scholarly journals DNA-foraging bacteria in the seafloor

2019 ◽  
Author(s):  
Kenneth Wasmund ◽  
Claus Pelikan ◽  
Margarete Watzka ◽  
Andreas Richter ◽  
Amy Noel ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Stable Isotope ◽  
Carbon Source ◽  
Marine Sediments ◽  
Ecosystem Function ◽  
Stable Isotope Probing ◽  
Extracellular Dna ◽  
Genetic Features ◽  
Close Relatives ◽  
Globally Distributed

AbstractExtracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of key DNA-foraging microorganisms in marine sediments are completely unknown. Here we combined microcosm experiments, stable isotope probing and genome-centric metagenomics to study microbial catabolism of DNA and its sub-components in anoxic marine sediments.13C-DNA added to sediment microcosms was degraded within ten days and mineralised to13CO2. Stable isotope probing showed that diverseCandidatusIzemoplasma,Lutibacter, Shewanella, FusibacteraceaeandNitrincolaceaeincorporated DNA-derived13C-carbon. Genomes representative of the13C-labelled taxa were recovered and all encoded enzymatic repertoires for catabolism of DNA. Comparative genomics indicated that DNA can be digested by diverse members of the orderCandidatusIzemoplasmatales (formerTenericutes), which appear to be specialised DNA-degraders that encode multiple extracellular nucleases.Fusibacteraceaelacked genes for extracellular nucleases but utilised various individual purine- and pyrimidine-based molecules, suggesting they ‘cheated’ on liberated sub-components of DNA. Close relatives of the DNA-degrading taxa are globally distributed in marine sediments, suggesting that these poorly understood taxa contribute widely to the key ecosystem function of degrading and recycling DNA in the seabed.

scholarly journals Subgroup level differences of physiological activities in marine Lokiarchaeota

2020 ◽  
Author(s):  
Xiuran Yin ◽  
Mingwei Cai ◽  
Yang Liu ◽  
Guowei Zhou ◽  
Tim Richter-Heitmann ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Marine Sediments ◽  
Inorganic Carbon ◽  
Bacterial Biomass ◽  
Stable Isotope Probing ◽  
Aromatic Compound Degradation ◽  
Lactate Degradation ◽  
Globally Distributed ◽  
Mud Area

Abstract Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus ‘Prometheoarchaeum syntrophicum’. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.

scholarly journals Linking Microbial Community Function to Phylogeny of Sulfate-Reducing Deltaproteobacteria in Marine Sediments by Combining Stable Isotope Probing with Magnetic-Bead Capture Hybridization of 16S rRNA

2009 ◽  
Vol 75 (15) ◽  
pp. 4927-4935 ◽  
Author(s):  
Tetsuro Miyatake ◽  
Barbara J. MacGregor ◽  
Henricus T. S. Boschker
Keyword(s):  
Microbial Community ◽  
Stable Isotope ◽  
16S Rrna ◽  
Marine Sediments ◽  
Magnetic Bead ◽  
Stable Isotope Probing ◽  
Target Range ◽  
Microbial Community Function ◽  
Sulfate Reducing ◽  
Community Function

ABSTRACT We further developed the stable isotope probing, magnetic-bead capture method to make it applicable for linking microbial community function to phylogeny at the class and family levels. The main improvements were a substantial decrease in the protocol blank and an approximately 10-fold increase in the detection limit by using a micro-elemental analyzer coupled to isotope ratio mass spectrometry to determine 13C labeling of isolated 16S rRNA. We demonstrated the method by studying substrate utilization by Desulfobacteraceae, a dominant group of complete oxidizing sulfate-reducing Deltaproteobacteria in marine sediments. Stable-isotope-labeled [13C]glucose, [13C]propionate, or [13C]acetate was fed into an anoxic intertidal sediment. We applied a nested set of three biotin-labeled oligonucleotide probes to capture Bacteria, Deltaproteobacteria, and finally Desulfobacteraceae rRNA by using hydrophobic streptavidin-coated paramagnetic beads. The target specificities of the probes were examined with pure cultures of target and nontarget species and by determining the phylogenetic composition of the captured sediment rRNA. The specificity of the final protocol was generally very good, as more than 90% of the captured 16S rRNA belonged to the target range of the probes. Our results indicated that Desulfobacteraceae were important consumers of propionate but not of glucose. However, the results for acetate utilization were less conclusive due to lower and more variable labeling levels in captured rRNA. The main advantage of the method in this study over other nucleic acid-based stable isotope probing methods is that 13C labeling can be much lower, to the extent that δ13C ratios can be studied even at their natural abundances.

scholarly journals Food Web Structure and Trophic Interactions Revealed by Stable Isotope Analysis in the Midstream of the Chishui River, a Tributary of the Yangtze River, China

Water ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 195
Author(s):  
Qiang Qin ◽  
Fubin Zhang ◽  
Fei Liu ◽  
Chunling Wang ◽  
Huanzhang Liu
Keyword(s):  
Stable Isotope ◽  
Carbon Source ◽  
Food Web ◽  
Food Chain ◽  
Yangtze River ◽  
Trophic Niche ◽  
The Yangtze River ◽  
Food Chain Length ◽  
Trophic Pathways ◽  
Chishui River

Understanding energy flow and nutrient pathways is crucial to reveal the dynamics and functions of riverine ecosystems and develop appropriate conservation strategies. In this study, we utilized stable isotopes of δ13C and δ15N to examine the fundamental characteristics of trophic position, trophic niche, and carbon source for the food web in the midstream of the Chishui River, a tributary to the Yangtze River. Our results showed that stable isotope signatures among different sorts of basal resources and consumers were significantly distinguishable and that the food chain consisted of four trophic levels, indicating the multiple trophic pathways and long food chain length here. The trophic guilds of fish were classified into four categories, in which herbivorous and carnivorous fish showed greater trophic diversity and omnivorous fish had higher trophic redundancy, which meant that there was a stable trophic niche structure in the study area. Phytoplankton and periphyton presented the largest contributions to consumers, indicating that autochthonous productivity was the dominant carbon source in the midstream of the Chishui River. Since the Chishui River is still in a natural condition without any dam constructions, the autochthonous productivity, stable trophic niche structure, multiple trophic pathways and long food chain length found here demonstrate its high conservation value. Therefore, the strategy to refrain from damming on this river should persist into the future.

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