Alexander Kozik ◽  
Rong Tao ◽  
Alexander Poulev ◽  
Isabel Armas ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Mobile Element ◽  
Bioinformatic Analysis ◽  
Relative Expression Level ◽  
Gene Coding ◽  
Genes Encoding ◽  
Key Enzyme ◽  
Natural Derivative ◽  
Dark Green ◽  
Transposon Insertions

Abstract Dietary flavonoids play an important role in human nutrition and health. Flavonoid biosynthesis genes have recently been identified in lettuce (Lactuca sativa); however, few mutants have been characterized. We now report the causative mutations in Green Super Lettuce (GSL), a natural light green mutant derived from red cultivar NAR; and GSL-Dark Green (GSL-DG), an olive-green natural derivative of GSL. GSL harbors CACTA 1 (LsC1), a 3.9-kb active nonautonomous CACTA superfamily transposon inserted in the 5′ untranslated region of anthocyanidin synthase (ANS), a gene coding for a key enzyme in anthocyanin biosynthesis. Both terminal inverted repeats (TIRs) of this transposon were intact, enabling somatic excision of the mobile element, which led to the restoration of ANS expression and the accumulation of red anthocyanins in sectors on otherwise green leaves. GSL-DG harbors CACTA 2 (LsC2), a 1.1-kb truncated copy of LsC1 that lacks one of the TIRs, rendering the transposon inactive. RNA-sequencing and reverse transcription quantitative PCR of NAR, GSL, and GSL-DG indicated the relative expression level of ANS was strongly influenced by the transposon insertions. Analysis of flavonoid content indicated leaf cyanidin levels correlated positively with ANS expression. Bioinformatic analysis of the cv Salinas lettuce reference genome led to the discovery and characterization of an LsC1 transposon family with a putative transposon copy number greater than 1,700. Homologs of tnpA and tnpD, the genes encoding two proteins necessary for activation of transposition of CACTA elements, were also identified in the lettuce genome.

scholarly journals Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters

2021 ◽  
Vol 9 (4) ◽  
pp. 757
Author(s):  
Qing-Mei Li ◽  
Ying-Li Zhou ◽  
Zhan-Fei Wei ◽  
Yong Wang
Keyword(s):  
Comparative Genomics ◽  
Deep Sea ◽  
Binding Protein ◽  
Glycerol Metabolism ◽  
Metabolic Reconstruction ◽  
Type Ii Secretion ◽  
Phylogenetic Groups ◽  
Genes Encoding ◽  
Epipelagic Zone ◽  
Chitin Binding Protein

Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.

An association between Exspina typica Lang (Tanaidacea) and deep-sea holothurians

1987 ◽  
Vol 67 (1) ◽  
pp. 11-15 ◽  
Author(s):  
Michael H. ◽  
Thurston D. S. M. ◽  
Billett-Al ◽  
Elizabeth Hassack
Keyword(s):  
Deep Sea ◽  
Cold Water

First reports of the association between Exspina typica and three species of abyssal holothurian are presented. These records suggest that the association is a real one, and not an artefact of sampling, but throw no light on the nature of the association. The geographic and bathymetric distributions of E. typica are summarized, and the species is shown to be a widely distributed cold water stenotherm.

scholarly journals Seabed mapping for selecting cold-water coral protection areas on Hatton Bank, Northeast Atlantic

2009 ◽  
Vol 66 (9) ◽  
pp. 2013-2025 ◽  
Author(s):  
P. Durán Muñoz ◽  
M. Sayago-Gil ◽  
J. Cristobo ◽  
S. Parra ◽  
A. Serrano ◽  
...  
Keyword(s):  
Deep Sea ◽  
Ad Hoc ◽  
Cold Water ◽  
Interdisciplinary Approach ◽  
Western Slope ◽  
Northeast Atlantic ◽  
Fisheries Science ◽  
Seabed Mapping ◽  
Del Rio ◽  
Water Coral

Abstract Durán Muñoz, P., Sayago-Gil, M., Cristobo, J., Parra, S., Serrano, A., Díaz del Rio, V., Patrocinio, T., Sacau, M., Murillo, F. J., Palomino, D., and Fernández-Salas, L. M. 2009. Seabed mapping for selecting cold-water coral protection areas on Hatton Bank, Northeast Atlantic. – ICES Journal of Marine Science, 66: 2013–2025. Research into vulnerable marine ecosystems (VMEs) on the high seas and the impacts of bottom fishing and ad hoc management measures are high priority today thanks to UN General Assembly Resolution 61/105. An interdisciplinary methodology (specifically designed for selecting cold-water coral protection areas) and a case study focused on the Hatton Bank (NE Atlantic) are presented. This interdisciplinary approach, developed under the ECOVUL/ARPA project, was based on conventional fisheries science, geomorphology, benthic ecology, and sedimentology. It contributes to defining practical criteria for identifying VMEs, to improving knowledge of their distribution off Europe's continental shelf, and to providing advice on negative fishing impacts and habitat protection. The approach was used to identify the bottom-trawl deep-sea fishery footprint on the western slope of Hatton Bank, to map the main fishing grounds and related deep-sea habitats (1000–1500 m deep), and to study the interactions between fisheries and cold-water corals. The results lead to a proposal to close the outcrop area (4645 km2) located on the western slope of Hatton Bank as a conservation measure for cold-water corals.

scholarly journals Megafaunal composition of cold-water corals and other deep-sea benthos in the southern Emperor Seamounts area, North Pacific Ocean

2017 ◽  
Vol 19 (1) ◽  
pp. 19-30 ◽  
Author(s):  
Mai MIYAMOTO ◽  
Masashi KIYOTA ◽  
Takeshi HAYASHIBARA ◽  
Masanori NONAKA ◽  
Yukimitsu IMAHARA ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
North Pacific ◽  
Deep Sea ◽  
Cold Water ◽  
North Pacific Ocean ◽  
Emperor Seamounts ◽  
Area North

scholarly journals Evidence that a Linear Megaplasmid Encodes Enzymes of Aliphatic Alkene and Epoxide Metabolism and Coenzyme M (2-Mercaptoethanesulfonate) Biosynthesis in XanthobacterStrain Py2

2001 ◽  
Vol 183 (7) ◽  
pp. 2172-2177 ◽  
Author(s):  
Jonathan G. Krum ◽  
Scott A. Ensign
Keyword(s):  
Ring Opening ◽  
Methanogenic Archaea ◽  
Hypothetical Protein ◽  
Epoxide Ring ◽  
Coenzyme M ◽  
Epoxide Ring Opening ◽  
Propylene Oxidation ◽  
Key Enzymes ◽  
Genes Encoding ◽  
Key Enzyme

ABSTRACT The bacterial metabolism of propylene proceeds by epoxidation to epoxypropane followed by a sequence of three reactions resulting in epoxide ring opening and carboxylation to form acetoacetate. Coenzyme M (2-mercaptoethanesulfonic acid) (CoM) plays a central role in epoxide carboxylation by serving as the nucleophile for epoxide ring opening and the carrier of the C3 unit that is ultimately carboxylated to acetoacetate, releasing CoM. In the present work, a 320-kb linear megaplasmid has been identified in the gram-negative bacterium Xanthobacter strain Py2, which contains the genes encoding the key enzymes of propylene oxidation and epoxide carboxylation. Repeated subculturing of Xanthobacter strain Py2 under nonselective conditions, i.e., with glucose or acetate as the carbon source in the absence of propylene, resulted in the loss of the propylene-positive phenotype. The propylene-negative phenotype correlated with the loss of the 320-kb linear megaplasmid, loss of induction and expression of alkene monooxgenase and epoxide carboxylation enzyme activities, and the loss of CoM biosynthetic capability. Sequence analysis of a hypothetical protein (XecG), encoded by a gene located downstream of the genes for the four enzymes of epoxide carboxylation, revealed a high degree of sequence identity with proteins of as-yet unassigned functions in the methanogenic archaeaMethanobacterium thermoautotrophicum andMethanococcus jannaschii and in Bacillus subtilis. The M. jannaschii homolog of XecG, MJ0255, is located next to a gene, MJ0256, that has been shown to encode a key enzyme of CoM biosynthesis (M. Graupner, H. Xu, and R. H. White, J. Bacteriol. 182: 4862–4867, 2000). We propose that the propylene-positive phenotype of Xanthobacter strain Py2 is dependent on the selective maintenance of a linear megaplasmid containing the genes for the key enzymes of alkene oxidation, epoxide carboxylation, and CoM biosynthesis.

scholarly journals Ashinkailepas kermadecensis, a new species of deep-sea scalpelliform barnacle (Thoracica: Eolepadidae) from the Kermadec Islands, southwest Pacific

Zootaxa ◽  
2009 ◽  
Vol 2021 (1) ◽  
pp. 57-65 ◽  
Author(s):  
JOHN S. BUCKERIDGE
Keyword(s):  
New Species ◽  
New Zealand ◽  
Deep Sea ◽  
Cold Water ◽  
The Other ◽  
Cold Seeps ◽  
Central Japan ◽  
Southwest Pacific ◽  
The North ◽  
A New Species

A new deep-sea stalked barnacle, Ashinkailepas kermadecensis sp. nov. has been recovered from a cold-water seep at depths of 1165 metres in the vicinity of the Kermadec Ridge to the northeast of the North Island, New Zealand. There are now two species of Ashinkailepas—the other, Ashinkailepas seepiophila Yamaguchi, Newman & Hashimoto, 2004, occurs in deep, cold seeps off central Japan. As there are two species within Ashinkailepas, formal diagnoses are provided for both taxa.

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