**1. Introduction**

302 The Dynamical Processes of Biodiversity – Case Studies of Evolution and Spatial Distribution

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*Trichoderma* species frequently are predominant over wide geographic regions in all climatic zones, where they are significant decomposers of woody and herbaceous materials. They are characterized by rapid growth, an ability to assimilate a diverse array of substrates, and by their production of an range of antimicrobials. Strains have been exploited for production of enzymes and antibiotics, bioremediation of xenobiotic substances, and as biological control agents against plant pathogenic fungi and nematodes. The main use of *Trichoderma* in global trade is derived from its high production of enzymes. *Trichoderma reesei* (teleomorph: *Hypocrea jecorina*) is the most widely employed cellulolytic organism in the world, although high levels of cellulase production are also seen in other species of this genus (Baig et al., 2003, Watanabe et al., 2006). Worldwide sales of enzymes had reached the figure of \$ 1.6 billion by the year 2000 (Demain 2000, cited by Karmakar and Ray, 2011), with an annual growth of 6.5 to 10% not including pharmaceutical enzymes (Stagehands, 2008). Of these, cellulases comprise approximately 20% of the enzymes marketed worldwide (Tramoy et al., 2009). Cellulases of microbial origin are used to process food and animal feed, biofuel production, baking, textiles, detergents, paper pulp, agriculture and research areas at all levels (Karmakar and Ray, 2011). Most cellulases are derived from *Trichoderma* (section Longibrachiatum in particular) and *Aspergillus* (Begum et al., 2009). *Trichoderma* is also an efficient degrader of heteropolysaccharides such as xylan, and xylanases and mannanases are of importance in the production of fine paper (Watanabe et al., 2006). In addition, some strains of *Trichoderma* are agents of bioremediation, capable of assimilating heavy metals (Akhtar et al., 2009; Guillermina et al., 2002) and of degrading cyanide (Ezzi and Lynch, 2005) and pesticides with high persistence in the environment (Cross, 1999, Tang et al., 2009). The genus *Trichoderma* includes strains altogether producing an extremely wide range of metabolites, including compounds with antifungal activities (phenolic compounds, 6-αpentyl-pyrone, viridofunginas, harzianopiridona), antibiotics (anthraquinone, harzianodiona, gliotoxin), plant growth regulators (ciclonerodiol, α-harzianopiridonapentyl-pyrone), antimicrobial peptides including more than 200 peptaibols, and even viridiol phytotoxic compounds with potential pharmaceutical uses as anti-tumor and immunomodulatory compounds (harzianodiona and gliotoxin). These and other metabolites that are unclassified inhibitors and anti-virus agents expand the prospects of industrial, pharmaceutical or other commercial uses of this organism (Sivasithanparam and Ghisalberti, 1998, Supothina et al., 2007, Vinal et al., 2006, Xiao-Yan et al., 2006).

Biodiversity of *Trichoderma* in Neotropics 305

species of *Trichoderma* are listed on the website of the International Commission on the Taxonomy of Fungi subcommision on *Trichoderma* and *Hypocrea* (www.isth.info, Druzhinina & Kopchinskiy 2008), and 193 named taxa are represented to date by sequences deposited in

In the past, species in *Trichoderma* were defined primarily by the application of the concept Morphological Species Recognition (MSR), sometimes in combination with other phenetic characters. However, morphological identifications are highly prone to error due to the lack of definitive morphological characteristics and variations in culture. Consequently, perhaps 50% or more of the *Trichoderma* isolates deposited in culture collections may be incorrectly named based on morphological identifications. Furthermore, *Trichoderma* strains evidently cannot consistently be crossed to apply the Biological Species Recognition (BSR) concept based on their reproductive behavior. Therefore, Genealogical Concordance Phylogenetic Species Recognition (GCPSR) (Taylor et al., 2000), based on the concordance of multiple gene phylogenies, is an attractive alternative to apply the Phylogenetic Species Concept

Complementary methodologies have been applied to differentiate and characterize *cryptic species* or *phylogenetic species* in a fungi, correlating morphological, biogeographic, biochemical, ecological and, most recently, phylogenetic traits (e.g. refs). Applying the PSC proposed by Taylor et al. (2000), Chaverri et al. (2003) examined the internal transcribed spacer regions of rDNA (ITS1 and ITS2), the large intron of the transcription elongation factor 1-α (*tef1α)*, and short fragments of the actin (*act*1) and calmodulin (*cal1*) exon sequences in *H. lixii/T. harzianum*, to determine seven phylogenetic lineages in *T. harzianum*. However, they declined to recognize the lineages as phylogenetic species since they could not be reliably distinguished morphologically. Similarly applying GCPSR, Samuels et al. (2006) found that the *T. koningii* species aggregate includes three well-separated main lineages defined by phenotypic characters, and further recognized twelve taxonomic species and one variety within the three lineages: (1) T. *koningii, T. ovalisporum* and the new taxa *T. caribbaeum* var. *caribbaeum, T. caribbaeum* var*. aequatoriale, T. dorotheae, T. dingleyae, T. intricatum, T. koningiopsis, T. petersenii and T. taiwanense*; (2) the new species *T. rogersonii* and *T. austrokoningii*, and (3) the new anamorph species *T. stilbohypoxyli*. Druzhinina et al (2010b) recently revisited the genetic diversity in *T. harzianum,* examining three unlinked gene loci for 93 strains isolated worldwide. Their data illustrated clearly the complex history of speciation in the *H. lixii*-*T. harzianum* species group, rejecting the anamorph/teleomorph combination in favour of separate species status for *H. lixii* and *T. harzianum*, with the phylogenetic position of most isolates not resolved and attributed to a diverse network of recombining strains lacking strict genetic borders. In a similar study employing multiple gene phylogenies and multiple methods of phenotype profiling, Druzhina et al. (2010a) demonstrated that isolates previously identified as *H. jecorina* comprised four phylogenetic species, including *H. jecorina*/*T. reesei sensu stricto* containing most of the teleomorph isolates and the wild-type strain of *T. reesei* (QM6a) that has subsequently been genetically modified and employed in biofuel production. Conversely, all of the strains isolated as anamorphs from soil were referred to *T. parareesei.* It becomes clear from these studies that

Genbank (www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=29859).

**2.1 Species concepts** 

(PSC) in recognizing species of *Trichoderma*.

**2.1.1 Cryptic species or phylogenetic species** 

Many species of *Trichoderma* are closely associated with plant roots and specific strains may form endophytic associations with their plant host (Bailey et al., 2006, Evans et al., 2003, Hoyos-Carvajal et al., 2009b; Manesh et al., 2006, Sette et al., 2006, Viterbo & Chet 2006, Yedidia et al., 2000). As endophytes they are particularly effective biological control agents of fungi in the rhizosphere, producing antimicrobials, activating plant defence mechanisms, and stimulating plant growth and vigour by solubilizing minerals and providing other nutrients and growth regulating compounds (Alfano et al., 2007; Altomare et al. 1999; Sharon et al., 2001; Vinale et al., 2006, Woo et al., 2006, Yedidia et al., 2000). The multiple roles of *Trichoderma* in biotrophic decomposition, parasitism and endophytic associations are of particular importance to the sustainability of agricultural and natural ecosystems (Harman et al. 2004). However, one of the great impediments to the study of *Trichoderma* has been the incorrect and confusing application of species names, making comparisons and generalizations from many published studies unreliable (Kopchinskiy et al., 2005). In addition, different isolates of *Trichoderma* species may exhibit as much variation in metabolic activity as observed among species, making careful study of their biodiversity essential to fully exploit the potential of these fungi.
