Global patterns and determinants of lake macrophyte taxonomic, functional and phylogenetic beta diversity

Authors

Jorge García-Girón, Jani Heino, Lars Baastrup-Spohr, Claudia P. Bove, John Clayton, Mary de Winton, Tõnu Feldmann, Margarita Fernández-Aláez, Frauke Eckeg, Patrick Grillas, Mark V. Hoyer, Agnieszka Kolada, Sarian Kosten, Balázs A. Lukács, Marit Mjelde, Roger P. Mormul, Laila Rhazi, Mouhssine Rhazi, Laura Sass, Jun Xu, Janne Alahuhta

Documenting the patterns of biological diversity on Earth has always been a central challenge in macroecology and biogeography. However, for the diverse group of freshwater plants, such research program is still in its infancy. Here, we examined global variation in taxonomic, functional and phylogenetic beta diversity patterns of lake macrophytes using regional data from six continents. A data set of ca. 480 lake macrophyte community observations, together with climatic, geographical and environmental variables, was compiled across 16 regions worldwide. We (a) built the very first phylogeny comprising most freshwater plant lineages; (b) exploited a wide array of functional traits that are important to macrophyte autoecology or that relate to lake ecosystem functioning; (c) assessed if different large-scale beta diversity patterns show a clear latitudinal gradient from the equator to the poles using null models; and (d) employed evolutionary and regression models to first identify the degree to which the studied functional traits show a phylogenetic signal, and then to estimate community-environment relationships at multiple spatial scales. Our results supported the notion that ecological niches evolved independently of phylogeny in macrophyte lineages worldwide. We also showed that taxonomic and phylogenetic beta diversity followed the typical global trend with higher diversity in the tropics. In addition, we were able to confirm that species, multi-trait and lineage compositions were first and foremost structured by climatic conditions at relatively broad spatial scales. Perhaps more importantly, we showed that large-scale processes along latitudinal and elevational gradients have left a strong footprint in the current diversity patterns and community-environment relationships in lake macrophytes. Overall, our results stress the need for an integrative approach to macroecology, biogeography and conservation biology, combining multiple diversity facets at different spatial scales.

Sampling effects drive the species–area relationship in lake zooplankton

Authors

Leana D. Gooriah, Jonathan M. Chase

The island species–area relationship (ISAR) describes how the numbers of species increases with increasing size of an island (or island‐like habitat, such as lakes), and is one of the oldest laws in ecology. Despite its conceptual importance, there remains a great deal of ambiguity regarding the ISAR and its underlying processes. We compiled data from sampled zooplankton assemblages from several hundred lakes in North America and Europe to examine the influence of the three main hypothesized mechanisms leading to ISARs – passive sampling, disproportionate effects and habitat heterogeneity. We compiled data on lake zooplankton assemblages that reported sample‐level and lake level species richness estimates, as well as relative abundance data. In both North American and European lakes, we found a consistent and strong increase in total species richness with increasing lake area. However, when we compared the number of species standardized by number of individuals, there was no relationship between lake area and sample‐level species richness or an estimate of species relative abundances, calculated as the probability of interspecific encounter (PIE; a measure of evenness). This was true even when multiple samples were taken across lakes and combined, reducing the likelihood that habitat heterogeneity was driving the results. Overall, our results suggest that the ISAR of zooplankton in these lakes was most likely determined by sampling effects rather than disproportionate effects or habitat heterogeneity leading to more species in larger lakes. Understanding the mechanisms driving ISAR results such as ours can also help us develop predictions for biodiversity change when the area of these habitats changes.

Biogeography and ecology of freshwater chrysophyte cysts in Finland

Authors

Sanna Korkonen, Jan Weckström, Atte Korhola

The occurrence of various chrysophyte cyst morphotypes is unknown in Finland, with the exception of a few isolated lake studies. We set out to chart which cyst types are found in Finland and what their ecological preferences are, focusing on cyst-air temperature relationships that could be further utilized in reconstructing past winter/spring air temperatures and ice-free periods from sedimentary cyst assemblages. Surface sediment samples from lakes across Finland were analysed for their chrysophyte stomatocyst assemblages. Multivariate ecological techniques (e.g. canonical correspondence analysis, principal component analysis) were used to identify the environmental variables that most strongly affected the distribution of the cysts. This survey expanded the known geographical range for several cyst types. Lake water pH and ice-free periods (surrogate for air temperature) explained the statistically significant distribution and composition of the cyst assemblages studied. The results broaden our knowledge of cyst biogeography and strengthen the findings of previous studies of the environmental factors contributing to the occurrence of cysts. Highly variable and rich chrysophyte cyst assemblages in Finland are clearly associated with temperature, pH, electrical conductivity and total phosphorus, with good potential in contemporary and retrospective environmental assessment.

Everything is not everywhere: a tale on the biogeography of cyanobacteria

Authors

Karine Felix Ribeiro, Leandro Duarte, Luciane Oliveira Crossetti

Microrganisms such as cyanobacteria have been often considered as exhibiting wide distribution mainly driven by environmental heterogeneity. Recently, however, new findings have evoked the role of previously neglected processes, such as dispersal limitation, determining the distribution of a wide range of microorganisms, including cyanobacteria. Here, we reviewed the biogeographic patterns of cyanobacteria with focus on molecular data and the evidences from the published literature for the processes driving these patterns. Also, considerations are made about concept of species, discordances in the taxonomic concepts, and level of taxonomic resolution, and how these affect the biogeographic study of cyanobacteria. From a overview, it can be observed that both environmental and historical factors are important to structure cyanobacteria diversity across time and space. Moreover, different species may exhibit significant differences in their distribution patterns, from possibly cosmopolitan species to other endemic species. However, distribution patterns are closely dependent on the concept of species, besides the taxonomic resolution, spatial and environmental scales, and the biases of the molecular methodologies applied in the studies. Thus, efforts to broaden sampling and sequencing of unknown and less-known species, as well as geographic regions and habitats poorly exploited, are crucial for a better understanding of cyanobacteria biogeography.

Environmental factors influencing the quantitative distribution of microcystin and common potentially toxigenic cyanobacteria in U.S. lakes and reservoirs

Authors

John R. Beaver, Claudia E. Tausz, Kyle C. Scotese, Amina I. Pollard, Richard M. Mitchell

Many species of cyanobacteria are capable of producing toxins and causing nuisance blooms, however response to environmental conditions is likely taxon-specific. Environmental factors influencing cyanobacterial composition and toxin production in lakes have been examined in many studies; yet are often confined to individual water bodies, or to a small number of systems within the same region. Here, data from the 2012 USEPA National Lakes Assessment are used to examine relationships between biovolume of common potentially-toxigenic cyanobacteria (Aphanizomenon spp., Cylindrospermopsisspp., Dolichospermum spp., Microcystis spp. and Planktothrix spp.) and environmental variables across the entire conterminous United States, and results are compared across nine distinct ecoregions. Total phosphorus and water clarity were identified as the most influential environmental factors correlated with phytoplankton community composition. The Northern, Southern and Temperate Plains ecoregions displayed the highest biovolumes of potentially toxigenic taxa on average, as well as highest mean concentrations of microcystin. In those three ecoregions, samples with microcystin concentrations greater than 1 ppb were primarily dominated by Planktothrix spp. while in all other ecoregions Dolichospermum spp. was the dominant genus. Canonical Correlation Analysis revealed a strong association between high microcystin concentrations and high nutrient concentrations (total nitrogen and total phosphorus), and between high microcystin concentrations and low percentage of watershed forest cover. Results from this study indicate that the likely occurrence of potentially toxigenic taxa in lakes and reservoirs is predictable on a biogeographical basis, depending on morphological and water quality characteristics. Data from this study may be useful to regional managers attempting to prevent or mitigate nuisance cyanobacterial blooms.

Temperature Effects Explain Continental Scale Distribution of Cyanobacterial Toxins

Authors

Evanthia Mantzouki, Miquel Lürling, Jutta Fastner, Lisette de Senerpont Domis, Elżbieta Wilk-Woźniak, Judita Koreivienė, Laura Seelen, Sven Teurlincx, Yvon Verstijnen, Wojciech Krztoń, Edward Walusiak, Jūratė Karosienė and many others

Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.

Estimating intraspecific genetic diversity from community DNA metabarcoding data

Authors

Vasco Elbrecht​, Ecaterina Edith Vamos, Dirk Steinke, Florian Leese

Background

DNA metabarcoding is used to generate species composition data for entire communities. However, sequencing errors in high-throughput sequencing instruments are fairly common, usually requiring reads to be clustered into operational taxonomic units (OTUs), losing information on intraspecific diversity in the process. While Cytochrome c oxidase subunit I (COI) haplotype information is limited in resolving intraspecific diversity it is nevertheless often useful e.g. in a phylogeographic context, helping to formulate hypotheses on taxon distribution and dispersal.

Methods

This study combines sequence denoising strategies, normally applied in microbial research, with additional abundance-based filtering to extract haplotype information from freshwater macroinvertebrate metabarcoding datasets. This novel approach was added to the R package “JAMP” and can be applied to COI amplicon datasets. We tested our haplotyping method by sequencing (i) a single-species mock community composed of 31 individuals with 15 different haplotypes spanning three orders of magnitude in biomass and (ii) 18 monitoring samples each amplified with four different primer sets and two PCR replicates.

Results

We detected all 15 haplotypes of the single specimens in the mock community with relaxed filtering and denoising settings. However, up to 480 additional unexpected haplotypes remained in both replicates. Rigorous filtering removes most unexpected haplotypes, but also can discard expected haplotypes mainly from the small specimens. In the monitoring samples, the different primer sets detected 177–200 OTUs, each containing an average of 2.40–3.30 haplotypes per OTU. The derived intraspecific diversity data showed population structures that were consistent between replicates and similar between primer pairs but resolution depended on the primer length. A closer look at abundant taxa in the dataset revealed various population genetic patterns, e.g. the stonefly Taeniopteryx nebulosa and the caddisfly Hydropsyche pellucidula showed a distinct north–south cline with respect to haplotype distribution, while the beetle Oulimnius tuberculatus and the isopod Asellus aquaticus displayed no clear population pattern but differed in genetic diversity.

Discussion

We developed a strategy to infer intraspecific genetic diversity from bulk invertebrate metabarcoding data. It needs to be stressed that at this point this metabarcoding-informed haplotyping is not capable of capturing the full diversity present in such samples, due to variation in specimen size, primer bias and loss of sequence variants with low abundance. Nevertheless, for a high number of species intraspecific diversity was recovered, identifying potentially isolated populations and taxa for further more detailed phylogeographic investigation. While we are currently lacking large-scale metabarcoding datasets to fully take advantage of our new approach, metabarcoding-informed haplotyping holds great promise for biomonitoring efforts that not only seek information about species diversity but also underlying genetic diversity.

Geospatial distribution of viromes in tropical freshwater ecosystems

Authors

Xiaoqiong Gu, Qi Xiang Martin Tay, Shu Harn Te, Nazanin Saeidi, Shin Giek Goh, Ariel Kushmaro, Janelle R. Thompson, Karina Yew-Hoong Gin

This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridaewere enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridaeand Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems.

Crustacean zooplankton in lakes of the far north of Ontario, Canada

Authors

Josef MacLeod, Wendel Keller, Andrew M. Paterson

The far north of Ontario, Canada, is a region that is very vulnerable to future change due to climate warming and resource extraction. Despite its vast size (~ 450,000 km²) and large numbers of lakes (> 700,000), there has been very little study of aquatic ecosystems in this remote area. To address this lack of limnological data, forty-one northern Ontario lakes spanning two physiographic regions, the Hudson Bay Lowlands and the Canadian Shield, were sampled during 2012 for crustacean zooplankton and water chemistry. These sub-Arctic lakes support diverse crustacean plankton communities with species richness similar to the richness of lakes in central and northeastern Ontario. While some of the species collected appear to be at the northern limit of their distributions, most relatively common Ontario species occurred throughout the 2012 study area. The physico-chemical characteristics showing relationships with species richness and relative abundances were variables associated with lake morphometry, ionic strength and nutrient status. There were differences in community richness and composition between Lowlands and Shield lakes; however, these differences do not seem attributable to biogeographical influences on species occurrences. Rather, the lower species richness and differences in community composition in Lowlands lakes relative to Shield lakes appear to be largely related to lake morphometry. The shallower and generally smaller Lowlands lakes provide much less habitat diversity, i.e. niche space, than the larger, deeper Shield lakes, leading to simpler communities.

On the geographic variability of a freshwater crustacean Polyphemus pediculus (Cladocera, Onychopoda)

Author

Butorina, Lyudmila G.

Specimens of Polyphemus pediculus (Linnaeus, 1761) from a shallow-water Yaroslavllocal population and a deep-water Michigan population at depths of 1.2, 9.3 and 23.6 m were compared by using nine quantitative and 12 meristic features. Experimental data were treated statistically by employing the methods of variance and multivariate analyses. The degree of reliability of morphometric differences between individuals was assessed by ratios of their sizes, coefficients of variation, ranges of variation, mean levels of variability and statistical differences of data by principal components. Geographic variability of morphometric features of P. pediculus is clearly expressed, but unstable. The variability magnitude and range vary depending on the geographic latitude, ecological conditions of habitation, crustacean age and sex, with differences evident with respect to certain quantitative and meristic features. The mean level of variability of P. pediculus quantitative features is approximately similar in the Yaros1av110ca1 population and in the Michigan population at a l.2-m depth (Cv = 22-23 %). At the depths of 9.3 and 23.6 m in Lake Michigan, the variability is lower by a factor of 1.5 and 2.7, respectively. The range of quantitative feature variability in the deep-water population (10.7 to 44.4 %) is wider, especially at the depth of 1.2 m, compared with the shallow-water population (9.5 %). In both populations, the quantitative features are most variable in parthenogenetic females. The mean level of P. pediculus meristic feature variability in the deep-water population (6.1 %) is 1.5-fo1d lower, and the range of variability is 1.7-fo1dwider, compared with the shallow-water population. The meristic features are most variable in immature specimens from the deep-water population (12.4 %), and in heterosexual individuals (9.4 %) from the shallow-water population. The level of geographic variability of morphometric features depends on the ecological conditions of existence of the local populations. Three ecological races, which differ reliably from each other, are distinguished in the deep-water Michigan population. The size of the crustacean body, antennae, caudal segment, the eye diameter, the length and the number of setae on the third segments of endopodites of limbs of I – III pairs are the principal discriminators of the species. Morphometric differences of the studied local populations indicate a considerable geographic variability of the species and a continuously proceeding gradual sympatric speciation.