The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

Growth and nutrition of birch seedlings in relation to potassium supply rate

Summary Growth of hydroponically cultivated birch seedlings (Betula pendula Roth.) at sub- and supra-optimum potassium supply rates was investigated. Potassium was supplied either as a relative addition rate (r _k = 5, 10, 15 and 20% increase day^-1) or as fixed concentrations (0.2, 3, 6, 12 and 15 mM) in the culture solution. After an acclimation period the growth rate of the seedlings in the suboptimum treatments reached values close to the treatment variable, the relative rate of K-addition. Deficiency symptoms, in the form of chlorosis and necroses along the leaf margins, developed initially in all suboptimum treatments, but very few new symptoms appeared once the seedlings had reached the phase of steady-state nutrition and growth. At supra-optimum K-supply levels, i.e. at 0.2–15 mM K in the culture solution, no symptoms of deficiency or toxicity developed, and the relative growth rate of the seedlings remained maximum. The relative growth rate of the seedlings was linearly related to the plant K-status for K contents ranging from 0.2 to 1.0% of dry weight (DW). At higher internal K-concentrations, 1.0–3.0% DW, no further increase in relative growth rate was achieved. A shortage of K resulted in a decrease in the net assimilation rate. This effect was counterbalanced by the absence of shift in he leaf weight ratio as well as by the production of relatively thin leaves. The fraction of dry matter allocated to roots decreased in K-limited plants, as did the leaf contents of soluble carbohydrates and starch.     

COMPETITION BETWEEN STAURASTRUM LUETKEMUELLERII (CHLOROPHYCEAE) AND MICROCYSTIS AERUGINOSA(CYANOPHYCEAE) UNDER VARYING MODES OF PHOSPHATE SUPPLY1

The desmid Staurastrum luetkemuellerii Donat et Ruttner and the cyanobacterium Microcystis aeruginosa Kütz. were grown in mixed cultures with various phosphate (P_i) additions. One pulse of P_i each day (semi-continuous cultures) favored M. aeruginosa whereas S. luetkemuellerii was favored when the same quantity of P_i was supplied continuously (chemostats). Both species coexisted under P limitation provided that the nutrient was supplied in an appropriate mode. The ability of each species to compete for P depended on their P_i uptake characteristics and their capability to retain the accumulated P_i. High affinity in uptake at low P_i concentrations contributed considerably to the growth eficiency of S. luetkemuellerii under continuous supply of P_iM. aeruginosa was, however, consistently superior to S. luetkemuellerii in accuniulatiug the newly added P, but had a high rate of P_i release. In both -types of cultures, a net high of P went from M. aeruginosa to S. luetkemuellerii. The kinetic characteristics of the two species were used to simulate the outcome of competition experiments. Simulations agreed with the experimental data f both uptake and P_i release were considered in the model. The zlariable P*(the concentration of P_i at which the net uptake is equal to μ·Q_P is a function of uptake and release of P_i but could not explain the chemostat results. S. luetkemuellerii was the winner in many experiments even if its P*was higher thou that of M. aeruginosa. Thus, in the present case P_c (the concentration at which the net uptake is zero) was a better predictor of the ability to compete for P_i under steady state as well as transient conditions in the P_i supply.     

A New Method for Finding Small Vertebrate Fossils: Ultraviolet Light At Night

Vertebrate fossils from many different formations fluoresce when exposed to ultraviolet (UV) light. In this paper field observations and controlled experiments in the Chadron Formation (White River Group, late Eocene) of Wyoming are used to assess the utility of searching for fossils at night using ultraviolet light. The results indicate that, especially for very small teeth and egg-shell fragments, searching with ultraviolet light at night can result in significantly more specimens than searching during daylight hours. This method has the potential to increase sample sizes for small vertebrate specimens that are often overlooked when using standard collecting techniques.     

Bacteria Associated with Cysts of the Soybean Cyst Nematode (Heterodera glycines)

The soybean cyst nematode (SCN), Heterodera glycines, causes economically significant damage to soybeans (Glycine max) in many parts of the world. The cysts of this nematode can remain quiescent in soils for many years as a reservoir of infection for future crops. To investigate bacterial communities associated with SCN cysts, cysts were obtained from eight SCN-infested farms in southern Ontario, Canada, and analyzed by culture-dependent and -independent means. Confocal laser scanning microscopy observations of cyst contents revealed a microbial flora located on the cyst exterior, within a polymer plug region and within the cyst. Microscopic counts using 5-(4,6-dichlorotriazine-2-yl)aminofluorescein staining and in situ hybridization (EUB 338) indicated that the cysts contained (2.6 ± 0.5) × 10⁵ bacteria (mean ± standard deviation) with various cellular morphologies. Filamentous fungi were also observed. Live-dead staining indicated that the majority of cyst bacteria were viable. The probe Nile red also bound to the interior polymer, indicating that it is lipid rich in nature. Bacterial community profiles determined by denaturing gradient gel electrophoresis analysis were simple in composition. Bands shared by all eight samples included the actinobacterium genera Actinomadura and Streptomyces. A collection of 290 bacteria were obtained by plating macerated surface-sterilized cysts onto nutrient broth yeast extract agar or on actinomycete medium. These were clustered into groups of siblings by repetitive extragenic palindromic PCR fingerprinting, and representative isolates were tentatively identified on the basis of 16S rRNA gene sequence. Thirty phylotypes were detected, with the collection dominated by Lysobacter and Variovorax spp. This study has revealed the cysts of this important plant pathogen to be rich in a variety of bacteria, some of which could presumably play a role in the ecology of SCN or have potential as biocontrol agents.     

Use of Plant Strategy Ordination,DCA and ANOVA to elucidate relationships among habitats of Salix planifolia and Salix monticola

Abstract. Detrended Correspondence Analysis (DCA) was used on a data set of 112 species from 14 stands dominated by Salix planifolia and/or S. monticola. Environmental variables were determined which might be important to explain differences in stand vegetation composition, and willow stature (height), in willow carrs in the Rocky Mountain National Park. Correlation of environmental variables with DCA stand scores indicate that peat depth and soil redox potential are highly related to the primary DCA axis. Soils in stands of S. planifolia are more reduced in the early summer and have greater peat depths, than soils in stands of S. monticola. The second DCA axis is related to a water chemistry gradient of hydrogen ion, sulphate, and ammonium concentration. Four environmental variables selected by correlation analysis were regressed on stand scores from the first two DCA axes. Regression coefficients of August soil redox potential and soil water pH were significantly non-zero on the primary DCA axis. In addition to overall vegetation relationships elucidated by DCA, the relationships between willow stature and environmental variables were tested by simultaneous ANOVAs. ANOVA results and DCA ordinations indicate that S. planifolia and S. monticola plants achieve the greatest stature in the least reduced soils, and in shallow peat. Competitive, stress tolerant, and ruderal plant strategy theory applied to the vegetation data produced an arrangement of stands highly correlated to the DCA Axis 1 stand arrangement. These correlations indicate that the primary axis of vegetation structure can be extracted either by species composition, or species morphology/physiology relationships. Concurrent use of DCA and plant strategy theory is suggested as a tool for the prediction of community composition.