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Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1
(2022)
Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.
As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.
Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.
(1) Background:
Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula.
(2) Methods:
To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs.
(3) Results:
We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches.
(4) Conclusions:
Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.
Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe.
While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts.
Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts.
To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany.
Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities.
Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower.
Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge.
However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities.
Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation.
Read the free Plain Language Summary for this article on the Journal blog.
Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe
(2022)
The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.
Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.