Introduction
Decomposition of organic matter is vitally important in ecosystem processes such as carbon and nitrogen cycling, soil formation and biodiversity maintenance (García‐Palacios, McKie, Handa, Frainer, & Hättenschwiler, 2016; Giweta, 2020). In nature, decomposition is highly dynamic with ever-changing interactions among decomposers and between substrate composition and successive development of microbial communities (Baldrian et al., 2016; Katagiri et al., 2019). Fungi are key components of the microbial communities in most natural decompositions with different fungal species and strains interacting with each other in multiple ways, leading to complete degradation of complex organic compounds such as lignocelluloses in wood and plant litter. Indeed, there is emerging evideince showing orderly succession among fungal members of microbial communities through the different stages of lignocellulose decomposition (Eichlerová et al., 2015).
As one of the most important members of microbial communities in forest ecosystems, saprophytic fungi (SPF) have diverse degradation mechanisms and play key roles in the degradations of dead organic matters (Baldrian et al., 2016; Rajala, Peltoniemi, Hantula, Mäkipää, & Pennanen, 2011). However, due to the limited resources across space and time in most ecological niches and the presence of many (potential) competitors, fungal decomposers have evolved mechanisms to allow them successfully colonizing one to several substrates/ecological niches (Boddy, 2000). Those colonizing only one type of ecological niche are called ecological “specialists” while others capable of colonizing many types of ecological niches are called “generalists” (Moor, Nordén, Penttil, Siitonen, & Snll, 2020). There are many who are in-between the obligate specialists and broad generalists, including those that are primarily found in one ecological niche but are capable of surviving and growing in other niches (Moor et al., 2020). Evidence for ecological specializations in fungi has been recorded since ancient times (Baldrian et al., 2016). In addition, most ecological niches and substrates have successions where different fungal communities may dominate different phases of substrate decomposition (Eichlerová et al., 2015).
There are many factors that can impact the composition and structure of saprophytic fungal community. Among these factors, the chemical composition of substrates plays a major role (Krah et al., 2018; Rajala, Peltoniemi, Pennanen, & Mäkipää, 2010). For example, on woody substrates, the decomposition rate of polymeric lignocellulosic components changes through the decomposition process, due to changes in substrate compositions and in the types and relative abundances of different microbes and their enzymes involved in degradations (Šnajdr et al., 2011). Traditionally, saprophytic fungi are broadly classified into two types, namely ligninolytic white-rot (WR) and cellulolytic brown-rot (BR), although there is a continuum between these two types (Boddy, 2000; Riley et al., 2014). In the process of decomposition, interaction (including competition) among fungi is likely very common, affecting the distribution, abundance, and the order of occurrence among these fungi in natural communities (Edman & Eriksson, 2016).
Different interaction strategies among species can lead to different orders of SPF emergence on substrates. Both biotic and abiotic factors can also influence their order of emergence and interactions (Boddy, 2000; Edman & Fällström, 2013; Fukami et al., 2010). Fungal competition on substrates is commonly classified into two major functional types: primary resource capture and secondary resource capture (Boddy, 2000; Sasha & Bhatnagar, 2019; Song, Vail, Sadowsky, & Schilling, 2012). Success of SPF in primary resource capture mainly depends on the ability to utilize previously uncolonized resources and on their ability to resist antifungal compounds in those substrates. In contrast, success in secondary resource capture mainly relies on antagonistic mechanisms, with different species competing with each other to obtain sufficient nurients for survival and reproduction (Boddy, 2000). Often, changes in microbial communities during decomposition are related to the secretion of antagonistic enzymes and metabolites (Boddy, 2000). On the one hand, SPFs have the ability to secrete various carbohydrate-active enzymes (CAZymes) to decompose and utilise the major constituents such as lignin, cellulose, and hemicellulose in wood and plant litter, facilitating nutrient cycling and energy flow in forest ecosystem (Cantarel et al., 2009; Kohler et al., 2015; Zhao, Liu, Wang, & Xu, 2013). Indeed, the compositions and characteristics of CAZymes often differ among fungi, likely shaped by characteristics of their substrates and the degree of adaptation to the specific environmental conditions (Zhao et al., 2013). Therefore, to understand decomposition, it is particularly important to study the compositions and characteristics of CAZymes to clarify the potential mechanisms for different nutritional modes, infection, and substrates specificity/preference (de Wit et al., 2012; Martin, Kohler, Murat, Veneault-Fourrey, & Hibbett, 2016; Nagy et al., 2016; Park, Jeong, & Kong, 2018; Zhao et al., 2013; Zhao et al., 2019). On the other hand, fungal secondary metabolites (SMs) are known to play crucial roles in defence against pathogens and competitors and provide advantages for their producers and/or those who have resistant mechanisms. Along with CAZymes, fungal SMs can provide important information for understanding the chemical basis of niche specialization during decompositions (Arfi, Levasseur, & Record, 2013; Saha & Roy-Barman, 2018).
Multiple groups of SPFs are frequently involved in plant litter decomposition. These fungi belong to diverse clades, but some of them are functionally interchangeable (Arfi et al., 2013; Niemela, Renvall, & Pentilla, 1995; Zhang & Wei, 2016; Figure S1). In forest ecosystems, due to its extractive composition and the presence of antifungal compounds such as resin, pinecone is a specialized substrate and a unique habitat for fungi (https://mycocosm.jgi.doe.gov/Aurvu1/Aurvu1.home.html). Indeed, only species in a few fungal genera (e.g., Strobilurus ,Auriscalpium , Baeospora and Mycena ) are known to colonize and decompose pinecones. Among these genera,Auriscalpium and Strobilurus are highly specialized on pinecones (Qin, Horak, Popa, Rexer, & Yang, 2018; Wang & Yang, 2019). Interestingly, species of Auriscalpium and Strobilurususually share the dead cones of the same plant species in a chronological order, with Auriscalpium fungi often appearing on newly fallen cones, while those of Strobilurus typically occurring on highly rotten cones during later stages of decomposition. At present, the mechanisms for their succession during pinecone decomposition are unknown.
In this study, we investigated three pinecone substrate-fungus pairs from Europe and East Asia to understand the potential mechanisms for substrate specificities and ecological succession during pinecone decomposition. The three fungal pairs as well as their substrates wereA . orientale -S . luchuensis on cones ofPinus yunnanensis , A . vulgare -S .stephanocystis on cones of P . sylvestris , andA . microsporum -S .pachcystidiatus /S .orientalis on cones of P . armandii . We obtained the genome sequences of these seven fungal species and quantified the main chemical compounds during pinecone decomposition. Our analyses revealed both shared and unique features in their substrate specificity and ecological successions among these fungal pairs.