Fungal Biodiversity in Salt Marsh Ecosystems

This review brings together the research efforts on salt marsh fungi, including their geographical distribution and host association. A total of 486 taxa associated with different hosts in salt marsh ecosystems are listed in this review. The taxa belong to three phyla wherein Ascomycota dominates the taxa from salt marsh ecosystems accounting for 95.27% (463 taxa). The Basidiomycota and Mucoromycota constitute 19 taxa and four taxa, respectively. Dothideomycetes has the highest number of taxa, which comprises 47.12% (229 taxa), followed by Sordariomycetes with 167 taxa (34.36%). Pleosporales is the largest order with 178 taxa recorded. Twenty-seven genera under 11 families of halophytes were reviewed for its fungal associates. Juncus roemerianus has been extensively studied for its associates with 162 documented taxa followed by Phragmites australis (137 taxa) and Spartina alterniflora (79 taxa). The highest number of salt marsh fungi have been recorded from Atlantic Ocean countries wherein the USA had the highest number of species recorded (232 taxa) followed by the UK (101 taxa), the Netherlands (74 taxa), and Argentina (51 taxa). China had the highest number of salt marsh fungi in the Pacific Ocean with 165 taxa reported, while in the Indian Ocean, India reported the highest taxa (16 taxa). Many salt marsh areas remain unexplored, especially those habitats in the Indian and Pacific Oceans areas that are hotspots of biodiversity and novel fungal taxa based on the exploration of various habitats.


Introduction
Salt marsh ecosystems are known for their high productivity, exceeding primary production estimates of species rich ecosystems (e.g., tropical rainforests, coral reefs) [1]. The flora in salt marsh ecosystems is mainly composed of grasses, herbs, and shrubs and these are terrestrial organisms variously adapted to, or tolerant of, a semi-marine environment. Halophytes are a diverse group of plants that have a worldwide distribution, and grow in different climatic regions, wherein soils have high salinity levels [2]. Halophytes are common in temperate and Mediterranean climates, and fewer both in the tropics and at high latitudes [3][4][5][6]. The vegetation in these ecosystems shows the vertical zonation of different communities as tidal submergence decreases with increasing elevation, and species tolerance to changing gradient conditions. Salt marsh vegetation generally increases the attenuation of both tidal currents and waves as they pass over the vegetated area and immobilize elements with their sediments. Furthermore, halophytes serve as a natural buffer, protecting other shoreline ecosystems from human impacts and disturbances. The    Major studies on halophytes focus on ecology and conservation [12][13][14]. One of these is the decomposition of vascular plant material wherein the detritus breakdown was reviewed in Pomeroy and Wiegert [15], Howarth and Hobbie [16], and Long and Mason [17]. The active decomposition processes in salt marsh ecosystems reflects to the relatively high rates of primary production. Three phases of plant decomposition were noted by Valiela et al. [18]. The early phase involves the leaching of soluble compounds, resulting in a fast rate of weight loss lasting for less than a month. Organic matter breakdown by microorganisms and continuous leaching of decayed products occurs in the second phase that lasts for a year. The last phase lasts for another year when there is a slow decay of refractory materials such as humates and fulvates [19].
The continuous breakdown of detritus into smaller fragments increases the surface-tovolume ratio and this is exposed to further microbial degradation. Bacteria and fungi are key decomposers in the salt marsh ecosystem that are essential for the transformation and recycling of nutrients through the environment. The colonization of fungi on standing dead halophytes commences during the early stages of decomposition before leaf fall to the salt marsh sediment surface [20,21]. The decomposition of the senescent tissues of halophytes by salt marsh fungi is brought about by the direct penetration of the host cell wall and the production of enzymes active in degrading lignocellulosic compounds, such as lignin, cellulose, and hemicellulose [22][23][24][25][26]. Bacterial communities are the major decomposers in the latter stage of decomposition [27,28]. Studies in salt marsh ecosystems not only consider microbial activity and the recycling of nutrients, but also bacterial [29,30] and fungal diversity [20,31,32].
The present review compiles the published data of fungi from halophytes, including their geographical distribution and host association. When compared to other fungal groups, salt marsh fungi are underexplored, and this review brings together the research efforts on these undiscovered habitats and plants. The pertinent literature from bibliographic databases (e.g., Scopus, Web of Science, Google Scholar) and published resources on salt marsh fungi documenting halophytes were compiled. Published works, wherein the documented fungal taxa were observed directly from halophytic substrates, are included ( Table  1). The different host parts, living and dead, that are either partly or wholly submerged are documented, as well as drift plant portions washed up in salt marsh areas. Salt marsh fungi isolated using cultivation-dependent techniques were not included since it is not known if these fungi were actively growing and reproducing on the halophytes. The taxa were listed based on the recent outline of fungi and fungus-like taxa by Wijayawardene et al. [33]. Since previous works only listed the taxa and the hosts [34][35][36], here we include the plant parts where the fungus was observed, the location (country: state/province) where the host was collected, the life mode of the fungus, and the pertinent literature citations are included ( Table 1). The accepted name of the host was based on the webpage of the World Flora Online consortium (http://www.worldfloraonline.org/; accessed on 10 May 2021), GrassBase (https://www.kew.org/data/grasses-db/sppindex.htm; accessed on 10 May 2021) and CRC World Dictionary of Grasses by Quattrocchi [37]. The graphs presented in the next sections summarizes the information from Table 1 and was developed using data visualization tools (Excel Office 365, Tableau Desktop Professional Edition 19.2.2). --Spartina townsedii UK [38] Mycosphaerella lineolata (Roberge ex Desm.) J. Schröt.

Poaceae
The association of fungi with grasses have been documented and most of the host plants are members of Poaceae. Ten genera of salt marsh grasses under Poaceae are included in this review wherein Spartina is the most studied of halophytic hosts for direct observation of marine fungi. In addition to Spartina, salt marsh grasses such as Phragmites and Distichlis were well studied also for their fungal associates.
Salt marsh fungi are not well-documented from grasses such as Spartina anglica, S. pectinata, Spergularia marina, Uniola paniculata, Elymus farctus, × Ammocalamagrostis baltica, and Agropyron sp. with one taxon recorded for each host [35]. Furthermore, there are few studies on the fungal composition of Arundo donax (4 taxa) [35] and Ammophila arenaria (four taxa). Marram grass (Ammophila arenaria) is more common in sand dunes and supports quite a diverse fungal community [157,158], while arbuscular mycorrhizal fungi (AMF) play a key role in the establishment, growth, and survival of plants [159].

Poaceae
The association of fungi with grasses have been documented and most of the host plants are members of Poaceae. Ten genera of salt marsh grasses under Poaceae are included in this review wherein Spartina is the most studied of halophytic hosts for direct observation of marine fungi. In addition to Spartina, salt marsh grasses such as Phragmites and Distichlis were well studied also for their fungal associates.
Salt marsh fungi are not well-documented from grasses such as Spartina anglica, S. pectinata, Spergularia marina, Uniola paniculata, Elymus farctus, × Ammocalamagrostis baltica, and Agropyron sp. with one taxon recorded for each host [35]. Furthermore, there are few studies on the fungal composition of Arundo donax (4 taxa) [35] and Ammophila arenaria (four taxa). Marram grass (Ammophila arenaria) is more common in sand dunes and supports quite a diverse fungal community [157,158], while arbuscular mycorrhizal fungi (AMF) play a key role in the establishment, growth, and survival of plants [159].

Distichlis spicata
Ascomycota dominates the taxa associated with Distichlis spicata (93.55%) wherein 16 and 13 species are members of Dothideomycetes and Sordariomycetes, respectively. Pleosporalean taxa constitute the majority of fungi associated with D. spicata (14 species), followed by Hypocreales with nine species recorded. Puccinia distichlidis and Tranzscheliella distichlidis represent the Basidiomycota. A total of 26 genera were recorded as associates of D. spicata and were mostly observed on senescent and decaying leaves.
ates of D. spicata and were mostly observed on senescent and decaying leaves.

Spartina
A total of 149 taxa (141 Ascomycota, 6 Basidiomycota, 2 Mucoromycota) were recorded in Spartina. The majority of the taxa belong to Dothideomycetes (70 taxa), followed by Sordariomycetes (59 taxa). Pleosporaceae and Halosphaeriaceae dominate the fungi documented in Spartina with 19 and 17 taxa recorded, respectively. Spartina alterniflora, S. maritima, and Spartina × townsendii harbor 79, 46, and 49 taxa, respectively ( Figure 11, Table 1). A total of 78 taxa were recorded in the unidentified Spartina species. The identification of the Spartina species can be challenging, wherein species are morphologically similar.
1 Figure 11. The distribution of fungal taxa associated with Spartina.

Geographical Distribution of Salt Marsh Fungi
The salt marsh fungi reported are from countries of three major oceans, as documented in Figure 14. The Atlantic Ocean consists of 12 countries, wherein the USA had the highest number of species recorded (232 taxa) followed by the UK (101 taxa), the Netherlands (74 taxa), and Argentina (51 taxa). China had the highest number of salt marsh fungi in the Pacific Ocean with 165 taxa reported, while in the Indian Ocean, India reported the highest taxa (16 taxa). Most of the biodiversity studies documenting salt marsh fungi in the Atlantic Ocean are mostly from the USA and the UK and this reflects the high number of taxa [32,36,38,49,61]. China ranked second with the most number of salt marsh fungal taxa, mainly due to the biodiversity study in Phragmites australis conducted by Poon et al. [41]. atus). Alva et al. [160] report Penicillium chrysogenum as an endophyte from Zostera japonica.

Geographical Distribution of Salt Marsh Fungi
The salt marsh fungi reported are from countries of three major oceans, as documented in Figure 14. The Atlantic Ocean consists of 12 countries, wherein the USA had the highest number of species recorded (232 taxa) followed by the UK (101 taxa), the Netherlands (74 taxa), and Argentina (51 taxa). China had the highest number of salt marsh fungi in the Pacific Ocean with 165 taxa reported, while in the Indian Ocean, India reported the highest taxa (16 taxa). Most of the biodiversity studies documenting salt marsh fungi in the Atlantic Ocean are mostly from the USA and the UK and this reflects the high number of taxa [32,36,38,49,61]. China ranked second with the most number of salt marsh fungal taxa, mainly due to the biodiversity study in Phragmites australis conducted by Poon et al. [41]. The geographical distribution of salt marsh fungi and the different halophytes are presented in Figure 15. The fungi associated with salt marsh grass Phragmites australis have been studied in different countries (Australia, Belgium, Egypt, France, Germany, China, Iraq, Japan, the Netherlands, South Australia, Thailand). Spartina alterniflora was recorded in countries along the Atlantic (Argentina, Canada, France, USA) and the Indian Ocean (India), but lacks data from countries in the Pacific Ocean. The geographical distribution of salt marsh fungi and the different halophytes are presented in Figure 15. The fungi associated with salt marsh grass Phragmites australis have been studied in different countries (Australia, Belgium, Egypt, France, Germany, China, Iraq, Japan, the Netherlands, South Australia, Thailand). Spartina alterniflora was recorded in countries along the Atlantic (Argentina, Canada, France, USA) and the Indian Ocean (India), but lacks data from countries in the Pacific Ocean.
1 Figure 15. Map of countries showing the global distribution of fungal diversity studies in halophytes. The different color of each pie chart represents the hosts, and the angle measured the number of their fungal associates.

United States of America
Most of the studies of halophytes-associated fungi were concentrated on the United States of America (USA) (Figure 16). Table 1

United States of America
Most of the studies of halophytes-associated fungi were concentrated on the United States of America (USA) (Figure 16). Table 1

Conclusions and Future Perspectives
Most studies of fungi on salt marsh plants are from Spartina, Juncus, and Phragmites, probably due to the huge biomass generated by these taxa. The mycota of less bulky halophytes (e.g., Limonium, Triglochin, Uniola) and litter from the surrounding sea grass

Conclusions and Future Perspectives
Most studies of fungi on salt marsh plants are from Spartina, Juncus, and Phragmites, probably due to the huge biomass generated by these taxa. The mycota of less bulky halophytes (e.g., Limonium, Triglochin, Uniola) and litter from the surrounding sea grass beds washed off to marsh areas (e.g., Zostera japonica, Z. marina, Z. noltii) are also less represented, or these hosts are yet to be explored. The checklist presented in the current study updates the list of Calado and Barata [34] and the inclusion of fungi associated with rarely studied halophytes record 486 taxa worldwide. Ascomycota dominate the taxa (463 taxa) and are comprised mostly of Dothideomycetes with their ability to eject their ascospores forcibly and widely, spore type, the formation of ascomata or ascostromata under a clypeus or just immersed in thin leaves, and an ability to decompose lignocellulose substrates [57,161]. Meyers et al. [162] showed that salt marsh yeasts and the ascomycete, Buergenerula spartinae, produce degradative enzymes and utilize simple carbon and nitrogen compounds. The yeast, Pichia spartinae, produces β-glucosidase and other degradative enzymes. Gessner [74] demonstrated that a number of salt marsh fungi isolated from Spartina alterniflora, Zostera sp., and Z. marina produced enzymes capable of degrading cellulose, cellobiose, lipids, pectin, starch, tannic acid, and xylan and, thus, play a key role in the degradation of storage and structural compounds. Salt marsh fungi might possess high biotransformation and metabolic abilities, which could be related to their ecology.
Basidiomycota (19 taxa) and Mucoromycota (4 taxa) are poorly represented in salt marsh ecosystems as they are in other marine habitats [163]. There are no records of Chytridiomycota listed in the present work and only a few authors detected this group, and other basal fungal lineages, in salt marsh ecosystems using molecular analysis [164][165][166][167]. These groups are worth exploring to determine the overall fungal communities in the salt marsh ecosystems. Many chytrids and other basal fungi are more challenging to cultivate and require different isolation methods (e.g., baiting techniques in liquid culture) than the saprobes, methods that have rarely been applied in the study of saltmarsh plants. When appropriate techniques are used, chytrids and other zoosporic organisms have been reported. For example, the fungal-like organism Phytophthora inundata has been recovered from the halophilic plants Aster tripolium and Salicornia europaea, while P. gemini and P. chesapeakensis occur on Zostera marina, and Salisapilia nakagirii on the decaying litter of Spartina alterniflora (www.marinefungi.org; accessed on 10 May 2021, [163]). Marine chytrids have been isolated from substrates such as seaweeds and mangrove leaves [163].
The taxa listed are mostly saprobes and these can be attributed to the inclusion of salt marsh fungi observed directly from the different host parts, which are mostly submerged decaying substrates. When compared to saprobic fungi in halophytes, few studies have been carried out on the diversity of endophytes and pathogens and their interaction in the salt marsh ecosystems. Surveys on endophytic fungi from halophytes using cultivation-dependent methods coupled with molecular approaches, showed that endophytes were dominated by Ascomycota and a few belonged to Basidiomycota and Zygomycota [168][169][170][171][172][173][174][175]. Pathogenic fungi from salt marsh ecosystems are poorly documented but play a significant role in the dynamics of the ecosystem [176][177][178]. For example, Govers et al. [179] reported that the fungal-like organisms Phytophthora gemini and P. inundata caused widespread infection of the common seagrass species, Zostera marina (eelgrass), across the northern Atlantic and Mediterranean that threatened the conservation and restoration of vegetated marine coastal systems. Likewise, Claviceps purpurea affects the viability of Spartina townsedii in south coast UK salt marshes. Fisher et al. [180] noted that Cl. purpea in the Alabama and Mississippi coastlines rendered the seeds of one of the primary salt marsh grasses sterile. Raybold et al. [181] recorded epidemics of C. purpurea on Spartina anglica in Poole Harbor (UK) and that ergot growth was detrimental to seed production. These underexplored fungal groups are worthy to be explored for their ecological and biotechnological importance.
This shows how salt marsh fungal studies were concentrated in countries in the Atlantic Ocean specifically the USA (232 taxa) and the UK (101 taxa). Many salt marsh areas remain unexplored, especially those in the Indian and Pacific Oceans, and these areas are hotspots of biodiversity and novel fungal taxa based on the exploration of various habitats [85,100,163,[182][183][184][185][186][187]. Recently, novel species were isolated in halophytes [85,100,145] and further taxa remain to be discovered, isolated, and sequenced, while vast areas worldwide have yet to be surveyed. For example, salt marsh plants are immensely numerous, diverse, and common along the south-east coast of Australia, yet little is known of their fungal associates [188].
The salt marsh vegetation and its fungal associates are adapted to salt stress and inundation and are subjected to extreme environmental conditions such as being periodically wet to different lengths of time leading to drying out at low tides and exposure to high temperatures and drying out at midday. Many are well adapted to prevailing conditions by their fleshy leaves (Suaeda australis), others can tolerate high flooding.
Few data are currently available on the specificity of fungi on their salt marsh hosts. Figure 17 shows the number of fungal taxa recorded from the three commonly studied hosts, Juncus, Phragmites, and Spartina, wherein there is little overlap in the species composition. One of the common species on Spartina plants is undoubtedly Halobyssothecium obiones, while Leptosphaeria pelagica is common. A common ascomycete on Atriplex portulacoides and Suaeda maritima is Decorospora gaudefroyi. Host plants that have been little surveyed for fungi are Limonium vulgare (sea lavender) and Atriplex portulacoides (sea purslane), yet they do support a number of taxa, e.g., Neocamarosporium obiones and Amarenomyces ammophilae. The fungal community reported on Juncus roemerianus in the salt marsh at North Carolina is significantly different from those on Spartina and Phragmites. It remains to be seen if this is due to the host plant or its geographical location. vast areas worldwide have yet to be surveyed. For example, salt marsh plants are immensely numerous, diverse, and common along the south-east coast of Australia, yet little is known of their fungal associates [188]. The salt marsh vegetation and its fungal associates are adapted to salt stress and inundation and are subjected to extreme environmental conditions such as being periodically wet to different lengths of time leading to drying out at low tides and exposure to high temperatures and drying out at midday. Many are well adapted to prevailing conditions by their fleshy leaves (Suaeda australis), others can tolerate high flooding.
Few data are currently available on the specificity of fungi on their salt marsh hosts. Figure 17 shows the number of fungal taxa recorded from the three commonly studied hosts, Juncus, Phragmites, and Spartina, wherein there is little overlap in the species composition. One of the common species on Spartina plants is undoubtedly Halobyssothecium obiones, while Leptosphaeria pelagica is common. A common ascomycete on Atriplex portulacoides and Suaeda maritima is Decorospora gaudefroyi. Host plants that have been little surveyed for fungi are Limonium vulgare (sea lavender) and Atriplex portulacoides (sea purslane), yet they do support a number of taxa, e.g., Neocamarosporium obiones and Amarenomyces ammophilae. The fungal community reported on Juncus roemerianus in the salt marsh at North Carolina is significantly different from those on Spartina and Phragmites. It remains to be seen if this is due to the host plant or its geographical location. Another groups of fungi that have not been fully studied in the salt marsh habitat are yeasts, as these also require specific techniques for their isolation from the water column or from plant tissue. Spencer et al. [189] recovered a number of yeasts from the vicinity of Spartina townsendii, as follows: very numerous Cryptococcus spp.; Trichosporon cutaneum; Trichosporon pullulans; the relatively rare species, Metschnikowia bicuspidata and Cryptococcus flavus; and Saturnospora ahearnii [190]. Although marine yeasts are common in sea water and deep seawater vents [163], their large-scale sampling in salt marshes remains a challenge for the future.
Currently, the salt marsh ecosystem has been threatened both by global warming and human activity. Sea-level rises brought about by climate change alter the location and character of the land-sea interface wherein salt marsh vegetation moves upward and inland. The increase in the sea level may not lead to the loss of coastal marshes, but the resiliency will depend on the ability of halophytes to migrate upland. Susceptible areas are organogenic marshes and areas where sediment is limited, potentially leading to catastrophic shifts and marsh loss. In this paper, a total of 57 plant taxa under 27 genera were reviewed for their fungal associates. The halophytes included here are only ap- Another groups of fungi that have not been fully studied in the salt marsh habitat are yeasts, as these also require specific techniques for their isolation from the water column or from plant tissue. Spencer et al. [189] recovered a number of yeasts from the vicinity of Spartina townsendii, as follows: very numerous Cryptococcus spp.; Trichosporon cutaneum; Trichosporon pullulans; the relatively rare species, Metschnikowia bicuspidata and Cryptococcus flavus; and Saturnospora ahearnii [190]. Although marine yeasts are common in sea water and deep seawater vents [163], their large-scale sampling in salt marshes remains a challenge for the future.
Currently, the salt marsh ecosystem has been threatened both by global warming and human activity. Sea-level rises brought about by climate change alter the location and character of the land-sea interface wherein salt marsh vegetation moves upward and inland. The increase in the sea level may not lead to the loss of coastal marshes, but the resiliency will depend on the ability of halophytes to migrate upland. Susceptible areas are organogenic marshes and areas where sediment is limited, potentially leading to catastrophic shifts and marsh loss. In this paper, a total of 57 plant taxa under 27 genera were reviewed for their fungal associates. The halophytes included here are only approximately 11% of the total number of species of salt marsh plants worldwide. Thus, many salt marsh fungi await discovery with wider host plant sampling and the use of a wider range techniques for their isolation. For this reason, it is imperative to study the halophytic fungi to document not just biodiversity but also to discover novel taxa restricted only to this kind of habitat.