scholarly journals Long-chain diols in rivers: distribution and potential biological sources

2018 ◽  
Vol 15 (13) ◽  
pp. 4147-4161 ◽  
Author(s):  
Julie Lattaud ◽  
Frédérique Kirkels ◽  
Francien Peterse ◽  
Chantal V. Freymond ◽  
Timothy I. Eglinton ◽  
...  
Keyword(s):  
River Flow ◽  
River System ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
River Systems ◽  
Eukaryotic Diversity ◽  
Fractional Abundance ◽  
Biological Sources ◽  
Rrna Gene Sequencing ◽  
Long Chain

Abstract. Long-chain diols (LCDs) occur widespread in marine environments and also in lakes and rivers. Transport of LCDs from rivers may impact the distribution of LCDs in coastal environments, however relatively little is known about the distribution and biological sources of LCDs in river systems. In this study, we investigated the distribution of LCDs in suspended particulate matter (SPM) of three river systems (Godavari, Danube, and Rhine) in relation with precipitation, temperature, and source catchments. The dominant long-chain diol is the C32 1,15-diol followed by the C30 1,15-diol in all studied river systems. In regions influenced by marine waters, such as delta systems, the fractional abundance of the C30 1,15-diol is substantially higher than in the river itself, suggesting different LCD producers in marine and freshwater environments. A change in the LCD distribution along the downstream transects of the rivers studied was not observed. However, an effect of river flow is observed; i.e., the concentration of the C32 1,15-diol is higher in stagnant waters such as reservoirs and during seasons with river low stands. A seasonal change in the LCD distribution was observed in the Rhine, likely due to a change in the producers. Eukaryotic diversity analysis by 18S rRNA gene sequencing of SPM from the Rhine showed extremely low abundances of sequences (i.e., < 0.32 % of total reads) related to known algal LCD producers. Furthermore, incubation of the river water with 13C-labeled bicarbonate did not result in 13C incorporation into LCDs. This indicates that the LCDs present are mainly of fossil origin in the fast-flowing part of the Rhine. Overall, our results suggest that the LCD producers in rivers predominantly reside in lakes or side ponds that are part of the river system.

scholarly journals Long-chain diols in rivers: distribution and potential biological sources

2018 ◽  
Author(s):  
Julie Lattaud ◽  
Frédérique Kirkels ◽  
Francien Peterse ◽  
Chantal V. Freymond ◽  
Timothy I. Eglinton ◽  
...  
Keyword(s):  
River Flow ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
River Systems ◽  
Eukaryotic Diversity ◽  
Suspended Particulate ◽  
Fractional Abundance ◽  
Biological Sources ◽  
Rrna Gene Sequencing ◽  
Long Chain

Abstract. Long chain diols (LCDs) occur widespread in marine environments and also in lakes and rivers. Transport of LCDs from rivers may impact the distribution of LCDs in coastal environments, however relatively little is known about the distribution and biological sources of LCDs in river systems. In this study, we investigated the distribution of LCDs in suspended particulate matter (SPM) of three river systems (Godavari, Danube, and Rhine) in relation with season, precipitation, temperature, and source catchments. The dominant long-chain diol is the C32 1,15-diol followed by the C30 1,15-diol in all studied river systems. In regions influenced by marine waters, such as delta systems, the fractional abundance of the C30 1,15-diol is substantially higher than in the river itself, suggesting different LCD producers in marine and freshwater environments. A change in the LCD distribution along the downstream transects of the rivers studied was not observed. However, an effect of river flow is observed, i.e. the concentration of the C32 1,15-diol is higher in stagnant waters, such as reservoirs and during seasons with river low stands. A seasonal change in the LCD distribution was observed in the Rhine, likely due to a change in the producers. Eukaryotic diversity analysis by 18S rRNA gene sequencing of SPM from the Rhine showed extremely low abundances of sequences (i.e.

scholarly journals A quest for the biological sources of long chain alkyl diols in the western tropical North Atlantic Ocean

2018 ◽  
Vol 15 (19) ◽  
pp. 5951-5968 ◽  
Author(s):  
Sergio Balzano ◽  
Julie Lattaud ◽  
Laura Villanueva ◽  
Sebastiaan W. Rampen ◽  
Corina P. D. Brussaard ◽  
...  
Keyword(s):  
Atlantic Ocean ◽  
Water Column ◽  
North Atlantic ◽  
18S Rrna ◽  
North Atlantic Ocean ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Tropical North Atlantic ◽  
Biological Sources ◽  
Long Chain

Abstract. Long chain alkyl diols (LCDs) are widespread in the marine water column and sediments, but their biological sources are mostly unknown. Here we combine lipid analyses with 18S rRNA gene amplicon sequencing on suspended particulate matter (SPM) collected in the photic zone of the western tropical North Atlantic Ocean at 24 stations to infer relationships between LCDs and potential LCD producers. The C30 1,15-diol was detected in all SPM samples and accounted for >95 % of the total LCDs, while minor proportions of C28 and C30 1,13-diols, C28 and C30 1,14-diols, as well as C32 1,15-diol were found. The concentration of the C30 and C32 diols was higher in the mixed layer of the water column compared to the deep chlorophyll maximum (DCM), whereas concentrations of C28 diols were comparable. Sequencing analyses revealed extremely low contributions (≈0.1 % of the 18S rRNA gene reads) of known LCD producers, but the contributions from two taxonomic classes with which known producers are affiliated, i.e. Dictyochophyceae and Chrysophyceae, followed a trend similar to that of the concentrations of C30 and C32 diols. Statistical analyses indicated that the abundance of 4 operational taxonomic units (OTUs) of the Chrysophyceae and Dictyochophyceae, along with 23 OTUs falling into other phylogenetic groups, were weakly (r≤0.6) but significantly (p value <0.01) correlated with C30 diol concentrations. It is not clear whether some of these OTUs might indeed correspond to C28−32 diol producers or whether these correlations are just indirect and the occurrence of C30 diols and specific OTUs in the same samples might be driven by other environmental conditions. Moreover, primer mismatches were unlikely, but cannot be excluded, and the variable number of rRNA gene copies within eukaryotes might have affected the analyses leading to LCD producers being undetected or undersampled. Furthermore, based on the average LCD content measured in cultivated LCD-producing algae, the detected concentrations of LCDs in SPM are too high to be explained by the abundances of the suspected LCD-producing OTUs. This is likely explained by the slower degradation of LCDs compared to DNA in the oxic water column and suggests that some of the LCDs found here were likely to be associated with suspended debris, while the DNA from the related LCD producers had been already fully degraded. This suggests that care should be taken in constraining biological sources of relatively stable biomarker lipids by quantitative comparisons of DNA and lipid abundances.

scholarly journals Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

2022 ◽  
Vol 12 ◽  
Author(s):  
Elizabeth A. Suter ◽  
Maria Pachiadaki ◽  
Gordon T. Taylor ◽  
Virginia P. Edgcomb
Keyword(s):  
Food Web ◽  
Parasitic Infection ◽  
18S Rrna Gene ◽  
Microbial Food Web ◽  
Rrna Gene ◽  
Eukaryotic Diversity ◽  
Domains Of Life ◽  
Path Lengths ◽  
Rrna Gene Sequencing ◽  
Microbial Productivity

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

scholarly journals Validation of a PNA clamping method for reducing host DNA amplification and increasing eukaryotic diversity in rhizosphere microbiome studies

2020 ◽  
Author(s):  
Stephen J. Taerum ◽  
Blaire Steven ◽  
Daniel J. Gage ◽  
Lindsay R. Triplett
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Universal Primers ◽  
Rrna Gene ◽  
Plant Host ◽  
Eukaryotic Diversity ◽  
Rrna Gene Sequencing

AbstractProtists and microscopic animals are important but poorly understood determinants of plant health. Plant-associated eukaryotes could be surveyed by high-throughput sequencing of 18S ribosomal RNA (rRNA) genes, but the abundance of plant DNA in rhizosphere samples makes 18S rRNA gene amplification with universal primers unfeasible. Here we applied a pipeline to generate peptide nucleic acid (PNA) clamps to suppress the amplification of plant host DNA during 18S rRNA gene library preparation. We designed a PNA clamp, PoacV9_01, specific to the V9 region of the 18S rRNA gene for plants in the family Poaceae. PoacV9_01 suppressed the amplification of five species of grain crops in quantitative PCR reactions. In an 18S rRNA gene sequencing survey of the rhizosphere of maize, PoacV9_01 reduced the relative abundance of plant reads from 65% to 0.6%, while drastically increasing the number and diversity of animal, fungal, and protist reads detected. Thus, PoacV9_01 can be used to facilitate the study of eukaryotes present in grass phytobiomes. In addition, the pipeline developed here can be used to develop PNA clamps that target other plant species.

scholarly journals A quest for the biological sources of the ubiquitous long chain alkyl diols in the marine realm

2018 ◽  
Author(s):  
Sergio Balzano ◽  
Julie Lattaud ◽  
Laura Villanueva ◽  
Sebastiaan Rampen ◽  
Corina P. D. Brussaard ◽  
...  
Keyword(s):  
Water Column ◽  
18S Rrna ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Phylogenetic Groups ◽  
Suspended Particulate ◽  
Marine Realm ◽  
Biological Sources ◽  
Long Chain

Abstract. Long chain alkyl diols (LCDs) are widespread in the marine water column and sediments but their biological sources are mostly unknown. Here we combine lipid analyses with 18S rRNA gene amplicon sequencing on suspended particulate matter (SPM) collected in the photic zone of the tropical North Atlantic at 24 stations to infer relationships between LCDs and potential LCD-producers. The C30 1,15-diol was detected in all SPM samples and accounted for > 95 % of the total LCDs, while minor proportions of C28 and C30 1,13-diols, C28 and C30 1,14-diols as well as C32 1,15-diol were found. The concentration of the C30 and C32 diols was higher in the mixed layer of the water column compared to the deep chlorophyll maximum (DCM), whereas concentrations of C28 diols were comparable. Sequencing analyses revealed extremely low contributions (≈ 0.1 % of the 18S rRNA gene reads) of known LCD-producers but the contributions from two taxonomic classes to which known producers are affiliated, i.e. Dictyochophyceae and Chrysophyceae, followed a trend similar to that of the concentrations of C30 and C32 diols. Statistical analyses indicated that the abundance of 4 operational taxonomic units (OTUs) of the Chrysophyceae and Dictyochophyceae, along with 23 OTUs falling in other phylogenetic groups, were significantly correlated with C30 diol concentrations. However, it is not clear whether some of these OTUs might indeed correspond to LCD-producers or whether these correlations are just indirect. Furthermore, based on the average LCD-content measured in cultivated LCD-producing algae, the detected concentrations of LCDs in SPM are too high to be explained by the abundances of the suspected LCD-producing OTUs. This is likely explained by the slower degradation of LCDs compared to DNA in the oxic water column and suggests that some of the LCDs found here were likely to be associated to suspended debris, while the DNA from the related LCD-producers had been already fully degraded. This suggests that care should be taken in constraining biological sources of relatively stable biomarker lipids by quantitative comparisons of DNA and lipid abundances.

scholarly journals Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring

Pathogens ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 586
Author(s):  
Manuel Alejandro Borquez-Román ◽  
Luis Fernando Lares-Jiménez ◽  
Libia Zulema Rodriguez-Anaya ◽  
Jose Reyes Gonzalez-Galaviz ◽  
Paul A. Fuerst ◽  
...  
Keyword(s):  
Thermal Spring ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Likelihood Analysis ◽  
Ribosomal Ribonucleic Acid ◽  
Pcr Products ◽  
Northwestern Mexico ◽  
Rrna Gene Sequencing ◽  
A New Species

Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using universal eukaryotic primers for the small subunit ribosomal ribonucleic acid (SSU rRNA) gene. Sequencing primers were designed to allow the comparison of the 18S rRNA gene sequences of the new isolates with previous sequences reported for Stenamoeba. Phylogenetic relationships among sequences from Stenamoeba were determined using Maximum Likelihood analysis. The results showed the two "Agua Caliente" sequences to be closely related, while clearly separating them from those of other Stenamoeba taxa. The degrees of sequence differentiation from other taxa were considered sufficient to allow us to propose that the Mexican isolates represent a new species.

scholarly journals The cultivation of Pyropia haitanensis has important impacts on the seawater microbial community

2020 ◽  
Vol 32 (4) ◽  
pp. 2561-2573
Author(s):  
Wenlei Wang ◽  
Lei Wu ◽  
Kai Xu ◽  
Yan Xu ◽  
Dehua Ji ◽  
...  
Keyword(s):  
Microbial Community ◽  
Growth And Development ◽  
Alpha Diversity ◽  
18S Rrna Gene ◽  
Pyropia Haitanensis ◽  
Rrna Gene ◽  
Cultivation Period ◽  
Rrna Gene Sequencing ◽  
Bacteria And Fungi ◽  
Surrounding Seawater

Abstract Microorganisms play important roles in the growth and development of macroalgae. Still, the biodiversity of the epiphytic microbial community associated with the economically important red alga Pyropia haitanensis during the cultivation period remains uncharacterized, especially the effects of P. haitanensis cultivation on the microbial community of surrounding seawater. Here, we isolated epiphytic microbes from P. haitanensis during the thallus stage during oceanic cultivation and the conchocelis stage during industrial cultivation. The dynamic diversity patterns, as determined by 16S and 18S rRNA gene sequencing of the bacterial and fungal communities, respectively, associated with P. haitanensis and seawater in the presence and absence of algal cultivation were investigated. A notable distinction was observed between the microbial communities of seawater with and without P. haitanensis cultivation. Additionally, the alpha-diversity of seawater with P. haitanensis cultivation was significantly greater than without P. haitanensis cultivation. Cyanobacteria were the dominant species in the latter, while Rhodobacteraceae was enriched in the former. Furthermore, there were significant differences in the microbial community of P. haitanensis at the thallus and conchocelis stages. Seawater properties had significant direct effects on the microbial diversity of P. haitanensis and cultivation seawater, but not on non-cultivation seawater. The enriched microbial presence might promote thallus morphogenesis and be beneficial for the growth and development of both the thallus and conchocelis stages. These findings expand our knowledge of the bacteria and fungi that are beneficial for Pyropia nursery seeding and cultivation, as well as the effects of P. haitanensis cultivation on the seawater microbial community.

scholarly journals Fungi found in Mediterranean and North Sea sponges: how specific are they?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3722 ◽  
Author(s):  
Mohd Azrul Naim ◽  
Hauke Smidt ◽  
Detmer Sipkema
Keyword(s):  
North Sea ◽  
Ribosomal Rna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Anaerobic Digesters ◽  
Operational Taxonomic Units ◽  
The North ◽  
Hypervariable Regions ◽  
The North Sea ◽  
Biological Sources

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

scholarly journals Biodegradation of thiocyanate in groundwater by a native aquifer microbial consortium

2018 ◽  
Author(s):  
Liam P Spurr ◽  
Mathew P Watts ◽  
Han Ming Gan ◽  
John W Moreau
Keyword(s):  
18S Rrna Gene ◽  
Ex Situ ◽  
Contaminated Groundwater ◽  
Rrna Gene ◽  
Proof Of Concept ◽  
Tailings Dams ◽  
Ore Processing ◽  
Rrna Gene Sequencing ◽  
Culturing Conditions

Gold ore processing typically generates large amounts of thiocyanate (SCN-)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN--contaminated groundwater, either in situ or through ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN--degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ~135 mgL-1 SCN-, was collected from an aquifer below an unlined tailings dam. An SCN--degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN--degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulfur-oxidising bacteria. Interestingly, few recognised SCN--degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN- degradation in groundwater by native aquifer microorganisms.

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