Abstract Background Most fungi, including entomopathogenic fungi, have two different conidiation patterns, normal and microcycle conidiation, under different culture conditions, eg, in media containing different nutrients. However, the mechanisms underlying the conidiation pattern shift are poorly understood. Results In this study, Metarhizium acridum undergoing microcycle conidiation on sucrose yeast extract agar (SYA) medium shifted to normal conidiation when the medium was supplemented with sucrose, nitrate, or phosphate. By linking changes in nutrients with the conidiation pattern shift and transcriptional changes, we obtained conidiation pattern shift libraries by Solexa/Illumina deep-sequencing technology. A comparative analysis demonstrated that the expression of 137 genes was up-regulated during the shift to normal conidiation, while the expression of 436 genes was up-regulated at the microcycle conidiation stage. A comparison of subtractive libraries revealed that 83, 216, and 168 genes were related to sucrose-induced, nitrate-induced, and phosphate-induced conidiation pattern shifts, respectively. The expression of 217 genes whose expression was specific to microcycle conidiation was further analyzed by the gene expression profiling via multigene concatemers method using mRNA isolated from M. acridum grown on SYA and the four normal conidiation media. The expression of 142 genes was confirmed to be up-regulated on standard SYA medium. Of these 142 genes, 101 encode hypothetical proteins or proteins of unknown function, and only 41 genes encode proteins with putative functions. Of these 41 genes, 18 are related to cell growth, 10 are related to cell proliferation, three are related to the cell cycle, three are related to cell differentiation, two are related to cell wall synthesis, two are related to cell division, and seven have other functions. These results indicate that the conidiation pattern shift in M. acridum mainly results from changes in cell growth and proliferation. Conclusions The results indicate that M. acridum shifts conidiation pattern from microcycle conidiation to normal conidiation when there is increased sucrose, nitrate, or phosphate in the medium during microcycle conidiation. The regulation of conidiation patterning is a complex process involving the cell cycle and metabolism of M. acridum. This study provides essential information about the molecular mechanism of the induction of the conidiation pattern shift by single nutrients. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2971-0) contains supplementary material, which is available to authorized users. Keywords: Conidiation pattern shift, Normal and microcycle conidia, Metarhizium acridum, Pathway analysis Background Conidia (spores) are the beginning and end of the differentiation process in the lifecycle of fungi [[29]1, [30]2], and they play important roles in reproduction and survival [[31]2]. Most filamentous fungi have two conidiation patterns: normal and microcycle conidiation [[32]3]. Normal conidiation is the most common reproductive mode of filamentous fungi [[33]4], and microcycle conidiation is a survival mechanism under stress conditions, whereby the normal lifecycle is bypassed [[34]3, [35]5–[36]8]. To date, microcycle conidiation has been described in more than 100 fungal species [[37]3, [38]5, [39]7], and it has been divided into four basic categories based on the morphological characteristics of conidia [[40]9]. The conidiation patterns can be shifted from normal to microcycle conidiation under various conditions, such as high and/or low temperature [[41]6, [42]10, [43]11], high and/or low pH [[44]12, [45]13], high salt concentration [[46]14], and the presence of certain nutrients [[47]7, [48]10, [49]15, [50]16]. Nutrients are the most common factors that affect fungal conidiation patterns. In Colletotrichum gloeosporioides, microcycle conidiation occurs in substrate-limited liquid cultures [[51]17]. In Beauveria bassiana, microcycle conidiation is observed in the absence of a carbon source in the basal medium [[52]15]. In Aspergillus flavus, exogenous putrescine inhibits microcycle conidiation and induces mycelial development [[53]18]. In Neurospora intermedia, microcycle conidiation occurs under low sugar and nitrogen conditions [[54]19]. The culture conditions for normal and microcycle conidiation are different, and even a subtle change in culture conditions can cause a substantially different conidiation pattern. The conidiation pattern shift in response to nutrients may be regulated by some sensors and pathways [[55]20]. However, the molecular mechanisms of the conidiation pattern shift in response to nutrients have not been elucidated. The conidia of entomopathogenic fungi are formulated as myco-insecticides [[56]21–[57]23]. Metarhizium acridum is a model system for entomopathogenic fungi, and it is widely used for locust control in Africa, Asia, and Australia [[58]24–[59]26]. The entomopathogenic fungus M. acridum displays two conidiation patterns: normal conidiation on 1/4 strength Sabouraud’s dextrose agar medium (1/4 SDAY), but microcycle conidiation on sucrose yeast extract (SYA) medium [[60]27]. In the present study, the effects of single nutrients on the conidiation pattern of M. acridum were investigated by the addition of 7.5 % sucrose (sucrose-rich (SR) medium), 0.75 % nitrate (nitrate-rich (NR) medium) or 0.25 % phosphate (phosphate-rich (PR) medium) to the microcycle conidiation medium (SYA). The results showed that normal conidiation occurred on 1/4 SDAY and the three nutrient-rich media, and conidiophores and normal conidiation occurred 21 h post-inoculation (hpi), while microcycle conidia were produced on SYA medium during this period. The transcripts of M. acridum derived from SYA medium, the three nutrient-rich media, and 1/4 SDAY medium were compared. The genes involved in the conidiation pattern shift and the genes involved in the regulation of the conidiation pattern shift in the three nutrient-rich media were identified. Then, the mechanisms of the conidiation pattern shift of M. acridum in response to different nutrients were explored. Results Conidiation pattern shift of M. acridum in response to different nutrients To investigate the effects of single nutrients on the conidiation pattern shift, M. acridum was grown on the microcycle conidiation medium (SYA), normal conidiation medium (1/4 SDAY), and SYA medium supplemented with sucrose, nitrate, or phosphate. On 1/4 SDAY, SR, NR, and PR media, conidiophores appeared without conidia at 21 hpi. Normal conidiation took place after 24 hpi, while microcycle conidia were produced on SYA medium during this period. The morphology of the normal and microcycle conidia differed significantly, with microcycle conidia having a more uniform size than normal conidia (Fig. [61]1). These results indicate that all the nutrients, including sucrose, nitrate, and phosphate, can influence the conidiation pattern shift and cause morphological changes in the conidia of M. acridum. Fig. 1. Fig. 1 [62]Open in a new tab Different conidiation patterns of M. acridum CQMa102 on different agar media following incubation at 28 °C. Plates were inverted and photographed (400×). Scale bar = 100 μm Characterization of a digital gene expression (DGE) database To elucidate the molecular mechanisms of the conidiation pattern shift that was regulated by single nutrients, mRNA derived from M. acridum cultured on SYA, SR, NR, PR, and 1/4 SDAY media was used to construct five digital gene expression (DGE) libraries. Approximately 6 million sequence tags, 2 million of which were distinct, were obtained for all five DGE libraries. For each library, more than 60 % of the tags were mapped to the transcription reference database of M. acridum [[63]28]. Major characteristics of the libraries are shown in Table [64]1. The copy number of a tag reflected the mRNA expression level in clean tags, and the distribution of clean tag expression could be used to evaluate the normality of all the data. The distribution of total tags and distinct tags suggests that a small number of mRNAs were highly abundant, but the majority of mRNAs were expressed at low levels, thus meeting the heterogeneity law of gene expression (Additional file [65]1). The results indicated that our sequencing data are credible and suitable for further analysis. Table 1. Major characteristics of all the DGE libraries Category Parameter Value for conidiation library 1/4SDAY SYA C-source rich N-source rich P-source rich Raw tag Total no. of tags 6,183,315 5,825,445 6,065,919 6,013,042 6,248,039 No. of distinct tags 281,640 270,988 261,287 310,019 284,707 Clean tag Total no. of tags 6,002,447 5,654,488 5,893,027 5,810,564 6,062,673 No. of distinct tags 114,124 111,004 102,142 118,874 113,434 Unambiguous tag-mapped genes No. of genes 6340 6520 5854 6448 6371 % of reference genes 62.85 64.63 58.03 63.92 63.15 [66]Open in a new tab Using a gene ontology (GO) analysis of the genes mapped in the reference database of the M. acridum genome, we constructed a particular GO hierarchy of (i) biological process, (ii) cellular component, and (iii) molecular function for each library ([67]http://wego.genomics.org.cn/cgi-bin/wego/index.pl) (Fig. [68]2). For molecular function, the most significant enrichment was observed among various binding genes (GO: 0005488) and catalytic activity genes (GO: 0003824). For biological process, the most significant enrichment was observed among cellular process (GO: 0009987) and metabolic process (0008152). For cellular component, about 71 % of the differentially expressed genes (DEGs) were found to be involved in “cell” structure; these included genes related to the plasma membrane and external encapsulating structures, such as the cell wall and cell envelope (Additional file [69]2). Fig. 2. Fig. 2 [70]Open in a new tab Histogram of GO classification of putative gene functions from the five libraries. The functions of identified genes cover three main categories: biological process, cellular component, and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in a main category. GO analysis showed that the distributions of gene functions for the five libraries are similar DEGs of M. acridum during normal and microcycle conidiation To elucidate the molecular mechanism of the conidiation pattern shift, genes whose expression was up-regulated genes during normal and microcycle conidiation were screened by constructing four subtractive libraries based on the five DGE libraries. A comparison of the four subtractive libraries revealed that the expression of 137 genes was up-regulated in the four normal conidiation media (Fig. [71]3a), and the expression of 436 genes was up-regulated in the microcycle conidiation medium (SYA) (Fig. [72]3b). Among the 137 genes whose expression was up-regulated during the normal conidiation stage, there were three transcription factors, seven absorption- and transportation-related genes, including one amino acid transporter, two major facilitator superfamily (MFS) transporters, two ATP-binding cassette (ABC) transporters, one sulfate transporter, and one oligopeptide transporter, six stress-related genes, including two cytochrome P450 genes, and four nutrient and energy metabolism-related genes, such as one glycolysis-related gene, one tricarboxylic acid (TCA)-cycle-related genes, and two phosphorylation-related genes (Additional file [73]3). A GO analysis showed that the genes are mainly involved in catalytic activity, transporter activity, and binding function processes (Additional file [74]2). These genes are mainly involved in amino acid metabolism, cell growth and death, energy metabolism, lipid metabolism, metabolism of terpenoids and polyketides, xenobiotics biodegradation and metabolism, biosynthesis of secondary metabolites, and carbohydrate metabolism pathways (Additional file [75]4). The results indicate that normal conidiation in M. acridum is a complex process that involves multiple genes and biological processes. Fig. 3. Fig. 3 [76]Open in a new tab Screening of differentially expressed genes involved in conidiation pattern shift. a The genes were up-regulated during the normal conidiation. The boundaries of each subtractive library are delimited by specific colors: 1/4SDAY vs. SYA subtractive library (black); SYA+Phosphate vs. SYA subtractive library (red); SYA+Nitrate vs. SYA subtractive library (green); SYA+Sucrose vs. SYA subtractive library (blue). b The genes were up-regulated during the microcycle conidiation. The boundaries of each subtractive library are delimited by specific colors: SYA vs. 1/4SDAY subtractive library (black); SYA vs. SYA+Phosphate subtractive library (red); SYA vs. SYA+Nitrate subtractive library (green); SYA vs. SYA+Sucrose subtractive library (blue) Among the 436 genes whose expression was up-regulated during microcycle conidiation, there were 16 transcription factors, including five zinc finger protein (ZFP) transcription factors, one basic leucine zipper domain (bZIP) family transcription factor, and one helix-loop-helix (HLH) transcription factors, five mitogen-activated protein (MAP) kinases, 15 absorption- and transportation-related genes, including three carbohydrate and water reabsorption genes, six RNA transport proteins, five stress-related genes, including two cytochrome P450 genes, two peroxidase genes, and one glutathione-disulfide reductase gene, and 13 nutrient and energy metabolism-related genes, including four glycolysis-related genes, three TCA-cycle-related genes, and six phosphorylation-related genes (Additional file [77]5). A GO analysis revealed that these genes are mainly involved in catalytic activity, transporter activity, and binding function processes (Additional file [78]1: Table S1). These genes are mainly involved in amino acid metabolism, microbial metabolism in diverse environments, carbohydrate metabolism, cell growth and death, energy metabolism, lipid metabolism, xenobiotics biodegradation and metabolism, metabolism of terpenoids and polyketides, nucleotide metabolism, replication and repair, signal transduction, translation, transcription, biosynthesis of secondary metabolites, glycan biosynthesis and metabolism, transport and catabolism, and metabolism of cofactors and vitamins pathways (Additional file [79]4). Many genes whose expression was up-regulated during microcycle conidiation encode proteins that function in cell division, cell proliferation, cell wall formation, and cytoskeletal rearrangement, including a tyrosine-protein phosphatase [[80]29], a transcriptional coactivator [[81]30], a zinc knuckle domain protein [[82]31], a serine-type carboxypeptidase [[83]32], sedoheptulose-1, 7-bisphosphatase [[84]33], a catalase [[85]34, [86]35], cytochrome P450 [[87]36], a mannan endo-1, 6-α-mannosidase-like protein [[88]37, [89]38], an actin-associated protein [[90]39], and a HLH transcription factor [[91]40], suggesting that these up-regulated genes play a role in microcycle conidiation. Interestingly, members of the normal conidiation FluG pathway, including snaD, GNAT, fluG, pkaA [[92]41], fadA [[93]42], and gasA [[94]43], were up-regulated during microcycle conidiation (Additional file [95]5). These results indicate that genes related to both normal and microcycle conidiation are mainly involved in amino acid metabolism, cell growth and death, energy metabolism, lipid metabolism, metabolism of terpenoids and polyketides, translation pathways, and other pathways (Additional file [96]4). These pathways participate in cell proliferation, cell development, cell cycle, and cytoskeletal rearrangement processes. The common pathways in the conidiation pattern shift indicate that normal and microcycle conidiation have similar developmental processes and can be regulated through some common pathways, eg, the FluG pathway. However, compared with normal conidiation, microcycle conidiation involved two more pathways, more genes in 10 pathways (Additional file [97]4), and higher gene expression in common pathways, such as the FluG pathway. These genes and pathways might be related to the shift between normal and microcycle conidiation. Genes involved in the conidiation pattern shift related to different nutrients Because the conidiation pattern of M. acridum could be regulated by single nutrients, including sucrose, nitrate, and phosphate, we constructed three subtractive libraries to screen for genes that are specifically expressed in the conidiation pattern shift in response to these nutrients. The three subtractive libraries were compared individually with the genes expressed in 1/4 SDAY medium and the other two nutrient-rich media libraries, which showed that 83, 216, and 168 genes were specifically expressed on SR, NR, and PR media, respectively, indicating that they are involved in the regulation of the conidiation pattern shift by these nutrients (Fig. [98]4). Among the 83 sucrose-regulated genes, the expression of 75 genes was up-regulated, and the expression of eight genes was down-regulated (Additional file [99]6). Among them, there were four transcription factors, five stress-related genes, including three cytochrome P450 genes, one lipoxygenase, and one phytanoyl-CoA dioxygenase, six metabolism-related genes, including three glycolysis-related genes, two binding proteins, and one protein tyrosine phosphatase, and two genes involved in the cell cycle process. A GO analysis found that most of the genes played roles in catalytic activity, oxidoreductase activity, hydrolase activity, and metal ion binding (Additional file [100]6). A pathway analysis found that these DEGs are mainly involved in amino acid metabolism, biosynthesis of secondary metabolites, lipid metabolism, xenobiotics biodegradation and metabolism, metabolism of cofactors and vitamins, and transcription pathways (Additional file [101]7). The results indicate that sucrose could facilitate cell growth and inhibit sporulation by changing metabolic pathways. Fig. 4. Fig. 4 [102]Open in a new tab Screening of differentially expressed genes involved in conidiation pattern shift when related to different special nutrients. a The differentially expressed genes invovled in conidiation pattern shift were regulated by sucrose. b The differentially expressed genes invovled in conidiation pattern shift were regulated by nitrate. c The differentially expressed genes invovled in conidiation pattern shift were regulated by phosphate. The non-simple Venn diagram shows unique and overlapping sets of transcripts between the libraries. The boundaries of each library are delimited by specific colors: 1/4 SDAY medium library (black); SYA+Phosphate medium library (red); SYA+Nitrate medium library (green); SYA+Sucrose medium library (blue) With respect to the nitrate-rich medium, 216 specifically expressed genes were screened in the target libraries. Of these, the expression of 203 genes was up-regulated, and the expression of 13 genes was down-regulated (Additional file [103]8). Among these, there were seven transcription factors, including four zinc finger transcription factors and one GATA-binding transcription factor, three stress-related genes, including two cytochrome P450 genes and one dioxygenase, 41 metabolism-related genes, including three binding proteins and one protein tyrosine phosphatase, and five genes involved in the cell cycle process. A pathway analysis found that these genes are mainly involved in amino acid metabolism, carbohydrate metabolism, cell growth and death, lipid metabolism, xenobiotics biodegradation and metabolism, nucleotide metabolism, transport and catabolism pathways, and microbial metabolism in diverse environments pathways (Additional file [104]7). A GO analysis found that most of the genes had roles in catalytic activity, protein kinase activity, transporter activity, transferase activity, hydrolase activity, and adenyl ribonucleotide binding. The results showed that at a high nitrate level, the expression of catalytic-, hydrolase-, transferase-, and ribonucleotide-binding-related genes was up-regulated. A reasonable explanation is that nitrogen affects cell morphology by controlling amino acid metabolism. For the phosphate-rich medium, 168 specifically expressed genes were filtered in the target libraries. Of these, the expression of 151 genes was up-regulated, and the expression of 17 genes was down-regulated (Additional file [105]9). Among these, there were five transcription factors, including three zinc finger transcription factors, seven stress-related genes, including two cytochrome P450 genes and three dioxygenases, 24 metabolism-related genes, including two TCA-cycle-related genes, one phosphorylation-related gene, five binding proteins, and three phosphatases, and two cell cycle genes. A pathway analysis found that the genes are mainly involved in amino acid metabolism, carbohydrate metabolism, cell growth and death, lipid metabolism, xenobiotics biodegradation and metabolism, transport and catabolism, and microbial metabolism in diverse environment pathways (Additional file [106]7). A GO analysis found that most of the genes are involved in catalytic activity, nucleic acid binding, protein kinase activity, transferase activity, adenyl ribonucleotide binding, ATPase activity, and peptidase activity. The results showed that phosphate might affect cell division, proliferation, and differentiation by controlling the formation of ATP and affecting the cytoskeleton. Carbon, nitrogen, and phosphorus are basic components of the cell. They are constituents of nucleic acids, sugar-phosphate backbones, and phospholipid bilayers, and they are required for cell division and membrane formation [[107]44]. However, the conidiation pattern shifts in response to these nutrients were controlled by different genes, some of which played roles in the same pathway. MAP kinase [[108]45], the origin recognition complex subunit [[109]46], and a serine/threonine protein kinase [[110]47] are located in the cell growth and death pathway, and they played roles in the conidiation pattern shift in response to sucrose, nitrate, and phosphate, respectively. The conidiation pattern shift in response to nutrients involved different pathways. Exo-beta-D-glucosaminidase is involved in the sucrose-induced conidiation pattern shift, and it has an effect on hyphal growth at low sugar concentrations [[111]48]. Acyltransferase is involved in the nitrate-induced conidiation pattern shift, and it participates in the composition of the membrane at high nitrogen concentrations [[112]49]. L-asparaginase is involved in the phosphate-induced conidiation pattern shift, and it has an effect on growth under certain phosphate concentrations [[113]50, [114]51]. These results indicate that carbon, nitrogen, and phosphorus influence the fungal conidiation pattern by perturbing the cell cycle, nutrient metabolism, and related pathways of M. acridum. DEGs involved in conidiation were confirmed by the gene expression profiling via multigene concatemers (MgC-GEP) method To confirm the reliability of the DEGs related to conidiation patterns and their shifts, the expression profiles of the 217 genes that were specific to microcycle conidiation were further analyzed by the MgC-GEP method [[115]52] using the mRNA of M. acridum grown on SYA and the four normal conidiation media. One hundred and eighty genes were found using primer pairs targeting the 217 genes, and the expression of 142 genes was confirmed to be up-regulated on SYA medium in comparison with the four normal conidiation media (Additional files [116]10 and [117]11). Of these 142 genes, 101 genes encode hypothetical proteins or proteins of unclear function, and only 41 genes encode proteins with putative functions. Of these 41 genes, 18 are related to cell growth, 10 are related to cell proliferation, three are related to the cell cycle, three are related to cell differentiation, two are related to cell wall synthesis, two are related to cell division, and seven have other functions (Table [118]2). These results indicate that the conidiation pattern shift in M. acridum mainly results from changes in cell growth and proliferation. Table 2. Functions of some microcycle conidiation-relate genes screened by Gene Expression profiling via Multigene Concatemers Functions Gene ID Name References