Eubacterium rectale detoxification mechanism increases resilience of the gut environment.

Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment. We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and ROS levels. Cell free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells. We demonstrated through an array of multi-omics and molecular techniques that glutathione (GSH) biosynthesized by E. rectale was able to alleviate host ROS damage. We further showed downregulation of cell stress and immune response genes by host RNA sequencing, which is evidence that E. rectale microbial products promote recovery and alleviate ROS stress.

Arbuscular mycorrhizal fungal contribution towards plant resilience to drought conditions.

Climate changes cause altering rainfall patterns resulting in an increase in drought occurrences globally. These events are disrupting plants and agricultural productivity. To evade droughts, plants try to adapt and modify in the best capacities possible. The plants have adapted by structurally modifying roots, stems, and leaves, as well as modifying functions. Lately, the association of microbial communities with plants has also been proven to be an important factor in aiding resilience. The fungal representatives of the microbial community also help safeguard the plants against drought. We discuss how these fungi associate with plants and contribute to evading drought stress. We specifically focus on Arbuscular mycorrhizal fungi (AMF) mediated mechanisms involving antioxidant defenses, phytohormone mediations, osmotic adjustments, proline expressions, fungal water absorption and transport, morphological modifications, and photosynthesis. We believe understanding the mechanisms would help us to optimize the use of fungi in agricultural practices. That way we could better prepare the plants for the anticipated future drought events.

Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model.

IMPORTANCE: Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.

Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy.

Background: Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results: We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions: The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities.

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

The Contribution of the Human Oral Microbiome to Oral Disease: A Review.

The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.

Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience.

BACKGROUND: Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. RESULTS: In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. CONCLUSIONS: Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.

Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress.

Environmental change, especially frequent droughts, is predicted to detrimentally impact the North American perennial grasslands. Consistent dry spells will affect plant communities as well as their associated rhizobiomes, possibly altering the plant host performance under environmental stress. Therefore, there is a need to understand the impact of drought on the rhizobiome, and how the rhizobiome may modulate host performance and ameliorate its response to drought stress. In this study, we analyzed bacterial and fungal communities in the rhizospheres of three ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii. The ecotypes were established in 2010 in a common garden design and grown for a decade under persistent dry conditions at the arid margin of the species' range in Colby, Kansas. The experiment aimed to answer whether and to what extent do the different ecotypes maintain or recruit distinct rhizobiomes after 10 years in an arid climate. In order to answer this question, we screened the bacterial and fungal rhizobiome profiles of the ecotypes under the arid conditions of western Kansas as a surrogate for future climate environmental stress using 16S rRNA and ITS2 metabarcoding sequencing. Under these conditions, bacterial communities differed compositionally among the A. gerardii ecotypes, whereas the fungal communities did not. The ecotypes were instrumental in driving the differences among bacterial rhizobiomes, as the ecotypes maintained distinct bacterial rhizobiomes even after 10 years at the edge of the host species range. This study will aid us to optimize plant productivity through the use of different ecotypes under future abiotic environmental stress, especially drought. IMPORTANCE In this study, we used a 10-year long reciprocal garden system, and reports that different ecotypes (dry, mesic, and wet) of dominant prairie grass, Andropogon gerardii can maintain or recruit distinct bacterial but not fungal rhizobiomes after 10 years in an arid environment. We used both 16S rRNA and ITS2 amplicons to analyze the bacterial and fungal communities in the rhizospheres of the respective ecotypes. We showed that A. gerardii might regulate the bacterial community to adapt to the arid environment, in which some ecotypes were not adapted to. Our study also suggested a possible tradeoff between the generalist and the specialist bacterial communities in specific environments, which could benefit the plant host. Our study will provide insights into the plant host regulation of the rhizosphere bacterial and fungal communities, especially during frequent drought conditions anticipated in the future.

Perspective: Simple State Communities to Study Microbial Interactions: Examples and Future Directions.

Microbial interactions in natural environments are intricately complex. High numbers and rich diversity of microorganisms, along with compositional heterogeneities complicate the cause. It is essential to simplify these complex communities to understand the microbial interactions. We proposed a concept of "simple state community," which represents a subset of microbes and/or microbial functions of the original population that is necessary to build a stable community. By combining microbial culturing and high-throughput sequencing, we can better understand microbe-microbe and microbe-host interactions. To support our proposed model, we used carbon-based and nitrogen-based media to capture the simple state communities. We used 16S rRNA amplicon sequencing and assigned taxonomic identity to the bacterial populations before and after simple state communities. We showed that simple state communities were a subset of the original microbial communities at both phyla and genera level. We further used shotgun metagenomics to gain insights into the functional potential of the assembled simple state communities. Our proposed model supported the goal of simplifying the complex communities across diverse systems to provide opportunity to facilitate comprehension of both the structure and function of the subset communities. Further applications of the concept include the high-throughput screening of simple state communities using the BIOLOG® system and continuous culturing (Chemostat). This concept has the potential to test diverse experimental hypotheses in simplified microbial communities, and further extend that knowledge to answer the overarching questions at a more holistic level.

D155Y substitution of SARS-CoV-2 ORF3a weakens binding with Caveolin-1.

The clinical manifestation of the recent pandemic COVID-19, caused by the novel SARS-CoV-2 virus, varies from mild to severe respiratory illness. Although environmental, demographic and co-morbidity factors have an impact on the severity of the disease, contribution of the mutations in each of the viral genes towards the degree of severity needs a deeper understanding for designing a better therapeutic approach against COVID-19. Open Reading Frame-3a (ORF3a) protein has been found to be mutated at several positions. In this work, we have studied the effect of one of the most frequently occurring mutants, D155Y of ORF3a protein, found in Indian COVID-19 patients. Using computational simulations we demonstrated that the substitution at 155th changed the amino acids involved in salt bridge formation, hydrogen-bond occupancy, interactome clusters, and the stability of the protein compared with the other substitutions found in Indian patients. Protein-protein docking using HADDOCK analysis revealed that substitution D155Y weakened the binding affinity of ORF3a with caveolin-1 compared with the other substitutions, suggesting its importance in the overall stability of ORF3a-caveolin-1 complex, which may modulate the virulence property of SARS-CoV-2.

Remarkably high Pb2+ binding capacity of a novel, regenerable bioremediator Papiliotrema laurentii RY1: Functional in both alkaline and neutral environments.

The ability of P. laurentii strain RY1 to remediate lead (Pb2+) from water was investigated in batch and column studies. The lead removal ability of non-viable biomass, non-viable biomass immobilised on agar-agar (biobeads) and agar-agar at different pH was compared in batch studies. It was found that among the three, biobeads have maximum ability to remove Pb2+ followed by biomass and agar-agar beads. Maximum and almost equal lead removal by biobeads was observed at both neutral and alkaline pH making it a novel and more applicable bioremediator as all other reported bioremediators have a single pH for optimum activity. Studies were performed to determine the optimum conditions for lead removal from aqueous solutions for biobeads. The physical and chemical characterization of the biobeads before and after Pb2+ biosorption was done by using S.E.M. and F.T.I.R. respectively. The adsorption of Pb2+ on biobeads obeyed the Langmuir adsorption isotherm and pseudo first order kinetics. These mean that the Pb2+ binding sites are identical, located on the surface of the adsorbant and the rate of Pb2+ removal from aqueous solution is directly proportional to the number of Pb2+ binding sites on the biobeads. The thermodynamics of the biosorption process is also investigated. The binding capacity of the biobeads in batch study was found to be 52.91mg/gm which is higher in comparison to other reported yeast bioremediators. The used biobeads can be desorbed using 0.1(M) CaCl2. The desorbed biobeads can be used subsequently for several cycles of lead removal making it cost-effective. Column studies were also performed for biobeads with the help of Thomas model for examining its suitability for industrial application. Maximum specific lead uptake of the biobeads when applied in the column was found to be 58.26mg/gm which being promising makes it suitable for application in industries involved in the treatment of wastewater contaminated with high amounts of lead. The high mass transfer co-efficient indicate that small sized column can be used effectively to remove high amounts of lead which makes the bioremediation process by the biobeads more economical and advantageous for industrial application. Several factors like effectiveness of the biobeads in Pb2+removal at both neutral and alkaline pH, reusability, high mass transfer co-efficient, regenerability and high binding capacity makes it a novel versatile, cost-effective and high utility bioremediator.

Anti-virulence activity of polyphenolic fraction isolated from Kombucha against Vibrio cholerae.

The use of traditional foods and beverages or their bioactive compounds as anti-virulence agents is a new alternative method to overcome the increased global emergence of antimicrobial resistance in enteric pathogens. In the present study, we investigated the anti-virulence activity of a polyphenolic fraction previously isolated from Kombucha, a 14-day fermented beverage of sugared black tea, against Vibrio cholerae O1. The isolated fraction was mainly composed of the polyphenols catechin and isorhamnetin. The fraction, the individual polyphenols and the combination of the individual polyphenols significantly inhibited bacterial swarming motility and expression of flagellar regulatory genes motY and flaC, even at sub-inhibitory concentrations. The polyphenolic compounds also decreased bacterial protease secretion and mucin penetration in vitro. In vivo study revealed that the polyphenolic fraction significantly inhibited V. cholerae induced fluid accumulation in the rabbit ileal loop model and intestinal colonization in suckling mice model. Therefore, the anti-virulence activity of the Kombucha polyphenolic fraction involved inhibition of motility and protease secretion of V. cholerae, thus preventing bacterial penetration through the mucin layer as well as fluid accumulation and bacterial colonization in the intestinal epithelial cells. The overall results implied that Kombucha might be considered as a potential alternative source of anti-virulence polyphenols against V. cholerae. To the best of our knowledge, this is the first report on the anti-virulence activity of Kombucha, mostly attributed to its polyphenolic content.

DMSO strengthens chitin deacetylase-chitin interaction: Physicochemical, kinetic, structural and catalytic insights.

Chitin deacetylase, an enzyme isolated from Cryptococcus laurentii RY1, catalyzes the hydrolysis of acetamido group of N-acetyl-D-glucosamine unit of chitin. The primary objective of this study was to characterize and comprehend the activation of chitin deacetylase by DMSO. The secondary structure of the protein was determined by circular dichroism(CD).The interaction of protein with DMSO was evaluated by CD and tryptophan fluorescence spectroscopy which revealed that DMSO had no effect on overall secondary structure, but induced change in the tertiary structure of the enzyme. The interaction of chitin deacetylase with chitin in DMSO system when investigated by molecular dynamics simulation revealed stronger chitin deacetylase-chitin interaction involving several amino acid residues. The enhanced activity of the enzyme in presence of DMSO along with the fact that its kcat is highest of all other reported chitin deacetylases makes it a superior candidate in the industrial sector involved in chitosan production from chitin.

Removal of Pb (II), As (III), and Cr (VI) by nitrogen-starved Papiliotrema laurentii strain RY1.

Heavy metals such as lead, chromium, and metalloid like arsenic dominate the pinnacle in posing a threat to life. Being environment-friendly, elucidating the mechanism by which microorganisms detoxify such elements has always been an active field of research hitherto. In the present study, we have investigated the capability of nitrogen-deprived Papiliotrema laurentii strain RY1 toward enhanced tolerance and neutralizing toxic elements. There were biosorption and bioprecipitation of lead and chromium at the cell surfaces. Bioprecipitation mechanisms included the formation of lead phosphates and pyromorphites from lead, grimaldite from chromium. Transcripts such as metallothionein, aquaporins, and arsenical pump-driving ATPase have been surmised to be involved in the detoxification of elements. Furthermore, activation of antioxidant defense mechanisms for the cells for each of the elements should contribute towards yeast's propagation. The efficiency of removal of elements for live cells and immobilized cells were high for lead and chromium. To the best of our knowledge, this is the first report of such high tolerance of lead, arsenic, and chromium for any yeast. The yeast showed such varied response under dual stress due to nitrogen starvation and in the presence of respective elements. The yeast possesses promising potentials in nitrogen deprived and enriched environments to aid in bioremediation sectors.

Nitrogen deprivation elicits dimorphism, capsule biosynthesis and autophagy in Papiliotrema laurentii strain RY1.

Stress response due to the lack of essential nutrient(s) for an organism has been a focal point of several scientific investigations. The present study investigates the cellular adaptations behind the ability of Papiliotrema laurentii strain RY1 to perpetuate without added nitrogen and propagate robustly in growth- limiting amount of nitrogen. We executed phenotypic (using scanning electron microscopy, differential interference contrast microscopy and transmission electron microscopy), microbiological and computational analyses to show multiple responses of dimorphism, capsule formation and autophagy as a survival strategy by the yeast upon nitrogen starvation. The roles of phosphomannose isomerase, phosphomannomutase and several autophagy-related transcripts aiding in such a response have been discussed.

De novo RNA-Seq based transcriptome analysis of Papiliotrema laurentii strain RY1 under nitrogen starvation.

Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500. Trinity analysis and clustered transcripts annotation of the reads produced 17,611 unigenes, out of which 14,157 could be annotated. Gene Ontology term analysis generated 44.92% cellular component terms, 39.81% molecular function terms and 15.24% biological process terms. The most over represented pathways in general were translation, carbohydrate metabolism, amino acid metabolism, general metabolism, folding, sorting, degradation followed by transport and catabolism, nucleotide metabolism, replication and repair, transcription and lipid metabolism. A total of 4256 Single Sequence Repeats were identified. Differential gene expression analysis detected 996 P-significant transcripts to reveal transmembrane transport, lipid homeostasis, fatty acid catabolism and translation as the enriched terms which could be essential for Papiliotrema laurentii strain RY1 to adapt during nitrogen deprivation. Transcriptome data was validated by quantitative real-time PCR analysis of twelve transcripts. To the best of our knowledge, this is the first report of Papiliotrema laurentii strain RY1 transcriptome which would play a pivotal role in understanding the biochemistry of the yeast under acute nitrogen stress and this study would be encouraging to initiate extensive investigations into this Papiliotrema system.

Homology modeling, molecular docking and molecular dynamics studies of the catalytic domain of chitin deacetylase from Cryptococcus laurentii strain RY1.

This study provides structural insights into chitin deacetylase, over-expressing under nitrogen limiting condition in Cryptococcus laurentii strain RY1. The enzyme converts chitin, the second most abundant natural biopolymer, to chitosan, which offers tremendous applications in diverse fields. To elucidate the structure-function relationship of this biologically and industrially important enzyme, a homology model of the catalytic domain was constructed. The stability of the structure was assessed by molecular dynamics simulation studies. Tryptophan 151 of the domain was identified to form hydrogen bond and stacking interaction with chitin upon docking. In Silico substitution of Tryptophan (W) to Alanine (A), Phenylalanine (F) and Aspartate (D) corroborated the importance of the Tryptophan residue in interaction with the substrate. This is the first report of unravelling the structural characteristics of chitin deacetylase from Cryptococcus and understanding the approach of the enzyme towards its substrate. Our results would be helpful to perform experimental validations and apply quantum mechanics/molecular mechanics techniques to determine the detailed catalytic mechanism and enhance the industrial potency of the enzyme.

Antibacterial Activity of Polyphenolic Fraction of Kombucha Against Enteric Bacterial Pathogens.

The emergence of multi-drug-resistant enteric pathogens has prompted the scientist community to explore the therapeutic potentials of traditional foods and beverages. The present study was undertaken to investigate the efficacy of Kombucha, a fermented beverage of sugared black tea, against enterotoxigenic Escherichia coli, Vibrio cholerae, Shigella flexneri and Salmonella Typhimurium followed by the identification of the antibacterial components present in Kombucha. The antibacterial activity was evaluated by determining the inhibition zone diameter, minimal inhibitory concentration and minimal bactericidal concentration. Kombucha fermented for 14 days showed maximum activity against the bacterial strains. Its ethyl acetate extract was found to be the most effective upon sequential solvent extraction of the 14-day Kombucha. This potent ethyl acetate extract was then subjected to thin layer chromatography for further purification of antibacterial ingredients which led to the isolation of an active polyphenolic fraction. Catechin and isorhamnetin were detected as the major antibacterial compounds present in this polyphenolic fraction of Kombucha by High Performance Liquid Chromatography. Catechin, one of the primary antibacterial polyphenols in tea was also found to be present in Kombucha. But isorhamnetin is not reported to be present in tea, which may thereby suggest the role of fermentation process of black tea for its production in Kombucha. To the best of our knowledge, this is the first report on the presence of isorhamnetin in Kombucha. The overall study suggests that Kombucha can be used as a potent antibacterial agent against entero-pathogenic bacterial infections, which mainly is attributed to its polyphenolic content.

Expression of a chitin deacetylase gene, up-regulated in Cryptococcus laurentii strain RY1, under nitrogen limitation.

This study reports the identification of a chitin deacetylase gene in Cryptococcus laurentii strain RY1 over-expressing under nitrogen limitation by differential display. The up-regulation took place in robustly growing cells rather than in starving quiescent autophagic cells. Quantitative Real Time-PCR, enzyme activity in cell lysate and cell wall analysis corroborated the up-regulation of chitin deacetylase under nitrogen limitation. These results suggest chitin deacetylase might play a significant role in nitrogen limiting growth of Cryptococcus laurentii strain RY1.