Proteomic characterization of Pseudogymnoascus spp. isolates from polar and temperate regions.

Proteomics has been used extensively in the field of mycology, mainly in trying to understand the complex network of protein-protein interactions that has been implicated in the molecular functions of fungi. It is also a useful tool to compare metabolic differences within a genus. Species of Pseudogymnoascus, a genus under the phyla Ascomycota, have been shown to play an important role in the soil environment. They have been found in both polar and temperate regions and are a known producer of many extracellular hydrolases that contribute to soil decomposition. Despite the apparent importance of Pseudogymnoascus spp. in the soil ecosystem, investigations into their molecular functions are still very limited. In the present study, proteomic characterization of six Pseudogymnoascus spp. isolated from three biogeographic regions (the Arctic, Antarctic, and temperate regions) was carried out using tandem mass spectrometry. Prior to proteomic analysis, the optimization for protein extraction was carried out. Trichloroacetic acid­acetone­phenol was found to be the best extraction method to be used for proteomic profiling of Pseudogymnoascus spp. The proteomic analysis identified 2003 proteins that were successfully mapped to the UniProtKB database. The identified proteins were clustered according to their biological processes and molecular functions. The shared proteins found in all Pseudogymnoascus spp. (1201 proteins) showed a significantly close relationship in their basic cellular functions, despite differences in morphological structures. Analysis of Pseudogymnoascus spp. proteome also identified proteins that were unique to each region. However, a high number of these proteins belonged to protein families of similar molecular functions, namely, transferases and hydrolases. Our proteomic data can be used as a reference for Pseudogymnoascus spp. across different global regions and a foundation for future soil ecosystem function research.

Geographical Diversity of Proteomic Responses to Cold Stress in the Fungal Genus Pseudogymnoascus.

In understanding stress response mechanisms in fungi, cold stress has received less attention than heat stress. However, cold stress has shown its importance in various research fields. The following study examined the cold stress response of six Pseudogymnoascus spp. isolated from various biogeographical regions through a proteomic approach. In total, 2541 proteins were identified with high confidence. Gene Ontology enrichment analysis showed diversity in the cold stress response pathways for all six Pseudogymnoascus spp. isolates, with metabolic and translation-related processes being prominent in most isolates. 25.6% of the proteins with an increase in relative abundance were increased by more than 3.0-fold. There was no link between the geographical origin of the isolates and the cold stress response of Pseudogymnoascus spp. However, one Antarctic isolate, sp3, showed a distinctive cold stress response profile involving increased flavin/riboflavin biosynthesis and methane metabolism. This Antarctic isolate (sp3) was also the only one that showed decreased phospholipid metabolism in cold stress conditions. This work will improve our understanding of the mechanisms of cold stress response and adaptation in psychrotolerant soil microfungi, with specific attention to the fungal genus Pseudogymnoascus.

Evaluation of the Deterioration of Untreated Commercial Polystyrene by Psychrotrophic Antarctic Bacterium.

Polystyrene (PS) and microplastic production pose persistent threats to the ecosystem. Even the pristine Antarctic, which is widely believed to be pollution-free, was also affected by the presence of microplastics. Therefore, it is important to comprehend the extent to which biological agents such as bacteria utilise PS microplastics as a carbon source. In this study, four soil bacteria from Greenwich Island, Antarctica, were isolated. A preliminary screening of the isolates for PS microplastics utilisation in the Bushnell Haas broth was conducted with the shake-flask method. The isolate AYDL1 identified as Brevundimonas sp. was found to be the most efficient in utilising PS microplastics. An assay on PS microplastics utilisation showed that the strain AYDL1 tolerated PS microplastics well under prolonged exposure with a weight loss percentage of 19.3% after the first interval (10 days of incubation). Infrared spectroscopy showed that the bacteria altered the chemical structure of PS while a deformation of the surface morphology of PS microplastics was observed via scanning electron microscopy after being incubated for 40 days. The obtained results may essentially indicate the utilisation of liable polymer additives or "leachates" and thus, validate the mechanistic approach for a typical initiation process of PS microplastics biodeterioration by the bacteria (AYDL1)-the biotic process.

UV-B-induced DNA damage and repair pathways in polar Pseudogymnoascus sp. from the Arctic and Antarctic regions and their effects on growth, pigmentation and conidiogenesis.

Solar radiation regulates most biological activities on Earth. Prolonged exposure to solar UV radiation can cause deleterious effects by inducing two major types of DNA damage, namely, cyclobutane pyrimidine dimers (CPDs) and pyrimidine 6-4 pyrimidone photoproducts. These lesions may be repaired by the photoreactivation (Phr) and nucleotide excision repair (NER) pathways; however, the principal UV-induced DNA repair pathway is not known in the fungal genus Pseudogymnoascus. In this study, we demonstrated that an unweighted UV-B dosage of 1.6 kJ m-2 d-1 significantly reduced fungal growth rates (by between 22% and 35%) and inhibited conidia production in a 10 d exposure. The comparison of two DNA repair conditions, light or dark, which respectively induced photoreactivation (Phr) and NER, showed that the UV-B-induced CPDs were repaired significantly more rapidly in light than in dark conditions. The expression levels of two DNA repair genes, RAD2 and PHR1 (encoding a protein in NER and Phr respectively), demonstrated that NER rather than Phr was primarily activated for repairing UV-B-induced DNA damage in these Pseudogymnoascus strains. In contrast, Phr was inhibited after exposure to UV-B radiation, suggesting that PHR1 may have other functional roles. We present the first study to examine the capability of the Arctic and Antarctic Pseudogymnoascus sp. to perform photoreactivation and/or NER via RT-qPCR approaches, and also clarify the effects of light on UV-B-induced DNA damage repair in vivo by quantifying cyclobutene pyrimidine dimers and pyrimidine 6-4 pyrimidone photoproducts. Physiological response data, including relative growth rate, pigmentation and conidia production in these Pseudogymnoascus isolates exposed to UV-B radiation are also presented.

Protein homeostasis, regulation of energy production and activation of DNA damage-repair pathways are involved in the heat stress response of Pseudogymnoascus spp.

Proteome changes can be used as an instrument to measure the effects of climate change, predict the possible future state of an ecosystem and the direction in which is headed. In this study, proteomic and gene ontology functional enrichment analysis of six Pseudogymnoascus spp. isolated from various global biogeographical regions were carried out to determine their response to heat stress. In total, 2122 proteins were identified with high confidence. Comparative quantitative analysis showed that changes in proteome profiles varied greatly between isolates from different biogeographical regions. Although the identities of the proteins that changed varied between the different regions, the functions they governed were similar. Gene ontology analysis showed enrichment of proteins involved in multiple protective mechanisms, including the modulation of protein homeostasis, regulation of energy production and activation of DNA damage and repair pathways. Our proteomic analysis did not show any clear relationship between protein changes and the strains' biogeographical origins.

Biodeterioration of Untreated Polypropylene Microplastic Particles by Antarctic Bacteria.

Microplastic pollution is globally recognised as a serious environmental threat due to its ubiquitous presence related primarily to improper dumping of plastic wastes. While most studies have focused on microplastic contamination in the marine ecosystem, microplastic pollution in the soil environment is generally little understood and often overlooked. The presence of microplastics affects the soil ecosystem by disrupting the soil fertility and quality, degrading the food web, and subsequently influencing both food security and human health. This study evaluates the growth and biodegradation potential of the Antarctic soil bacteria Pseudomonas sp. ADL15 and Rhodococcus sp. ADL36 on the polypropylene (PP) microplastics in Bushnell Haas (BH) medium for 40 days. The degradation was monitored based on the weight loss of PP microplastics, removal rate constant per day (K), and their half-life. The validity of the PP microplastics' biodegradation was assessed through structural changes via Fourier transform infrared spectroscopy analyses. The weight loss percentage of the PP microplastics by ADL15 and ADL36 after 40 days was 17.3% and 7.3%, respectively. The optimal growth in the BH media infused with PP microplastics was on the 40th and 30th day for ADL15 and ADL36, respectively. The infrared spectroscopic analysis revealed significant changes in the PP microplastics' functional groups following the incubation with Antarctic strains.

Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus.

Rhodococci are renowned for their great metabolic repertoire partly because of their numerous putative pathways for large number of specialized metabolites such as biosurfactant. Screening and genome-based assessment for the capacity to produce surface-active molecules was conducted on Rhodococcus sp. ADL36, a diesel-degrading Antarctic bacterium. The strain showed a positive bacterial adhesion to hydrocarbon (BATH) assay, drop collapse test, oil displacement activity, microplate assay, maximal emulsification index at 45% and ability to reduce water surface tension to < 30 mN/m. The evaluation of the cell-free supernatant demonstrated its high stability across the temperature, pH and salinity gradient although no correlation was found between the surface and emulsification activity. Based on the positive relationship between the assessment of macromolecules content and infrared analysis, the extracted biosurfactant synthesized was classified as a lipopeptide. Prediction of the secondary metabolites in the non-ribosomal peptide synthetase (NRPS) clusters suggested the likelihood of the surface-active lipopeptide production in the strain's genomic data. This is the third report of surface-active lipopeptide producers from this phylotype and the first from the polar region. The lipopeptide synthesized by ADL36 has the prospect to be an Antarctic remediation tool while furnishing a distinctive natural product for biotechnological application and research.

Responses of soil microarthropod taxon (Hexapoda: Protura) to natural disturbances and management practices in forest-dominated subalpine lake catchment areas.

Disturbances are intrinsic drivers of structure and function in ecosystems, hence predicting their effects in forest ecosystems is essential for forest conservation and/or management practices. Yet, knowledge regarding belowground impacts of disturbance events still remains little understood and can greatly vary by taxonomic and functional identity, disturbance type and local environmental conditions. To address this gap in knowledge, we conducted a survey of soil-dwelling Protura, across forests subjected to different disturbance regimes (i.e. windstorms, insect pest outbreaks and clear-cut logging). We expected that the soil proturan assemblages would differ among disturbance regimes. We also hypothesized that these differences would be driven primarily by variation in soil physicochemical properties thus the impacts of forest disturbances would be indirect and related to changes in food resources. To verify that sampling included two geographically distant subalpine glacial lake catchments that differed in underlying geology, each having four different types of forest disturbance, i.e. control, bark beetle outbreak (BB), windthrow + BB (wind + BB) and clear-cut. As expected, forest disturbance had negative effects on proturan diversity and abundance, with multiple disturbances having the greatest impacts. However, differences in edaphic factors constituted a stronger driver of variability in distribution and abundance of proturans assemblages. These results imply that soil biogeochemistry and resource availability can have much stronger effects on proturan assemblages than forest disturbances.

Protura in Arctic Regions, with Description of Mastodonentomon n. gen. (Acerentomidae, Nipponentominae) and a Key to Known Arctic Taxa.

Protura are widespread, but their presence in the Arctic was first noted only ca. 70 years ago and is still little acknowledged. This work compiles taxonomic information on proturans in the Arctic regions and adds unpublished data from Northern Siberia. Currently, this fauna is represented by 23 species in two orders and 14 genera. The large cosmopolitan genus Eosentomon is represented by only four species, whereas Acerentomidae is much more diverse, with 19 species in 13 genera (eight Nipponentominae, five Acerentominae). Most of the Arctic species possess a larger number of setae than species living in temperate regions. Based on several unique characters, a new genus, Mastodonentomon, is erected for Nipponentomon macleani, and the species is re-described with the original description supplemented with new characters, including head chaetotaxy, seta length, and porotaxy. Proturan occurrence in the Arctic is limited to Beringia, but the majority of species have restricted distributions and none have been found in both the American Arctic and Siberia. This implies relict origins and high levels of proturan endemism in the Arctic. This emerging view on biogeographical history is, however, hampered by the limited extent of available data, which highlights the need for considerably greater survey efforts. A key to Arctic proturans is provided to facilitate further studies.

Biohydrogen Production by Antarctic Psychrotolerant Klebsiella sp. ABZ11.

Lower temperature biohydrogen production has always been attractive, due to the lower energy requirements. However, the slow metabolic rate of psychrotolerant biohydrogen-producing bacteria is a common problem that affects their biohydrogen yield. This study reports on the improved substrate synthesis and biohydrogen productivity by the psychrotolerant Klebsiella sp. strain ABZ11, isolated from Antarctic seawater sample. The isolate was screened for biohydrogen production at 30°C, under facultative anaerobic condition. The isolate is able to ferment glucose, fructose and sucrose with biohydrogen production rate and yield of 0.8 mol/l/h and 3.8 mol/g, respectively at 10 g/l glucose concentration. It also showed 74% carbohydrate uptake and 95% oxygen uptake ability, and a wide growth temperature range with optimum at 37°C. Klebsiella sp. ABZ11 has a short biohydrogen production lag phase, fast substrate uptake and is able to tolerate the presence of oxygen in the culture medium. Thus, the isolate has a potential to be used for lower temperature biohydrogen production process.

Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species.

Population genetics patterns of marine fish in general and of Southern Ocean fish in particular range from virtual panmixia over ocean-wide scale to deeply fragmented populations. However the causes underlying these different patterns are not properly understood. In this paper, we tested the hypotheses that population connectivity is positively related to a combination of life history traits, namely duration of pelagic larval period and the tendency towards pelagic life style in the adulthood. To do so, we analysed the variability of six microsatellite and one mitochondrial marker (cytochrome b) in three Southern Ocean fish species (Trematomus newnesi, Trematomus hansoni and Trematomus bernacchii). They share a recent common ancestor but notably differ in their duration of pelagic larval period as well as pelagic versus benthic lifestyle. We sampled over a range of more than 5000 km for all three species and used a number of population genetics tools to investigate past and contemporary levels of connectivity. All species experienced population fluctuations, but coalescent simulations suggested that contemporary populations are in migration-drift equilibrium. Although global F(ST) values were rather low, a significant population structure separated the High-Antarctic from the Peninsular regions in all species. The level of genetic differentiation was much lower in the pelagic versus benthic species. Present data suggest that past and present genetic structuring in the Southern Ocean are indeed related with the ecological traits of Antarctic fish, however the relative importance of individual factors remains unclear.

Influence of solar UV radiation on the nitrogen metabolism in needles of Scots pine (Pinus sylvestris L.).

Needles of 20-year-old Scots pine (Pinus sylvestris L.) saplings were studied in an ultraviolet (UV) exclusion field experiment (from 2000 to 2002) in northern Finland (67 degrees N). The chambers held filters that excluded both UV-B and UV-A, excluded UV-B only, transmitted all UV (control), or lacked filters (ambient). UV-B/UV-A exclusion decreased nitrate reductase (NR) activity of 1-year-old needles of Scots pines compared to the controls. The proportion of free amino acids varied in the range 1.08-1.94% of total proteins, and was significantly higher in needles of saplings grown under UV-B/UV-A exclusion compared to the controls or UV-B exclusion. NR activity correlated with air temperature, indicating a "chamber effect". The study showed that both UV irradiance and increasing temperature are significant modulators of nitrogen (N) metabolism in Scots pine needles.