Low evolutionary diversification in a widespread and abundant uncultured protist (MAST-4)

Recent culture-independent studies of marine planktonic protists have unveiled a large diversity at all phylogenetic scales and the existence of novel groups. MAST-4 represents one of these novel uncultured lineages, and it is composed of small (~2 μm) bacterivorous eukaryotes that are widely distributed in marine systems. MAST-4 accounts for a significant fraction of the marine heterotrophic flagellates at the global level, playing key roles in the marine ecological network. In this study, we investigated the diversity of MAST-4, aiming to assess its limits and structure. Using ribosomal DNA (rDNA) sequences obtained in this study (both pyrosequencing reads and clones with large rDNA operon coverage), complemented with GenBank sequences, we show that MAST-4 is composed of only five main clades, which are well supported by small subunit and large subunit phylogenies. The differences in the conserved regions of the internal transcribed spacers 1 and 2 (ITS1 and ITS2) secondary structures strongly suggest that these five clades are different biological species. Based on intraclade divergence, ITS secondary structures and comparisons of ITS1 and ITS2 trees, we did not find evidence of more than one species within clade A, whereas as many as three species might be present within other clades. Overall, the genetic divergence of MAST-4 was surprisingly low for an organism with a global population size estimated to be around 10(24), indicating a very low evolutionary diversification within the group.     

Resurvey studies of terricolous bryophytes and lichens indicate a widespread nutrient enrichment in German forests

Questions

Vegetation resurveys, both single studies and meta-analyses, have predominantly been based on vascular plant data while bryophytes and lichens have largely been neglected. Our study aims to fill this gap and addresses the following research questions: has the overall species richness of terricolous bryophytes and lichens in forests changed over time? Which are the winners and losers among single species and ecological species groups? Do the results give a signal of the impact of nutrient enrichment, of changes in the light regime and of climate change?

Location

Deciduous and coniferous forests in Germany.

Methods

We compiled 35 single resurvey data sets, including 1096 plots in total (each sampled twice). The time interval between initial surveys and resurveys ranged from 10 to 65 years. The differences between old and new plots were analysed with respect to the frequency of single species, total species richness, and the absolute and relative numbers of taxa in the species groups. Trend scores of species were related to ecological indicator values to identify the main environmental drivers behind the observed changes.

Results

Total species richness did not systematically change, while pleurocarpous mosses had increased at the expense of acrocarpous mosses and, in coniferous forests, of lichens. Weak changes were generally observed in deciduous forests on base-rich soils. In coniferous forests and in deciduous forests on acid soils, species with high nitrogen demand and high shade tolerance had increased, whereas those being typical for more infertile and open forest sites had decreased. There were trends towards a larger share of taxa with a more oceanic distribution.

Conclusions

The changes in the vegetation of terricolous bryophytes and lichens in the studied forests indicate nutrient enrichment and increasingly shady conditions in forests on acid soils, likely caused by nitrogen deposition and shrub layer closure.     

Properties of an abundant RNA-binding protein in yeast mitochondria

We have previously identified a protein with Mr approximately 40,000 (p40) that binds with high specificity and affinity to the 5'-untranslated leaders of mitochondrial mRNAs in yeast. Here we show that this protein is abundant, comprising about 0.4% of total mitochondrial protein. p40 is present in a cytoplasmic (rho degree) petite mutant that lacks mitochondrial protein synthesis and is therefore nuclear encoded. p40 can be detected by immunological techniques in cell lysates of several different pet mutants, specifically disturbed in the translation of individual mitochondrial mRNAs. It is thus not one of the translation factors defined by any of these mutations. In the case of a pet111 mutant, which is specifically blocked in the translation of COX2 mRNA, extracts still display COX2 mRNA binding activity, indicating that p40 complex formation in vitro is not dependent on the presence of PET111.     

Archaea of the Miscellaneous Crenarchaeotal Group are abundant,diverse and widespread in marine sediments

Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes.     

Small increase in substratum [corrected] pH causes the dieback of one of Europe's most common lichens, Lecanora conizaeoides

Backgrounds and Aims

Lecanora conizaeoides was until recently western and central Europe''s most abundant epiphytic lichen species or at least one of the most common epiphytes. The species is adapted to very acidic conditions at pH values around 3 and high concentrations of SO₂ and its derivatives formed in aqueous solution, and thus spread with increasing SO₂ deposition during the 19th and 20th centuries. With the recent decrease of SO₂ emissions to nearly pre-industrial levels within 20 years, L. conizaeoides declined from most of its former range. If still present, the species is no longer the dominant epiphyte, but is occurring in small densities only. The rapid spread of the L. conizaeoides in Europe from an extremely rare species to the probably most frequent epiphytic lichen and the subsequent rapid dieback are unprecedented by any other organism. The present study aimed at identifying the magnitude of deacidification needed to cause the dieback of the lichen.

Methods

The epiphytic lichen diversity and bark chemistry of montane spruce forests in the Harz Mountains, northern Germany, were studied and the results were compared with data recorded with the same methods 13–15 years ago.

Key Results

Lecanora conizaeoides, which was the dominant epiphyte of the study area until 15 years ago, is still found on most trees, but only with small cover values of ≤1 %. The bark pH increased by only 0·4 pH units.

Conclusions

The data suggest that only slight deacidification of the substratum causes the breakdown of the L. conizaeoides populations. Neither competitors nor parasites of L. conizaeoides that may have profited from reduced SO₂ concentrations are likely causes of the rapid dieback of the species.     

The distribution, organization and evolution of two abundant and widespread repetitive DNA sequences in the genus Hordeum

The genomic organization and chromosomal distributions of two abundant tandemly repeated DNA sequences, dpTa1 and pSc119.2, were examined in six wild Hordeum taxa, representing the four basic genomes of the genus, by Southern and fluorescence in situ hybridization. The dpTa1 probe hybridized to between 30 and 60 sites on the chromosomes of all five diploid species studied, but hybridization patterns differed among the species. Hybridization of the pSc119.2 sequence to the chromosomes and Southern blots of digested DNA detected signals in Hordeum bulbosum, Hordeum chilense, Hordeum marinum and Hordeum murinum 4x, but not in Hordeum murinum 2x and Hordeum vulgare ssp. spontaneum. A maximum of one pSc119.2 signal was observed in the terminal or subterminal region of each chromosome arm in the species carrying this sequence. The species carrying the same I-genome differed in the presence (Hordeum bulbosum) or absence (Hordeum spontaneum) of pSc119.2. The presence of pSc119.2 in the tetraploid cytotype of Hordeum murinum, but its absence in the diploid cytotype, suggests that the tetraploid is not likely to be a simple autotetraploid of the diploid. Data about the inter- and intra-specific variation of the two independent repetitive DNA sequences give information about both the interrelationships of the species and the evolution of the repetitive sequences. Received: 17 March 1999 / Accepted: 16 June 1999     

Endemic and widespread coral reef fishes have similar mitochondrial genetic diversity

Endemic species are frequently assumed to have lower genetic diversity than species with large distributions, even if closely related. This assumption is based on research from the terrestrial environment and theoretical evolutionary modelling. We test this assumption in the marine environment by analysing the mitochondrial genetic diversity of 33 coral reef fish species from five families sampled from Pacific Ocean archipelagos. Surprisingly, haplotype and nucleotide diversity did not differ significantly between endemic and widespread species. The probable explanation is that the effective population size of some widespread fishes locally is similar to that of many of the endemics. Connectivity across parts of the distribution of the widespread species is probably low, so widespread species can operate like endemics at the extreme or isolated parts of their range. Mitochondrial genetic diversity of many endemic reef fish species may not either limit range size or be a source of vulnerability.     

Mating pheromone-induced alteration of cell surface proteins in the heterobasidiomycetous yeast Tremella mesenterica.

Mating pheromone-induced alteration of the cell surface proteins of haploid cells, presumed to play crucial roles in the specific cell-cell interactions during sexual conjugation of Tremella mesenterica , was investigated. Exposed surface proteins were revealed by lactoperoxidase-catalyzed iodination in combination with polyacrylamide gel electrophoresis and autoradiography. From comparison of the molecular species of 125I-labeled surface proteins of the vegetative and the gamete (mating pheromone-treated) cells of the two compatible mating types (ab and AB), it was suggested that a striking change in cell surface structure occurs during the differentiation; although labeled protein species of the vegetative cells of the two mating types were indistinguishable, several new species, both mating type specific and nonspecific, appeared in the gamete cells. Turnover of the labeled proteins of the vegetative cells was negligible, whereas that of the gamete cells was rapid with release of low-molecular-weight labeled proteins in the medium. A role for the labeled surface proteins of the gamete cells in the cell-cell interactions during sexual conjugation was suggested by the following: the surface changes were induced by mating pheromone; the labeled proteins were preferentially localized on the surface of the mating tube; the labeled species appeared sequentially during the differentiation; and mating type-specific species were present in both mating types.     

The new species Lecanora bicinctoidea, its position and considerations about phenotypic evolution in the Lecanora rupicola group

A phylogenetic analysis of the Lecanora rupicola group based on combined nITS rDNA and beta-tubulin sequences and a combined dataset of ITS, beta-tubulin and partial sequences of polyketide synthase genes reveals a previously unrecognized species, which here is introduced under the name Lecanora bicinctoidea. The new species is a sister group of the L. swartzii complex (including L. swartzii and L. lojkaeana), which is characterized by eucorticate ascomata, and a morphological diversity that includes also a dwarf-fruticose lineage. The preferential occurrence on vertical to overhanging siliceous rocks corresponds more closely to L. swartzii. A detailed investigation of phenotypic characters reveals that the new species differs from the superficially similar morphospecies L. bicincta in several ways, such as a thallus of comparatively small areoles and broadly sessile ascomata and the development of an amphithecial cortex devoid of algal remnants (i.e. an eucortex). L. bicinctoidea contains methyl 3alpha-hydroxy-4-O-demethylbarbatate, a chemical compound not known from other members of the L. rupicola group. We also discuss the importance of eucortex formation as one of several factors that are involved in the evolution of substrate-detached thallus structures.     

Functional diversity and traits assembly patterns of lichens as indicators of successional stages in a tropical rainforest

Understanding community assembly patterns with regard to functional traits, which may be common to different species, allows us to compare ecological communities in a wider range of environmental and phytogeographic conditions. Moreover, a functional approach may facilitate the comprehension of the relation between biotic changes and ecosystem functions in complex systems such as tropical forests. Considering the lack of information in relation to the influence of environmental conditions on lichen functional traits, on lichen functional patterns in tropical forests and the potential usage of this approach in bioindication studies, this paper aims at (i) determining the functional structure of the lichen communities along the forest succession gradient, (ii) assessing the relation of lichen functional traits to this gradient and (iii) verifying the potential of using lichen functional traits as indicators of successional stages in tropical rainforests. Lichens were sampled in 24 sampling units of three successional stages (6–10; 12–20; and 40–60 years of recovering). The results corroborated our main hypothesis that the functional structure of the lichen communities responds to structural changes along a forest regeneration gradient. Growth forms (foliose, fruticose and crustose) as well as some reproductive trait states (lirella, isidia and perithecia) were the most suitable lichen traits to be used as indicators of forest succession in the southern edge of the Atlantic Rainforest. Lirella, fruticose and foliose were more related to earlier successional stages; isidia was more related to intermediate stages, while perithecia and crustose were more related to older stages. These results reinforce the ability of lichens to be used as bioindicators of forest conditions.     

Correcting widespread misidentifications of the highly abundant and commercially important sardine species Sardinella lemuru,Bleeker, 1853 in the Philippines

Morphology, meristics, and molecular genetics tools were used to determine the species level identification of the most commonly landed sardine species in the Philippines. Results from this study indicated that the historical and widely applied nomenclature of the Indian oil sardine, Sardinella longiceps, is incorrect and that this species is instead the Bali sardinella Sardinella lemuru. Developing an effective strategy for managing one of the Philippines most important commodity sardine species first requires accurate identification of this species. Results of this study provide needed information that is now being applied to emerging management policies.     

Slow and fast visual motion channels have independent binocular-rivalry stages

We have previously reported a transparent motion after-effect indicating that the human visual system comprises separate slow and fast motion channels. Here, we report that the presentation of a fast motion in one eye and a slow motion in the other eye does not result in binocular rivalry but in a clear percept of transparent motion. We call this new visual phenomenon 'dichoptic motion transparency' (DMT). So far only the DMT phenomenon and the two motion after-effects (the 'classical' motion after-effect, seen after motion adaptation on a static test pattern, and the dynamic motion after-effect, seen on a dynamic-noise test pattern) appear to isolate the channels completely. The speed ranges of the slow and fast channels overlap strongly and are observer dependent. A model is presented that links after-effect durations of an observer to the probability of rivalry or DMT as a function of dichoptic velocity combinations. Model results support the assumption of two highly independent channels showing only within-channel rivalry, and no rivalry or after-effect interactions between the channels. The finding of two independent motion vision channels, each with a separate rivalry stage and a private line to conscious perception, might be helpful in visualizing or analysing pathways to consciousness.     

The yeast lichenosphere: high diversity of basidiomycetes from the lichens Tephromela atra and Rhizoplaca melanophthalma

Lichens are well-known examples of complex symbiotic associations between organisms from different Kingdoms. Microfungi in particular, establish diverse associations with the hosting lichen thallus, as species-specific parasites or transient co-inhabitants. The whole community of lichen-associated fungi constitute the ‘lichen mycobiome’ comprising both ascomycetes and basidiomycetes, including filamentous and yeast taxa. Metabarcoding results and microscopy analyses show that in some thalli, basidiomycetes are frequent lichen-associated fungi but still only a few species could be axenically isolated and morphologically characterized. Within a broad project aiming at characterizing the mycobiome diversity by culture-dependent and independent approaches in two lichen species selected as reference models – Rhizoplaca melanophthalma and Tephromela atra, we succeed in isolating and culturing 76 new strains of basidiomycetous yeasts. The lichen thalli were collected in different mountain regions worldwide and at relatively high elevation. The yeast strains were isolated on different growth media and were studied for their morphological and genetic diversity. Nuclear internal transcribed spacer (ITS) and ribosomal large subunit (LSU) sequence analyses identified them to belong to ten families within the orders Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes, Tremellomycetes and Ustilaginomycetes. The yeasts here detected showed patterns of host-preference in a few cases and they are potentially related to the ecological conditions.     

Laccase and tyrosinase activities in lichens

Phenoloxidase activity was found in lichenized ascomycetes belonging to different taxonomic groups. Most of the epigeic and epilithic lichens of the order Peltigerales were found to possess both laccase and tyrosinase activities; the lichens of the order Lecanorales possessed only laccase activity, which was an order of magnitude lower than that of Peltigerales. Water-soluble phenoloxidases were present only in peltigerous lichens: activity that could be washed out from intact thalli comprised 10% of that released from disrupted thalli. The activity of the peltigerous lichens and the release of soluble phenoloxidases into the medium increased when the thalli were rehydrated quickly. In some of the lichens tested, the phenoloxidase activity was stimulated by desiccation-rehydration cycles. The oxidases discovered may play an important role in the phenolic metabolism of lichens and be involved in the biochemical reaction of humus synthesis during primary soil formation, which may be a previously unknown geochemical function of these symbiotic microorganisms.