scholarly journals Diversity of Microbial Communities and Quantitative Chemodiversity in Layers of Marine Sediment Cores from a Causeway (Kaichu-Doro) in Okinawa Island, Japan

2017 ◽  
Vol 8 ◽  
Author(s):  
Taha Soliman ◽  
James D. Reimer ◽  
Sung-Yin Yang ◽  
Alejandro Villar-Briones ◽  
Michael C. Roy ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Marine Sediment ◽  
Sediment Cores ◽  
Okinawa Island

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

scholarly journals Effects of Macrofaunal Recolonization on Biogeochemical Processes and Microbiota—A Mesocosm Study

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1599
Author(s):  
Annika Fiskal ◽  
Aixala Gaillard ◽  
Sebastien Giroud ◽  
Dejan Malcic ◽  
Prachi Joshi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bottom Water ◽  
Surface Sediments ◽  
Sediment Cores ◽  
Lake Basin ◽  
Sediment Properties ◽  
Chironomid Larvae ◽  
Sediment Reworking ◽  
Mesocosm Experiments ◽  
Tubificid Worms

Macroinvertebrates are widespread in lake sediments and alter sedimentary properties through their activity (bioturbation). Understanding the interactions between bioturbation and sediment properties is important given that lakes are important sinks and sources of carbon and nutrients. We studied the biogeochemical impact of macrofauna on surface sediments in 3-month-long mesocosm experiments conducted using sediment cores from a hypoxic, macrofauna-free lake basin. Experimental units consisted of hypoxic controls, oxic treatments, and oxic treatments that were experimentally colonized with chironomid larvae or tubificid worms. Overall, the presence of O2 in bottom water had the strongest geochemical effect and led to oxidation of sediments down to 2 cm depth. Relative to macrofauna-free oxic treatments, chironomid larvae increased sediment pore water concentrations of nitrate and sulfate and lowered porewater concentrations of reduced metals (Fe2+, Mn2+), presumably by burrow ventilation, whereas tubificid worms increased the redox potential, possibly through sediment reworking. Microbial communities were very similar across oxic treatments; however, the fractions of α-, β-, and γ-Proteobacteria and Sphingobacteriia increased, whereas those of Actinobacteria, Planctomycetes, and Omnitrophica decreased compared to hypoxic controls. Sediment microbial communities were, moreover, distinct from those of macrofaunal tubes or feces. We suggest that, under the conditions studied, bottom water oxygenation has a stronger biogeochemical impact on lacustrine surface sediments than macrofaunal bioturbation.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals The Search for Supernova-Produced Radionuclides in Terrestrial Deep-Sea Archives

2012 ◽  
Vol 29 (2) ◽  
pp. 109-114 ◽  
Author(s):  
J. Feige ◽  
A. Wallner ◽  
S. R. Winkler ◽  
S. Merchel ◽  
L. K. Fifield ◽  
...  
Keyword(s):  
Solar System ◽  
Marine Sediment ◽  
Deep Sea ◽  
Massive Stars ◽  
Sediment Cores ◽  
Deep Ocean ◽  
Transport Mechanisms ◽  
Supernova Shell ◽  
Process Element ◽  
Insight Into

AbstractAn enhanced concentration of 60Fe was found in a deep ocean crust in 2004 in a layer corresponding to an age of ∼2 Myr. The confirmation of this signal in terrestrial archives as supernova-induced and the detection of other supernova-produced radionuclides is of great interest. We have identified two suitable marine sediment cores from the South Australian Basin and estimated the intensity of a possible signal of the supernova-produced radionuclides 26Al, 53Mn, 60Fe, and the pure r-process element 244Pu in these cores. The finding of these radionuclides in a sediment core might allow us to improve the time resolution of the signal and thus to link the signal to a supernova event in the solar vicinity ∼2 Myr ago. Furthermore, it gives us an insight into nucleosynthesis scenarios in massive stars, condensation into dust grains and transport mechanisms from the supernova shell into the solar system.

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