Phytoplankton assemblages and community structure in tropical temporary freshwater ponds in sub‐Saharan Africa1

Anthropogenic and climatic factors are important determinants of algal distribution in aquatic systems. This study aimed to identify temporary pond‐groups of phytoplankton assemblages and to establish the interactions between environmental variables and phytoplankton structure. Phytoplankton samples were collected and preserved with 5% formalin; water samples for chemical analysis were taken in August and September 2007, 2008, and 2009 in 86 ponds randomly selected in the Sahelian sector and the Sudanian sector (protected and unprotected areas) of Burkina Faso. Plankton species were examined using light microscopy and identified using standard methods. A Fuchs‐Rosenthal chamber was used for algal cell counting. NMDS ordination, indicator species analysis and canonical analysis were performed using Pc‐Ord and CANOCO. Kruskal–Wallis and Mann–Whitney U‐tests using the software Statistica were performed to compare parameters between pond‐groups. Three pond‐groups were identified: the Sahelian pond‐group, dominated by Lyngbya martensiana and Pseudanabaena constricta; the protected area pond‐group, dominated by Euglena caudata and Trachelomonas raciborskii; and the unprotected area pond‐group, dominated by Closterium venus and Euglena proxima. At P < 0.05, species composition and abundance in algal groups were mostly associated with nitrate, pH, dissolved oxygen, and conductivity. The Sahelian and the Sudanian sectors were different in pH, water transparency, and species richness. Univariate and multivariate analyses illustrate that variations in the physicochemical properties of water and algal structure followed climatic and anthropogenic gradients. The classification of ponds into algal associations demonstrated that algal assemblages may be used as reliable indicators of habitat conditions.     

Lipid and DNA Evidence of Dominance of Planktonic Archaea Preserved in Sediments of the South China Sea: Insight for Application of the TEX86 Proxy in an Unstable Marine Sediment Environment

The marine planktonic archaea are dominated by Thaumarchaeotal Marine Group I, which is characterized by the lipid biomarker thaumarchaeol. The marine benthic archaea are characterized by greater diversity of currently unknown species whose lipid biomarker signatures are uncertain. In this study, a sediment core from the northwestern part of the South China Sea (SCS) (water depth 1474 m) was analyzed using molecular DNA and lipid biomarker approaches. While 16S rRNA gene analysis showed changing archaeal community structures with sediment depth, this change had little impact on the fossil record of archaeal lipids that are characteristic of the planktonic community. As a result, the fossil archaeal lipids recorded paleo sea surface temperature of the SCS since the last glacial maxima by the TEX₈₆ proxy, which agreed generally with the winter temperature recorded by planktonic foraminiferas collected from the same area of the SCS that hosted mass-transported deposits. This suggests that this deep water deposit may have partially preserved paleoclimate record reflecting seasonal temperature variation in a near shore setting, which is in contrast to annual sea surface temperature or sub sea surface temperature variation recorded by TEX₈₆ in the open ocean.     

Proteome profile of a pandemic Vibrio parahaemolyticus SC192 strain in the planktonic and biofilm condition

Vibrio parahaemolyticus is one of the leading causative agents of foodborne diseases in humans. In this study, the proteome profiles of the pandemic strain V. parahaemolyticus SC192 belonging to the O3:K6 serovar during the planktonic and biofilm stages were analyzed by two-dimensional liquid chromatography coupled to tandem mass spectrometry. This non-gel-based multidimensional protein identification technology approach identified 45.5% of the proteome in the reference genome V. parahaemolyticus RIMD 2210633. This is the largest proteome coverage obtained so far in V. parahaemolyticus and provides evidence for expression of 27% of the hypothetical proteins. Comparison of the planktonic and biofilm proteomes based on their cluster of orthologous groups, gene ontologies and KEGG pathways provides basic information on biofilm specific functions and pathways. To the authors’ knowledge, this is the first study to generate a global proteome profile of the pandemic strain of V. parahaemolyticus and the method reported here could be used to rapidly obtain a snapshot of the proteome of any microorganism at a given condition.     

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T))

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.     

The membrane bioreactor: a novel tool to grow anammox bacteria as free cells

In a membrane bioreactor (MBR), fast growth of anammox bacteria was achieved with a sludge residence time (SRT) of 12 days. This relatively short SRT resulted in a--for anammox bacteria--unprecedented purity of the enrichment of 97.6%. The absence of a selective pressure for settling, and dedicated cultivation conditions led to growth in suspension as free cells and the complete absence of flocs or granules. Fast growth, low levels of calcium and magnesium, and possibly the presence of yeast extract and a low shear stress are critical for the obtainment of a completely suspended culture consisting of free anammox cells. During cultivation, a population shift was observed from Candidatus "Brocadia" to Candidatus "Kuenenia stuttgartiensis." It is hypothesized that the reason for this shift is the higher affinity for nitrite of "Kuenenia." The production of anammox bacteria in suspension with high purity and productivity makes the MBR a promising tool for the cultivation and study of anammox bacteria.     

Quantifying rotifer species richness in temperate lakes

1. Biodiversity assessments of lakes depend on the ability to identify the complement of species present, although the degree of sampling required is often uncertain. We utilise long‐term data to predict rotifer species richness in three habitats in three Polish lakes using rarefaction sampling methods. 2. Richness in littoral and psammon habitats did not saturate, even with up to 130 samples. Highest richness was observed in psammon habitat (119 species) in Lake Mikolajskie, followed by littoral habitat in Lakes ?uknajno (114 species) and Kuc (110 species). Littoral habitats in Lakes ?uknajno (56%) and Kuc (51%) had the most species not shared with other habitats in the same lake. 3. Species richness (Chao2) estimates ranged between 44 for pelagic and 135 for psammon habitat in Lake Mikolajskie, to 100 for psammon and 137 for littoral habitat in Lake Kuc, and 65 for pelagic and 162 for littoral habitat in Lake ?uknajno. Whole lake estimates were 167, 205 and 171 species, respectively, for these lakes, higher than the 150 to 160 species predicted by Dumont and Segers (Hydrobiologia, 1996, 341 , 125). 4. Using standardised sampling, richness was significantly higher in littoral than either pelagic or psammon habitats. Contrasts of standardised rarefaction curves revealed that richness in Lakes Kuc and Mikolajskie was described as well by littoral‐only or psammon‐only samples, respectively, as by those randomly drawn from across all habitats in the lake. 5. Species richness estimates for Lake Mikolajskie were highest in summer, followed by autumn and spring. Interannual estimates differed by up to 427%, nearly an order of magnitude greater than maximal seasonal variation of 70%. 6. Results indicate that much higher sampling intensity is required to establish species richness than is presently carried out in most lakes. Because many species can be detected only with very intensive sampling, conservation programmes must consider sampling intensity when designing studies.     

Complementary pathways of dissolved organic carbon removal pathways in clear-water Amazonian ecosystems: photochemical degradation and bacterial uptake

Dissolved organic carbon (DOC) photochemical reactions establish important links between DOC and planktonic bacteria. We hypothesize that seasonal changes in DOC quality, related to the flood pulse, drive the effects of light-DOC interactions on uptake by planktonic bacteria uptake in clear-water Amazonian ecosystems. Water samples from two ecosystems (one lake and one stream) were incubated in sunlight during different hydrological periods and were then exposed to bacterial degradation. Photochemical and bacterial degradation were driven by seasonal DOC inputs. Bacterial mineralization was the main degradation pathway of autochthonous DOC in the lake, while allochthonous DOC was more available for photochemical oxidation. We suggest that sunlight enhances the bacterial uptake of refractory DOC but does not alter uptake of labile forms. We also observed a positive relationship between sunlight and bacterial degradation of DOC, instead of competition. We conclude that photochemical reactions and bacteria complementarily degrade the different sources of DOC during the flood pulse in Amazonian clear-water aquatic ecosystems.     

Molecular evidence for an independent origin of modern triserial planktonic foraminifera from benthic ancestors

Gallitellia vivans is the only Recent representative of the triserial planktonic foraminiferal family Guembelitriidae. The origin and evolution of this interesting albeit poorly known family are enigmatic. To elucidate the phylogenetic relationships between G. vivans and other planktonic foraminifera, we sequenced the small subunit ribosomal DNA (SSU rDNA) for comparison to our extensive database of planktonic and benthic species. Our analyses suggest that G. vivans represents a separate lineage of planktonic foraminifera, which branches close to the benthic rotaliids Stainforthia and Virgulinella. Both genera resemble Gallitellia in general morphological appearance, having elongate triserial tests at least in their early ontogenic stages. The divergence time of G. vivans is estimated at ca. 18 Ma (early Miocene), suggesting an origin independent from the Cretaceous and Paleogene triserial planktonic foraminifera. Our study thus indicates that modern triserial planktonic foraminifera are not related to the Cretaceous–Paleogene triserial species, and that the sporadic occurrences in the fossil record are not the result of poor preservation, but reflect multiple transitions from benthic to planktonic mode of life.     

Surface water conditions in the Northern Benguela Region (SE Atlantic) during the last 450 ky reconstructed from assemblages of planktonic foraminifera

Planktonic foraminiferal records from Site 1083 (ODP Leg 175) were used to investigate changes in surface water conditions in the Northern Benguela Region over the past 450 ky. The assemblages of planktonic foraminifera are dominated by four species: sinistral coiling Neogloboquadrina pachyderma, dextral coiling N. pachyderma, Globigerina bulloides and Globorotalia inflata. Besides, tropical species deliver a small contribution to the assemblage.The most prominent temporal variations, displayed by N. pachyderma (s+d), represent changes in the coastal upwelling and the presence of cold, nutrient rich waters over the core site. Neogloboquadrina pachyderma (s+d) shows cyclic variability in the eccentricity and, to a less extent, precession frequencies. The changes indicate increased upwelling intensity in glacial maxima and precession maxima, and correlate well with the wind-strength record of Stuut et al. (2002). During glacial maxima, steep temperature gradients over the Southern Hemisphere caused strong SE trade winds and strong upwelling. Precession maxima cause a weak monsoonal circulation, more zonal SE trade winds, strong coastal upwelling, and nutrient-rich surface waters over ODP Site 1083.Advection of Angola Current (AC) surface water into the Walvis Basin, indicated by the tropical species, occurs when the Angola Benguela Front (ABF) is positioned southward. Occasionally, this happened during glacial maxima, as can be explained with the reconstructed and predicted meridional movements of the ABF. The amount of AC water was never sufficient to suppress the marine biological production at the core site.The contribution of Benguela Current (BC) water, reflected by Globorotalia inflata, is greatly determined by the upwelling. In periods of strong upwelling, the BC influence is suppressed.In several glacial substages, the temperature of the upwelling South Atlantic Central Water (SACW) may have been increased, as suggested by the dominance of Neogloboquadrina pachyderma (d) in the upwelling record. This phenomenon may be due to intensified subduction in the central South Atlantic that induces the formation of SACW, or to larger contributions of Eastern SACW to the upwelling water.Around 250–200 ky BP, a long-term shift to higher productivity occurred that is absent in the upwelling record. It was accompanied with a transition from a precession and obliquity variability to an eccentricity dominated variability in the Globorotalia inflata (BC) record. The shift was probably connected to a long-term southward shift of the circumpolar oceanic frontal systems south of the African continent.     

Evolutionary rates do not drive latitudinal diversity gradients

Among the several hypotheses invoked for explaining latitudinal diversity gradients (LDGs), some models classified within the 'evolutionary hypothesis' family assume that LDGs are the direct consequence of latitudinal variations in the speciation and/or extinctions rates. Spatially structured simulations of the biogeographical dispersal of a randomly generated clade refute the central tenet of these explanatory models and indicate that global diversity patterns are combined outcomes of geographic and thermal mid-domain effects under a phylogenetically controlled niche conservatism constraint. The positive correlation observed in several higher taxa between speciation rate and diversity does not involve any causal relationship between these two parameters but is most likely the first order by-product of a positive correlation between temperature and per capita speciation rate.