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 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 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 Genomics Reveals the Metabolic Potential and Functions in the Redistribution of Dissolved Organic Matter in Marine Environments of the Genus Thalassotalea

2020 ◽  
Vol 8 (9) ◽  
pp. 1412
Author(s):  
Minji Kim ◽  
In-Tae Cha ◽  
Ki-Eun Lee ◽  
Eun-Young Lee ◽  
Soo-Je Park
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Extracellular Enzymes ◽  
Marine Invertebrates ◽  
Carbon Sources ◽  
Marine Environments ◽  
Metabolic Potential ◽  
Carbohydrate Utilization ◽  
Genes Encoding ◽  
Metagenomic Study

Members of the bacterial genus Thalassotalea have been isolated recently from various marine environments, including marine invertebrates. A metagenomic study of the Deepwater Horizon oil plume has identified genes involved in aromatic hydrocarbon degradation in the Thalassotalea genome, shedding light on its potential role in the degradation of crude oils. However, the genomic traits of the genus are not well-characterized, despite the ability of the species to degrade complex natural compounds, such as agar, gelatin, chitin, or starch. Here, we obtained a complete genome of a new member of the genus, designated PS06, isolated from marine sediments containing dead marine benthic macroalgae. Unexpectedly, strain PS06 was unable to grow using most carbohydrates as sole carbon sources, which is consistent with the finding of few ABC transporters in the PS06 genome. A comparative analysis of 12 Thalassotalea genomes provided insights into their metabolic potential (e.g., microaerobic respiration and carbohydrate utilization) and evolutionary stability [including a low abundance of clustered regularly interspaced short palindromic repeats (CRISPR) loci and prophages]. The diversity and frequency of genes encoding extracellular enzymes for carbohydrate metabolism in the 12 genomes suggest that members of Thalassotalea contribute to nutrient cycling by the redistribution of dissolved organic matter in marine environments. Our study improves our understanding of the ecological and genomic properties of the genus Thalassotalea.

Stabilisation and mineralisation of sludge in reed bed systems after 10–20 years of operation

2013 ◽  
Vol 69 (3) ◽  
pp. 539-545 ◽  
Author(s):  
Steen Nielsen ◽  
Eleonora Peruzzi ◽  
Cristina Macci ◽  
Serena Doni ◽  
Grazia Masciandaro
Keyword(s):  
Organic Matter ◽  
Extracellular Enzymes ◽  
Wastewater Treatment Plants ◽  
Hydrolytic Enzymes ◽  
Biochemical Properties ◽  
Water Soluble ◽  
Biochemical Processes ◽  
C And N ◽  
Reed Bed ◽  
Urban Wastewater Treatment

Sludge stabilisation and mineralisation during periods of operation between 10 and 21 years were investigated in three different systems receiving sludge from urban wastewater treatment plants situated in Denmark. Samples were taken along the entire profiles, in order to compare the effectiveness of the sludge stabilisation process. Particular attention was given to the stabilisation process occurring within the reed beds; in fact, parameters correlated to biochemical properties of organic sludge matter were determined. Statistical procedures were used to evaluate how the biochemical processes influence the quality of sludge organic matter. The level of total organic carbon and total nitrogen had a similar trend along the profile: their concentration decreased with increasing depth, reaching very low levels at the deepest layers. The same trend was also observed for the water-soluble carbon, N-NH3, β-glucosidase and urease activities, and hydrolytic enzymes linked to C and N cycles: their values decreased dramatically with increasing depth, meaning that the level of mineralisation of the organic matter was higher in the deepest layers. The determination of extracellular enzymes bound to humic substances and humic carbon permitted evaluation of the stabilisation of organic sludge matter, and also allowed individuation of the ways in which the sludge was stabilised, in terms of mineralisation and humification of the organic matter.

scholarly journals Sediment Resuspension and Associated Extracellular Enzyme Activities Measured ex situ: A Mechanism for Benthic-Pelagic Coupling in the Deep Gulf of Mexico

2021 ◽  
Vol 8 ◽  
Author(s):  
Kai Ziervogel ◽  
Julia Sweet ◽  
Andrew R. Juhl ◽  
Uta Passow
Keyword(s):  
Organic Matter ◽  
Gulf Of Mexico ◽  
Deep Sea ◽  
Enzyme Activities ◽  
Bacterial Cell ◽  
Bottom Water ◽  
Extracellular Enzymes ◽  
Sediment Resuspension ◽  
Bottom Waters ◽  
Benthic Pelagic Coupling

Sediment resuspension caused by near-bed currents mediates exchange processes between the seafloor and the overlying water column, known as benthic-pelagic coupling. To investigate the effects of sediment resuspension on microbial enzyme activities in bottom waters (<500 m), we conducted onboard erosion experiments using sediment cores taken with a multi-corer from six deep-sea sites in the northern Gulf of Mexico. We then incubated the core-top water with resuspended sediments in roller tanks to simulate bottom water conditions following sediment resuspension. Bacterial cell abundance, particulate organic matter content, and potential rates of three hydrolytic enzymes (leucine aminopeptidases – PEP; β-glucosidases – GLU, lipases – LIP) were monitored during the experimentally-generated erosion events and subsequently in the roller tanks to examine whether resuspension of deep-sea sediments enhances activities of extracellular enzymes in overlying waters. Surficial sediments were resuspended at critical shear stress velocities between 1.4 and 1.7 cm s–1, which parallel bottom water currents of 28 and 34 cm s–1. Only one of our nine cores resisted experimentally generated bottom shear stresses and remained undisturbed, possibly as a result of oil residues from natural hydrocarbon seeps at the investigated site. The most notable enzymatic responses to sediment resuspension were found for LIP activities that increased in overlying waters of all eight of our resuspended cores and remained at high levels during the roller tank incubations. PEP and GLU showed orders of magnitude lower rates and more variable responses to experimentally resuspended sediments compared with LIP. We also found a disconnect between enzyme activities and bacterial cell numbers, indicating a major role of extracellular enzymes physically disconnected from microbial cells in our experiments. Our results demonstrate that sediment resuspension may promote organic matter breakdown in bottom waters by supplying extracellular enzymes without requiring a bacterial growth response. The marked increase in LIP activity suggests that resuspended enzymes may affect the degradation of petroleum hydrocarbons, including those from the natural seeps that are abundant in the investigation area.

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.

scholarly journals Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea

2016 ◽  
Vol 13 (9) ◽  
pp. 2815-2821 ◽  
Author(s):  
Federico Baltar ◽  
Catherine Legrand ◽  
Jarone Pinhassi
Keyword(s):  
Organic Matter ◽  
Baltic Sea ◽  
Extracellular Enzymes ◽  
Seasonal Pattern ◽  
Critical Factor ◽  
Hydrolytic Activity ◽  
Seasonal Temperature ◽  
The Baltic Sea ◽  
The Baltic ◽  
Hydrolysis Of

Abstract. Extracellular enzymatic activities (EEAs) are a crucial step in the degradation of organic matter. Dissolved (cell-free) extracellular enzymes in seawater can make up a significant contribution of the bulk EEA. However, the factors controlling the proportion of dissolved EEA in the marine environment remain unknown. Here we studied the seasonal changes in the proportion of dissolved relative to total EEA (of alkaline phosphatase (APase), β-glucosidase (BGase), and leucine aminopeptidase (LAPase)), in the Baltic Sea for 18 months. The proportion of dissolved EEA ranged between 37 and 100, 0 and 100, and 34 and 100 % for APase, BGase, and LAPase, respectively. A consistent seasonal pattern in the proportion of dissolved EEA was found among all the studied enzymes, with values up to 100 % during winter and  <  40 % during summer. A significant negative relation was found between the proportion of dissolved EEA and temperature, indicating that temperature might be a critical factor controlling the proportion of dissolved relative to total EEA in marine environments. Our results suggest a strong decoupling of hydrolysis rates from microbial dynamics in cold waters. This implies that under cold conditions, cell-free enzymes can contribute to substrate availability at large distances from the producing cell, increasing the dissociation between the hydrolysis of organic compounds and the actual microbes producing the enzymes. This might also suggest a potential effect of global warming on the hydrolysis of organic matter via a reduction of the contribution of cell-free enzymes to the bulk hydrolytic activity.

Gametogenesis and the reproductive cycle in the deep-sea anemone Paracalliactis stephensoni (Cnidaria: Actiniaria)

1990 ◽  
Vol 70 (1) ◽  
pp. 163-172 ◽  
Author(s):  
Michel Praet-Van
Keyword(s):  
Organic Matter ◽  
Shallow Water ◽  
Deep Sea ◽  
Phytoplankton Bloom ◽  
Sea Anemone ◽  
Bay Of Biscay ◽  
Sea Anemones ◽  
Spring Phytoplankton Bloom ◽  
Sea Floor ◽  
Ultrastructural Investigation

This ultrastructural investigation of gametogenesis in a deep-sea anemone of the Bay of Biscay trawled around 2000 m depth, contributes to the knowledge of biology and strategy of reproduction of deep-sea benthos.This sea anemone is dioecious. The sperm appears very similar to those of shallow water sea anemones of the genus, Calliactis. The ultrastructural investigation of oogenesis allows the characteristics of the stages of previtellogenesis and vitellogenesis to be defined. The latter begins with a period of lipogenesis correlated with the formation of a trophonema. Mature oocytes measure up to 180 (im in diameter. Study of spermatogenesis and oogenesis reveals that spawning occurs in April/May. In males, the main area of testicular cysts, full of sperm, reaches maximal development from March to May and, in females, the percentage of mature oocytes decreases from 33% in April to 1% in May.Spawning may be induced by the advent in the deep-sea of the products of the spring phytoplankton bloom. This period of spawning, during the increased deposition of organic matter to the deep-sea floor, may be an advantageous strategy for early development of Paracalliactis.

scholarly journals Production of dissolved organic matter by phytoplankton and its uptake by heterotrophic prokaryotes in large tropical lakes

2014 ◽  
Vol 59 (4) ◽  
pp. 1364-1375 ◽  
Author(s):  
Cedric Morana ◽  
Hugo Sarmento ◽  
Jean-Pierre Descy ◽  
Josep M. Gasol ◽  
Alberto V. Borges ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Tropical Lakes ◽  
Heterotrophic Prokaryotes
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