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Enrique Lara

University of Neuchâtel, Institute of Biology, Post-Doc

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I am studying evolution, diversity and biogeography of eukaryotic micro organisms, especially testate amoebae (Euglyphida).

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Lund University

María Schiaffino

Leonardo D Fernández

Bernardo O'Higgins University

Niels Daugbjerg

University of South Bohemia

isabelle domaizon

National Institute of Agricultural Research (INRA)

Nataliia Annenkova

Limnological Institute, Siberian Branch of Russian Academy of Science

University of Copenhagen

Johanna Laybourn-parry

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Papers by Enrique Lara

Geographical distance and local environmental conditions drive the genetic population structure of a freshwater microalga (Bathycoccaceae; Chlorophyta) in Patagonian lakes

by Leonardo D Fernández and Enrique Lara

FEMS Microbiology Ecology, 2017

ABSTRACT The patterns and mechanisms underlying the genetic structure of microbial populations re... more ABSTRACT The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the rst study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1–5.8S-ITS2 sequences revealed high levels of nucleotide and haplotype diversity within and among populations. Fixation index and a spatially explicit Bayesian analysis conrmed the occurrence of genetically distinct microalga populations in Patagonia. Isolation by distance and isolation by environment accounted for 38.5% and 17.7% of the genetic structure observed, respectively, whereas together these models accounted for 41% of the genetic differentiation. While our results highlighted isolation by distance and isolation by environment as important mechanisms in driving the genetic population structure of the microalga studied, none of these models (either alone or together) could explain the entire genetic differentiation observed. The unexplained variation in the genetic differentiation observed could be the result of founder events combined with rapid local adaptations, as proposed by the monopolisation hypothesis.

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes

by María Schiaffino, Leonardo D Fernández, and Enrique Lara

Environmental Microbiology, 2016

Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their dis... more Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (IlluminaHiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a 'core biosphere' containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.

Eukaryotic plankton diversity in the sunlit ocean

by Enrique Lara, Sabrina Speich, Stefan Engelen, and Lars Stemmann

Science, 2015

Marine plankton support global biological and geochemical processes. Surveys of their biodiversit... more Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

Taxonomie morphologique, moléculaire, et barcoding du genre Euglyphavers une calibration de l'horloge moéculaire

unil.ch

Le genre Euglypha regroupe de nombreuses espèces de thécamoebiens caractérisés par une thèque (co... more

A molecular perspective on ciliates as soil bioindicators

European Journal of Soil Biology, 2012

Ciliates (or Ciliophora) are probably the most popular group of protists, with some classroom lab... more Ciliates (or Ciliophora) are probably the most popular group of protists, with some classroom lab favorites such as Paramecium spp. These highly conspicuous micro-organisms are easier to identify than many other eukaryotic microbes, at least for trained specialists. As a result, a large amount of data has been produced on their taxonomy, ecology and biogeography. Their relatively short generation times and their ubiquity in virtually all ecosystems on Earth make them excellent bioindicator organisms, particularly in soil systems. However, their practical use is hampered by long and tedious procedures of handling and preparing of specimens for identification, a task which is rendered even more difficult by the existence of cryptic species. A comfortable way to overcome these pitfalls is through the application of environmental molecular diversity screening methods that have been developed in the last two decades to the ciliate communities, and also more modern approaches such as next generation sequencing (454 pyrosequencing). As a complement, several approaches already developed for the prokaryotic communities (functional gene screening, environmental RNA clone libraries, fluorescent in situ hybridization) have not been considered today but could be easily applied to ciliate communities in soils. Still, before these methods can be applied to monitor natural ciliate communities, a considerable effort in species description and culturing (i.e. "classical protistology") must be achieved in order to interpret optimally the data obtained by molecular-based techniques. Here, we provide an overview of these methods as potential monitor strategies of environmental ciliate communities and its contribution to bioindication in soils, and also their limitations.

Molecular analysis of the biodiversity of protists in hydrocarbon-polluted and pristine soils

Institute of Sciences and …, 2005

Eukaryotic microorganisms are an essential component of the Earth's global diversity. It is ... more

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

European journal of protistology, 2015

Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how... more Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matche...

Checklist, diversity and distribution of testate amoebae in Chile

by Enrique Lara and Leonardo D Fernández

European Journal of Protistology, Feb 2015

Bringing together more than 170 years of data, this study represents the first attempt to constru... more Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species-accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25° S-47° S). These findings are here thoroughly discussed in a biogeographical and evolutionary context.

Eukaryotic plankton diversity in the sunlit ocean

by Lars Stemmann, Enrique Lara, and D. Iudicone

Science, 2015

Relationships between testate amoeba communities and water quality in Lake Donghu, a large alkaline lake in Wuhan, China

Frontiers of Earth Science, 2013

The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes i... more The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes in this area have suffered from eutrophication and serious environmental pollution during recent decades. The aquatic biodiversity in the lakes of the area is thus currently under significant threat from continuous human activities. Testate amoebae (TA) are benthic (rarely planktonic) microorganisms characterized by an agglutinated or autogenous shell. Owing to their high abundance, preservation potential in lacustrine sediments, and distinct response to environmental stress, they are increasingly used as indicators for monitoring water quality and reconstructing palaeoenvironmental changes. However this approach has not yet been developed in China. This study presents an initial assessment of benthic TA assemblages in eight lakes of Lake Donghu in the region of Wuhan, China. Testate amoeba community structure was most strongly correlated to water pH. In more alkaline conditions, communities were dominated by Centropyxis aculeata, Difflugia oblonga, Pontigulasia compressa, P. elisa and Lesquereusia modesta. These results are consistent with previous studies and show that TA could be useful for reconstructing past water pH fluctuations in China. To achieve this, the next step will be to expand the database and build transfer function models.

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

by Enrique Lara, Edward Mitchell, and Anush Kosakyan

European journal of protistology, 2015

We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested p... more We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these o...

Morphological and Molecular Diversification of Asian Endemic Difflugia tuberspinifera (Amoebozoa, Arcellinida): A Case of Fast Morphological Evolution in Protists?

by Enrique Lara and Edward Mitchell

Protist, Jan 5, 2014

Planktonic arcellinid testate amoebae exhibit a broad-range of morphological variability but it i... more Planktonic arcellinid testate amoebae exhibit a broad-range of morphological variability but it is currently unclear to what extent this variability represents phenotypic plasticity or if it is genetically determined. We investigated the morphology and phylogenetic relationships of three endemic east-asian Difflugia taxa 1) the vase-shaped D. mulanensis, 2) and a spinose and a spineless morphotypes of D. tuberspinifera using scanning electron microscopy and two ribosomal genetic markers (SSU rDNA and ITS sequences). Our phylogenetic analyses shows that all three taxa are genetically distinct and closely related to D. achlora and Netzelia oviformis. The genetic variations between the spineless and spinose morphotypes of D. tuberspinifera were low at the SSU rRNA level (0.4%), but ten times higher at the ITS level (4.5-6%). Our data suggest that the two forms of D. tuberspinifera are sufficiently differentiated in terms of morphology and genetic characteristics to constitute two separ...

Multiple barcode assessment within the <I>Saprolegnia-Achlya</I> clade (<I>Saprolegniales, Oomycota, Straminipila</I>) brings order in a neglected group of pathogens

IMA Fungus, 2014

The Saprolegnia-Achlya clade comprises species of major environmental and economic importance due... more

DNA bar-coding: biodiversité des lombriciens de Suisse

Insights from Different Approaches from Descriptive Field Studies to Microcosm Studies

Comparative Phylogeny of the Mixotrophic Testate Amoeba Hyalosphenia Papilio Leidy and Its" Zoochlorella" Endosymbiont (Trebouxiophyceae)

Euglyphid Diversity: Business as Usual or Terra Incognita?

Dna Barcoding of Protists in Soils: A Case Study Using Arcellinid Testate Amoebae (Amoebozoa)

Thécamoebiens muscicoles d'un mur d’enceinte du château de Neuchâtel–les protistes constituent-ils une partie négligeable de la biodiversité ou plutôt une «majorité silencieuse»?

Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida)

Protist, 2011

The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barc... more The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to six Cyphoderia morphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500 bp) was much shorter than the SSU sequences (1600 bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.

Geographical distance and local environmental conditions drive the genetic population structure of a freshwater microalga (Bathycoccaceae; Chlorophyta) in Patagonian lakes

by Leonardo D Fernández and Enrique Lara

FEMS Microbiology Ecology, 2017

ABSTRACT The patterns and mechanisms underlying the genetic structure of microbial populations re... more ABSTRACT The patterns and mechanisms underlying the genetic structure of microbial populations remain unresolved. Herein we investigated the role played by two non-mutually exclusive models (i.e. isolation by distance and isolation by environment) in shaping the genetic structure of lacustrine populations of a microalga (a freshwater Bathycoccaceae) in the Argentinean Patagonia. To our knowledge, this was the rst study to investigate the genetic population structure in a South American microorganism. Population-level analyses based on ITS1–5.8S-ITS2 sequences revealed high levels of nucleotide and haplotype diversity within and among populations. Fixation index and a spatially explicit Bayesian analysis conrmed the occurrence of genetically distinct microalga populations in Patagonia. Isolation by distance and isolation by environment accounted for 38.5% and 17.7% of the genetic structure observed, respectively, whereas together these models accounted for 41% of the genetic differentiation. While our results highlighted isolation by distance and isolation by environment as important mechanisms in driving the genetic population structure of the microalga studied, none of these models (either alone or together) could explain the entire genetic differentiation observed. The unexplained variation in the genetic differentiation observed could be the result of founder events combined with rapid local adaptations, as proposed by the monopolisation hypothesis.

Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes

by María Schiaffino, Leonardo D Fernández, and Enrique Lara

Environmental Microbiology, 2016

Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their dis... more Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (IlluminaHiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a 'core biosphere' containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.

Eukaryotic plankton diversity in the sunlit ocean

by Enrique Lara, Sabrina Speich, Stefan Engelen, and Lars Stemmann

Science, 2015

Marine plankton support global biological and geochemical processes. Surveys of their biodiversit... more Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

Taxonomie morphologique, moléculaire, et barcoding du genre Euglyphavers une calibration de l'horloge moéculaire

unil.ch

Le genre Euglypha regroupe de nombreuses espèces de thécamoebiens caractérisés par une thèque (co... more

A molecular perspective on ciliates as soil bioindicators

European Journal of Soil Biology, 2012

Ciliates (or Ciliophora) are probably the most popular group of protists, with some classroom lab... more Ciliates (or Ciliophora) are probably the most popular group of protists, with some classroom lab favorites such as Paramecium spp. These highly conspicuous micro-organisms are easier to identify than many other eukaryotic microbes, at least for trained specialists. As a result, a large amount of data has been produced on their taxonomy, ecology and biogeography. Their relatively short generation times and their ubiquity in virtually all ecosystems on Earth make them excellent bioindicator organisms, particularly in soil systems. However, their practical use is hampered by long and tedious procedures of handling and preparing of specimens for identification, a task which is rendered even more difficult by the existence of cryptic species. A comfortable way to overcome these pitfalls is through the application of environmental molecular diversity screening methods that have been developed in the last two decades to the ciliate communities, and also more modern approaches such as next generation sequencing (454 pyrosequencing). As a complement, several approaches already developed for the prokaryotic communities (functional gene screening, environmental RNA clone libraries, fluorescent in situ hybridization) have not been considered today but could be easily applied to ciliate communities in soils. Still, before these methods can be applied to monitor natural ciliate communities, a considerable effort in species description and culturing (i.e. "classical protistology") must be achieved in order to interpret optimally the data obtained by molecular-based techniques. Here, we provide an overview of these methods as potential monitor strategies of environmental ciliate communities and its contribution to bioindication in soils, and also their limitations.

Molecular analysis of the biodiversity of protists in hydrocarbon-polluted and pristine soils

Institute of Sciences and …, 2005

Eukaryotic microorganisms are an essential component of the Earth's global diversity. It is ... more

Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae)

European journal of protistology, 2015

Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how... more Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matche...

Checklist, diversity and distribution of testate amoebae in Chile

by Enrique Lara and Leonardo D Fernández

European Journal of Protistology, Feb 2015

Bringing together more than 170 years of data, this study represents the first attempt to constru... more Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species-accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25° S-47° S). These findings are here thoroughly discussed in a biogeographical and evolutionary context.

Eukaryotic plankton diversity in the sunlit ocean

by Lars Stemmann, Enrique Lara, and D. Iudicone

Science, 2015

Relationships between testate amoeba communities and water quality in Lake Donghu, a large alkaline lake in Wuhan, China

Frontiers of Earth Science, 2013

The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes i... more The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes in this area have suffered from eutrophication and serious environmental pollution during recent decades. The aquatic biodiversity in the lakes of the area is thus currently under significant threat from continuous human activities. Testate amoebae (TA) are benthic (rarely planktonic) microorganisms characterized by an agglutinated or autogenous shell. Owing to their high abundance, preservation potential in lacustrine sediments, and distinct response to environmental stress, they are increasingly used as indicators for monitoring water quality and reconstructing palaeoenvironmental changes. However this approach has not yet been developed in China. This study presents an initial assessment of benthic TA assemblages in eight lakes of Lake Donghu in the region of Wuhan, China. Testate amoeba community structure was most strongly correlated to water pH. In more alkaline conditions, communities were dominated by Centropyxis aculeata, Difflugia oblonga, Pontigulasia compressa, P. elisa and Lesquereusia modesta. These results are consistent with previous studies and show that TA could be useful for reconstructing past water pH fluctuations in China. To achieve this, the next step will be to expand the database and build transfer function models.

Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida, Hyalospheniidae), a new species described from a Swiss raised bog

by Enrique Lara, Edward Mitchell, and Anush Kosakyan

European journal of protistology, 2015

We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested p... more We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these o...

Morphological and Molecular Diversification of Asian Endemic Difflugia tuberspinifera (Amoebozoa, Arcellinida): A Case of Fast Morphological Evolution in Protists?

by Enrique Lara and Edward Mitchell

Protist, Jan 5, 2014

Planktonic arcellinid testate amoebae exhibit a broad-range of morphological variability but it i... more Planktonic arcellinid testate amoebae exhibit a broad-range of morphological variability but it is currently unclear to what extent this variability represents phenotypic plasticity or if it is genetically determined. We investigated the morphology and phylogenetic relationships of three endemic east-asian Difflugia taxa 1) the vase-shaped D. mulanensis, 2) and a spinose and a spineless morphotypes of D. tuberspinifera using scanning electron microscopy and two ribosomal genetic markers (SSU rDNA and ITS sequences). Our phylogenetic analyses shows that all three taxa are genetically distinct and closely related to D. achlora and Netzelia oviformis. The genetic variations between the spineless and spinose morphotypes of D. tuberspinifera were low at the SSU rRNA level (0.4%), but ten times higher at the ITS level (4.5-6%). Our data suggest that the two forms of D. tuberspinifera are sufficiently differentiated in terms of morphology and genetic characteristics to constitute two separ...

Multiple barcode assessment within the <I>Saprolegnia-Achlya</I> clade (<I>Saprolegniales, Oomycota, Straminipila</I>) brings order in a neglected group of pathogens

IMA Fungus, 2014

The Saprolegnia-Achlya clade comprises species of major environmental and economic importance due... more

DNA bar-coding: biodiversité des lombriciens de Suisse

Insights from Different Approaches from Descriptive Field Studies to Microcosm Studies

Comparative Phylogeny of the Mixotrophic Testate Amoeba Hyalosphenia Papilio Leidy and Its" Zoochlorella" Endosymbiont (Trebouxiophyceae)

Euglyphid Diversity: Business as Usual or Terra Incognita?

Dna Barcoding of Protists in Soils: A Case Study Using Arcellinid Testate Amoebae (Amoebozoa)

Thécamoebiens muscicoles d'un mur d’enceinte du château de Neuchâtel–les protistes constituent-ils une partie négligeable de la biodiversité ou plutôt une «majorité silencieuse»?

Comparing Potential COI and SSU rDNA Barcodes for Assessing the Diversity and Phylogenetic Relationships of Cyphoderiid Testate Amoebae (Rhizaria: Euglyphida)

Protist, 2011

The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barc... more The mitochondrial Cytochrome Oxidase Subunit 1 gene (COI) has been promoted as an ideal "DNA barcode" for animal species and other groups of eukaryotes. However, the utility of the COI marker for species level discrimination and for phylogenetic analyses has yet to be tested within the Rhizaria. Accordingly, we analysed mitochondrial COI gene sequences and nuclear small subunit rDNA (SSU) sequences from several morphospecies of euglyphid testate amoebae (Cercozoa, Rhizaria) in order to evaluate the utility of these DNA markers for species discrimination and phylogenetic reconstructions. Sequences were obtained from eleven populations belonging to six Cyphoderia morphospecies that were isolated from field samples in North America and Europe. Mean inter-population COI sequence dissimilarities were on average 2.9 times greater than in the SSU, while the intra-population sequence dissimilarities were higher in the SSU (0-0.95%) than in the COI (0%); this suggests that the COI fragment is valuable for discriminating Cyphoderiidae isolates. Our study also demonstrated that COI sequences are useful for inferring phylogenetic relationships among Cyphoderiidae isolates. COI and SSU tree topologies were very similar even though the COI fragment used in these analyses (500 bp) was much shorter than the SSU sequences (1600 bp). Altogether, these results demonstrate the utility of the COI as a potential taxonomic DNA barcode for assessing cyphoderiid species diversity and for inferring phylogenetic relationships within the group.

Soil testate amoeba diversity follows a unimodal latitudinal pattern in southwestern South America caused by short- and long-term processes

by Leonardo D Fernández, Enrique Lara, and Reinaldo Javier Rivera

[2015]: 34th annual meeting of the German Society of Protozoology. March, Magdeburg, Germany. Ora... more