Functional Characterization of Core Regulatory Genes Involved in Sporulation of the Nematophagous Fungus Purpureocillium lavendulum

Analysis of justification for author order and gender bias in author order among those contributing equally

The practice of designating two or more authors as equal contributors (ECs) on a scientific publication is increasingly common as a form of sharing credit. However, EC authors are often unclearly attributed on curriculum vitae (CVs) or citation engines, and it is unclear how research teams determine author order within an EC listing. In response to studies showing that male authors were more likely to be placed first in an EC listing, the American Society for Microbiology (ASM) required that authors explain the reasons for author order beginning in 2020. In this study, we analyze data from over 2,500 ASM publications to see how this policy affected gender bias and how research teams are making decisions on author order. Data on publications from 2018 to 2021 show that gender bias was largely nonsignificant both before and after authors were asked by ASM to provide an EC statement. The most likely reasons for EC order included alphabetical order, seniority, and chance, although there were differences for publications from different geographic regions. However, many research teams used unique methods in order selection, highlighting the importance of EC statements to provide clarity for readers, funding agencies, and tenure committees.

IMPORTANCE

First-author publications are important for early career scientists to secure funding and educational opportunities. However, an analysis published in eLife in 2019 noted that female authors are more likely to be placed second even when both authors report they have contributed equally. American Society for Microbiology announced in response that they would require submissions to include a written justification of author order. In this paper, we analyze the resultant data and show that laboratories are most likely to use some combination of alphabetical order, seniority, and chance to determine author order. However, the prevalence of these methods varies based on the research team's geographic location. These findings highlight the importance of equal contributor statements to provide clarity for readers, funding agencies, and tenure committees. Furthermore, this work is critically important for understanding how these decisions are made and provides a glimpse of the sociology of science.

Analysis of justification for and gender bias in author order among those contributing equally

The practice of designating two or more authors as equal contributors (EC) on a scientific publication is increasingly common as a form of sharing credit. However, EC authors are often unclearly attributed on CVs or citation engines, and it is unclear how research teams determine author order within an EC listing. In response to studies showing that male authors were more likely to be placed first in an EC listing, the American Society of Microbiology (ASM) required that authors explain the reasons for author order beginning in 2020. In this study we analyze data from over 2500 ASM publications to see how this policy affected gender bias and how research teams are making decisions on author order. Data on publications from 2018-2021 show that gender bias was largely nonsignificant both before and after authors were asked by ASM to provide an EC statement. The most likely reasons for EC order included alphabetical order, seniority, and chance, although there were differences for publications from different geographic regions. However, many research teams used unique methods in order selection, highlighting the importance of EC statements to provide clarity for readers, funding agencies, and tenure committees.

Characterization of regulatory genes Plhffp and Plpif1 involved in conidiation regulation in Purpureocillium lavendulum

Purpureocillium lavendulum is an important biocontrol agent against plant-parasitic nematodes, primarily infecting them with conidia. However, research on the regulatory genes and pathways involved in its conidiation is still limited. In this study, we employed Agrobacterium tumefaciens-mediated genetic transformation to generate 4,870 random T-DNA insertion mutants of P. lavendulum. Among these mutants, 131 strains exhibited abnormal conidiation, and further in-depth investigations were conducted on two strains (designated as #5-197 and #5-119) that showed significantly reduced conidiation. Through whole-genome re-sequencing and genome walking, we identified the T-DNA insertion sites in these strains and determined the corresponding genes affected by the insertions, namely Plhffp and Plpif1. Both genes were knocked out through homologous recombination, and phenotypic analysis revealed a significant difference in conidiation between the knockout strains and the wild-type strain (ku80). Upon complementation of the ΔPlpif1 strain with the corresponding wildtype allele, conidiation was restored to a level comparable to ku80, providing further evidence of the involvement of this gene in conidiation regulation in P. lavendulum. The knockout of Plhffp or Plpif1 reduced the antioxidant capacity of P. lavendulum, and the absence of Plhffp also resulted in decreased resistance to SDS, suggesting that this gene may be involved in the integrity of the cell wall. RT-qPCR showed that knockout of Plhffp or Plpif1 altered expression levels of several known genes associated with conidiation. Additionally, the analysis of nematode infection assays with Caenorhabditis elegans indicated that the knockout of Plhffp and Plpif1 indirectly reduced the pathogenicity of P. lavendulum towards the nematodes. The results demonstrate that Agrobacterium tumefaciens - mediated T-DNA insertion mutagenesis, gene knockout, and complementation can be highly effective for identifying functionally important genes in P. lavendulum.

LOX1- and PLP1-dependent transcriptional reprogramming is essential for injury-induced conidiophore development in a filamentous fungus

IMPORTANCE

In addition to being considered a biocontrol agent, the fungus Trichoderma atroviride is a relevant model for studying mechanisms of response to injury conserved in plants and animals that opens a new landscape in relation to regeneration and cell differentiation mechanisms. Here, we reveal the co-functionality of a lipoxygenase and a patatin-like phospholipase co-expressed in response to wounding in fungi. This pair of enzymes produces oxidized lipids that can function as signaling molecules or oxidative stress signals that, in ascomycetes, induce asexual development. Furthermore, we determined that both genes participate in the regulation of the synthesis of 13-HODE and the establishment of the physiological responses necessary for the formation of reproductive aerial mycelium ultimately leading to asexual development. Our results suggest an injury-induced pathway to produce oxylipins and uncovered physiological mechanisms regulated by LOX1 and PLP1 to induce conidiation, opening new hypotheses for the novo regeneration mechanisms of filamentous fungi.

Ethanol mediates the interaction between Caenorhabditis elegans and the nematophagous fungus Purpureocillium lavendulum

Accurately recognizing pathogens by the host is vital for initiating appropriate immune response against infecting microorganisms. Caenorhabditis elegans has no known receptor to recognize pathogen-associated molecular pattern. However, recent studies showed that nematodes have a strong specificity for transcriptomes infected by different pathogens, indicating that they can identify different pathogenic microorganisms. However, the mechanism(s) for such specificity remains largely unknown. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum can infect the intestinal tract of the nematode C. elegans and the infection led to the accumulation of reactive oxygen species (ROS) in the infected intestinal tract, which suppressed fungal growth. Co-transcriptional analysis revealed that fungal genes related to anaerobic respiration and ethanol production were up-regulated during infection. Meanwhile, the ethanol dehydrogenase Sodh-1 in C. elegans was also up-regulated. Together, these results suggested that the infecting fungi encounter hypoxia stress in the nematode gut and that ethanol may play a role in the host-pathogen interaction. Ethanol production in vitro during fungal cultivation in hypoxia conditions was confirmed by gas chromatography-mass spectrometry. Direct treatment of C. elegans with ethanol elevated the sodh-1 expression and ROS accumulation while repressing a series of immunity genes that were also repressed during fungal infection. Mutation of sodh-1 in C. elegans blocked ROS accumulation and increased the nematode's susceptibility to fungal infection. Our study revealed a new recognition and antifungal mechanism in C. elegans. The novel mechanism of ethanol-mediated interaction between the fungus and nematode provides new insights into fungal pathogenesis and for developing alternative biocontrol of pathogenic nematodes by nematophagous fungi. IMPORTANCE Nematodes are among the most abundant animals on our planet. Many of them are parasites in animals and plants and cause human and animal health problems as well as agricultural losses. Studying the interaction of nematodes and their microbial pathogens is of great importance for the biocontrol of animal and plant parasitic nematodes. In this study, we found that the model nematode Caenorhabditis elegans can recognize its fungal pathogen, the nematophagous fungus Purpureocillium lavendulum, through fungal-produced ethanol. Then the nematode elevated the reactive oxygen species production in the gut to inhibit fungal growth in an ethanol dehydrogenase-dependent manner. With this mechanism, novel biocontrol strategies may be developed targeting the ethanol receptor or metabolic pathway of nematodes. Meanwhile, as a volatile organic compound, ethanol should be taken seriously as a vector molecule in the microbial-host interaction in nature.

In-depth comparative transcriptome analysis of Purpureocillium sp. CB1 under cadmium stress

Fungal bioremediation is a very attractive tool to cope with environmental pollution. We aimed to decipher the cadmium (Cd) response of Purpureocillium sp. CB1, isolated from polluted soil, at transcriptome level by RNA-sequencing (RNA-seq). We used 500 and 2500 mg/L of Cd²⁺ concentrations at two time points (t_6;36). RNA-seq determined 620 genes that were co-expressed in all samples. The highest number of differentially expressed genes (DEGs) was obtained within the first six h of exposure to 2500 mg/L of Cd²⁺. Several genes encoding transcriptional regulators, transporters, heat shock proteins, and oxidative stress-related genes were differentially expressed under Cd²⁺ stress. Remarkably, the genes that encode salicylate hydroxylase, which is involved in naphthalene biodegradation pathway, were significantly overexpressed. Utilization of diesel as the sole carbon source by CB1 even in the presence of Cd²⁺ supported concomitant upregulation of hydrocarbon degradation pathway genes. Furthermore, leucinostatin-related gene expression levels increased under Cd²⁺ stress. In addition, leucinostatin extracts from Cd²⁺-treated CB1 cultures showed higher antifungal activity than the control. Notably, Cd²⁺ in CB1 was mainly found as bound to the cell wall, thus confirming its adsorption potential. Cd²⁺ stress slightly reduced growth and led to mycelial malformation due to Cd²⁺ adsorption, especially at a concentration of 2500 mg/L at t₃₆. A strong correlation was recorded between RNA-seq and reverse-transcriptase-quantitative polymerase chain reaction (RT-qPCR) data. In conclusion, the study represents the first transcriptome analysis of Purpureocillium sp. under Cd²⁺ stress, providing insights into the primary targets for rational engineering to construct strains with remarkable bioremediation potency. KEY POINTS: • Upregulation of genes encoding salicylate hydroxylases under Cd²⁺ stress • Maximum Cd²⁺ adsorption at 500 mg/L at t₃₆ as tightly bound to the cell wall • Concordant bioremediation potential of CB1 on Cd²⁺ and diesel.

The Growth and Conidiation of Purpureocillium lavendulum Are Co-Regulated by Nitrogen Sources and Histone H3K14 Acetylation

Plant-parasitic nematodes cause severe economic losses to agriculture. As important biocontrol agents, nematophagous fungi evolved the ability to obtain nitrogen sources from nematodes. However, the impact of nitrogen sources on the growth and development of these fungi is largely unknown. In this study, we aimed to better understand how nitrogen sources could influence vegetative growth and conidiation through epigenetic regulation in the nematophagous fungus, Purpureocillium lavendulum. Through nutrition screening, we found a phenomenon of the fungus, limited colony extension with a large amount of conidia production when cultured on PDA media, can be altered by adding ammonia nitrate. Characterized by site-directed mutagenesis, the histone H3K14 acetylation was found to be involved in the alternation. Furthermore, the acetyltransferase PlGCN5 was responsible for H3K14 acetylation. Knockout of Plgcn5 severely diminished conidiation in P. lavendulum. Chip-seq showed that H3K14ac distributed in conidiation regulating genes, and genes in the MAPK pathway which may be the downstream targets in the regulation. These findings suggest that histone modification and nitrogen sources coordinated lifestyle regulation in P. lavendulum, providing new insight into the mechanism of growth regulation by nutritional signals for the carnivorous fungus.

Pathogenicity and Metabolites of Purpureocillium lavendulum YMF1.00683 against Meloidogyne incognita

Purpureocillium lavendulum is a biological control agent with several registered products that can parasitize the eggs and larvae of various pathogenic nematodes. In this study, the pathogenicity and secondary metabolites of the fungus P. lavendulum YMF1.00683 were investigated. The strain YMF1.00683 had infection efficiency against the plant root-knot nematode Meloidogyne incognita. The strain’s process of infecting nematodes was observed under a microscope. Moreover, seven metabolites, including a new sterol (1), were isolated and identified from cultures of YMF1.0068 in Sabouraud’s dextrose agar. A bioassay showed that 5-methoxymethyl-1H-pyrrole-2-carboxaldehyde (7) is toxic to M. incognita and affects the egg hatching. It caused 98.23% mortality in M. incognita and could inhibit 80.78% of the hatching eggs at 400 μg/mL over a period of 96 h. Furthermore, 5-methoxymethyl-1H-pyrrole-2-carboxaldehyde (7) showed a strong avoidance effect at 40 ppm, and its chemotactic index value was −0.37. The results indicate that P. lavendulum could produce active metabolites against M. incognita.

Identification of Nematicidal Metabolites from Purpureocillium lavendulum

Purpureocillium lavendulum is a fungus with promising biocontrol applications. Here, transcriptome data acquired during the infection of Caenorhabditis elegans by Purpureocillium lavendulum showed that the transcription of metabolite synthesis genes was significantly up-regulated after 24 and 48 h of the fungus-nematode interaction. Then, the up-regulated transcription level of lipoxygenase was confirmed by RT-qPCR. The ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) analysis of differential metabolites revealed that this interaction resulted in the emergence of new metabolites or enhanced the production of metabolites. The results of the UPLC-MS analysis and the nematicidal assay were used to establish optimal culturing conditions under which 12 metabolites, including 3 hydroxylated C18 fatty acids and 9 steroids, were isolated and identified. Among them, hydroxylated fatty acids showed pronounced nematicidal activity against Meloidogyne incognita, and two degradative sterols showed chemotaxis activity to M. incognita. This study lays a foundation for the function of lipoxygenase and its products during the infection of Purpureocillium lavendulum.

Characterization of the complete mitochondrial genome of the nematophagous fungus Purpureocillium lavendulum

The complete mitochondrial genome of Purpureocillium lavendulum was characterized in this study. This mitogenome is a closed circular molecule of 23,567 bp in length with a GC content of 28.46%, including 15 protein-coding genes, 25 transfer RNA genes, 2 ribosomal RNA genes. Phylogenetic analyses based on sequences at the 14 concatenated mitochondrial protein-coding genes showed that P. lavendulum was closely related to Hirsutella minnesotensis.