Comparative Transcriptome and WGCNA RevealKey Genes Involved in Lignocellulose Degradation in Sarcomyxa Edulis

In order to explore the molecular mechanism of Sarcomyxa edulis response to lignocelluloses degradation, the developmental transcriptomes was analyzed for six stages covering the whole developmental process, including mycelium growing to half bag (B1), mycelium in cold stimulation after full bag (B2), mycelium in primordia appearing (B3), primordia (B4), mycelium at the harvest stage (B5) and mature fruiting body (B6). A total of 6 samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, we constructed a co-expression network of weighted genes associated with extracellular enzyme physiological traits by WGCNA, and obtained 19 gene co-expression modules closely related to lignocelluloses degradation. In addition, a number of key genes involved in lignocelluloses degradation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of Sarcomyxa edulis lignocelluloses degradation.

The lolB gene in Xanthomonas campestris pv. campestris is required for bacterial attachment, stress tolerance, and virulence

Background Xanthomonas campestris pv. campestris (Xcc) is a Gram-negative bacterium that can cause black rot disease in crucifers. The lipoprotein outer membrane localization (Lol) system is involved in the lipoprotein sorting to the outer membrane. Although Xcc has a set of annotated lol genes, there is still little known about the physiological role in this phytopathogen. In this study, we aimed to characterize the role of LolB of Xcc in bacterial attachment, stress tolerance, and virulence. Results To characterize the role of LolB, lolB mutant was constructed and phenotypic evaluation was performed. The lolB mutant revealed reductions in bacterial attachment, extracellular enzyme production, and virulence. Mutation of lolB also resulted in reduced tolerance to a myriad of stresses, including heat and a range of membrane-perturbing agents. Trans-complementation of lolB mutant with intact lolB gene reverted these altered phenotypes to the wild-type levels. From subsequent reporter assay and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) analysis, the expression of genes that encode the major extracellular enzymes and the stress-related proteins was reduced after lolB mutation. Conclusions The results in this work contribute to the functional understanding of lolB in Xanthomonas for the first time, and provide new insights into the function of lolB in bacteria.

Extracellular Enzyme Activities and Carbon/Nitrogen Utilization in Mycorrhizal Fungi Isolated From Epiphytic and Terrestrial Orchids

Fungi employ extracellular enzymes to initiate the degradation of organic macromolecules into smaller units and to acquire the nutrients for their growth. As such, these enzymes represent important functional components in terrestrial ecosystems. While it is well-known that the regulation and efficiency of extracellular enzymes to degrade organic macromolecules and nutrient-acquisition patterns strongly differ between major fungal groups, less is known about variation in enzymatic activity and carbon/nitrogen preference in mycorrhizal fungi. In this research, we investigated variation in extracellular enzyme activities and carbon/nitrogen preferences in orchid mycorrhizal fungi (OMF). Previous research has shown that the mycorrhizal fungi associating with terrestrial orchids often differ from those associating with epiphytic orchids, but whether extracellular enzyme activities and carbon/nitrogen preference differ between growth forms remains largely unknown. To fill this gap, we compared the activities of five extracellular enzymes [cellulase, xylanase, lignin peroxidase, laccase, and superoxide dismutase (SOD)] between fungi isolated from epiphytic and terrestrial orchids. In total, 24 fungal strains belonging to Tulasnellaceae were investigated. Cellulase and xylanase activities were significantly higher in fungi isolated from terrestrial orchids (0.050 ± 0.006 U/ml and 0.531 ± 0.071 U/ml, respectively) than those from epiphytic orchids (0.043 ± 0.003 U/ml and 0.295 ± 0.067 U/ml, respectively), while SOD activity was significantly higher in OMF from epiphytic orchids (5.663 ± 0.164 U/ml) than those from terrestrial orchids (3.780 ± 0.180 U/ml). Carboxymethyl cellulose was more efficiently used by fungi from terrestrial orchids, while starch and arginine were more suitable for fungi from epiphytic orchids. Overall, the results of this study show that extracellular enzyme activities and to a lesser extent carbon/nitrogen preferences differ between fungi isolated from terrestrial and epiphytic orchids and may indicate functional differentiation and ecological adaptation of OMF to local growth conditions.

Production and Quantification of Virulence Factors in Malassezia Species

A total of 77 strains of Malassezia were included in this study. Biofilm production and hydrolytic enzymes were studied by using specific solid media. Real-time Reverse Transcriptase qPCR method was applied to determine overexpression of genes encoding extracellular enzyme. All included Malassezia species produced biofilms. No statistical significant difference was observed between biofilm formation of the Malassezia species (P = 0.567) . All Malassezia species produced lipase and 95% of M. globosa showed a strong enzymatic activity (Pz=0.55 ± 0.02). Statistical significant difference was observed between the mean keratinase indices of M. slooffiae and the others Malassezia species ( P = 0.005). The overexpression of one or more genes was observed in 100% of strains isolated from patients with folliculitis, in 87.5% for pityriasis versicolor isolates and in 57.14% for the control group isolates. A statistical significant difference of the lipase gene expression ( P = 0.072) was associated with the strains collected from patients with folliculitis vs group control. This investigation provides more information about the frequency of the production of the major enzymes considered to be virulence factors of Malassezia species. Interestingly, the overexpression of one or more genes was observed in strains isolated from patients with Malassezia disorder.

Purification efficiency of eight aquatic plant species in an artificial floating island system in relation to extracellular enzyme activity and microbial community

The floating island system exploits the combination of aquatic plants, microorganisms, and extracellular enzymes to purify wastewater. We investigated the purification efficiency of eight aquatic plant species cultured in wastewater. The relationships of plant purification capacity with extracellular enzyme activity and microbial community were analyzed to explore the crucial factors that affect the plant purification capacity and the mechanism of pollutants removal in different plant systems. Three plant species, namely Oenanthe javanica, Thalia dealbata, and lris pseudacorus, were most effective for purification of ammonium-nitrogen (NH4⁺-N), total phosphate (TP), and chemical oxygen demand (COD) with maximum efficiencies of 76.09, 85.87, and 89.10%, respectively. Urease, alkaline phosphatase (AP), and β-glucosidase activities were significantly and positively correlated with root system development (P < 0.05). Activities of urease and AP were positively correlated with NH4⁺-N and TP removal, respectively. The magnitude of urease and AP activity was generally consistent with the plant’s capacity to remove NH4⁺-N and TP. β-Glucosidase activity and COD removal were not significantly correlated. The dominant microbial phylum in each species treatment was Proteobacteria. Alphaproteobacteria and Bacteroidia showed > 1% relative abundance and greater involvement in degradation of pollutants in the experimental system.

Beneficial effect of Achromobacter insolitus MB20 and manures in reducing Pythium aphanidermatum disease in cucumber

The increased global livestock production, such as chickens, cows, goats, and rabbits causes increased animal waste in both liquid and solid forms. The utilization of animal manures are considered as a beneficial way to minimize the livestock waste problems. Application of manure is advantageous to the soil nutrient balance, soil structure and moisture-holding capacity, and facilitates environmental protection. A combination of biocontrol agent of Achromobacter insolitus MB20 and manures was studied as alternative to chemical fungicides to protect crop from diseases without damaging the environment and human health. The chemical fungicides cannot be used continously and do not represent a sustainable method control. Result showed that an application of A. insolitus alone reduced cucumber damping-off as high as 60%, and in combination of A. insolitus with chicken manure was 80%, goat manure 70%, cow manure and rabbit urine 65%. The in vitro test indicated that A. insolitus inhibited P. aphanidermatum growth by 28%. This antagonist bacterium also produced extracellular enzyme of protease and cellulase with proteolytic index (PI) value was 1.4 and cellulolytic index (CI) value was 1.7. An application of A. insolitus with chicken manure resulted the best combination and the most effective in reducing of cucumber damping-off.

Depth dependence of climatic controls on soil microbial community activity and composition

Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.