scholarly journals Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments

2019 ◽  
Author(s):  
Mingwei Cai ◽  
Yang Liu ◽  
Xiuran Yin ◽  
Zhichao Zhou ◽  
Michael W. Friedrich ◽  
...  

ABSTRACTAsgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the “Gerdarchaeota”. Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involving in the tetrahydromethanopterin-based Wood–Ljungdahl pathway. Transcriptomic evidence showed that all known Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, in different ecological niches in sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

1981 ◽  
Vol 32 (2) ◽  
pp. 245 ◽  
Author(s):  
DJW Moriarty ◽  
MC Barclay

The food of seven species of penaeid prawns from the Gulf of Carpentaria consists predominantly of Foraminifera, small molluscs, crustaceans and polychaetes. Measurements of organic and inorganic carbon, organic nitrogen and bacterial biomass were made. Foregut contents of adult prawns contained between 72 and 223 mg organic carbon/g dry wt. Protein constituted between 43 and 64% of the organic matter. Approximate assimilation efficiencies of food in prawns caught in the gulf, determined for four species, varied from 48 to 77% of organic carbon and from 42 to 77% of organic nitrogen. The food of juvenile Penaeus merguiensis was examined for two growing seasons. In the 1976-1977 season the foregut contents contained a mean of 41 mg organic nitrogen /g dry wt and 181 mg organic carbon /g dry wt. In the 1977-1978 season, significantly lower proportions of organic nitrogen and carbon were eaten, viz, 21 mg organic nitrogenlg dry wt and 101 mg organic carbon /g dry wt. Improved assay procedures for muramic acid have shown that bacteria are less important in the food of prawns than previously reported. Bacteria constituted less than 2% of the organic matter in the adults of all species, but in many juvenile P. merguiensis bacteria were more important, constituting up to 14% of organic matter.


2019 ◽  
Author(s):  
Christine Rooks ◽  
James Kar-Hei Fang ◽  
Pål Tore Mørkved ◽  
Rui Zhao ◽  
Hans Tore Rapp ◽  
...  

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.


DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Nolan Bornowski ◽  
John P Hamilton ◽  
Pan Liao ◽  
Joshua C Wood ◽  
Natalia Dudareva ◽  
...  

Abstract Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.


2012 ◽  
Vol 9 (5) ◽  
pp. 1915-1933 ◽  
Author(s):  
J. M. Mogollón ◽  
A. W. Dale ◽  
H. Fossing ◽  
P. Regnier

Abstract. Arkona Basin (southwestern Baltic Sea) is a seasonally-hypoxic basin characterized by the presence of free methane gas in its youngest organic-rich muddy stratum. Through the use of reactive transport models, this study tracks the development of the methane geochemistry in Arkona Basin as this muddy sediment became deposited during the last 8 kyr. Four cores are modeled each pertaining to a unique geochemical scenario according to their respective contemporary geochemical profiles. Ultimately the thickness of the muddy sediment and the flux of particulate organic carbon are crucial in determining the advent of both methanogenesis and free methane gas, the timescales over which methanogenesis takes over as a dominant reaction pathway for organic matter degradation, and the timescales required for free methane gas to form.


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