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 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 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 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 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 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.

scholarly journals Ecological assessment of phytoplankton community via microscopic method and 18S rRNA gene sequencing in Pearl River Estuary

2019 ◽  
Vol 131 ◽  
pp. 01043 ◽  
Author(s):  
Bo Peng ◽  
Yuannan Wang ◽  
Hengjun Zhang ◽  
Chen Chen ◽  
Hailin Luo ◽  
...  
Keyword(s):  
18S Rrna ◽  
Phytoplankton Community ◽  
Diversity Index ◽  
River Estuary ◽  
Gene Sequencing ◽  
Pearl River Estuary ◽  
Ecological Assessment ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Monitoring phytoplankton community underpins our understanding of water quality and ecological functions. In this study, we approached phytoplankton abundance, community composition, and diversity by both microscopy and 18S rRNA gene sequencing. Environmental variances influencing the phytoplankton were evaluated as well. There were 6 phyla and 62 species identified by microscopy, and the diversity index Shannon-Wiener and evenness index Pielou index indicated phytoplankton community had high diversity; however, the high density of dominance genus suggested that our research region had potential red tide effects. The canonical correspondence analysis illustrated that suspended solids, phosphate and temperature were three major factors that affected the distribution and components of phytoplankton community. The DNA barcoding sequencing of 18S rRNA gene supported the main results via microscopic methods while providing more identified community components, which implied that 18S rRNA gene sequencing can be used as a supplemental method for fast ecological assessment of phytoplankton community.

Association between diet and rumen microbiota in wild roe deer

2019 ◽  
Vol 366 (6) ◽  
Author(s):  
Robert Wilson ◽  
Kjartan Østbye ◽  
Inga Leena Angell ◽  
Knut Rudi
Keyword(s):  
18S Rrna ◽  
Roe Deer ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Rumen Microbiota ◽  
Dietary Components ◽  
Rrna Gene Sequencing ◽  
Insight Into

ABSTRACT The association between diet and the rumen microbiota for wild animals remains largely unexplored. Here, we explored this association using a combination of 16S rRNA gene sequencing to determine the prokaryote microbiota and 18S rRNA gene sequencing to determine the dietary components for wild roe deer. These analyses revealed a wide diversity of dietary components, with over-representation of Bacteroidetes for the diet-correlating bacteria. Ruminococcus, on the other hand, dominated the stable diet-independent part of the microbiota. Taken together, the combination of 16S and 18S rRNA gene analyses provide novel insight into rumen microbiota ecology.

Diversity and distribution of nematodes associated with terrestrial slugs in the Western Cape Province of South Africa

2011 ◽  
Vol 86 (2) ◽  
pp. 215-221 ◽  
Author(s):  
J.L. Ross ◽  
E.S. Ivanova ◽  
W.F. Sirgel ◽  
A.P. Malan ◽  
M.J. Wilson
Keyword(s):  
South Africa ◽  
18S Rrna ◽  
Parasitic Nematode ◽  
Gene Sequencing ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Western Cape ◽  
Western Cape Province ◽  
Rrna Gene Sequencing ◽  
Three New Species

AbstractA survey of nematodes associated with native and introduced species of terrestrial slugs was conducted in the Western Cape Province of South Africa, in order to gather new data regarding diversity and distribution. A total of 521 terrestrial slugs were collected from 35 localities throughout the Western Cape. All slugs were dissected and examined for the presence of internal nematodes. Extracted nematodes were identified using a combination of molecular (18S rRNA gene sequencing) and morphological techniques. Nematodes were found parasitizing slugs at 14 of the 35 sites examined, amounting to 40% of sample sites. Of all slugs, 6% were infected with nematodes. A total of seven species of nematode were identified in the province, includingAgfa flexilis,Angiostomasp.,Phasmarhabditissp. SA1,Phasmarhabditissp. SA2,Caenorhabditis elegans,Panagrolaimussp. andRhabditissp. Of these species, four were thought to be parasitic to slugs (A. flexilis, Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2), as opposed to forming necromenic or phoretic associations. Three new species of slug-parasitic nematode were identified during this study (Angiostomasp.,Phasmarhabditissp. SA1 andPhasmarhabditissp. SA2).

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