Plant functional group diversity promotes soil protist diversity

We tested whether effects of plant diversity can propagate through food webs, down to heterotrophic protists not linked directly to plants. To this end we synthesised grassland ecosystems with varying numbers of plant functional groups (FGN) and assessed corresponding changes in testate amoebae communities. The number of plant species was kept constant. When FGN was increased from 1 to 3, species number and total community density of live testate amoebae were enhanced according to a linear and a saturating function, respectively. From FGN 1 to 2, the appearance of new testate amoebae species did not affect the presence of the resident species, whereas, from FGN 2 to 3 about one quarter of the resident testate amoebae species was replaced, without altering the total species number. Overall, density by species increased, while evenness of the testate amoebae community was not affected by FGN; although Trinema lineare, one of the most common species, became more abundant. The observed relationship between plant functional group diversity and testate amoebae diversity could shed new light on the biogeographical distribution patterns of protists.     

The promise of a protist: the Dictyostelium genome project

The genome of Dictyostelium discoideum is being sequenced by an international consortium and is scheduled for completion in the next few years. The sequence will accelerate research into a number of phenomena carried out by these versatile soil amoebae, providing insight into analogous processes that operate in a wide range of eukaryotes. These include the dynamic regulation of the cytoskeleton during chemotaxis, intercellular communication during multicellular development and the intracellular growth of bacterial pathogens. The current state of the genome project is summarized and the challenges of sequencing a genome with unusually low guanine and cytosine content and with a bimodal base composition distribution are discussed. The prospects for functional analyses at the genomic scale are also considered. Electronic Publication     

利用环境胁迫提高破囊壶菌二十二碳六烯酸生产的研究进展

破囊壶菌由于具备生产多种高值天然活性物质的能力,如二十碳五烯酸(eicosapentaenoic acid, EPA)、二十二碳六烯酸(docosahexaenoic acid, DHA)、角鲨烯和类胡萝卜素等,目前已被视为商业脂质生产的优质来源。本文首先对破囊壶菌的生态作用和生物技术价值进行介绍,并概述了脂肪酸的两条生物合成途径;其次重点阐述了NaCl、温度、溶氧和pH这4种环境胁迫因子对破囊壶菌生长、脂质积累、脂肪酸组成和DHA生产的影响;随后总结了当前利用环境胁迫因子的渗透调节策略、分段发酵策略和缓解氧化应激策略提升破囊壶菌DHA生物合成能力的研究现状;最后指出了破囊壶菌在环境胁迫的分子调控机制、分段式发酵策略、菌株进化及代谢工程等方面存在的问题,并对如何改进这些问题以及未来可能的发展方向进行了展望。该综述旨在为破囊壶菌实现高效工业化生产DHA提供有效的参考。     

Pycnogonid affinities: a review

Early authors regarded Pycnogonida (sea spiders) either as aquatic arachnids, ‘degraded’ crustaceans or as some sort of intermediate form between the two. Subsequently, pycnogonids were either placed among the Chelicerata or considered as an isolated group, unrelated to other arthropods. The latter model is untenable under phylogenetic systematics and recent cladistic studies have supported one of two alternative hypotheses. The first is the traditional Chelicerata s.lat. concept, i.e. (Pycnogonida + Euchelicerata). This, however, has only one really convincing synapomorphy: chelate chelicerae. The second hypothesis recognizes (Pycnogonida + all other Euarthropoda) and has been recovered in various ‘total evidence’ studies. Morphologically some characters – the presence of gonopores on the trunk and absence of a labrum, nephridia and intersegmental tendons – support Cormogonida (Euarthropoda excluding pycnogonids). Advances in developmental biology have proposed clear interpretations of segmentation homologies. However, so far there is also a confrontation of the two hypotheses depending on whether the last walking leg segment is considered part of the prosoma. In this case pycnogonids have too many prosomal segments compared with Euchelicerata; perhaps implying they are not sister groups. Alternatively, if part of the postprosomal region, the last leg pair could correspond to the chilarial segment in euchelicerates and its uniramous state could be apomorphic with respect to other euarthropods. Molecular phylogenies need to be more rigorously analysed, better supported by data from different sources and technique‐sensitive aspects need to be explored. Chelicerata s.lat. may emerge as the more convincing model, yet even the putative autapomorphy of chelicerae needs to be treated with caution as there are fossil ‘great appendage’ arthropods in the early Palaeozoic which also have a robust, food‐gathering, pair of head limbs and which may lie on the chelicerate, or even the euarthropod, stem lineage.     

The affinities of mites and ticks: a review

Mites and ticks can be divided into two well-defined clades, Anactinotrichida and Actinotrichida, for which a recent work formalized a suite of putative autapomorphies and reciprocal differences. Whether they are sister-taxa – forming a monophyletic Acari – is more controversial. Earlier supporters of two independent origins for mites largely failed to demonstrate convincing synapomorphies between either of the two lineages and other arachnid orders; although recent work on reproductive biology revealed explicit characters of this nature. Furthermore, some of the characters proposed in support of a monophyletic Acari do not stand up to detailed scrutiny when compared with Arachnida in general. Effective morphological comparisons between mites and other arachnids are hindered by incompatible nomenclature and long-standing, mite-specific characters which are difficult to score for other arachnids. Furthermore, taxon-specific characters restricted to individual mite groups have sometimes been treated erroneously as 'typical' for all Acari. Here, previous hypotheses of mite affinities are reviewed. Historically, authors have debated whether mites are basal arachnids or highly derived. Excluding weakly supported early hypotheses, mites have been resolved – in whole or in part – as sister-group of all other Arachnida (based on tagmosis), closely related to Opiliones (based mostly on genital morphology), Palpigradi (based on controversial interpretations of limb morphology), Solifugae (based mostly on the mouthparts, but now perhaps also reproductive characters) and Ricinulei (based on hexapodal larvae and perhaps mouthparts). We cannot provide a final resolution here, but we aim to highlight important character sets which should be included in subsequent phylogenetic analyses, as well as useful areas for future investigations: particularly tagmosis and the nature of the gnathosoma.     

The phylogenetic affinities of the chaetognaths: a molecular analysis

The chaetognaths, or arrowworms, constitute a small and enigmatic phylum of marine invertebrates whose phylogenetic affinities have long been uncertain. A popular hypothesis is that the chaetognaths are the sister group of the major deuterostome phyla: chordates, hemichordates, and echinoderms. Here we attempt to determine the affinities of the chaetognaths by using molecular sequence data. We describe the isolation and nucleotide sequence determination of 18S ribosomal DNA from one species of chaetognath and one acanthocephalan. Extensive phylogenetic analyses employing a suite of phylogenetic reconstruction methods (maximum parsimony, maximum likelihood, evolutionary parsimony, and two distance methods) suggest that the hypothesized relationship between chaetognaths and the deuterostomes is incorrect. In contrast, we propose that the lineage leading to the chaetognaths arose prior to the advent of the coelomate metazoa.      

ThePulmonaria dacica group: Its affinities with central and south-east European allies and with the genusParaskevia (Boraginaceae)

Comparative morphological, karyological and chorological studies prove the distinctness of the SE European and Asiatic populations ofPulmonaria mollis s.l., to be treated asP. dacica (Figs. 4, 5).P. mollis s.str. is interpreted as a relatively young taxon, which probably has evolved from an older stock ofP. dacica ancestors during the Pleistocene (Figs. 6, 8) and might have migrated, perhaps with oak woodland communities, from SE to C. Europe. A similar evolution can be postulated for S—SE European dysploidP. rubra-carnica-stiriaca-vallarsae group; this may have involved still unknown tetraploids (P. carnica?, Fig. 7). This group is linked via the hypertriploid speciesP. vallarsae with theP. saccharata group and at least the eastern species of theP. australis group. The monotypic genusParaskevia apparently marks the earliest divergence from the common Tertiary ancestral stock (Fig. 8). It exhibits a tetraploid chromosome number (2n = 28) but has preserved the most primitive characters. — Some comments on the systematics and nomenclature ofP. australis andParaskevia are added.     

Telonemia, a new protist phylum with affinity to chromist lineages

Recent molecular investigations of marine samples taken from different environments, including tropical, temperate and polar areas, as well as deep thermal vents, have revealed an unexpectedly high diversity of protists, some of them forming deep-branching clades within important lineages, such as the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed Telonema as a distinct group of species branching off close to chromist lineages. Consistent with these gene trees, Telonema possesses ultrastructures revealing both the distinctness of the group and the evolutionary affinity to chromist groups. Altogether, the data suggest that Telonema constitutes a new eukaryotic phylum, here defined as Telonemia, possibly representing a key clade for the understanding of the early evolution of bikont protist groups, such as the proposed chromalveolate supergroup.     

Clustering in linear‐mixed models with a group fused lasso penalty

A method is proposed that aims at identifying clusters of individuals that show similar patterns when observed repeatedly. We consider linear‐mixed models that are widely used for the modeling of longitudinal data. In contrast to the classical assumption of a normal distribution for the random effects a finite mixture of normal distributions is assumed. Typically, the number of mixture components is unknown and has to be chosen, ideally by data driven tools. For this purpose, an EM algorithm‐based approach is considered that uses a penalized normal mixture as random effects distribution. The penalty term shrinks the pairwise distances of cluster centers based on the group lasso and the fused lasso method. The effect is that individuals with similar time trends are merged into the same cluster. The strength of regularization is determined by one penalization parameter. For finding the optimal penalization parameter a new model choice criterion is proposed.     

Phylogeographical pattern of Euplotes nobilii,a protist ciliate with a bipolar biogeographical distribution

Nuclear (18S and ITS) and mitochondrial (16S) ribosomal RNA gene sequences were determined from genetically distinct wild‐type strains of Antarctic (nine strains), Fuegian (four strains), Greenland (nine strains) and Svalbard (three strains) populations of the marine ciliate, Euplotes nobilii, and analysed for their nucleotide polymorphisms. A close genetic homogeneity was found within and between the Antarctic and Fuegian populations, while more significant levels of genetic differentiation were detected within and between the two Arctic populations, as well as between these populations and the Antarctic/Fuegian ones. The phylogeographical pattern that was derived from these data indicates that gene flow is not limited among Arctic populations; it equally connects the Arctic and Antarctic populations either directly, or through the Fuegian population. This indication reinforces previous evidence from laboratory assays of mating interactions between some of the strains analysed in this work that Southern and Northern polar populations of E. nobilii belong to a unique, panmictic population that substantially share the same gene pool.     

Recent evolutionary diversification of a protist lineage

Here, we have identified a protist (dinoflagellate) lineage that has diversified recently in evolutionary terms. The species members of this lineage inhabit cold-water marine and lacustrine habitats, which are distributed along a broad range of salinities (0–32) and geographic distances (0–18 000 km). Moreover, the species present different degrees of morphological and sometimes physiological variability. Altogether, we analysed 30 strains, generating 55 new DNA sequences. The nuclear ribosomal DNA (nrDNA) sequences (including rapidly evolving introns) were very similar or identical among all the analysed isolates. This very low nrDNA differentiation was contrasted by a relatively high cytochrome b (COB) mitochondrial DNA (mtDNA) polymorphism, even though the COB evolves very slowly in dinoflagellates. The 16 Maximum Likelihood and Bayesian phylogenies constructed using nr/mtDNA indicated that the studied cold-water dinoflagellates constitute a monophyletic group (supported also by the morphological analyses), which appears to be evolutionary related to marine-brackish and sometimes toxic Pfiesteria species. We conclude that the studied dinoflagellates belong to a lineage which has diversified recently and spread, sometimes over long distances, across low-temperature environments which differ markedly in ecology (marine versus lacustrine communities) and salinity. Probably, this evolutionary diversification was promoted by the variety of natural selection regimes encountered in the different environments.     

A necrotic cell death model in a protist

While necrotic cell death is attracting considerable interest, its molecular bases are still poorly understood. Investigations in simple biological models, taken for instance outside the animal kingdom, may benefit from less interference from other cell death mechanisms and from better experimental accessibility, while providing phylogenetic information. Can necrotic cell death occur outside the animal kingdom? In the protist Dictyostelium, developmental stimuli induced in an autophagy mutant a stereotyped sequence of events characteristic of necrotic cell death. This sequence included swift mitochondrial uncoupling with mitochondrial 2',7'-dichlorofluorescein diacetate fluorescence, ATP depletion and increased oxygen consumption. This was followed by perinuclear clustering of dilated mitochondria. Rapid plasma membrane rupture then occurred, which was evidenced by time-lapse videos and quantified by FACS. Of additional interest, developmental stimuli and classical mitochondrial uncouplers triggered a similar sequence of events, and exogenous glucose delayed plasma membrane rupture in a nonglycolytic manner. The occurrence of necrotic cell death in the protist Dictyostelium (1) provides a very favorable model for further study of this type of cell death, and (2) strongly suggests that the mechanism underlying necrotic cell death was present in an ancestor common to the Amoebozoa protists and to animals and has been conserved in evolution.     

The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes

Classical studies on protist diversity of freshwater environments worldwide have led to the idea that most species of microbial eukaryotes are known. One exemplary case would be constituted by the ciliates, which have been claimed to encompass a few thousands of ubiquitous species, most of them already described. Recently, molecular methods have revealed an unsuspected protist diversity, especially in oceanic as well as some extreme environments, suggesting the occurrence of a hidden diversity of eukaryotic lineages. In order to test if this holds also for freshwater environments, we have carried out a molecular survey of small subunit ribosomal RNA genes in water and sediment samples of two ponds, one oxic and another suboxic, from the same geographic area. Our results show that protist diversity is very high. The majority of phylotypes affiliated within a few well established eukaryotic kingdoms or phyla, including alveolates, cryptophytes, heterokonts, Cercozoa, Centroheliozoa and haptophytes, although a few sequences did not display a clear taxonomic affiliation. The diversity of sequences within groups was very large, particularly that of ciliates, and a number of them were very divergent from known species, which could define new intra-phylum groups. This suggests that, contrary to current ideas, the diversity of freshwater protists is far from being completely described.     

The statistical-thermodynamic basis for computation of binding affinities: a critical review.

Although the statistical thermodynamics of noncovalent binding has been considered in a number of theoretical papers, few methods of computing binding affinities are derived explicitly from this underlying theory. This has contributed to uncertainty and controversy in certain areas. This article therefore reviews and extends the connections of some important computational methods with the underlying statistical thermodynamics. A derivation of the standard free energy of binding forms the basis of this review. This derivation should be useful in formulating novel computational methods for predicting binding affinities. It also permits several important points to be established. For example, it is found that the double-annihilation method of computing binding energy does not yield the standard free energy of binding, but can be modified to yield this quantity. The derivation also makes it possible to define clearly the changes in translational, rotational, configurational, and solvent entropy upon binding. It is argued that molecular mass has a negligible effect upon the standard free energy of binding for biomolecular systems, and that the cratic entropy defined by Gurney is not a useful concept. In addition, the use of continuum models of the solvent in binding calculations is reviewed, and a formalism is presented for incorporating a limited number of solvent molecules explicitly.