Correspondence: Cathrine Sumathi Manohar, B1-12, Biological Oceanography Division, Council of Scientific and Industrial Research – National Institute of Oceanography, Dona Paula, Goa 403 004, India. Tel.: 00 91 832-2450441; fax: 00 91 832-2450606; e-mail: firstname.lastname@example.org
Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large number of marine habitats such as deep-sea habitats, pelagic waters, coastal regions, hydrothermal vent ecosystem, anoxic habitats, and ice-cold regions. This is of interest to a variety of research disciplines like ecology, evolution, biogeochemistry, and biotechnology. In this review, we have summarized how molecular tools have helped to broaden our understanding of the fungal diversity in various marine habitats. Majority of the environmental phylotypes could be grouped as novel clades within Ascomycota, Basidiomycota, and Chytridiomycota or as basal fungal lineages. Deep-branching novel environmental clusters could be grouped within Ascomycota as the Pezizomycotina clone group, deep-sea fungal group-I, and soil clone group-I, within Basidiomycota as the hydrothermal and/or anaerobic fungal group, and within Chytridiomycota as Cryptomycota or the Rozella clade. However, a basal true marine environmental cluster is still to be identified as most of the clusters include representatives from terrestrial regions. The challenge for future research is to explore the true marine fungi using molecular techniques.
Molecular description of the microbial diversity from a number of natural habitats has revealed hitherto unknown microbial wealth (Nelson et al., 2010). The marine ecosystem is no exemption, and the diversity estimates using molecular tools have brought to light, rich microbial diversity (Treusch et al., 2010). Surveys have been carried out in the marine habitats to study the diversity and distribution of prokaryotic and micro-eukaryotic kingdoms (Richards & Bass, 2005; Epstein & López-García, 2007; López-García & Moreira, 2008; Jones & Pang, 2012). Molecular studies on micro-eukaryotic diversity have revealed that fungal sequences could be retrieved from a number of marine habitats. Several of these environmental fungal sequences are highly divergent from the well-described fungal taxa and have phylogenetic importance (López-García et al., 2007; Le Calvez et al., 2009; Jones et al., 2011). A few studies have exclusively studied the fungal diversity from marine habitats. They have also added to the list of environmental fungal sequences that are divergent from the known fungal taxa (Bass et al., 2007; Gao et al., 2008, 2010; Jebaraj et al., 2010; Singh et al., 2011, 2012a,b; Arfi et al., 2012; Thaler et al., 2012).
Understanding the fungal diversity in the marine ecosystem is important to study the fungal evolutionary history as early fungal divergence is known to have taken place in the marine realm (López-García & Moreira, 2008; Le Calvez et al., 2009). There are increasing evidences to show the active participation of fungi in the marine habitats and their involvement in the biogeochemical processes (Stoeck et al., 2007; Alexander et al., 2009; Stock et al., 2009; Edgcomb et al., 2011). Molecular diversity estimates have shown that fungi occupy an important ecological niche in the marine environment. But still the extent of fungal distribution in the marine habitats is debatable (Richards et al., 2012). Here, we have summarized the fungal diversity unraveled from the marine habitats, especially the unique fungal sequences and clusters identified from these regions. An evaluation of these studies will be of immense help for further explorations of the marine environment and aid future research to retrieve true marine fungal phylotypes and isolates.
Marine habitats can be broadly classified into coastal and deep-sea regions, and the molecular diversity of fungi has been reported from both these regions. However, studies from the coastal regions (Table 1) are very few in comparison with the studies from the deep-sea regions (Table 2). Each of these major marine habitats harbors a number of unique, self-contained niches such as the coral reef, the mangrove, and hydrothermal vent systems. Two of these niches, the hydrothermal vent and oxygen-depleted habitats have been studied extensively. The molecular diversity understood from both these biogeochemically active regions is listed individually (Tables 3 and 4).
Table 1. Phylogenetic affiliation of environmental fungal sequences from coastal regions
Coastal regions are characterized by eutrophication from terrestrial run-off and high primary production (Danovaro & Pusceddu, 2007). This leads to large availability of organic matter to consumers as detritus. Prokaryotic heterotrophs are known to play a huge role as primary degraders in the coastal waters, followed by eukaryotic heterotrophs (Strom, 2008). Although planktonic forms of fungi have been reported from coastal waters, only a few studies have been carried out on fungi as they are generally not known to be free-living. Diversity of fungi has been studied only from a few selected coastal locations along the coasts off Brazil (Cury et al., 2011), coral reef regions off Hawaii (Gao et al., 2008, 2010), and mangrove areas (Arfi et al., 2012). These molecular studies have retrieved fungal sequences belonging to Ascomycota, Basidiomycota, and Chytridiomycota and some of them grouped into novel environmental clusters (Table 1).
The coral reef ecosystem in the coastal waters of the tropical regions is a dynamic, self-sustained system with vast biodiversity, and fungi were largely considered to be pathogens in this system (Kim et al., 2006; Yarden et al., 2007; Vega Thurber et al., 2009). However, metagenomic analysis and the functional diversity of coral-associated microorganisms show that fungi are a dominant community and they are involved in the nitrogen cycling within the coral reef ecosystem (Wegley et al., 2007). The macroorganisms such as sponges, oysters, and sea anemones also are important members within the coral reef ecosystem. These organisms are micro-habitats for the microbial communities. Highly diverse environmental sequences have been identified from these regions (Gao et al., 2008, 2010; Singh et al., 2012b). Studies on the culturable fungal diversity and their biotechnological potential have shown that many novel fungi are associated with it. The secondary metabolites produced by them are also very varied and have wide applications (Zhou et al., 2011; Raghukumar & Ravindran, 2012). The mangrove ecosystems situated along some coastal marine environments are another important niche for identification of marine fungi, and many true obligate marine species have been isolated from these regions (Suetrong et al., 2009). A large number of true marine fungi were also described from mangrove regions, but their phylogenetic significance has not been understood clearly (Sarma & Hyde, 2001; Fryar et al., 2004; Jones et al., 2009). These barriers have been removed by the application of molecular techniques as the taxonomic affiliation of fungal cultures and environmental sequences are assigned based on the phylogenetic analysis of the marker gene sequence (Hyde et al., 2011). A recent study by Arfi et al. (2012) from the coastal mangrove regions using pyrosequencing approach has shown a rich fungal diversity, and Agaricomycetes are shown to be the dominant groups. This study is the first and only known report on the molecular diversity of mangrove regions. However, studies on the molecular diversity of fungi from the coastal regions are just a handful, and these regions need to be further explored.
Low temperatures, high hydrostatic pressure, absence of light, and very low biological diversity are the salient features of the deep-sea regions. Species counts in the deep-sea sediments are very low in comparison with coastal sediments, and majority of the culturable fungi isolated are common terrestrial forms (Damare et al., 2008; Singh et al., 2010). The majority of the fungi obtained from deep-sea habitats belonged to Ascomycota, Basidiomycota with a large representation of yeasts belonging to both the phyla (Bass et al., 2007; Lai et al., 2007). Molecular studies have revealed the presence of many deep-branching novel sequences belonging to the major fungal phyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (Table 2). There has been a large interest in the deep-sea habitats, because these regions are known to be the cradle of molecular evolution. Unexpectedly, large diverse types of micro-eukaryotes, novel marine alveolates, stramenopiles, heterokonts, and dinoflagellates were retrieved from the deep-sea regions (López-García et al., 2001, 2003, 2007; Edgcomb et al., 2002).
The molecular divergence of fungi is hypothesized to have taken place in the marine realm. And unique niches such as the thermal vents and the oxygen-depleted regions were studied specifically to understand the fungal evolution (Tables 3 and 4). These regions are the hub of taxonomic diversity and are of special importance for evolutionary studies, as they could harbor a large number of deep-branching ancient fungal phylotypes (Heckman et al., 2001). True to this hypothesis, novel fungal phylotypes were retrieved from this region using universal micro-eukaryotic primers (Edgcomb et al., 2002; López-García et al., 2003, 2007). A large number of novel fungal cultures were isolated, and unsuspected species richness was brought to light through studies using fungal-specific primers for metagenomic analysis (Le Calvez et al., 2009). Although rich knowledge of the fungal diversity from the vent region has been obtained using molecular tools, the information is rather incomplete. Novel fungal clades could be identified only within Ascomycota, Basidiomycota, and Chytridiomycota, and no representatives are reported from the basal fungal groups (Table 3). Diversity estimates using specific primer sets for each phylum with special focus on the basal groups can help us to further characterize the fungal distribution in this region.
Vast diversity of novel environmental phylotypes was also found through molecular investigations of marine oxygen-depleted environments (listed in Jebaraj et al., 2012) and a few oxygen-depleted freshwater environments (Dawson & Pace, 2002; Luo et al., 2005; Slapeta et al., 2005). Most of the studies focused on the molecular ecology using universal eukaryotic primers and revealed a large diversity of novel Ciliates, Cercomonads, Stramenopiles, Radiolarians, and Ophisthokonts from this region (Dawson & Pace, 2002; Stoeck & Epstein, 2003; Stoeck et al., 2003; Luo et al., 2005; Takishita et al., 2005; Behnke et al., 2006; Alexander et al., 2009). Fungal sequences have been a major component from these studies, and some of the sequences obtained were restricted to known and well-described taxa (Table 4). Wide distribution of fungi from anoxic habitats shows their adaptability to a variety of environmental conditions (Jebaraj et al., 2012). Representative phylotypes belonging to the major known environmental clusters and also novel environmental clusters were isolated from the vent regions and ODEs.
The number of novel phylotypes obtained from the deep-sea habitats is higher compared with the other marine habitats (Fig. 1). RNA-based libraries could also be used to recover novel sequences, and it was possible to show that these sequences were metabolically active and have a role in the deep-sea ecosystem (Edgcomb et al., 2011). This emphasizes the fact that fungi play an active ecological role in the deep-sea habitats. Development of probes and combination of genomic and culture-based techniques can help us to understand the significance of these clusters in marine habitats. This is of great interest to the mycologist as the early fungal divergence is known to have taken place in the marine realm, and molecular studies such as these could give us an insight into the fungal evolution.
Highly diverse and novel clusters of environmental fungal sequences identified from marine habitats
Environmental fungal sequences obtained from the marine habitats clustered within the major fungal phyla Ascomycota, Basidiomycota, and Chytridiomycota or grouped as basal fungal clades. A very few representation of fungal sequences belonging to Zygomycota were retrieved, and phyla such as Glomeromycota, Blastocladiomycota, and Neocallimastigomycota had no representation in any of the molecular studies. The taxonomic position of the fungal sequences that clustered close to known fungal taxa could be clearly identified. However, many of the environmental sequences clustered away from the known fungal taxa and grouped to form environmental clades. Analysis of these environmental sequences shows that a few distinct environmental clusters can be identified within Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (Fig. 1).
Environmental sequences retrieved from marine habitats grouped into three major environmental groups within Ascomycota (Fig. 1). A major cluster of sequences identified within Saccharomycotina is the deep-sea fungal group (DSF Group-I) with Candida sp. as its closest described taxa (Nagano et al., 2010; Thaler et al., 2012). This group was described by Nagano et al. (2010) with fungal sequences from the deep-sea regions off Japan based on ITS and LSU rRNA clone library analysis (Table 2). A similar cluster can also be delineated based on the phylogenetic analysis of SSU rRNA sequences obtained from other deep-sea regions (Bass et al., 2007; Nagahama et al., 2011) and oxygen-depleted environments (Takishita et al., 2007b). This was evident from the phylogenetic analysis of the environmental sequences from deep-sea regions, which included environmental phylotypes (CYSGM-19, KD10 BASS, S04H05) from these studies (Nagahama et al., 2011). Studies from the South China Sea and the Arabian Sea have also retrieved environmental sequences that cluster close to Candida sp. (Lai et al.,2007, Jebaraj et al., 2010). But these studies were not useful to determine their taxonomic affiliation to this cluster because representative environmental sequences belonging to this cluster were not included during phylogenetic analysis. Inclusion of representative sequences from major environmental clusters can be of great help for taxonomic characterization.
Another set of highly diverse fungal sequence clusters within Pezizomycotina as an environmental clone group (PCG). It branches close to well-known fungal cultures Penicillium sp., Eupenicillium sp., and Aspergillus sp. and clusters around single fungal phylotypes (DH148-5-EKD21, BOLA831, AT2-4) obtained from the pioneering molecular studies of the marine regions (López-García et al., 2001, 2003; Dawson & Pace, 2002).This PCG can be observed distinctly when representative environmental phylotypes [BOLA831, AT2-4, TAGIRI 22, UI1104B, UI12H09 from marine habitats such as the anoxic coastal sediments (Dawson & Pace, 2002)], anoxic fumaroles (Takishita et al., 2005), and hypersaline anoxic Mediterranean deep-sea basin (Alexander et al., 2009) were included during analysis (Takishita et al., 2005; Jebaraj et al., 2010), Penicillium sp. and Aspergillus sp. are ubiquitously distributed species that are capable of anaerobic denitrification (Takasaki et al., 2004; Jebaraj & Raghukumar, 2009). This cluster like the DSF Group-I can also be identified through the ITS and LSU rRNA sequence analysis (Gao et al., 2008; Nagano et al., 2010).
A third soil clone group (SCGI), clusters between Taphrinomycotina and Saccharomycotina as a monophyletic clade (Nagahama et al., 2011). It has representative fungal sequences from soils of terrestrial origin and is a well-supported clade within Ascomycota. It is placed in a high taxonomic order, and is almost equivalent to a subphylum (Porter et al., 2008). The phylotype S08fH11 is the first representative from marine habitats in the SCGI cluster and is distinctly diverse to the known SCGI terrestrial sequences. Targeted studies to specifically understand the occurrence of this novel cluster in marine habitats could give us new insights and widen our perception of the marine fungal diversity (Nagahama et al., 2011).
Novel environmental sequences grouped together into the hydrothermal and/or anaerobic fungal group (Hy-An Group) within Basidiomycota, Ustilaginomycotina (López-García et al., 2007). This cluster is so-called because it was first described during the survey at the marine, anoxic vent habitat; however, studies have added a number of environmental sequences belonging to this group from all the major marine habitats (Fig. 1). It has representative sequences obtained from all the molecular surveys from the deep-sea hydrothermal vent regions (Edgcomb et al., 2002, 2011; López-García et al., 2003, 2007; Le Calvez et al., 2009). Environmental sequences obtained from the coastal (Gao et al., 2008, 2010), deep-sea (Bass et al., 2007; Lai et al., 2007), oxygen-depleted environments (Dawson & Pace, 2002; Alexander et al., 2009; Jebaraj et al., 2010) also cluster within this group. Their distribution is rather ubiquitous from marine and is reported from fresh water (Euringer & Lueders, 2008; Lesaulnier et al., 2008) and terrestrial habitats (Moon-van der Staay et al., 2006). The first known representative to this group was obtained during the molecular survey of the Guaymas Basin vent region (Edgcomb et al., 2002). This phylotype (A1_E024) was not included during the phylogenetic analysis and was probably removed as it was highly divergent. But its availability at the public database and inclusion during later analyses made it possible to define its phylogenetic affiliation and define the Hy-An Group. Interestingly, Malassezia sp. is the closest known fungal taxa to this group, which is a well-known pathogenic fungus. Attempts to cultivate this fungus from marine habitats have not been very successful because of its special growth requirements (Nagahama et al., 2011). This is a big challenge for the culture-based fungal diversity studies, as the laboratory conditions may not be always conducive for isolation of fungal cultures. It also calls for immediate attention to improve our growth media and laboratory set-up as we aim to cultivate the uncultured from the marine habitats. Environmental sequences belonging to this cluster were also identified from RNA-based clone libraries constructed from hydrothermal vent regions (Edgcomb et al., 2011). It is highly probable that the fungi belonging to this cluster are having an important ecological role that is worth investigating.
Chytridiomycota and basal fungal lineages
The largest number of novel environmental sequences belonging to Kingdom Fungi is recovered within Chytridiomycota. A large clade of environmental sequences almost contributing to about more than half of the known chytrid population has been identified. This cluster, Cryptomycota, has the largest number of representatives from a vast range of ecosystems including the freshwater, marine, and agriculture systems (Jones et al., 2011). A combination of molecular techniques has helped in the characterization of the morphology and life cycle of this novel group of organisms that cluster close to the chytrid Rozella sp. This clade has been identified in a large number of marine environments and was identified as Rozella and LKM 11 cluster (Bass et al., 2007; Takishita et al., 2007a; Stock et al., 2009; Nagahama et al., 2011). This can be regarded as one of the most important contributions of molecular taxonomy to Kingdom Fungi. Such a basal clade from the marine habitats with ancient fungal forms could be very interesting and may hold the key for understanding the animal–fungal evolutionary history. Many other clusters could also be identified from marine habitats such as the basal clone group (BCGI). Phylotypes belonging to this clade have so far been isolated from the oxygen-depleted habitats, arctic regions, and deep-sea habitats (Bass et al., 2007; Takishita et al., 2007b; Tian et al., 2009; Nagahama et al., 2011). Other independent novel clusters also group within the Chytridiomycota, which are well supported and highly divergent from known forms (Le Calvez et al., 2009). Phyla Chytridiomycota and Zygomycota are polyphyletic, and a large number of environmental sequences within these phyla are only categorized as basal fungal lineages. Occurrences and study of Zygomycota from marine habitats have been scanty (Stoeck & Epstein, 2003; Stoeck et al., 2006; Jebaraj et al., 2010). The environmental phylotypes (M1_18C05, CCW24, CCW 35, and FAS_49) obtained within this group have to be characterized further through phylogenetic analysis. Additional environmental sequences from this cluster may be required to prove the taxonomic position of these clone groups.
Application of molecular tools has added a new dimension to fungal diversity by bringing to light the presence of novel environmental phylotypes from a variety of marine habitats. Majority of these fungal phylotypes were obtained as a subsection from the metagenomic analysis of the micro-eukaryotes (Tables 1-4). In many instances, the wide taxonomic diversity of these sequences has overshadowed the fungal sequences retrieved along with it. The studies of the micro-eukaryotes also used universal primer sets for a large number of samplings, and this has helped in the identification of a number of novel clades such as the uncultured marine alveolate group-I, group-II, and uncultured marine stramenopile clade repeatedly. However, there are a large number of primer sets available for studying fungal diversity (Pang & Mitchell, 2005). Molecular surveys across the oceanic systems using chosen universal fungal primer sets and sampling up to saturation could aid in the identification of novel marine clusters. Development of probes for the clades identified from the various studies can be of great importance in characterizing undescribed and uncultured marine fungi.
Phylogenetic analysis of the environmental sequences generated from molecular diversity surveys is crucial to understand their taxonomic assessment. The sequences that cluster close to known cultures and well-described taxa can be assigned their proper phylogenetic place with ease. However, appropriate selection of molecular data available from databases and careful construction of various models are essential to understand the phylogenetic relationship of environmental phylotypes that are divergent from known taxa. It has been a general practice to include representative sequences from all major groups of interest for analysis. Thus, the divergent sequences fit as novel clades within the major taxonomic ranks. Environmental phylotypes during analysis from other studies along with its taxonomic representatives has aided in the identification of major environmental clusters (López-García et al., 2007; Nagano et al., 2010; Nagahama et al., 2011; Thaler et al., 2012). But some phylotypes that belong to these environmental clusters could not be assigned their rightful place within these clades because representatives of these clusters were not included during analysis (Lai et al.,2007; Jebaraj et al., 2010). Increasing the availability of molecular data for each taxonomic group and diligent implementation of phylogenetic analysis are promising approaches to unravel the yet to be described marine fungal diversity.
The authors have no conflict of interest on this publication.