As a model organism for studies of cell and environmental biology, the free‐living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), “gene‐sized” chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high‐quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete “gene‐sized” nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5′‐TA‐3′ is conserved at nearly all internally‐eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature‐resistance to the evolved loss of temperature stress‐sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.

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Evidence is mounting that microorganisms originating from livestock impact the air quality of the animal houses themselves and the public in the surrounding neighborhoods. The aim of this study was to develop efficient bacterial source tracking capabilities to identify sources of Escherichia coli aerosol pollution caused by pigs. Airborne E. coli were isolated from indoor air, upwind air (10 and 50 m away) and downwind air samples (10, 50, 100, 200 and 400 m away) for five swine houses using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli strains from pig fecal samples were also collected simultaneously. The enterobacterial repetitive intergenic consensus polymerize chain reaction (ERIC-PCR) and the repetitive extragenic palindromic (REP-PCR) approaches were used to study the genetic variability and to determine the strain relationships among E. coli isolated from different sites in each swine house. Results showed that 35.1% (20/57) of the bacterial DNA fingerprints from the fecal isolates matched with the corresponding strains isolated from indoor and downwind air samples (similarity > or = 90%). E. coli strains from the indoor and downwind air samples were closely related to the E. coli strains isolated from feces, while those isolated from upwind air samples (swine house C) had low similarity (61-69%). Our results suggest that some strains isolated from downwind and indoor air originated in the swine feces. Effective hygienic measures should be taken in animal farms to prevent or minimize the downwind spread of microorganism aerosol.

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To better understand the effect of different disinfectants on the types and quantities of microorganisms in a broiler chicken house, five different types of disinfectants, including ozone, available chlorine, quaternary ammonium salt, glutaraldehyde, and mixed disinfectant, were used. The broiler house microbial communities were analyzed by high-throughput sequencing combined with air sampling. The results showed that the concentrations of airborne aerobic bacteria in the empty broiler houses after application of different disinfectants were significantly reduced compared to a house untreated with disinfectant (P < 0.05 or P < 0.01), and the number of inhalable particles of airborne aerobic bacteria sharply decreased after disinfection. Of the five disinfectants, the mixed disinfectant had the best disinfection efficacy on the total microbial communities (P < 0.05). A total of 508,143 high-quality sequences were obtained by high-throughput sequencing, which identified 1995 operational taxonomic units. In total, 42 phyla and 312 genera were identified. The structures of airborne microbial communities in the broiler houses after the different disinfectants were applied differed. In the house treated with the mixed disinfectant, the microbial communities containing opportunistic pathogens, such as Escherichia-Shigella, Bacillus, and Pseudomonas, had the lowest abundance, with a significant decrease compared to the house untreated with disinfectant. The alpha diversity index showed low diversity of the microbial communities in the house treated with mixed disinfectant. In contrast to the other four disinfectants, only a small amount of bacteria was detected in the air sample in the house treated with the mixed disinfectant; specifically, only four phyla were found (Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes). The mixed disinfectant produced a positive effect on disinfection for four phyla; however, it didn’t thoroughly eliminate them. At genus level, Bacillus, Arenimonas, and Shinella could not be detected in the house treated with the mixed disinfectant, but were detected in houses treated with other disinfectants. The high-throughput sequencing results revealed that the combination of multiple disinfectants exhibited a good disinfection efficacy and that this technique could disinfect the air of broiler houses. These results will help guide the development of a reasonable program for broiler house disinfection.

Fungi play an irreplaceable role in drug discovery in the course of human history, as they possess unique abilities to synthesize diverse specialized metabolites with significant medicinal potential. Trichoderma are well-studied filamentous fungi generally observed in nature, which are widely marketed as biocontrol agents. The secondary metabolites produced by Trichoderma have gained extensive attention since they possess attractive chemical structures with remarkable biological activities. A large number of metabolites have been isolated from Trichoderma species in recent years. A previous review by Reino et al. summarized 186 compounds isolated from Trichoderma as well as their biological activities up to 2008. To update the relevant list of reviews of secondary metabolites produced from Trichoderma sp., we provide a comprehensive overview in regard to the newly described metabolites of Trichoderma from the beginning of 2009 to the end of 2020, with emphasis on their chemistry and various bioactivities. A total of 203 compounds with considerable bioactivities are included in this review, which is worth expecting for the discovery of new drug leads and agrochemicals in the foreseeable future. Moreover, new strategies for discovering secondary metabolites of Trichoderma in recent years are also discussed herein.