Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships’ Ballast Water: Implications for Biogeography and Infectious Diseases

Lohan, Katrina M. Pagenkopp; Fleischer, Robert C.; Carney, Katharine J.; Holzer, Kimberly K.; Ruiz, Gregory M.

doi:10.1007/s00248-015-0684-6

Cited by 49 publications

(55 citation statements)

References 61 publications

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“…3). For example, reads belonging to the Pseudoperkinsidae lineage of protist parasites 38 increased to 48.2% of the amplicons in the larval sample with 7.5 μM PNA, as compared to less than 1% of the amplicons without PNA blocker.…”

Section: Resultsmentioning

confidence: 99%

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome

Belda

Coulibaly

Fofana

et al. 2017

Sci Rep

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Anopheles mosquitoes are vectors of the human malaria parasite, Plasmodium falciparum. The vector microbiota is a likely factor influencing parasite transmission. The prokaryotic microbiota of mosquitoes is efficiently surveyed by sequencing of hypervariable regions of the 16s ribosomal RNA (rRNA) gene. However, identification of the eukaryotic microbiota by targeting the 18s rRNA gene is challenging due to simultaneous amplification of the abundant 18s rRNA gene target in the mosquito host. Consequently, the eukaryotic microbial diversity of mosquitoes is vastly underexplored. An efficient methodology is needed to identify this component of the microbiota, expected to include relatives of Plasmodium. Here, we use defined panels of Anopheles samples from West Africa to test two experimental PCR clamp approaches to maximize the specific amplification of 18s rRNA gene hypervariable regions from eukaryotic microbes: anneal-inhibiting blocking primers and peptide-nucleic acid (PNA) oligonucleotide blockers. Of the two, PNA blockers were the only efficient blocking strategy, allowing a reduction of mosquito 18s rRNA gene sequences by more than 80% for the V4 hypervariable region. These PNA blockers will facilitate taxonomic profiling of the eukaryotic microbiota of the A. gambiae species complex, and contribute to a better understanding of microbial influence upon immunity and pathogen infection.

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Section: Resultsmentioning

confidence: 99%

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome

Belda

Coulibaly

Fofana

et al. 2017

Sci Rep

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“…First, metabarcoding is a highly sensitive method for detection of a variety of taxa, allowing researchers to identify a greater breadth of microbial taxa from vectors (e.g. BW) than previously feasible (Brinkmeyer, ; Kim et al., ; Pagenkopp Lohan et al., ). Metabarcoding can detect organisms in low abundance (Zhan et al., ), the parasites and symbionts of organisms (Lindeque, Parry, Harmer, Somerfield, & Atkinson, ) and even potential invaders (Brown, Chain, Crease, MacIsaac, & Cristescu, 2015).…”

Section: Discussionmentioning

confidence: 99%

“…Our approach for removing OTUs in negative controls is detailed in Pagenkopp Lohan et al. (). Briefly, we removed OTUs in negative controls ( n = 8 OTUs, Table ) and all identified as organelle or mitochondrial ( n = 85).…”

Section: Methodsmentioning

confidence: 99%

Molecular characterisation of protistan species and communities in ships’ ballast water across three U.S. coasts

Lohan

Fleischer

Carney

et al. 2017

Diversity and Distributions

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Aim We characterised protistan taxa in ships’ ballast water (BW) arriving to port systems across three U.S. coasts. Our goals were to compare (1) diversity and (2) community composition of protists in BW among and between port systems. Location Chesapeake Bay in Virginia (Port of Hampton Roads), Galveston Bay in Texas (Ports of Texas City, Houston and Bayport) and Prince William Sound in Alaska (Port of Valdez). Methods We collected 61 BW samples from 39 vessels from May to August 2013. We conducted amplicon‐based high‐throughput sequencing (HTS) using the hypervariable V4 domain of the small subunit (SSU) gene of the ribosomal RNA (rRNA) complex to identify protistan taxa. Results We detected 8,561 OTUs from protistan taxa, including 35 taxonomic groups. We found high protistan diversity in the BW entering all three port systems, with the dominant taxa belonging to the Alveolata, Rhizaria and Stramenopiles. Thirty‐eight taxa were found in high relative abundance (>10,000 sequences), and some were recovered from multiple samples within and across ports, indicating both a high relative abundance and frequency of introduction events. The composition of the protistan communities entering each of the port systems appeared to vary depending on BW source, with those entering Valdez being consistently more similar to each other than those entering other port systems. Main conclusions This study is the most comprehensive assessment of protistan diversity in BW and has important implications for microbial biogeography and invasions. Ships’ BW is importing distinct and diverse protistan communities to U.S. coasts with high propagule pressure for some taxa, creating opportunity for invasion by novel taxa. Further, our results demonstrate the broad‐scale movement of marine protists that has occurred through BW, highlighting a discrepancy between the large magnitude of introductions and limited number of known microbial invasions.

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“…Furthermore, microbes can be transported—and survive—over long distances in several ways e.g. by aerial movement, migratory birds and ballast water [3]. The above properties, high abundance and dispersion potential, are what lead to the assumption “everything is everywhere, but the environment selects” [4], an issue that still provokes intense discussions [5].…”

Section: Introductionmentioning

confidence: 99%

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms

et al. 2017

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Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions.

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Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships’ Ballast Water: Implications for Biogeography and Infectious Diseases

Cited by 49 publications

References 61 publications

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome

Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome

Molecular characterisation of protistan species and communities in ships’ ballast water across three U.S. coasts

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms

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