Genetic diversity of eukaryotic plankton assemblages in Eastern Tibetan Lakes differing by their salinity and altitude

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, we compared the biodiversity characteristics of diverse taxonomic groups across water depths and in surface sediments from a freshwater lake and a hypersaline lake on the northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, we detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, and 28 vertebrate taxa. Each group had a substantially different community composition in the two lakes, and differences were also found between water and sediments within each lake. Cooccurrence network analysis revealed higher network complexity, lower modularity, and fewer negative cohesions in the hypersaline lake, suggesting that high salinity may destabilize ecological networks. Our results provide the first holistic view of Tibetan lake biodiversity under contrasting salinity levels and reveal structural differences in the ecological networks that may impact ecosystem resilience.

Testate amoebae (Protozoa) in lakes of the Qinghai-Tibet Plateau: Biodiversity, community structures, and protozoic biosilicification in relation to environmental properties and climate warming

The Qinghai-Tibet Plateau (QTP) is characterized by a vast number of frozen and unfrozen freshwater reservoirs, which is why it is also called "the third pole" of the Earth or "Asian Water Tower". We analyzed testate amoeba (TA) biodiversity and corresponding protozoic biosilicification in lake sediments of the QTP in relation to environmental properties (freshwater conditions, elevation, and climate). As TA are known as excellent bio-indicators, our results allowed us to derive conclusions about the influence of climate warming on TA communities and microbial biogeochemical silicon (Si) cycling. We found a total of 113 TA taxa including some rare and one unknown species in the analyzed lake sediments of the QTP highlighting the potential of this remote region for TA biodiversity. >1/3 of the identified TA taxa were relatively small (<30 μm) reflecting the relatively harsh environmental conditions in the examined lakes. TA communities were strongly affected by physico-chemical properties of the lakes, especially water temperature and pH, but also elevation and climate conditions (temperature, precipitation). Our study reveals climate-related changes in TA biodiversity with consequences for protozoic biosilicification. As the warming trend in the QTP is two to three times faster compared to the global average, our results provide not only deeper insights into the relations between TA biodiversity and environmental properties, but also predictions of future developments in other regions of the world. Moreover, our results provide fundamental data for paleolimnological reconstructions. Thus, examining the QTP is helpful to understand microbial biogeochemical Si cycling in the past, present, and future.

Human impact on current environmental state in Chinese lakes

Anthropogenic and natural disturbance to inland aquatic ecosystems displays a notable spatial difference, yet data to measure these differences are scarce. This study encompasses 217 lakes distributed over five lake regions of China and elucidates the environmental factors determining the spatial variability of the water quality and trophic status. A significant correlation between human modification index in surrounding terrestrial systems (HMT) and trophic status of lake ecosystems (TSI) was found, and the regression slope in each region was similar except in the Qinghai-Tibet Plateau region. It was further noted that the pattern of environmental factor network (EF network) differed among freshwater and saline lakes. The EF network was complex for freshwater lakes in less human-influenced areas, but intensive man-made influence disrupted most relationships except for those between total nitrogen, total phosphorus, chlorophyll-a, and water turbidity. As for regions including saline lakes, correlations among water salinity and organic forms of carbon and nitrogen were apparent. Our results suggest that HMT and EF network can be useful indicators of the ecological integrity of local lake ecosystems, and integrating spatial information on a large scale provides conservation planners the option for evaluating the potential risk on inland aquatic systems.

Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau

Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.

Salinity Is a Key Determinant for the Microeukaryotic Community in Lake Ecosystems of the Inner Mongolia Plateau, China

The arid and semiarid areas experienced remarkable lake shrinkage during recent decades due to intensive human activities and climate change, which would result in unprecedented changes of microeukaryotic communities. However, little is known about how climate change affects the structure and ecological mechanisms of microeukaryotic communities in this area. Here, we used an 18S rRNA gene-based high-throughput sequencing approach to explore the structure, interspecies interaction, and assembly processes of the microeukaryotic community in lake ecosystems of the Inner Mongolia Plateau. As a direct result of climate change, salinity has become the key determinant of the lacustrine microeukaryotic community in this region. The microeukaryotic community in this ecosystem can be divided into three groups: salt (Lake Daihai), brackish (Lake Dalinuoer) and freshwater lakes. Co-occurrence network analysis revealed that salinity shapes the interspecies interactions of the microeukaryotic community. This causes interspecies interactions to change from antagonistic to cooperative with an increase in salinity. Phylogenetic-based β-nearest taxon distance analyses revealed that stochastic processes mainly dominated the microeukaryotic community assembly in lake ecosystems of the Inner Mongolia Plateau, and salinity stress drove the assembly processes of the microeukaryotic community from stochastic to deterministic. Overall, these findings expand the current understanding of interspecies interactions and assembly processes of microeukaryotic communities during climate change in lake ecosystems of the Inner Mongolia Plateau.

Where the Little Ones Play the Main Role-Picophytoplankton Predominance in the Soda and Hypersaline Lakes of the Carpathian Basin

The extreme environmental conditions of the diverse saline inland waters (soda lakes and pans, hypersaline lakes and ponds) of the Carpathian Basin are an advantage for picophytoplankton. The abundance of picophytoplankton in these waters can be up to several orders of magnitude higher than that in freshwater shallow lakes, but differences are also found within different saline water types: higher picophytoplankton abundances were observed in hypersaline lakes compared to humic soda lakes, and their highest numbers were detected in turbid soda lakes. Moreover, their contribution to phytoplankton biomass is higher than that in shallow freshwater lakes with similar trophic states. Based on long-term data, their ratio within the phytoplankton increased with turbidity in the case of turbid soda lakes, while, in hypersaline lakes, their proportion increased with salinity. Picocyanobacteria were only detected with high abundance (>106−107 cells/mL) in turbid soda lakes, while picoeukaryotes occurred in high numbers in both turbid and hypersaline lakes. Despite the extreme conditions of the lakes, the diversity of picophytoplankton is remarkable, with the dominance of non-marine Synechococcus/Cyanobium, Choricystis, Chloroparva and uncultured trebouxiophycean green algae in the soda lakes, and marine Synechococcus and Picochlorum in the hypersaline lakes.

Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes

East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.

Patterns of protist distribution and diversification in alpine lakes across Europe

Biogeography in Europe is known to be crucially influenced by the large mountain ranges serving as biogeographical islands for cold-adapted taxa and geographical barriers for warm-adapted taxa. While biogeographical patterns are well-known for plants and animals in Europe, we here investigated diversity and distribution patterns of protist freshwater communities on a European scale (256 lakes) in the light of the well-studied post-glacial distribution patterns of macroorganisms. Thus, our study compared 43 alpine protist communities of lakes located in the Alps, Carpathians, Pyrenees, and the Sierra Nevada with that of surrounding lowland lakes. We verified altitudinal diversity gradients of freshwater protists with decreasing richness and diversity across altitudes similar to those observed for plants and animals. Alpine specialists and generalists could be identified differing significantly in richness and diversity, but hardly in occurrence and proportions of major taxonomic groups. High proportions of region-specific alpine specialists indicate an increased occurrence of distinct lineages within each mountain range and thus, suggested either separated glacial refugia or post-glacial diversification within mountain ranges. However, a few alpine specialists were shared between mountain ranges suggesting a post-glacial recolonization from a common lowland pool. Our results identified generalists with wide distribution ranges and putatively wide tolerance ranges toward environmental conditions as main drivers of protist diversification (specification) in alpine lakes, while there was hardly any diversification in alpine specialists.

Local factors drive bacterial and microeukaryotic community composition in lake surface sediment collected across an altitudinal gradient

Lake surface sediments are dominated by microorganisms that play significant roles in biogeochemical cycling within lakes. There is limited knowledge on the relative importance of local environmental factors and altitude on bacterial and microeukaryotic community richness and composition in lake sediments. In the present study, surface sediment samples were collected from 40 lakes along an altitude gradient (2-1215 m). Microbial communities were characterized using 16S (bacteria) and 18S (microeukaryotes) rRNA gene metabarcoding. Bacterial and microeukaryotic richness were not correlated with altitude but instead to environmental variables (e.g. area of water in the catchment (bacteria: R = -0.43). For both bacteria and microeukaryotes, dissimilarity in the community structure had a higher correlation to combined environmental variables (without altitude) (bacteria: R = 0.53; microeukaryotes: R = 0.55) than altitude alone (bacteria: R = 0.34; microeukaryotes: R = 0.47). Sediment sulfur and productive grassland were important variables in determining the relative abundance of sulfate reducing bacteria. Nitrospira, was positively related to altitude but negatively to water column total organic carbon and the proportion of productive grassland in the catchment. Little overlap in amplicon sequence variants was shown amongst lakes. This has important considerations for management decisions, suggesting that to protect biodiversity, conservation of numerous lakes and lake types is required.

Distribution Patterns of Microeukaryotic Community Between Sediment and Water of the Yellow River Estuary

Water and sediment have always been closely tied in aquatic systems. However, little information regarding the full extent of microeukaryotic composition in both the two habitats did we know especially in estuaries. In the present study, the microeukaryotic abundance, diversity, composition, and their response to environmental factors between sediment and water in the Yellow River Estuary (YRE) were investigated. The microeukaryotic 18S rRNA gene abundance ranged from 1.03 × 10⁶ to 5.48 × 10⁷ copies/g dry for sediment, and 3.01 × 10⁴ to 1.25 × 10⁶ copies/mL for water. The distribution patterns of eukaryotic microorganisms could be clustered into two different branches. And the compositions of microeukaryotes in the two habitats were distinct obviously. Metazoa, Fungi, Streptophyta, Ochrophyta, Cercozoa, and Dinophyta were more abundant in sediment. The dominant phyla in water were Dinophyta, followed by Metazoa, Ochrophyta, Cryptophyta, Chloroplyta, Cercozoa, Fungi, Katablepharidophyta, Choanoflagellida, and Haptophyta. Interestingly, the eukaryotic microorganisms detected in sediment were much less sensitive to environmental variables compared with water. Furthermore, their potential co-occurrence networks in particular were also discovered in the present study. As such, we have provided baseline data to support further research on estuarine microeukaryotes in both sediment and water, which was useful for guiding the practical application of ecosystem management and biodiversity protection.

Community response of microbial primary producers to salinity is primarily driven by nutrients in lakes

Higher microbial diversity was frequently observed in saline than fresh waters, but the underlying mechanisms remains unknown, particularly in microbial primary producers (MPP). MPP abundance and activity are notably constrained by high salinity, but facilitated by high nutrients. It remains to be ascertained whether and how nutrients regulate the salinity constraints on MPP abundance and community structure. Here we investigated the impact of nutrients on salinity constraints on MPP abundance and diversity in undisturbed lakes with a wide salinity range on the Tibetan Plateau. MPP community was explored using quantitative PCR, terminal restriction fragment length polymorphism and sequencing of cloning libraries targeting form IC cbbL gene. The MPP community structure was sorted by salinity into freshwater (salinity<1‰), saline (1‰ < salinity<29‰) and hypersaline (salinity>29‰) lakes. Furthermore, while MPP abundance, diversity and richness were significantly constrained with increasing salinity, these constraints were mitigated by enhancing total organic carbon (TOC) and total nitrogen (TN) contents in freshwater and saline lakes. In contrast, the MPP diversity increased significantly with the salinity in hypersaline lakes, due to the mitigation of enhancing TOC and TN contents and salt-tolerant MPP taxa. The mitigating effect of nutrients was more pronounced in saline than in freshwater and hypersaline lakes. The MPP compositions varied along salinity, with Betaproteobacteria dominating both the freshwater and saline lakes and Gammaproteobacteria dominating the hypersaline lakes. We concluded that high nutrients could mitigate the salinity constraining effects on MPP abundance, community richness and diversity. Our findings offer a novel insight into the salinity effects on primary producers and highlight the interactive effects of salinity and nutrients on MPP in lakes. These findings can be used as a baseline to illuminate the effects of increased anthropogenic activities altering nutrient dynamics on the global hydrological cycle and the subsequent responses thereof by MPP communities.

Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution

BACKGROUND

The class Diphyllatea belongs to a group of enigmatic unicellular eukaryotes that play a key role in reconstructing the morphological innovation and diversification of early eukaryotic evolution. Despite its evolutionary significance, very little is known about the phylogeny and species diversity of Diphyllatea. Only three species have described morphology, being taxonomically divided by flagella number, two or four, and cell size. Currently, one 18S rRNA Diphyllatea sequence is available, with environmental sequencing surveys reporting only a single partial sequence from a Diphyllatea-like organism. Accordingly, geographical distribution of Diphyllatea based on molecular data is limited, despite morphological data suggesting the class has a global distribution. We here present a first attempt to understand species distribution, diversity and higher order structure of Diphyllatea.

RESULTS

We cultured 11 new strains, characterised these morphologically and amplified their rRNA for a combined 18S-28S rRNA phylogeny. We sampled environmental DNA from multiple sites and designed new Diphyllatea-specific PCR primers for long-read PacBio RSII technology. Near full-length 18S rRNA sequences from environmental DNA, in addition to supplementary Diphyllatea sequence data mined from public databases, resolved the phylogeny into three deeply branching and distinct clades (Diphy I - III). Of these, the Diphy III clade is entirely novel, and in congruence with Diphy II, composed of species morphologically consistent with the earlier described Collodictyon triciliatum. The phylogenetic split between the Diphy I and Diphy II + III clades corresponds with a morphological division of Diphyllatea into bi- and quadriflagellate cell forms.

CONCLUSIONS

This altered flagella composition must have occurred early in the diversification of Diphyllatea and may represent one of the earliest known morphological transitions among eukaryotes. Further, the substantial increase in molecular data presented here confirms Diphyllatea has a global distribution, seemingly restricted to freshwater habitats. Altogether, the results reveal the advantage of combining a group-specific PCR approach and long-read high-throughput amplicon sequencing in surveying enigmatic eukaryote lineages. Lastly, our study shows the capacity of PacBio RS when targeting a protist class for increasing phylogenetic resolution.

People, pollution and pathogens - Global change impacts in mountain freshwater ecosystems

Mountain catchments provide for the livelihood of more than half of humankind, and have become a key destination for tourist and recreation activities globally. Mountain ecosystems are generally considered to be less complex and less species diverse due to the harsh environmental conditions. As such, they are also more sensitive to the various impacts of the Anthropocene. For this reason, mountain regions may serve as sentinels of change and provide ideal ecosystems for studying climate and global change impacts on biodiversity. We here review different facets of anthropogenic impacts on mountain freshwater ecosystems. We put particular focus on micropollutants and their distribution and redistribution due to hydrological extremes, their direct influence on water quality and their indirect influence on ecosystem health via changes of freshwater species and their interactions. We show that those changes may drive pathogen establishment in new environments with harmful consequences for freshwater species, but also for the human population. Based on the reviewed literature, we recommend reconstructing the recent past of anthropogenic impact through sediment analyses, to focus efforts on small, but highly productive waterbodies, and to collect data on the occurrence and variability of microorganisms, biofilms, plankton species and key species, such as amphibians due to their bioindicator value for ecosystem health and water quality. The newly gained knowledge can then be used to develop a comprehensive framework of indicators to robustly inform policy and decision making on current and future risks for ecosystem health and human well-being.

Growth and Grazing Kinetics of the Facultative Anaerobic Nanoflagellate, Suigetsumonas clinomigrationis

The functional and numerical responses of the facultative anaerobic heterotrophic nanoflagellate, Suigetsumonas clinomigrationis NIES-3647 to prey density were examined under oxic and anoxic conditions. S. clinomigrationis grew at temperatures between 10 and 30°C and in the salinity range of 3.9–36.9 psu. The maximum specific growth and ingestion rates of S. clinomigrationis were lower under anoxic conditions than under oxic conditions. Half-saturation constants for the growth of S. clinomigrationis were within or greater than the range of bacterial densities in the water column of Lake Suigetsu, suggesting that its growth rate is limited by bacterial prey densities in natural environments.

Metagenomics Reveals a Novel Virophage Population in a Tibetan Mountain Lake

Virophages are parasites of giant viruses that infect eukaryotic organisms and may affect the ecology of inland water ecosystems. Despite the potential ecological impact, limited information is available on the distribution, diversity, and hosts of virophages in ecosystems. Metagenomics revealed that virophages were widely distributed in inland waters with various environmental characteristics including salinity and nutrient availability. A novel virophage population was overrepresented in a planktonic microbial community of the Tibetan mountain lake, Lake Qinghai. Our study identified coccolithophores and coccolithovirus-like phycodnaviruses in the same community, which may serve as eukaryotic and viral hosts of the virophage population, respectively.

Halomonas xiaochaidanensis sp. nov., isolated from a salt lake sediment

A short-rod-shaped moderately halophilic bacterium, designated CUG 00002(T), was isolated from the sediment of Xiaochaidan salt lake in Qinghai Province, China by using R2A medium. The cells were Gram-staining negative, aerobic, forming creamy and circular colonies with diameters of 2-3 mm on R2A agar when incubated at 30 °C for 3 days. 16S rRNA gene-based phylogenetic analysis indicated that strain CUG 00002(T) belonged to the genus Halomonas in the class Gammaproteobacteria, showing highest sequence similarity of 97.1 and 96.7 % to Halomonas mongoliensis Z-7009(T) (=DSM 17332=VKM B2353) and Halomonas shengliensis SL014B-85(T) (=CGMCC 1.6444(T)=LMG 23897(T)), respectively. The predominant isoprenoid quinone was ubiquinone-9 (Q9), and the major fatty acids were C16:0, summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (comprising C18:1 ω7c or C18:1 ω6c). The genomic DNA G+C content of strain CUG 00002(T) was 61.8 mol%. The above characteristics were consistent with the placement of the organism in the genus Halomonas. The level of DNA-DNA relatedness between CUG 00002(T) and its most closely related strain H. mongoliensis Z-7009(T) was 41.0 ± 1.6 %. Based on the results of phenotypic, phylogenetic and biochemical analyses, strain CUG 00002(T) represents a novel species of the genus Halomonas, for which the name Halomonas xiaochaidanensis sp. nov. is proposed. The type strain is CUG 00002(T) (=CCTCC AB 2014152(T)=KCTC 42685(T)).

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.

Temporal Succession of Ancient Phytoplankton Community in Qinghai Lake and Implication for Paleo-environmental Change

Tibetan lake sediments in NW China are sensitive recorders of climate change. However, many important plankton members do not leave any microscopic features in sedimentary records. Here we used ancient DNA preserved in Qinghai Lake sediments to reconstruct the temporal succession of plankton communities in the past 18,500 years. Our results showed that seven classes and sixteen genera of phytoplankton in the lake underwent major temporal changes, in correlation with known climatic events. Trebouxiophyceae and Eustigmatophyceae were predominant during the cold periods, whereas Chlorophyceae, Phaeophyceae, Xanthophyceae, Bacillariophyceae, and Cyanophyceae were abundant during the warm periods. The inferred changes in temperature, nutrients, precipitation, and salinity, as driven by the Westerlies and summer Monsoon strength, likely contributed to these observed temporal changes. Based on these correlations, we propose the phytoplankton index as a proxy to reconstruct the stadial versus interstadial climate change history in Qinghai Lake. This taxon-specific index is free of terrestrial contamination, sensitive to short-term climatic oscillations, and continuous in recording all climatic events in the lake. The validity of this index and its applicability to other lakes is demonstrated by its good correlations with multiple climate records of Qinghai Lake and another lake on the Tibetan Plateau, Kusai Lake.

Prokaryotic Community Structure Driven by Salinity and Ionic Concentrations in Plateau Lakes of the Tibetan Plateau

The prokaryotic community composition and diversity and the distribution patterns at various taxonomic levels across gradients of salinity and physiochemical properties in the surface waters of seven plateau lakes in the Qaidam Basin, Tibetan Plateau, were evaluated using Illumina MiSeq sequencing. These lakes included Lakes Keluke (salinity, <1 g/liter), Qing (salinity, 5.5 to 6.6 g/liter), Tuosu (salinity, 24 to 35 g/liter), Dasugan (salinity, 30 to 33 g/liter), Gahai (salinity, 92 to 96 g/liter), Xiaochaidan (salinity, 94 to 99 g/liter), and Gasikule (salinity, 317 to 344 g/liter). The communities were dominated by Bacteria in lakes with salinities of <100 g/liter and by Archaea in Lake Gasikule. The clades At12OctB3 and Salinibacter, previously reported only in hypersaline environments, were found in a hyposaline lake (salinity, 5.5 to 6.6 g/liter) at an abundance of ∼1.0%, indicating their ecological plasticity. Salinity and the concentrations of the chemical ions whose concentrations covary with salinity (Mg(2+), K(+), Cl(-), Na(+), SO4 (2-), and Ca(2+)) were found to be the primary environmental factors that directly or indirectly determined the composition and diversity at the level of individual clades as well as entire prokaryotic communities. The distribution patterns of two phyla, five classes, five orders, five families, and three genera were well predicted by salinity. The variation of the prokaryotic community structure also significantly correlated with the dissolved oxygen concentration, pH, the total nitrogen concentration, and the PO4 (3-) concentration. Such correlations varied depending on the taxonomic level, demonstrating the importance of comprehensive correlation analyses at various taxonomic levels in evaluating the effects of environmental variable factors on prokaryotic community structures. Our findings clarify the distribution patterns of the prokaryotic community composition in plateau lakes at the levels of individual clades as well as whole communities along gradients of salinity and ionic concentrations.

High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin

Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs) in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau

Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

Primer pairs for the specific environmental detection and T-RFLP analysis of the ubiquitous flagellate taxa Chrysophyceae and Kinetoplastea

Bacterivorous protists play a key role in microbial soil food webs, however due to the lack of specific PCR protocols targeting selected protist taxa, knowledge on the diversity and dynamics of these groups is scarce. We developed specific PCR primers in combination with a T-RFLP protocol for the cultivation-independent analysis of two important taxa of bacterivorous flagellates, the Chrysophyceae and Kinetoplastea, in soil samples. Sequence analysis of clone libraries originating from two soils in temperate regions demonstrated the specificity of the respective primer pairs. Clone sequences affiliating to the Chrysophyceae mainly clustered within the clade C2, which has been known so far for its presence mainly in cold climatic regions, whereas Kinetoplastea sequences were mainly related to the Neobodonid clade. Based on an in silico restriction analysis of database sequence entries, suitable restriction enzymes for a T-RFLP approach were selected. This in silico approach revealed the necessity to use a combination of two restriction enzymes for T-RFLP analysis of the Chrysophyceae. Soil T-RFLP profiles reflected all T-RFs of the clone library sequences obtained from the same soils and allowed to distinguish flagellate communities from different sites. We propose to use these primer pairs for PCR detection and rapid fingerprint screening in environmental samples and envisage their use also for quantitative PCR or next generation sequencing approaches.

Unique picoeukaryotic algal community under multiple environmental stress conditions in a shallow, alkaline pan

Winter phytoplankton communities in the shallow alkaline pans of Hungary are frequently dominated by picoeukaryotes, sometimes in particularly high abundance. In winter 2012, the ice-covered alkaline Zab-szék pan was found to be extraordinarily rich in picoeukaryotic green algae (42-82 × 10(6) cells ml(-1)) despite the simultaneous presence of multiple stressors (low temperature and light intensity with high pH and salinity). The maximum photosynthetic rate of the picoeukaryote community was 1.4 μg C μg chlorophyll a (-1) h(-1) at 125 μmol m(-2) s(-1). The assimilation rates compared with the available light intensity measured on the field show that the community was considerably light-limited. Estimated areal primary production was 180 mg C m(-2) d(-1). On the basis of the 18S rRNA gene analysis (cloning and DGGE), the community was phylogenetically heterogeneous with several previously undescribed chlorophyte lineages, which indicates the ability of picoeukaryotic communities to maintain high genetic diversity under extreme conditions.

Assimilation of cellulose-derived carbon by microeukaryotes in oxic and anoxic slurries of an aerated soil

Soil microeukaryotes may trophically benefit from plant biopolymers. However, carbon transfer from cellulose into soil microeukaryotes has not been demonstrated so far. Microeukaryotes assimilating cellulose-derived carbon in oxic and anoxic soil slurries were therefore examined by rRNA-based stable-isotope probing. Bacteriovorous flagellates and ciliates and, likely, mixotrophic algae and saprotrophic fungi incorporated carbon from supplemental [U-(13)C]cellulose under oxic conditions. A previous study using the same soil suggested that cellulolytic Bacteria assimilated (13)C of supplemental cellulose. Thus, it can be assumed that ciliates, cercozoa, and chrysophytes assimilated carbon by grazing upon and utilizing metabolic products of Bacteria that hydrolyzed cellulose in the soil slurries.

Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes

Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.

Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis

Tibetan lakes represent a unique microbial environment and are a good ecosystem to investigate the microbial diversity of high mountain lakes and their relationship with environmental factors. The diversity and community structure of bacterioplankton in Tibetan lakes was determined using DNA fingerprinting analysis, high-density 16S rRNA gene microarray (PhyloChip) analysis, and extensive clone library analysis of bacterial 16S rRNA genes. A previously unseen high microbial diversity (1732 operational taxonomic units based on PhyloChip data) and numerous novel bacterial 16S rRNA gene sequences were observed. Abundant SAR11-like sequences retrieved from saline Lake Qinghai demonstrated a unique SAR11 phylogenetic sister clade related to the freshwater LD12 clade. Water chemistry (e.g. salinity) and altitude played important roles in the selection of bacterial taxa (both presence and relative abundance) in Tibetan lakes. The ubiquity and uniqueness of bacterial taxa, as well as the correlation between environmental factors and bacterial taxa, was observed to vary gradually with different phylogenetic levels. Our study suggested high microbial cosmopolitanism and high endemicity observed at higher and lower phylogenetic levels, respectively.

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4-1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r=0.443, P=0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.

Do patterns of bacterial diversity along salinity gradients differ from those observed for macroorganisms?

It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.

Use of mycelia as paths for the isolation of contaminant-degrading bacteria from soil

Mycelia of fungi and soil oomycetes have recently been found to act as effective paths boosting bacterial mobility and bioaccessibility of contaminants in vadose environments. In this study, we demonstrate that mycelia can be used for targeted separation and isolation of contaminant‐degrading bacteria from soil. In a ‘proof of concept’ study we developed a novel approach to isolate bacteria from contaminated soil using mycelia of the soil oomycete Pythium ultimum as translocation networks for bacteria and the polycyclic aromatic hydrocarbon naphthalene (NAPH) as selective carbon source. NAPH‐degrading bacterial isolates were affiliated with the genera Xanthomonas, Rhodococcus and Pseudomonas. Except for Rhodococcus the NAPH‐degrading isolates exhibited significant motility as observed in standard swarming and swimming motility assays. All steps of the isolation procedures were followed by cultivation‐independent terminal 16S rRNA gene terminal fragment length polymorphism (T‐RFLP) analysis. Interestingly, a high similarity (63%) between both the cultivable NAPH‐degrading migrant and the cultivable parent soil bacterial community profiles was observed. This suggests that mycelial networks generally confer mobility to native, contaminant‐degrading soil bacteria. Targeted, mycelia‐based dispersal hence may have high potential for the isolation of bacteria with biotechnologically useful properties.

Short-term disturbance of a grazer has long-term effects on bacterial communities--relevance of trophic interactions for recovery from pesticide effects

Little is known about the transfer of pesticide effects from higher trophic levels to bacterial communities by grazing. We investigated the effects of pulse exposure to the pyrethroid Fenvalerate on a grazer-prey system that comprised populations of Daphnia magna and bacterial communities. We observed the abundance and population size structure of D. magna by image analysis. Aquatic bacteria were monitored with regard to abundance (by cell staining) and community structure (by a 16S ribosomal RNA fingerprinting method). Shortly after exposure (2 days), the abundance of D. magna decreased. In contrast, the abundance of bacteria increased; in particular fast-growing bacteria proliferated, which changed the bacterial community structure. Long after pulse exposure (26 days), the size structure of D. magna was still affected and dominated by a cohort of small individuals. This cohort of small D. magna grazed actively on bacteria, which resulted in low bacterial abundance and low percentage of fast-growing bacteria. We identified grazing pressure as an important mediator for translating long-term pesticide effects from a grazer population on its prey. Hence, bacterial communities are potentially affected throughout the period that their grazers show pesticide effects concerning abundance or population size structure. Owing to interspecific interactions, the recovery of one species can only be assessed by considering its community context.

East Tibetan lakes harbour novel clusters of picocyanobacteria as inferred from the 16S-23S rRNA internal transcribed spacer sequences

Planktonic picocyanobacteria abundance and diversity were investigated in nine lakes on the East Tibetan Plateau spanning a salinity gradient of 0.4-22.6 g l(-1). The investigation was conducted using epifluorescence microscopy (EFM) and terminal restriction fragment polymorphism analysis of 16S-23S rRNA internal transcribed spacer (ITS) PCR amplicons followed by sequence analyses of large ITS clone libraries of seven selected samples. EFM showed that picocyanobacteria comprised 7-19% of the total prokaryotic cells found in surface water. Most of the clones were classified into six clusters and grouped within the "picocyanobacterial clade", which consists exclusively of freshwater Synechococcus. Four new phylogenetic clusters and one new subcluster of Synechococcus spp. were found, none of which are members of any known picocyanobacterial clusters. The new clusters and subcluster were the most abundant picocyanobacteria (about 96% of the sequences) in the samples collected. Sequence analyses indicated that members of the four new Synechococcus groups were only found in freshwater lakes (<1.0 g l(-1) of total dissolved solid), while members of the new subcluster were found in all the investigated Tibetan lakes, over a large salinity gradient of 0.4-22.6 g l( -1). This suggests that there is ecologically significant microdiversity within the observed Synechococcus group as defined by ITS sequences. Collectively our study demonstrated abundant and potentially novel Synechococcus in East Tibetan lakes that are likely the result of evolutionary adaptations to regional conditions.

Application of the denaturing gradient gel electrophoresis (DGGE) technique as an efficient diagnostic tool for ciliate communities in soil

Ciliates (or Ciliophora) are ubiquitous organisms which can be widely used as bioindicators in ecosystems exposed to anthropogenic and industrial influences. The evaluation of the environmental impact on soil ciliate communities with methods relying on morphology-based identification may be hampered by the large number of samples usually required for a statistically supported, reliable conclusion. Cultivation-independent molecular-biological diagnostic tools are a promising alternative to greatly simplify and accelerate such studies. In this present work a ciliate-specific fingerprint method based on the amplification of a phylogenetic marker gene (i.e. the 18S ribosomal RNA gene) with subsequent analysis by denaturing gradient gel electrophoresis (DGGE) was developed and used to monitor community shifts in a polycyclic aromatic hydrocarbon (PAH) polluted soil. The semi-nested approach generated ciliate-specific amplification products from all soil samples and allowed to distinguish community profiles from a PAH-polluted and a non-polluted control soil. Subsequent sequence analysis of excised bands provided evidence that polluted soil samples are dominated by organisms belonging to the class Colpodea. The general DGGE approach presented in this study might thus in principle serve as a fast and reproducible diagnostic tool, complementing and facilitating future ecological and ecotoxicological monitoring of ciliates in polluted habitats.

Low taxon richness of bacterioplankton in high-altitude lakes of the eastern tibetan plateau, with a predominance of Bacteroidetes and Synechococcus spp

Plankton samples were collected from six remote freshwater and saline lakes located at altitudes of 3,204 to 4,718 m and 1,000 km apart within an area of ca. 1 million km(2) on the eastern Tibetan Plateau to comparatively assess how environmental factors influence the diversity of bacterial communities in high-altitude lakes. The composition of the bacterioplankton was investigated by analysis of large clone libraries of 16S rRNA genes. Comparison of bacterioplankton diversities estimated for the six Tibetan lakes with reference data previously published for lakes located at lower altitudes indicated relatively low taxon richness in the Tibetan lakes. The estimated average taxon richness in the four Tibetan freshwater lakes was only one-fifth of the average taxon richness estimated for seven low-altitude reference lakes. This cannot be explained by low coverage of communities in the Tibetan lakes by the established libraries or by differences in habitat size. Furthermore, a comparison of the taxonomic compositions of bacterioplankton across the six Tibetan lakes revealed low overlap between their community compositions. About 70.9% of the operational taxonomic units (99% similarity) were specific to single lakes, and a relatively high percentage (11%) of sequences were <95% similar to publicly deposited sequences of cultured or uncultured bacteria. This beta diversity was explained by differences in salinity between lakes rather than by distance effects. Another characteristic of the investigated lakes was the predominance of Cyanobacteria (Synechococcus) and Bacteroidetes. These features of bacterioplankton diversity may reflect specific adaptation of various lineages to the environmental conditions in these high-altitude lakes.