scholarly journals Disentangling the mechanisms shaping the surface ocean microbiota

2019 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Pedro C. Junger ◽  
Caterina R. Giner ◽  
Anders K. Krabberød ◽  
...  
Keyword(s):  
Sequence Data ◽  
Spatial Differentiation ◽  
Dispersal Limitation ◽  
Rrna Genes ◽  
Dna Sequence Data ◽  
Surface Ocean ◽  
Ecological Mechanisms ◽  
Global Biogeochemical Cycles ◽  
Main Components ◽  
18S Rrna Genes

Abstract Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlaying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore the previous, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans. Results We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. Conclusions The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear.

scholarly journals Disentangling the mechanisms shaping the surface ocean microbiota

2020 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Pedro C. Junger ◽  
Caterina R. Giner ◽  
Anders K. Krabberød ◽  
...  
Keyword(s):  
Sequence Data ◽  
Spatial Differentiation ◽  
Dispersal Limitation ◽  
Rrna Genes ◽  
Dna Sequence Data ◽  
Surface Ocean ◽  
Ecological Mechanisms ◽  
Global Biogeochemical Cycles ◽  
Main Components ◽  
18S Rrna Genes

Abstract Background The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have largescale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here we investigate how fundamental ecological mechanisms ( selection , dispersal and ecological drift ) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore the previous, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans . Results We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts. Conclusions The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear.

scholarly journals Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

2018 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Caterina. R. Giner ◽  
Anders K. Krabberød ◽  
Thomas S. B. Schmidt ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Sequence Data ◽  
Scale Effects ◽  
Dispersal Limitation ◽  
Global Scale ◽  
Global Ocean ◽  
Ecosystem Functions ◽  
Ecological Processes ◽  
Surface Ocean

ABSTRACTThe smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts thatselection,dispersalanddriftare main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.SIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmentalselection,dispersaland random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

scholarly journals Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

2014 ◽  
Vol 80 (14) ◽  
pp. 4363-4373 ◽  
Author(s):  
Alle A. Y. Lie ◽  
Zhenfeng Liu ◽  
Sarah K. Hu ◽  
Adriane C. Jones ◽  
Diane Y. Kim ◽  
...  
Keyword(s):  
Species Richness ◽  
Sanger Sequencing ◽  
18S Rrna ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Hypervariable Region ◽  
Full Length ◽  
Rrna Genes ◽  
Data Sets ◽  
18S Rrna Genes

ABSTRACTNext-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

Investigating the amphiatlantic status of Facelina bostoniensis (Couthouy, 1838) (Nudibranchia: Aeolidida)

2020 ◽  
Vol 86 (1) ◽  
pp. 64-71
Author(s):  
Leila Carmona
Keyword(s):  
Mediterranean Sea ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Mitochondrial Cytochrome ◽  
Molecular Systematic ◽  
Dna Sequence Data ◽  
Eastern Atlantic Ocean ◽  
The Mediterranean

ABSTRACT The aeolid species Facelina bostoniensis (Couthouy, 1838) was originally described from Massachusetts and was later reported from the Eastern Atlantic Ocean and the Mediterranean Sea. So far, no molecular systematic study of its amphiatlantic status has been carried out. Phylogenetic analyses (maximum likelihood and Bayesian) of DNA sequence data for the mitochondrial cytochrome c oxidase subunit I and 16S rRNA genes confirm the amphiatlantic status of F. bostoniensis. My findings show that this species is restricted to the Atlantic realm and that the species recorded from the Mediterranean is not F. bostoniensis but F. vicina (Bergh, 1882). It is hypothesized that previous records of F. bostoniensis from the Mediterranean Sea were actually misidentifications of F. vicina.

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽  
2013 ◽  
Vol 141 (5) ◽  
pp. 646-651 ◽  
Author(s):  
GASTÓN MORÉ ◽  
NIKOLA PANTCHEV ◽  
DALAND C. HERRMANN ◽  
MAJDA GLOBOKAR VRHOVEC ◽  
SABINE ÖFNER ◽  
...  
Keyword(s):  
18S Rrna ◽  
Sequence Data ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intermediate Hosts ◽  
Apicomplexan Parasites ◽  
Large Numbers ◽  
Wide Range ◽  
18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

Molecular markers for Peristenus spp. (Hymenoptera: Braconidae) parasitoids associated with Lygus spp. (Hemiptera: Miridae)

2003 ◽  
Vol 135 (1) ◽  
pp. 71-83 ◽  
Author(s):  
M. Erlandson ◽  
L. Braun ◽  
D. Baldwin ◽  
J. Soroka ◽  
M. Ashfaq ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequence ◽  
Sequence Data ◽  
Pcr Primers ◽  
Species Level ◽  
Rrna Genes ◽  
Specific Primers ◽  
Canadian Prairies ◽  
Dna Sequence Data ◽  
Species Specific

AbstractMolecular markers for identifying Peristenus spp. parasitoids to species level and preliminary molecular markers to distinguish two groups of Lygus spp. common to the Canadian prairies were developed. Peristenus species-specific polymerase chain reaction (PCR) primers were developed based on DNA sequence data from a 1600-bp region of the internal transcribed spacer region between the 5.8S and 18S nuclear rRNA genes (ITS2). These primers were able to distinguish Peristenus digoneutis Loan, Peristenus stygicus Loan, and Peristenus pallipes (Curtis). Their ability to identify to species-level parasites dissected from field-collected Lygus spp. nymphs was examined by analysis of DNA from 100 parasite samples. Of those samples showing positive PCR amplification with both control (ITS2) and species-specific primers, all were positive for P. pallipes; none of the samples amplified appropriately sized products with P. digoneutis specific or P. stygicus specific primers. These findings were validated using restriction enzyme digests of amplified regions of the Peristenus spp. cytochrome oxidase 1 gene. Both methods were consistent with earlier studies that showed P. pallipes to be the only species of the genus Peristenus to be associated with Lygus spp. on the Canadian prairies. PCR primers based on DNA sequence data from a 550-bp region of the mitochondrial 16S rRNA gene were designed to discriminate Lyguslineolaris (Palisot de Beauvois) from Lygus borealis (Kelton), and Lygus elisus (Van Duzee). These PCR primers were used to identify field-collected nymphs, with most being identified as either L. borealis/L. elisus (72–82%) orL. lineolaris (14–18%). These estimates of species composition closely reflected those of subsequent adult population surveys from the same fields.

scholarly journals Dix-seq: An integrated pipeline for fast amplicon data analysis

2020 ◽  
Author(s):  
Yongjun wei ◽  
Tianqi Ren ◽  
Lei Zhang
Keyword(s):  
Sequence Data ◽  
Gene Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Technologies ◽  
Functional Gene Diversity ◽  
Internal Transcribed Spacer Sequences ◽  
The Common ◽  
18S Rrna Genes ◽  
Multiple Samples

AbstractThe amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.

The phylogeography of Asian Schistosoma (Trematoda: Schistosomatidae)

Parasitology ◽  
2002 ◽  
Vol 125 (2) ◽  
pp. 99-112 ◽  
Author(s):  
S. W. ATTWOOD ◽  
E. S. UPATHAM ◽  
X. H. MENG ◽  
D.-C. QIU ◽  
V. R. SOUTHGATE
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Rrna Genes ◽  
12S Rrna ◽  
28S Rrna ◽  
Asian Origin ◽  
Dna Sequence Data ◽  
African Group ◽  
Mitochondrial 12S Rrna ◽  
Central Thailand

Partial (DNA) sequences are presented for 2 nuclear (18S and 28S rRNA genes) and 2 mitochondrial (12S rRNA and ND1 genes) loci for 5 species belonging to the Schistosoma japonicum, S. sinensium and S. indicum groups of Asian Schistosoma. Fresh field isolates were collected and cultured for the following taxa: S. incognitum (S. indicum group, central Thailand), S. mekongi (S. japonicum group, southern Laos), S. ovuncatum (S. sinensium group, northern Thailand), S. spindale (S. indicum group, northeast Thailand and central Thailand isolates) and S. sinensium (S. sinensium group, Sichuan Province, China). This represents the first published DNA sequence data for S. ovuncatum and for S. sinensiums.s. from the type locality in China. The paper also presents the first sequence data at the above loci for S. incognitum (except for the 28S sequences) and S. sinensium. Congruence was observed between the phylogenies estimated for each locus, although the relationships of S. incognitum were not so well resolved. Fitch–Margoliash, maximum likelihood (ML) and maximum parsimony methods were used to estimate the phylogenies and the agreement between them was similar to that observed between loci. The ML tree was considered to best represent the data and additional 28S sequences (taken from the GenBank), for S. haematobium, S. japonicum, S. mansoni and Orientobilharzia turkestanicum, were used to construct an overall phylogeny. The S. indicum group taxa showed considerable divergence from the other Asian species and closest affinity with the African group. S. ovuncatum and S. sinensium appeared as sister taxa but their status as sibling species remained supported. The findings are discussed in the context of phylogeographical hypotheses for the origin of Schistosoma. An Asian origin for Schistosoma is also considered.

scholarly journals Patterns of Cryptic Diversity and Phylogeography in Four Freshwater Copepod Crustaceans in European Lakes

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 448
Author(s):  
Elena Kochanova ◽  
Abhilash Nair ◽  
Natalia Sukhikh ◽  
Risto Väinölä ◽  
Arild Husby
Keyword(s):  
Sequence Data ◽  
Rrna Genes ◽  
Phylogeographic Structure ◽  
Cryptic Diversity ◽  
Widespread Species ◽  
Geographical Patterns ◽  
Mtdna Coi ◽  
Nuclear Its ◽  
Freshwater Copepods ◽  
18S Rrna Genes

Comparative phylogeography has become a powerful approach in exploring hidden or cryptic diversity within widespread species and understanding how historical and biogeographical factors shape the modern patterns of their distribution. Most comparative phylogeographic studies so far focus on terrestrial and vertebrate taxa, while aquatic invertebrates (and especially freshwater invertebrates) remain unstudied. In this article, we explore and compare the patterns of molecular diversity and phylogeographic structure of four widespread freshwater copepod crustaceans in European water bodies: the harpacticoids Attheyella crassa, Canthocamptus staphylinus and Nitokra hibernica, and the cyclopoid Eucyclops serrulatus, using sequence data from mtDNA COI and nuclear ITS/18S rRNA genes. The three taxa A. crassa, C. staphylinus and E. serrulatus each consist of deeply diverged clusters and are deemed to represent complexes of species with largely (but not completely) non-overlapping distributions, while in N. hibernica only little differentiation was found, which may however reflect the geographically more restricted sampling. However, the geographical patterns of subdivision differ. The divisions in A. crassa and E. serrulatus follow an east–west pattern in Northern Europe whereas that in C. staphylinus has more of a north–south pattern, with a distinct Fennoscandian clade. The deep mitochondrial splits among populations of A. crassa, C. staphylinus and E. serrulatus (model-corrected distances 26–36%) suggest that divergence of the lineages predate the Pleistocene glaciations. This study provides an insight into cryptic diversity and biogeographic distribution of freshwater copepods.

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