Microbial ecology of submerged marine caves and holes characterized by high levels of hydrogen sulphide

Submarine caves, cavities and niches characterised by H₂S elevated concentrations are particularly interesting for their inhabiting microflora as well as for the overall chemical, geological and biological parameters. These ecosystems are usually populated by well adapted living forms, physically distributed following the in situ concentration and gradient of micronutrients, O₂ and H₂S, and also according to the values of temperature and pH. The biota is primarily characterised by prokaryotes (both autotrophic and heterotrophic) adapted to anoxic and/or microaerophilic condition and capable to form extensive biofilms on the rocky surfaces and even on the bottom sediment. These habitats can be defined as extreme, because the scarcity or absence of solar irradiation, the chemo-physical traits and the fact that specialised prokaryotes are often the only inhabitants. This review is focused on the microbial ecology of marine caves and holes characterised by high levels of hydrogen sulphide. Ecological and geological data are already available but very few insights as far as regard microbiology were achieved in order to describe these fascinating habitats. The autochthonous mesophilic and thermotolerant microorganisms living in these caves may have interesting physiological traits and eventually may lead to potential application in biotechnological processes.     

Peptaibol production by sepedonium strains parasitizing boletales

Fungi of the genus Sepedonium (anamorphic ascomycetes) are known to infect fruiting bodies of Basidiomycetes of the order Boletales. We have characterized twelve Sepedonium isolates by intact-cell mass spectrometry (IC-MS) with the help of respective biomarkers and their metabolite spectra focusing on peptaibol production. A strain of mycoparasitic S. chalcipori was grown in solid-state fermentation, and tylopeptin production was found, suggesting an ascomycete origin of these peptaibols, which were first described in the basidiomycete Tylopilus neofelleus. In addition, the structures of two new peptaibols, chalciporin A (=Ac-Trp-Val-Aib-Val-Ala-Gln-Ala-Aib-Ser-Leu-Ala-Leu-Aib-Gln-Leuol) and chalciporin B (=Ac-Trp-Val-Aib-Val-Ala-Gln-Ala-Aib-Gln-Aib-Ala-Leu-Aib-Gln-Leuol) are presented. The IC-MS technique was applied for in situ peptaibol analysis of Sepedonium strains growing on Boletales, in particular S. chrysospermum infecting Xerocomus cf. badius. We found chrysospermins at the surface and within basidiomycete tissue, as well as in the cultivated parasite.     

Dryland Salinity and Ecosystem Distress Syndrome: Human Health Implications

Clearing of native vegetation for agriculture has left 1.047 million hectares of southwest Western Australia affected by dryland salinity, and this area may expand up to a further 1.7–3.4 million hectares if trends continue. Ecosystems in saline-affected regions display many of the classic characteristics of Ecosystem Distress Syndrome, one outcome of which has not yet been investigated in relation to dryland salinity: adverse human health implications. This article seeks to review existing information and identify potential adverse human health effects. Three key potential impacts on human health resulting from dryland salinity are identified: wind-borne dust and respiratory health; altered ecology of the mosquito-borne disease Ross River virus; and mental health consequences of salinity-induced environmental degradation. Given the predicted increase in extent and severity of dryland salinity over coming decades, adverse outcomes of salinity are likely to be further exacerbated, including those related to human health. There is a clear need to investigate the issues discussed in this review and also to identify other potential adverse health effects of dryland salinity. Investigations must be multidisciplinary to sufficiently examine the broad scope of these issues. The relationship between human health and salinity may also be relevant beyond Australia in other countries where secondary soil salinization is occurring.     

Serum proteomics of lung adenocarcinomas induced by targeted overexpression of c-raf in alveolar epithelium identifies candidate biomarkers

We previously reported a proteome map of lung adenocarcinomas in serine-threonine kinase of the Raf family (c-raf) transgenic mice. We now extend our initial studies to serum proteins at early stage (1 month) and advanced stages of tumorigenesis (12 months). Notably, serum proteins from wild-type and tumor bearing mice were extracted with a lysis buffer containing 5 mol/L urea, 2 mol/L thiourea, 40 mmol/L Tris, 4% CHAPS, 100 mmol/L DTT, 0.5% BioLyte 3-10, separated by 2-DE and studied by image analysis. On average 400 protein spots per gel were excised and analyzed by MALDI-TOF MS. We identified 45 common and 5 uniquely expressed proteins in wild-type and tumor bearing mice. Apart from uniquely identified proteins we observed for n = 9 proteins differential expression when wild-type and tumor bearing mice were compared. This included serpins and other protease inhibitors, lipocalins, transthyretins, globins, and Igs. Notably, we demonstrate significant regulation of alpha-1-antitrypsin, alpha-2-macroglobulin, hemoglobin subunit alpha, vitamin D-binding protein, major urinary proteins, and transthyretin (up to eight-fold) in serum of lung tumor bearing mice. Disease association of these proteins in human malignancies has been reported. Thus, an identification of regulated serum proteins in this lung cancer disease model provides excellent opportunities for the search of novel biomarkers.     

Detection of IncP replicon-specific regions in DNA from Antarctic microbiota

Plasmids capable of horizontal transfer contribute to the adaptability of bacteria, as they may provide genes that enable their hosts to cope with different selective pressures. Only limited information is available on plasmids from Antarctic habitats, and up until now surveys have only used traditional methods of endogenous plasmid isolation. The method based on primer systems, designed on the basis of published sequences for plasmids from different incompatibility (Inc) groups, is appropriate to detect the replicon-specific regions of corresponding plasmids in cultured bacteria, or in total community DNA, which share sufficient DNA similarity with reference plasmids at the amplified regions. In this study, we applied broad-host-range plasmid-specific primers to DNA from microbial samples collected at six different locations in Northern Victoria Land (Antarctica). DNA preparations were used as targets for PCR (polymerase chain reaction) amplification with primers for the IncP (trfA2) and IncQ (oriV ) groups. PCR products were Southern blotted and hybridized with PCR-derived probes for trfA2 and oriV regions. This approach detected the occurrence of IncP-specific sequences in eight out of fifteen DNA samples, suggesting a gene-mobilizing capacity within the original habitats.     

Potential biomarkers of an exaggerated response to endotoxemia

Serial plasma protein analysis was used to study the acute plasma proteome response to endotoxemia (presence of toxic bacterial products called endotoxins in the blood stream). Plasma samples from healthy volunteers before and multiple time points up to 24 h following administration of low-dose endotoxin were evaluated. Plasma protein profiles were obtained by rapid extraction of whole plasma followed by analysis with matrix-assisted laser desorption ionisation-time of flight mass spectrometry. The profiles were unique to each individual and stable over the time of the experiment. Administration of low-dose endotoxin caused profound change in six of 18 individuals. At 8 h many proteins showed quantitative oxidation, in addition to the appearance of new components and disappearance of common baseline components. An exceptionally intense new component at 4154 mass units was identified as the activation peptide of C1 esterase inhibitor. While recovery of baseline protein structure was nearly complete by 24 h, serum amyloid A, an acute-phase reactant, was still increasing and minor profile changes persisted. Clinical features did not distinguish these extreme responders from others, suggesting that plasma proteome changes offered unique insights into and potential biomarkers of subclinical events following endotoxin exposure.     

Epistemological issues in the study of microbial life: alternative terran biospheres?

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.     

Exposure to solar UV-B radiation accelerates mass and lignin loss of <Emphasis Type="Italic">Larrea tridentata</Emphasis> litter in the Sonoran Desert

We assessed whether exposure to solar ultraviolet-B radiation (UV-B) affects the mass loss of Larrea tridentata (creosotebush) litter in the Sonoran Desert of central Arizona. We placed three types of litter (leaves, twigs, or a natural mixture of leaves, twigs, and seeds) in bags constructed of UV-B-transmitting or UV-B-absorbing filter material that allowed either 85% (near-ambient UV-B treatment) or 15% (reduced UV-B treatment) of the biologically effective solar UV-B to reach litter inside the bags. Bags were placed outdoors for 4–5 months during the winter at two sites: a balcony or on the soil surface of the desert. Mass loss of leaf litter was greater under near-ambient UV-B than reduced UV-B at both sites: 21 (near-ambient) vs. 18% (reduced) on the balcony, and 18 vs. 14% at the desert site. Mass loss of twig litter was also greater under near-ambient UV-B at the desert site. Mass loss of the natural mixture of litter was also greater when exposed to near-ambient UV-B on the balcony, and tended to be greater at the desert site. We estimate that about 14–22% of the total mass loss of leaf litter during our 4–5 month experiments was attributable to solar UV-B exposure. Leaf litter exposed to near-ambient UV-B had lower concentrations of lignin, and fats and lipids, and slightly higher concentrations of holocellulose. The greater mass loss of litter under near-ambient UV-B appeared mainly attributable to loss of lignin, although losses of fats and lipids were also appreciable. A primary reason for greater mass loss of litter under solar UV-B appeared to be photodegradation, particularly of lignin.     

The influence of ice scour on benthic communities at three contrasting sites at Adelaide Island,Antarctica

Abstract Ice scouring is a key structuring force acting on high latitude shallow benthic communities. Despite its importance, detailed studies of scoured communities are still rare. Here we report the ecological effects of 12 iceberg impacts, across three contrasting study sites, at Adelaide Island, West Antarctic Peninsula. Grounded icebergs were marked with GPS and the newly formed scours (at 10–17 m depth) were sampled within 20 days of formation. Comparisons between scoured and adjacent unscoured assemblages were made using measures of abundance, biomass, taxon richness and the relative abundance of secondary consumers. Ice scouring was catastrophic at all sites, despite differences in substratum type, exposure and background community. Compared with undisturbed areas, scour assemblages were 95% lower in mean macrofaunal abundance and 75.9% lower in species richness. There was no general trend across all sites of ice scouring selecting for secondary consumers. The echinoid Sterechinus neumayeri and bivalve mollusc Mysella charcoti were highly abundant in undisturbed areas and were the biggest contributors to the observed differences between scours and undisturbed areas.     

Deep Endichnial Cruziana from the Lower-Middle Ordovician of Spain — A Unique Trace Fossil Record of Trilobitomorph Deep Burrowing Behavior

Full reliefs of Cruziana furcifera from the Lower-Middle Ordovician quartzite sandstone beds (Pochico Formation, southern Spain) points to deep, infaunal burrowing of trilobites. Some specimens show an unusual vertical extension with a wider lower part and a narrower upper part in cross section. They are referred to trilobites, which burrowed deeply in the sediment and were oriented obliquely head down and tail up. Deep burrowing seems to be common for other members of the Cruziana rugosa group, foremost C. rugosa and C. furcifera, less for C. goldfussi. The deep burrowing recorded in the discussed trace fossils can be referred to the earliest common infaunalization caused by trilobites and other arthropods during the Ordovician, probably in a response to a food competition on the sea floor, which promoted a behavioral plasticity within the same taxon or closely related taxa of trilobites.