Covariation of taxonomic and functional facets of ß-diversity in Chilean freshwater fish assemblages: Implications for current and future processes of biotic homogenization.

The biodiversity of assemblages that experience the introduction and extinction of species may lead to responses in two important facets: The taxonomic and functional diversity. The way in which these facets are associated may reveal important implications and consequences for the conservation of those assemblages. Considering the critical situation of freshwater fishes in continental Chile (30° - 56° S), we analyzed how the taxonomic (TDß) and functional (FDß) facets of ß-diversity, and their components of turnover and nestedness, are associated. We evaluated changes in ß-diversity (ΔTDß and ΔFDß), turnover (ΔTDtur and ΔFDtur), and nestedness (ΔTDnes and ΔFDnes) in 20 fish assemblages from their historical (pre-European) to current composition. We also simulated future trends of these changes, assuming that native species with conservation issues would become extinct. Our results show that the fish assemblages studied are in a process of loss of ß-diversity, both in taxonomic and functional facets (ΔTDß = -3.9%; ΔFDß = -30.4%); also, that these facets are positively correlated in the assemblages studied (r = 0.617; P < 0.05). Both components showed by loss in nestedness (ΔTDnes = -36.9%; ΔFDnes = -60.9%) but gain in turnover (ΔTDtur = 9.2%; ΔFDtur = 12.3%). The functional ß-diversity decreased more than the taxonomic (ΔFDß > ΔTDß), which was caused chiefly by six exotic species of Salmonidae, whose geographical spread was wider and that at the same time shared several morpho-functional traits. Our forecasts, assuming an intensification in the extinction of Endangered and Vulnerable native species, indicate that the process of homogenization will continue, though at a lower rate. Our study shows that the freshwater ichthyofauna of continental Chile is undergoing biotic homogenization, and that this process involves the facets of taxonomic and functional ß-diversity, which are show high correlation between historical and current compositions. Both facets show that process is influenced by nestedness, and while turnover contributes to differentiation (both taxonomic and functional), its importance is overshadowed by nestedness.

Bacterioplankton Zonation Does Exist in High Elevation, Polymictic Lakes.

The assessment of distribution patterns or zonation of planktonic microbes along the water column is a crucial step to interpret their function in the ecosystem. In lakes without seasonal thermal stratification or polymictic systems such as high elevation tropical lakes, planktonic bacterial taxa are probably homogeneously distributed in the water column in contrast to what is known for thermally stratified lakes. However, we know little about bacterial distribution patterns in polymictic lakes and their relation to environmental gradients other than temperature. Here we assessed the diversity, microdiversity, and bacterial community composition at different discrete depths in three high elevation lakes (4,400-4,550 m above sea level) from the Andean plateau to test whether bacterial zonation patterns exist along the water column. For this objective, we analyzed bulk DNA and the putatively active fraction (cDNA) of the 16S rRNA gene. Although a clear gradient of temperature and oxygen was not detected along the water column, a significant vertical spatial zonation of the bacterial communities was present in two out of the three lakes, with microdiversity contributing to such pattern. Our results provide a reference for understanding how changing environmental conditions could affect high elevation aquatic ecosystems, particularly when warming is amplified with elevation, accelerating changes in hydrological regimes and biodiversity. Finally, our results highlight the importance of incorporating the whole water column in ecological studies of aquatic ecosystems lacking temporal or permanent thermal stratification.

Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish.

From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.

Partitioning ß-diversity reveals that invasions and extinctions promote the biotic homogenization of Chilean freshwater fish fauna.

AIM: Exotic species' introductions together with extinction of native species represent the main mechanisms driving biotic homogenization of freshwater fish assemblages around the world. While generally ichtyofaunistic realms transit towards biotic homogenization, for conservation purposes it is essential to understand what specific mechanisms are promoting it on particular areas or regions. Here, we report the occurrence of biotic homogenization in 29 Chilean watersheds, analyzing its ß-diversity (including turnover and nestedness) and predicting future trends. LOCATION: Continental Chile (18o-56o S). METHODS: We determined fish composition per basin for historical and current assemblages; extant native, exotic, and extinct species were recorded as 1 (presence) or 0 (absence) in two matrices basins × species. For each matrix, we calculated the turnover (ßsim), nestedness (ßnes), and ß-diversity (ßsor); then, we obtained Δßsim, Δßnes, and Δßsor, as the arithmetical difference between basin pairs over time. In addition, we search for explanatory variables correlating Δßsim, Δßnes, and Δßsor with geographical and land use variables. Finally, simulating events of species introduction (i.e., invasion) and extinction, we generated 15 hypothetical assemblages, looking to establish future trends towards biotic change in Chilean basins. RESULTS: Species turnover and ß-diversity significantly decreased from historical to current assemblages (Δßsim = -0.084; Δßsor = -0.061, respectively), while the species nestedness did not show significant changes (Δßnes = 0.08). Biotic changes have been driven mainly by the introduction of 28 exotic species, with a minor role of extinctions (one species) and translocations (0 species) of native species. Changes in ß-diversity were negatively correlated with area, elevation, and geographical distance between basins but not with land-use nor human population. Finally, the analysis of 15 future assemblages predicts a significant decrease of ß-diversity and turnover, and an increase for species nestedness, this time promoted by an increase in the extinction of native species. MAIN CONCLUSION: Chilean basins show a significant decrease of the distributional ß-diversity and species turnover of the freshwater fish fauna, evidencing a trend towards biotic homogenization. This trend is shared with other Neotropical basins; however, specific mechanisms driving it show different magnitude. Changes in the ß-diversity components do not show correlation with variables associated to land use, thus suggesting that casual introductions of freshwater fishes in Chile follow an opportunistic mode related to commercial use. According to future scenarios simulated, biotic homogenization should increase further, mainly as consequence of increased native extinctions.

Bacterial Communities Associated With Spherical Nostoc Macrocolonies.

Species of the genus Nostoc (Cyanobacteria) can form large colonies of up to several centimeters in diameter that may represent a unique habitat for bacteria in freshwaters. Bacteria inside the colony are probably segregated from the surrounding water and largely dependent on the metabolism of this primary producer. However, the existence of a specific bacterial community associated with free-living representatives of Nostoc from lakes and streams is unknown. Here, we studied large Nostoc spp. colonies (ca. 2-10 cm in diameter) from two adjacent, high altitude aquatic environments and assessed the diversity, and community composition of the bacterial community associated with the inner gelatinous matrix (GM). Further, we compared this community with that of the lake's littoral zone where the colonies live or with the outer layer (OL) of the colony in samples collected from a stream. Alpha bacterial diversity in the inner GM of the colonies from both sites was lower than in the littoral zone or than in the OL. Significant differences in community composition were found between the inner and the OL, as well as between the inner GM, and the littoral zone. Further, these differences were supported by the putative metabolic processes of the bacterial communities. Our results indicate the existence of a specific bacterial community inside macrocolonies of Nostoc spp. and also imply that the inner environment exerts a strong selection. Finally, these large colonies represent not only a unique habitat, but probably also a hotspot of bacterial activity in an otherwise oligotrophic environment.

Bacterioplankton composition in tropical high-elevation lakes of the Andean plateau.

High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbor a unique genomic repertoire, but their composition and diversity are largely unknown. Here, we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (≥4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. Operational taxonomic units (OTUs) composition was significantly different among lakes and between seasons. Members of the class Opitutae, Spartobacteria, Burkholderiales and Actinobacteria were dominant, but only the hgcI clade (Actinobacteria) and the Comamonadaceae family (Burkholderiales) were shared between seasons among the three lakes. In general, a large percentage (up to 42%) of the rare OTUs was unclassified even at the family level. In one lake, a pycnocline and an anoxic water layer with high abundance of Thiocapsa sp. was found in the wet season indicating that the known polymictic thermal condition is not always given. Our study highlights the particular BCC of tropical high-elevation lakes and also how little is known about the variability in physico-chemical conditions of these ecosystems.

Morphological and taxonomic descriptions of a new genus and species of killifishes (Teleostei: Cyprinodontiformes) from the high Andes of northern Chile.

A new genus and species, Pseudorestias lirimensis, is described from the southern part of the Chilean Altiplano. While sharing several characters that clearly align the new species with Orestias, this new fish is characterized by numerous autapomorphies: the Meckel cartilage is a continuous cartilage that broadly expands posteriorly (in large specimens, it keeps its anterior part and is resorbed posteriorly), the basibranchials are fused into one long element, the second pharyngobranchial is not displaced dorsally over pharyngobranchial tooth plate 3+4, but they are aligned, the anterior and posterior ceratohyals are closely articulated keeping a scarce amount of cartilage between both bones and ventral to them, ossified middle and distal dorsal radials are present in females as well as ossified middle and distal anal radials. Pseudorestias lirimensis presents strong sexual dimorphism associated to size. Females are almost twice as large and long than males, neuromast lines are absent in males, a mesethmoid is present in males, squamation on head is reduced in males, and ossified middle and distal radial of dorsal fin are cartilaginous in males. Pseudorestias and Orestias are suggested as the sole members of the tribe Orestiini. A list of characters diagnosing the tribe is provided. The presence of the new genus is interpreted as a possible result of the ecosystem isolation where the fish is living from surrounding basins-as early as possibly from the Miocene-Pliocene times-and its physical and chemical characteristics. Small populations, living conditions, small habitat, and reduced distribution make this species a strong candidate to be considered critically endangered, a situation already established for all other Chilean species living in the Altiplano. There is high probability it will become extinct due to water demands and climate change in the region.

Correction: Pattern of genetic differentiation of an incipient speciation process: The case of the high Andean killifish Orestias.

[This corrects the article DOI: 10.1371/journal.pone.0170380.].

Pattern of genetic differentiation of an incipient speciation process: The case of the high Andean killifish Orestias.

During the Pleistocene and Holocene, the southwest Andean Altiplano (17°-22°S) was affected by repeated fluctuations in water levels, high volcanic activity and major tectonic movements. In the early Holocene the humid Tauca phase shifted to the arid conditions that have lasted until the present, producing endorheic rivers, lakes, lagoons and wetlands. The endemic fish Orestias (Cyprinodontidae) represents a good model to observe the genetic differentiation that characterizes an incipient speciation process in allopatry since the morphospecies described inhabit a restricted geographic area, with present habitat fragmentation. The genetic diversity and population structure of four endemic morphospecies of Orestias (Cyprinodontidae) found in the Lauca National Park (LNP) analyzed with mitochondrial markers (Control Region) and eight microsatellites, revealed the existence of genetic groups that matches the fragmentation of these systems. High values of genetic and phylogeographic differentiation indices were observed between Chungará Lake and Piacota lagoon. The group composed of the Lauca River, Copapujo and Chuviri wetlands sampling sites showed a clear signal of expansion, with a star-like haplotype network. Levels of genetic differentiation were lower than in Chungará and Piacota, suggesting that these localities would have differentiated after the bottlenecks linked to the collapse of Parinacota volcano. The Parinacota sample showed a population signal that differed from the other localities revealing greater genetic diversity and a disperse network, presenting haplotypes shared with other LNP localities. A mixing pattern of the different genetic groups was evident using the microsatellite markers. The chronology of the vicariance events in LNP may indicate that the partition process of the Orestias populations was gradual. Considering this, and in view of the genetic results, we may conclude that the morphospecies from LNP are populations in ongoing differentiation process.

Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.

The complete mitochondrial genome of the killifish Orestias sp. (Cyprinodontiformes, Cyprinodontidae) from the high Andean range.

The killifish genus Orestias is endemic to freshwater ecosystems in the High Andes of Peru, Bolivia and Chile. Phylogenetic and phylogeographic studies with partial mitochondrial genes have failed to resolve relationship among species, needing more comprehensive approaches. In this study, we described the complete mitochondrial genome of Orestias sp. from Lirima, northern Chile, with the aim to provide useful data for phylogenetic purposes and species delimitation. The mitochondrial genome was assembled with 2.6 million of reads obtained through an Ion Torrent (chip 318) sequencer. The circular sequence of 16,617 bp showed the following nucleotide composition: A, 26.7%, C, 27.1%, G, 17.0%, and T, 29.2%. Gene composition and structure were similar to other fish sequences available, and comprised 13 protein-coding genes, 12S and 16S rRNA, 22 tRNA genes, and a control region.

The complete mitochondrial genome of the endemic and threatened killifish Orestias ascotanensis Parenti, 1984 (Cyprinodontiformes, Cyprinodontidae) from the High Andes.

The killifish Orestias ascotanensis is endemic to the small isolated springs of Ascotán salt pan in the Central High Andes, Chile. Due to small populations, mining activity, and increasing aridity, this species is catalogued in danger of extinction. The complete mitochondrial genome of O. ascotanesis was assembled with an Ion Torrent sequencer (chip 318) that produced 2.61 million of reads. The 16 617 bp of the entire genome consisted of 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes, and a control region, showing that the gene composition and arrangement match to that reported for most fishes.

Unique clusters of Archaea in Salar de Huasco, an athalassohaline evaporitic basin of the Chilean Altiplano.

Analyses of clone libraries from water and sediments of different sites from Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano, revealed the presence of five unique clusters of uncultured Archaea that have not been previously reported or specifically assigned. These sequences were distantly related (83-96% sequence identity) to a limited number of other clone sequences and revealed no identity to cultured Archaea. The abundance of Archaea and Bacteria was estimated using qPCR and community composition was examined through the construction of clone libraries of archaeal 16S rRNA gene. Archaea were found to be dominant over Bacteria in sediments from two saline sites (sites H4: 6.31 x 10(4) and site H6: 1.37 x 10(4) microS cm(-1)) and in one of the water samples (freshwater from site H0: 607 muS cm(-1)). Euryarchaeotal sequences were more abundant than crenarchaeotal sequences. Many of the clone sequences (52%) were similar to uncultured archaeal groups found in marine ecosystems having identity values between 99% and 97%. A major fraction of the sequences (40%) were members of Methanobacteria, while others were included in the Marine Benthic Groups B and D, the Miscellaneous Crenarchaeotic Group, the Terrestrial Miscellaneous Euryarchaeotal Group, Marine Group I and Halobacteria. The presence of uncultured archaeal groups in Salar de Huasco extends their known distribution in inland waters, providing new clues about their possible function in the environment.

Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in northern Chile: an example of geographical dispersion?

The diversity of Cyanobacteria in water and sediment samples from four representative sites of the Salar de Huasco was examined using denaturing gradient gel electrophoresis and analysis of clone libraries of 16S rRNA gene PCR products. Salar de Huasco is a high altitude (3800 m altitude) saline wetland located in the Chilean Altiplano. We analyzed samples from a tributary stream (H0) and three shallow lagoons (H1, H4, H6) that contrasted in their physicochemical conditions and associated biota. Seventy-eight phylotypes were identified in a total of 268 clonal sequences deriving from seven clone libraries of water and sediment samples. Oscillatoriales were frequently found in water samples from sites H0, H1 and H4 and in sediment samples from sites H1 and H4. Pleurocapsales were found only at site H0, while Chroococcales were recovered from sediment samples of sites H0 and H1, and from water samples of site H1. Nostocales were found in sediment samples from sites H1 and H4, and water samples from site H1 and were largely represented by sequences highly similar to Nodularia spumigena. We suggest that cyanobacterial communities from Salar de Huasco are unique - they include sequences related to others previously described from the Antarctic, along with others from diverse, but less extreme environments.

Molecular analysis of enrichment cultures of ammonia oxidizers from the Salar de Huasco, a high altitude saline wetland in northern Chile.

We analyzed enrichment cultures of ammonia-oxidizing bacteria (AOB) collected from different areas of Salar de Huasco, a high altitude, saline, pH-neutral water body in the Chilean Altiplano. Samples were inoculated into mineral media with 10 mM NH4+ at five different salt concentrations (10, 200, 400, 800 and 1,400 mM NaCl). Low diversity (up to three phylotypes per enrichment) of beta-AOB was detected using 16S rDNA and amoA clone libraries. Growth of beta-AOB was only recorded in a few enrichment cultures and varied according to site or media salinity. In total, five 16S rDNA and amoA phylotypes were found which were related to Nitrosomonas europaea/Nitrosococcus mobilis, N. marina and N. communis clusters. Phylotype 1-16S was 97% similar with N. halophila, previously isolated from Mongolian soda lakes, and phylotypes from amoA sequences were similar with yet uncultured beta-AOB from different biofilms. Sequences related to N. halophila were frequently found at all salinities. Neither gamma-AOB nor ammonia-oxidizing Archaea were recorded in these enrichment cultures.