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Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Furthermore, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line ecotone. Using a space-time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.
Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Furthermore, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line ecotone. Using a space-time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.
Lakes cover large parts of the climatically sensitive Arctic landscape and respond rapidly to environmental change. Arctic lakes have different origins and include the predominant thermokarst lakes, which are small, young and highly dynamic, as well as large, old and stable glacial lakes. Freshwater diatoms dominate the primary producer community in these lakes and can be used to detect biotic responses to climate and environmental change. We used specific diatom metabarcoding on sedimentary DNA, combined with next-generation sequencing and diatom morphology, to assess diatom diversity in five glacial and 15 thermokarst lakes within the easternmost expanse of the Siberian treeline ecotone in Chukotka, Russia. We obtained 163 verified diatom sequence types and identified 176 diatom species morphologically. Although there were large differences in taxonomic assignment using the two approaches, they showed similar high abundances and diversity of Fragilariceae and Aulacoseiraceae. In particular, the genetic approach detected hidden within-lake variations of fragilarioids in glacial lakes and dominance of centric Aulacoseira species, whereas Lindavia ocellata was predominant using morphology. In thermokarst lakes, sequence types and valve counts also detected high diversity of Fragilariaceae, which followed the vegetation gradient along the treeline. Ordination analyses of the genetic data from glacial and thermokarst lakes suggest that concentrations of sulfate (SO42-), an indicator of the activity of sulfate-reducing microbes under anoxic conditions, and bicarbonate (HCO3-), which relates to surrounding vegetation, have a significant influence on diatom community composition. For thermokarst lakes, we also identified lake depth as an important variable, but SO42- best explains diatom diversity derived from genetic data, whereas HCO3- best explains the data from valve counts. Higher diatom diversity was detected in glacial lakes, most likely related to greater lake age and different edaphic settings, which gave rise to diversification and endemism. In contrast, small, dynamic thermokarst lakes are inhabited by stress-tolerant fragilarioids and are related to different vegetation types along the treeline ecotone. Our study demonstrated that genetic investigations of lake sediments can be used to interpret climate and environmental responses of diatoms. It also showed how lake type affects diatom diversity, and that such genetic analyses can be used to track diatom community changes under ongoing warming in the Arctic.
Shallow inland water bodies in Malawi continue to be threatened by various environmental challenges despite their importance to the fisheries industry. Due to the complex interaction between natural and anthropogenic disturbances, disentangling the effect of the two may be a complicated process. The littoral zone of most water bodies is important in environmental reconstructions including pollution and lake level monitoring. This study used a littoral zone, transect-based approach employing multi-proxy palaeolimnological techniques to reconstruct recent environmental change (ca. 100 yrs.) in Lake Malombe in the Malawi Rift, East Africa. The results of the study could inform fisheries management in Lake Malombe, which experienced a catastrophic decline in fish stocks. Results support documentary evidence for the complete desiccation of the lake less than 100 years ago. Subsequently, there is evidence for accelerated eutrophication in the recent past. In light of these results, it is concluded that transect sampling approaches rather than relying on single core measurements, and the need for careful consideration of the types of proxy, are significant considerations in palaeoenvironmental reconstructions.
Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.
Rapid population growth and economic development have led to increased anthropogenic pressures on the Tibetan Plateau, causing significant land cover changes with potentially severe ecological consequences. To assess whether or not these pressures are also affecting the remote montane-boreal lakes on the SE Tibetan Plateau, fossil pollen and diatom data from two lakes were synthesized. The interplay of aquatic and terrestrial ecosystem response was explored in respect to climate variability and human activity over the past 200 years. Nonmetric multidimensional scaling and Procrustes rotation analysis were undertaken to determine whether pollen and diatom responses in each lake were similar and synchronous. Detrended canonical correspondence analysis was used to develop quantitative estimates of compositional species turnover. Despite instrumental evidence of significant climatic warming on the southeastern Plateau, the pollen and diatom records indicate very stable species composition throughout their profiles and show only very subtle responses to environmental changes over the past 200 years. The compositional species turnover (0.36-0.94 SD) is relatively low in comparison to the species reorganizations known from the periods during the mid-and early-Holocene (0.64-1.61 SD) on the SE Plateau, and also in comparison to turnover rates of sediment records from climate-sensitive regions in the circum arctic. Our results indicate that climatically induced ecological thresholds are not yet crossed, but that human activity has an increasing influence, particularly on the terrestrial ecosystem in our study area. Synergistic processes of post-Little Ice Age warming, 20th century climate warming and extensive reforestations since the 19th century have initiated a change from natural oak-pine forests to seminatural, likely less resilient pine-oak forests. Further warming and anthropogenic disturbances would possibly exceed the ecological threshold of these ecosystems and lead to severe ecological consequences.
The understanding of environmentally induced changes in the biochemical composition of phytoplankton species is of great importance in both physiological studies and ecological food web research. In extensive laboratory experiments we tested the influence of two different temperatures (10 degrees C and 25 degrees C) and a phosphorus supply gradient on the sterol concentrations of the three freshwater phytoplankton species Scenedesmus quadricauda, Cryptomonas ovata and Cyclotella meneghiniana. The diatom C. meneghiniana was additionally exposed to a silicate gradient. In two separate experiments we analysed (1) possible interactive effects of temperature and phosphorus supply and (2) the effect of four phosphorus levels and three silicate levels on algal sterol concentrations. We observed that sterol concentrations were higher at 25 degrees C than at 10 degrees C in S. quadricauda and C. meneghiniana, but were not affected by temperature in C. ovata. Interactive effects of temperature and phosphorus supply on sterol concentrations were found in C. meneghiniana. This presumably was due to the bioconversion of one sterol (24-methylenecholesterol) into another (22-dihydrobrassicasterol). Increasing phosphorus supply resulted in species-specific effects on sterol concentrations, viz. an optimum curve response in S. quadricauda, a saturation curve response in C. meneghiniana and no change in sterol concentration in C. ovata. Effects of silicate supply on the sterols of C. meneghiniana equalled the effects of phosphorus supply. Albeit we did not observe a general trend in the three phytoplankton species tested, we conclude that sterol concentrations of phytoplankton are strongly affected by temperature and nutrient supply. Interactive effects point out the importance of taking into account more than just one environmental factor when assessing the effects of environmentally induced changes on phytoplankton sterol concentrations.
Hidden diversity in diatoms of Kenyan Lake Naivasha a genetic approach detects temporal variation
(2012)
This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (7667 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.
1. The polyunsaturated fatty acid eicosapentaenoic acid (EPA) plays an important role in aquatic food webs, in particular at the primary producerconsumer interface where keystone species such as daphnids may be constrained by its dietary availability. Such constraints and their seasonal and interannual changes may be detected by continuous measurements of EPA concentrations. However, such EPA measurements became common only during the last two decades, whereas long-term data sets on plankton biomass are available for many well-studied lakes. Here, we test whether it is possible to estimate EPA concentrations from abiotic variables (light and temperature) and the biomass of prey organisms (e.g. ciliates, diatoms and cryptophytes) that potentially provide EPA for consumers. 2. We used multiple linear regression to relate size- and taxonomically resolved plankton biomass data and measurements of temperature and light intensity to directly measured EPA concentrations in Lake Constance during a whole year. First, we tested the predictability of EPA concentrations from the biomass of EPA-rich organisms (diatoms, cryptophytes and ciliates). Secondly, we included the variables mean temperature and mean light intensity over the sampling depth (020 m) and depth (08 and 820 m) as factors in our model to check for large-scale seasonal- and depth-dependent effects on EPA concentrations. In a third step, we included the deviations of light and temperature from mean values in our model to allow for their potential influence on the biochemical composition of plankton organisms. We used the Akaike Information Criterion to determine the best models. 3. All approaches supported our proposition that the biomasses of specific plankton groups are variables from which seston EPA concentrations can be derived. The importance of ciliates as an EPA source in the seston was emphasised by their high weight in our models, although ciliates are neglected in most studies that link fatty acids to seston taxonomic composition. The large-scale seasonal variability of light intensity and its interaction with diatom biomass were significant predictors of EPA concentrations. The deviation of temperature from mean values, accounting for a depth-dependent effect on EPA concentrations, and its interaction with ciliate biomass were also variables with high predictive power. 4. The best models from the first and second approaches were validated with measurements of EPA concentrations from another year (1997). The estimation with the best model including only biomass explained 80%, and the best model from the second approach including mean temperature and depth explained 87% of the variability in EPA concentrations in 1997. 5. We show that it is possible to predict EPA concentrations reliably from plankton biomass, while the inclusion of abiotic factors led to results that were only partly consistent with expectations from laboratory studies. Our approach of including biotic predictors should be transferable to other systems and allow checking for biochemical constraints on primary consumers.
In this work, an approach of paleoclimate reconstruction for tropical East Africa is presented. After giving a short summary of modern climate conditions in the tropics and the East African climate peculiarity, the potential of reconstructing climate from paleolake sediments is discussed. As demonstrated, the hydrologic sensitivity of high-elevated closed-basin lakes in the Central Kenya Rift yields valuable guaranties for the establishment of long-term climate records. Temporal fluctuations of the limnological characteristics saved in the lake sediments are used to define variations in the Quaternary climate history. Based on diatom analyses in radiocarbon- and 40Ar/39Ar-dated sediments, a chronology of paleoecologic fluctuations is developed for the Central Kenya Rift -lakes Nakuru, Elmenteita and Naivasha. At least during the penultimate interglacial (around 140 to 60 kyr BP) and during the last interglacial (around 12 to 4 kyr BP), these lakes experienced several transgression-regression cycles on time intervals of about 11,000 years. Additionally, a long-term trend of lake evolution is found suggesting the general succession from deep freshwater lakes towards more saline waters during the last million years. Using ecologic transfer functions and a simple lake-balance model, the observed paleohydrologic fluctuations are linked to potential precipitation-evaporation changes in the lake basins. Though also tectonic influences on the drainage pattern and the effect of varied seepage are investigated, it can be shown that already a small increase in precipitation of about 30±10 % may have affected the hydrologic budget of the intra-rift lakes within the reconstructed range. The findings of this study help to assess the natural climate variability of East Africa. They furthermore reflect the sensitivity of the Central Kenya Rift -lakes to fluctuations of large-scale climate parameters, such as solar radiation and sea-surface temperatures of the Indian Ocean.