Development and evaluation of specific 16S rDNA primers for marine Cytophaga–Flavobacteria cluster

Through multiple alignment analysis of 16S rDNA sequences from all known genera of Cytophaga–Flavobacteria (CF) cluster, a new primer pair specifically targeting this cluster was developed, greatly facilitating their diversity and function's exploration in marine ecosystems. Compared with previously reported primers, the new primer pair could theoretically retrieve broader CF diversity without decreasing specificity. The effectiveness for field samples was further evaluated by testing the community DNA samples from various marine environments using the optimal polymerase chain reaction (PCR) conditions established in this work. The results showed its robustness and high specificity for amplifying CF cluster's 16S rDNA fragments from complex marine environments.     

Rodent middens reveal episodic,long‐distance plant colonizations across the hyperarid Atacama Desert over the last 34,000 years

Aim To document the impact of late Quaternary pluvial events on plant movements between the coast and the Andes across the Atacama Desert, northern Chile. Location Sites are located along the lower and upper fringes of absolute desert (1100–2800 m a.s.l.), between the western slope of the Andes and the Coastal Ranges of northern Chile (24–26° S). Methods We collected and individually radiocarbon dated 21 rodent middens. Plant macrofossils (fruits, seeds, flowers and leaves) were identified and pollen content analysed. Midden assemblages afford brief snapshots of local plant communities that existed within the rodents’ limited foraging range during the several years to decades that it took the midden to accumulate. These assemblages were then compared with modern floras to determine the presence of extralocal species and species provenance. Results Five middens span the last glacial period (34–21 ka) and three middens are from the last glacial–interglacial transition (19–11 ka). The remaining 13 middens span the last 7000 years. Coastal hyperarid sites exhibit low taxonomic richness in middens at 19.3, 1.1, 1.0, 0.9, 0.5 ka and a modern sample. Middens are also dominated by the same plants that occur today. In contrast, middens dated to 28.1, 21.3, 17.3, 3.7 and 0.5 ka contain more species, including Andean extralocals. Precordillera middens (c. 2700 m) show a prominent increase in plant macrofossil richness, along with the appearance of Andean extralocals and sedges at 34.5 and 18.9 ka. Six younger middens dated to 6.1–0.1 ka are similar to the modern local vegetation. Main conclusions Increased species richness and Andean extralocal plants occurred along the current lower fringes of absolute desert during the last glacial–interglacial transition and late Holocene. The absence of soil carbonates indicates the persistence of absolute desert throughout the Quaternary. Colonization by Andean plants could have been accomplished through long‐distance seed dispersal either by animals or floods that originated in the Andes. We postulate that dispersal would have been most frequent during regional pluvial events and associated increases in groundwater levels, forming local wetlands in the absolute desert, and generating large floods capable of crossing the Central Depression.     

The Scarab

Abstract

Joseph McBride Searching for John Ford: A Life St. Martin's Press 834 pp. $40.00     

What Can Environmental Sequences Tell Us About the Distribution of Low‐Rank Taxa? The Case of Euplotes (Ciliophora,Spirotrichea), Including a Description of Euplotes enigma sp. nov.

Environmental sequences have become a major source of information. High‐throughput sequencing (HTS) surveys have been used to infer biogeographic patterns and distribution of broad taxa of protists. This approach is, however, more questionable for addressing low‐rank (less inclusive) taxa such as species and genera, because of the increased chance of errors in identification due to blurry taxonomic boundaries, low sequence divergence, or sequencing errors. The specious ciliate genus Euplotes partially escapes these limitations. It is a ubiquitous, monophyletic taxon, clearly differentiated from related genera, and with a relatively well‐developed internal systematics. It has also been the focus of several ecological studies. We present an update on Euplotes biogeography, taking into consideration for the first time environmental sequences, both traditional (Sanger) and HTS. We inferred a comprehensive small subunit rRNA gene phylogeny of the genus including a newly described marine species, Euplotes enigma, characterized by a unique question mark‐shaped macronucleus. We then added available environmental sequences to the tree, mapping associated metadata. The resulting scenario conflicts on many accounts with previously held views, suggesting, for example, that a large diversity of anaerobic Euplotes species exist, and that marine representatives of mainly freshwater lineages (and vice‐versa) might be more common than previously thought.     

Monopolar electromyographic signals recorded by a current amplifier in air and under water without insulation

It was recently proposed that one could use signal current instead of voltage to collect surface electromyography (EMG). With EMG-current, the electrodes remain at the ground potential, thereby eliminating lateral currents. The purpose of this study was to determine whether EMG-currents can be recorded in Tap and Salt water, as well as in air, without electrically shielding the electrodes. It was hypothesized that signals would display consistent information between experimental conditions regarding muscle responses to changes in contraction effort. EMG-currents were recorded from the flexor digitorum muscles as participant’s squeezed a pre-inflated blood pressure cuff bladder in each experimental condition at standardized efforts. EMG-current measurements performed underwater showed no loss of signal amplitude when compared to measurements made in air, although some differences in amplitude and spectral components were observed between conditions. However, signal amplitudes and frequencies displayed consistent behavior across contraction effort levels, irrespective of the experimental condition. This new method demonstrates that information regarding muscle activity is comparable between wet and dry conditions when using EMG-current. Considering the difficulties imposed by the need to waterproof traditional bipolar EMG electrodes when underwater, this new methodology is tremendously promising for assessments of muscular function in aquatic environments.     

Photosynthesis and Leaf Structure in Domesticated Cassava (Euphorbiaceae) and a Close Wild Relative: Have Leaf Photosynthetic Parameters Evolved Under Domestication?

Broad patterns across wild plant species show that leaf composition and morphology vary predictably among habitats, richer habitats favoring resource‐acquisition strategies and poorer habitats favoring resource‐conservation strategies. Domestication is often accompanied by a shift to richer habitats, and might thus be expected to lead to a shift in leaf composition and morphology and hence in photosynthetic parameters. We compared leaf photosynthetic parameters in domesticated cassava (Manihot esculenta) and a close wild relative, using greenhouse‐grown plants. In domesticated cassava, CO₂ exchange rate expressed per unit mass and specific leaf area (SLA, m²/kg dry mass) were greater than in the wild relative, whereas leaf dry matter content (LDMC, dry mass/fresh mass) was lower in the domesticate. These results suggest that SLA and net photosynthetic rates may both have increased in the evolution of cassava under domestication, enabling more rapid growth in relatively resource‐rich and protected agricultural habitats. Previous comparisons of photosynthetic rates in domesticated plants and wild relatives have usually considered only leaf area‐based measures. Here, we discuss the interest of using mass‐based rates to study the evolution of ecological strategies under domestication.     

Enhancing Causal Assessment of Estuarine Fishkills Using Graphical Models

It is not possible to determine the causal relationship between fishkills and the toxic dinoflagellate Pfiesteria piscicida in the Neuse River Estuary, North Carolina, using observational data on these two variables alone. However, consideration of a third variable, indicating the presence of a broader class of more easily measured Pfiesteria-like organisms (PLOs), leads to causal model structures from which the nature of this relationship can be distinguished. We use reported field data to evaluate alternative models and find that the suggestion that toxic Pfiesteria cause fishkills is inconsistent with observation. The data are more indicative of a model in which PLOs (including potentially toxic Pfiesteria) are stimulated to become actively toxic by the presence of already dead or dying fish. Laboratory experiments performed to date do not provide evidence contradictory to this finding. However, neither can the existence of a common cause of both Pfiesteria toxicity and fishkills be ruled out. The differing implications for ecosystem management suggest that these causal associations should be further investigated through additional modeling and data collection efforts. Graphical methods of model construction and evaluation can assist in this process. Received 22 May 2002; accepted 3 October 2002.     

Use of toxicity assays for enantiomeric discrimination of pharmaceutical substances

Toxicity assays are commonly used as general indicators of environmental water pollution. In the study described here, selected toxicity tests have been used to evaluate the different toxicity levels of enantiomers of different pharmaceutical drugs that can be found as potential contaminants in water environments. Isomers of dopa, fluoxetine, and atenolol were tested with three aquatic organisms corresponding to different trophic levels: Daphnia magna (a crustacean), Pseudokirchneriella subcapitata (a microalga), and Tetrahymena thermophila (a protozoan). Different levels of toxicity were observed for each enantiomer, suggesting that significant enantioselectivity occurs in aquatic toxicity and that such enantiomeric differences must be considered when evaluating the ecological effects of these compounds.