Niches within a niche: ecological differentiation of subterranean amphipods across Europe's interstitial waters

Species that successfully colonized subterranean environments are subject to two opposing selection processes. Stringent abiotic factors select for convergent adaptations, such as loss of eyes and pigments, while interspecific competition drives between‐species divergence. Subterranean species can resolve opposing selection by adaptation to physically different microhabitats. Yet, species frequently co‐occur in physically homogeneous subterranean habitats, like interstitial. These co‐occurrences in such a narrow ecological context can be explained either by equalizing mechanisms, in which neither of the co‐occurring species has a competitive advantage, or by more complex niche models that include species’ differentiation along a trophic niche axis. We tested these hypotheses using the amphipod genus Niphargus. We analysed Europe‐wide co‐occurrence records of Niphargus species from interstitial habitats, split into six independent large‐scale regions. Firstly, we addressed whether species’ pairwise co‐occurrences are random using a probabilistic model. Secondly, we tested whether species cluster into distinct functional–morphological groups and whether ecologically or phylogenetically distinct species are more likely to co‐occur. We found that 68% of species co‐occurrences were not different from random expectation, indicating that most species had access to most sites within each region. The remaining 32% co‐occurred either significantly more or less often than expected by chance. Cluster analysis of functional morphological characters showed that interstitial species belong to two feeding types, micro‐ and macrofeeders, likely representing two peaks of the interstitial adaptive landscape, and hinting that niche divergence, as a mechanism allowing coexistence, is favoured. Finally, we found that the number of co‐occurrences increases with increasing differentiation of functional morphology, but not phylogenetic differences. We conclude that ecological differentiation may be important in shaping such interstitial communities.     

Characterization of ndh gene of isoniazid resistant and susceptible Mycobacterium tuberculosis isolates from Brazil

Resistance in Mycobacterium tuberculosis to isoniazid (INH) is caused by mutations in the catalase-peroxidase gene (katG), and within the inhA promoter and/or in structural gene. A small percentage (approximately 10%) of INH-resistant strains do not present mutations in both of these loci. Other genes have been associated with INH resistance including the gene encoding for NADH dehydrogenase (ndh). Here we report the detection of two ndh locus mutations (CGT to TGT change in codon 13 and GTG to GCG change in codon 18) by analyzing 23 INH-resistant and in none of 13 susceptible isolates from Brazilian tuberculosis patients. We also detected two isolates without a mutation in ndh, or any of the other INH resistance-associated loci examined, suggesting the existence of additional, as yet to be described, INH resistance mechanisms.     

<Emphasis Type="Italic">Neisseria meningitidis</Emphasis> strains from patients with invasive meningococcal disease differ in stimulation of cytokine production

Cytokine production was determined in vitro after stimulation with three different Neisseria meningitidis (NM) strains. Virulent NM B strain isolated from a patient with mild course of invasive meningococcal disease (IMD) elicited higher cytokine production than NM B and NM C hypervirulent strains isolated from patients with moderate and fatal course of IMD, respectively. Endotoxin concentration after in vitro stimulation correlated with cytokine production: the highest endotoxin levels were observed with virulent NM B strain. Serum cytokines and endotoxin levels showed an opposite trend. These results suggest that inflammatory response during IMD is predominantly influenced by host factors.     

Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist

The black yeast Aureobasidium pullulans is a textbook example of a generalistic and ubiquitous fungus thriving in a wide variety of environments. To investigate whether A. pullulans is a true generalist, or alternatively, whether part of its versatility can be attributed to intraspecific specialization masked by cryptic diversification undetectable by traditional phylogenetic analyses, we sequenced and analysed the genomes of 50 strains of A. pullulans from different habitats and geographic locations. No population structure was observed in the sequenced strains. Decay of linkage disequilibrium over shorter physical distances (<100 bp) than in many sexually reproducing fungi indicates a high level of recombination in the species. A homothallic mating locus was found in all of the sequenced genomes. Aureobasidium pullulans appears to have a homogeneous population genetics structure, which is best explained by good dispersal and high levels of recombination. This means that A. pullulans is a true generalist that can inhabit different habitats without substantial specialization to any of these habitats at the genomic level. Furthermore, in the future, the high level of A. pullulans recombination can be exploited for the identification of genomic loci that are involved in the many biotechnologically useful traits of this black yeast.     

Can Environment Predict Cryptic Diversity? The Case of Niphargus Inhabiting Western Carpathian Groundwater

In the last decade, several studies have shown that subterranean aquatic habitats harbor cryptic species with restricted geographic ranges, frequently occurring as isolated populations. Previous studies on aquatic subterranean species have implied that habitat heterogeneity can promote speciation and that speciation events can be predicted from species’ distributions. We tested the prediction that species distributed across different drainage systems and karst sectors comprise sets of distinct species. Amphipods from the genus Niphargus from 11 caves distributed along the Western Carpathians (Romania) were investigated using three independent molecular markers (COI, H3 and 28S). The results showed that: 1) the studied populations belong to eight different species that derive from two phylogenetically unrelated Niphargus clades; 2) narrow endemic species in fact comprise complexes of morphologically similar species that are indistinguishable without using a molecular approach. The concept of monophyly, concordance between mitochondrial and nuclear DNA, and the value of patristic distances were used as species delimitation criteria. The concept of cryptic species is discussed within the framework of the present work and the contribution of these species to regional biodiversity is also addressed.     

Insertion of a Specific Fungal 3′-phosphoadenosine-5′-phosphatase Motif into a Plant Homologue Improves Halotolerance and Drought Tolerance of Plants

Soil salinity and drought are among the most serious agricultural and environmental problems of today. Therefore, investigations of plant resistance to abiotic stress have received a lot of attention in recent years. In this study, we identified the complete coding sequence of a 3′-phosphoadenosine-5′-phosphatase protein, ApHal2, from the halotolerant yeast Aureobasidium pullulans. Expression of the ApHAL2 gene in a Saccharomyces cerevisiae hal2 mutant complemented the mutant auxotrophy for methionine, and rescued the growth of the hal2 mutant in media with high NaCl concentrations. A 21-amino-acids-long region of the ApHal2 enzyme was inserted into the Arabidopsis thaliana homologue of Hal2, the SAL1 phosphatase. The inserted sequence included the META motif, which has previously been implicated in increased sodium tolerance of the Hal2 homologue from a related fungal species. Transgenic Arabidopsis plants overexpressing this modified SAL1 (mSAL1) showed improved halotolerance and drought tolerance. In a medium with an elevated salt concentration, mSAL1-expressing plants were twice as likely to have roots in a higher length category in comparison with the wild-type Arabidopsis and with plants overexpressing the native SAL1, and had 5% to 10% larger leaf surface area under moderate and severe salt stress, respectively. Similarly, after moderate drought exposure, the mSAL1-expressing plants showed 14% increased dry weight after revitalisation, with no increase in dry weight of the wild-type plants. With severe drought, plants overexpressing native SAL1 had the worst rehydration success, consistent with the recently proposed role of SAL1 in severe drought. This was not observed for plants expressing mSAL1. Therefore, the presence of this fungal META motif sequence is beneficial under conditions of increased salinity and moderate drought, and shows no drawbacks for plant survival under severe drought. This demonstrates that adaptations of extremotolerant fungi should be considered as a valuable resource for improving stress-tolerance in plant breeding in the future.     

Understanding the effect of organic pollutant fluoranthene on pea in vitro using cytokinins,ethylene, ethane and carbon dioxide as indicators

Environmental contaminants like polycyclic aromatic hydrocarbons can influence many biochemical and physiological processes in plants. The effect of 0.1, 1 and 5 mg l⁻¹ of fluoranthene (FLT) in combination with indole-3-acetic acid (IAA, 0.1 mg l⁻¹) or a combination of IAA and N⁶-benzyladenine (BA, both 0.1 mg l⁻¹) on the growth and production of ethylene, ethane and CO₂ in Pisum sativum L. cultivated for 21 days in vitro was investigated. In 21 days old plants also net photosynthesis rate, content of FLT and cytokinins were evaluated. FLT 5 mg l⁻¹ significantly inhibited the growth of pea after 21 days in both IAA and IAA + BA treatments, increased production of ethylene (by 11% in IAA and 14% in IAA + BA treatments, respectively) and ethane (by 28 and 18%) and decreased production of CO₂ (by 23 and 29%). The net photosynthesis rate decreased in response to FLT concentration by up to 51% under saturating irradiation (600–1,200 μmol m⁻² s⁻¹), as found in IAA + BA + FLT 5 mg l⁻¹ treatment. The content of FLT in pea plant shoots well correlated with increasing FLT treatment in both IAA and IAA + BA medium. The content of cytokinins in pea shoots changed in response to FLT treatment. FLT 5 mg l⁻¹ caused a rise in level of trans-zeatin (by 16% in IAA and 9% in IAA + BA treatments, respectively), dihydrozeatin riboside (by 27 and 50%), benzyladenine (by 3 and 80%), benzyladenine riboside (by 44 and 17%) and meta-topolin riboside (by 139 and 214%), no change in isopentenyladenine level and a decrease in meta-topolin level (by 33% in IAA and 36% in IAA + BA treatments, respectively). Cultivation of plants in vitro allowed not only to assess their growth, photosynthetic activity and the level of cytokinins, but also to extend the knowledge about the effect of PAHs on production of gaseous stress indicators like ethylene, ethane and CO₂. Recorded changes in all studied parameters show, that persistent organic pollutants like PAHs can negatively influence plant growth and development.