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Fungi in Deep-Sea Environments and Metagenomics

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Abstract

This chapter discusses the fact that fungi are living in the oceans and form diverse communities. The constant increase of molecular data using clone libraries or high-throughput sequencing is permitting a revision of the definition of marine fungi. Molecular approaches are cogent methods to describe fungal diversity in deep-sea ecosystems. The continual recovery of novel operational taxonomic units (OTUs) using different kinds of samples and different primer pairs reinforce the hypothesis that marine fungal diversity is higher than previously thought. Many factors govern biodiversity in the oceans. High-pressure is mainly used by microbial ecologists to understand the ecological role of marine microorganisms. It is also used by food technologists to inactivate microorganisms and by biotechnologists to enhance the productivity of bioprocesses. The deep subsurface biosphere and hydrothermal ecosystems represent large biomes on Earth characterized by a set of extreme conditions.

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... Therefore, the need for redefining marine fungi has been recently realized and emphasized. The development of a functionalscale classification by combining the existing definition of marine fungi with a threelevel active and passive roles-based re-grouping was among the first to be suggested [6]. Thereafter, marine fungi have been defined either as those recovered repeatedly from marine habitats [7] or individuals with a long-term presence and metabolic activities in a marine habitat [8]. ...
... Particularly, studies based on metagenomics and metatranscriptomics provided evidence for the fungi-associated metabolic processes in the marine and water columns. Metagenomic studies discovered genes involved in amino acid metabolism, the aerobic carboxylation of glucose, anaerobic decarboxylation of pyruvate, urea, sulfur metabolism, etc. [6,22]. Fungal genes involved in complex C and fatty acid metabolism have been found across all depths and regions, and it is suggested that fungi might replace phytoplankton for vitamin supplies in deep waters [22]. ...
Article
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Fungi are considered terrestrial and oceans are a “fungal desert”. However, with the considerable progress made over past decades, fungi have emerged as morphologically, phylogenetically, and functionally diverse components of the marine water column. Although their communities are influenced by a plethora of environmental factors, the most influential include salinity, temperature, nutrients, and dissolved oxygen, suggesting that fungi respond to local environmental gradients. The biomass carbon of planktonic fungi exhibits spatiotemporal dynamics and can reach up to 1 μg CL−1 of seawater, rivaling bacteria on some occasions, which suggests their active and important role in the water column. In the nutrient-rich coastal water column, there is increasing evidence for their contribution to biogeochemical cycling and food web dynamics on account of their saprotrophic, parasitic, hyper-parasitic, and pathogenic attributes. Conversely, relatively little is known about their function in the open-ocean water column. Interestingly, methodological advances in sequencing and omics approach, the standardization of sequence data analysis tools, and integration of data through network analyses are enhancing our current understanding of the ecological roles of these multifarious and enigmatic members of the marine water column. This review summarizes the current knowledge of the diversity and abundance of planktonic fungi in the world’s oceans and provides an integrated and holistic view of their ecological roles.
... low temperature, high hydrostatic pressure, and oligotrophy, it has been reported that fungi are abundant and diverse in these environments [3][4][5]. According to literature surveys, the first documented deep-sea fungi were isolated from the Atlantic Ocean at a depth of 4450 m approximately 50 years ago [6]; however, it was not until 2006 that the first bioactive metabolite of the deep-sea fungus Chromocleista sp. was described by Park et al. [7]. ...
... Eight new chromones, engyodontiumones A-H (1)(2)(3)(4)(5)(6)(7)(8), and eight known polyketides (9)(10)(11)(12)(13)(14)(15)(16) (Figure 1) have been isolated from the deep-sea fungus Engyodontium album DFFSCS021. These polyketide compounds show a significant selective cytotoxicity against human histiocytic lymphoma U937 cell line with IC50 of 4.9-8.8 ...
Article
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Deep-sea fungi, the fungi that inhabit the sea and the sediment at depths of over 1000 m below the surface, have become an important source of industrial, agricultural, and nutraceutical compounds based on their diversities in both structure and function. Since the first study of deep-sea fungi in the Atlantic Ocean at a depth of 4450 m was conducted approximately 50 years ago, hundreds of isolates of deep-sea fungi have been reported based on culture-dependent methods. To date more than 180 bioactive secondary metabolites derived from deep-sea fungi have been documented in the literature. These include compounds with anticancer, antimicrobial, antifungal, antiprotozoal, and antiviral activities. In this review, we summarize the structures and bioactivities of these metabolites to provide help for novel drug development.
... To a large extent, it is related to the isolation and cultivation of unknown deep-sea microorganisms and the discovery of related secondary metabolites. Although it is supposed that microorganisms are huge in number and rich in diversity in these environments [5], few have been characterized so far [6]. In fact, the discovery of deep-sea microbial diversity can lead to the discovery of compounds with new biological activities, further promoting the drug development process [7]. ...
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Deep sea has an extreme environment which leads to biodiversity of microorganisms and their unique physical and biochemical mechanisms. Deep-sea derived microorganisms are more likely to produce novel bioactive substances with special mechanism of action for drug discovery. This article reviews secondary metabolites with biological activities such as anti-tumor, anti-bacterial, anti-viral, and anti-inflammatory isolated from deep-sea fungi and bacteria during 2018–2020. Effective methods for screening and obtaining natural active compounds from deep-sea microorganisms are also summarized, including optimizing the culture conditions, using genome mining technology, biosynthesis and so on. The comprehensive application of these methods makes broader prospects for the development and application of deep sea microbial bioactive substances.
... The deep-sea biosphere covers more than 65% of the Earth's surface and comprises the environments located at least 1000 m below sea level (mbsl) [2]. The current knowledge on fungi in the marine environment, particularly in the deep-sea biosphere, is scarce compared to what is known for the terrestrial environment. ...
Article
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The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.
... The Kohlmeyers' definition of marine fungi, which was well suited to describe the fungi occurring vertically on salt marsh and mangrove plants, was commonly accepted for more than 30 y. However, recently, it has been considered too restrictive by several specific studies (Mah e et al. 2014;Jones et al. 2015). Thus, a new broad definition was proposed by Pang et al. (2016): "any fungus that is recovered repeatedly from marine habitats because: 1) it is able to grow and/or sporulate (on substrata) in marine environments; 2) it forms symbiotic relationships with other marine organisms; or 3) it is shown to adapt and evolve at the genetic level or be metabolically active in marine environments". ...
Article
Posidonia oceanica leaves and their epiphytic algae Dictyota dichotoma and Sphaerococcus coronopifolius were sampled to investigate their culturable mycobiota. A total of 102 isolates were obtained; after rejection of duplicates, 32 morphotypes and 27 species were identified using morphological and molecular methods. The highest diversity was observed on P. oceanica with 18 species, followed by D. dichotoma (9 species) and S. coronopifolius (4 species). The phylogenetic analyses suggested the presence of possible new species of Aspergillus, Phaeosphaeria, Preussia and Tamaricicola. The fungal communities detected on the various substrata appeared quite distinct; no species were detected on the three substrata and only four were present on two of them. Strains were investigated for growth preference with respect to salinity and temperature to discriminate marine-from marine-derived fungi. Most strains (90%) were halophiles with a marked euryhalinism, while some (10%) were halotolerant. The majority of isolates had a mesophilic behaviour with some mesophilic-psychrotolerant strains.
... Species of the genus Tilletiopsis sensu lato are ubiquitous and can be found in various environments, and the most frequently reported habitats of these yeasts include diverse, either dead or living, plant material (Boekhout, 1991). Additionally, the propagules have been detected in the air, from where these yeasts can be transferred to flowers, plant surfaces, soils, sewage and deep-sea sediments, seawater and even sea animals (Gokhale, 1972;Shivas and Brown, 1989;Fairs et al., 2010;Li et al., 2011;Mahé et al., 2014;Yue et al., 2015). T. minor is the only known species of this genus, that was reported from clinical specimens and is a possible causing agent of pneumonia and corneal abscess (Ramani et al., 1997;Kechkekian et al., 2007;AL-Zaydani et al., 2014). ...
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In 2006 several yeast-like fungi were isolated from apples that showed a postharvest disorder named ‘white haze’. These strains were morphologically and molecularly assigned to the genus Tilletiopsis. Following the recent reclassification of yeasts in Ustilaginomycotina and the genus Tilletiopsis in particular, species that caused ‘white haze’ disorder were re-identified based on the phylogenetic analysis of five DNA-loci (ITS, LSU, SSU, RPB2 and TEF1) and analysis of D1/D2 domains of the 26S/28S rRNA (LSU). Six novel species belonging to three orders in the Exobasidiomycetes, namely Entyloma belangeri (holotype: CBS 111600; ex-type: DSM 29114) MB 823155, E. davenportii (holotype: CBS 111604; ex-type: DSM 100135) MB 823154, E. elstari (holotype: CBS 111593; ex-type: DSM 29113) MB 823153, E. randwijkense (holotype: CBS 111606; ex-type: DSM 100136) MB 823156, Jamesdicksonia mali (holotype: CBS 111625; ex-type: DSM 29121) MB 823151 and Golubevia heteromorpha (holotype: CBS 111610; ex-type: DSM 100176) MB 823152 are proposed to accommodate these strains. In addition, sequences representing phylogenetically related but yet undescribed fungi were obtained from GenBank in order to show the diversity of Tilletiopsis-like yeast states in Exobasidiomycetes.
... Likewise former definitions of a marine fungus were merely based on physiological capacities such as the ability to grow (Johnson and Sparrow 1961), sporulate (Kohlmeyer and Kohlmeyer 1979), or be metabolically active in the marine environment or under marine/estuarine salinity conditions (Mahé et al. 2014). However, the recently revised definition by Pang et al. (2016) also considers distinct genetic and evolutionary traits, defining a marine fungi those that are recovered repeatedly from marine habitats because of their ability to grow and/or sporulate (on substrata) in marine environments; establish symbiotic relationships with other marine organisms; and adapt, evolve, and be metabolically active in the marine milieu. ...
Chapter
In most ecosystems salinity shapes biotic assemblages, representing a key environmental factor. This variable is regarded as a major threat to microbial communities in terrestrial systems, modifying considerably a number of important ecosystem processes, including turnover of organic matter and nutrients acquisition. However, complex effects of salinity remain poorly understood, especially for non-model aquatic microbial assemblages, which account for most of the biodiversity in natural systems. Aquatic fungi are a widespread and phylogenetically heterogeneous group of microorganisms, occurring in marine, estuarine, and freshwater systems. These osmotrophs are completely adapted to rapidly colonize, grow, and reproduce in aquatic systems, where salinity represents a frequently fluctuating environmental variable. Some investigations have approached aquatic fungal response to salinity, suggesting that despite these microorganisms are able to survive under osmotic stress conditions, this variable may select for distinctive community compositions. At large, fungal responses to salinity stress are determined by taxon-specific underlying physiological traits, leading to distinctive tolerance thresholds. Herein, we review the impact of salinity on growth and development of aquatic fungi, integrating literature reports on marine and freshwater species, and recent advances introducing molecular techniques to provide better understanding of the phenomenon of aquatic fungal salinity tolerance.
... It has been hypothesized that extreme habitats harbor greater changes for novel drug discovery (Thatoi et al., 2013;Chávez et al., 2015). Interestingly, rich fungal species diversity inhabits extreme environments such as deep-sea sediments and mangrove ecosystems (Kumaresan and Suryanarayanan, 2001;Mahé et al., 2013). Many of ascomycetous species found in these habitats have been discovered having antiviral and other biological activities (Desmukh et al., 2018). ...
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Viral infections are amongst the most common diseases affecting people worldwide. New viruses emerge all the time and presently we have limited number of vaccines and only few antivirals to combat viral diseases. Fungi represent a vast source of bioactive molecules, which could potentially be used as antivirals in the future. Here, we have summarized the current knowledge of fungi as producers of antiviral compounds and discuss their potential applications. In particular, we have investigated how the antiviral action has been assessed and what is known about the molecular mechanisms and actual targets. Furthermore, we highlight the importance of accurate fungal species identification on antiviral and other natural products studies.
... Thanks to their unique adaptive capabilities, marine fungi are able to colonize different marine habitats, even the most extreme ones, including deep-sea environments. Although several studies have reported that fungi are abundant and diverse in these habitats [40], it is anticipated that many remain to be discovered. Access to the actual fungal biodiversity present in the deep-sea could lead to the discovery of new bioactive compounds useful for drug discovery [41]. ...
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The increasing emergence of new forms of multidrug resistance among human pathogenic bacteria, coupled with the consequent increase of infectious diseases, urgently requires the discovery and development of novel antimicrobial drugs with new modes of action. Most of the antibiotics currently available on the market were obtained from terrestrial organisms or derived semisynthetically from fermentation products. The isolation of microorganisms from previously unexplored habitats may lead to the discovery of lead structures with antibiotic activity. The deep-sea environment is a unique habitat, and deep-sea microorganisms, because of their adaptation to this extreme environment, have the potential to produce novel secondary metabolites with potent biological activities. This review covers novel antibiotics isolated from deep-sea microorganisms. The chemical classes of the compounds, their bioactivities, and the sources of organisms are outlined. Furthermore, the authors report recent advances in techniques and strategies for the exploitation of deep-sea microorganisms.
... Also the strict application of the dichotomic definition of obligate and facultative marine fungi has led to the exclusion of facultative fungi in the marine count. The three-level ecological classification proposed by Mahé et al (Mahé et al., 2013) would further increase this number as fungi are estimated to represent a significant fraction in the marine environment and include a wide range of forms including unicellular and multicellular forms from diverse lieages (Burgaud et al., 2012). ...
Research
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Unpublished MSc assignment for fungal diversity module. Project looking at the diversity of fungi in hydrothermal vent systems.
... Deep-sea fungi inhabit at depths of thousand meters or below the surface (Swathi et al., 2013) where the sea environments are extreme; which are typically characterized by the absence of sunlight irradiation, predominantly low temperature, high hydrostatic pressure, and oligotrophy. Many reports indicate abundance and diversity of fungi in these environments (Hua et al., 2011;Mahé et al., 2013). Here, we present an account of metabolites reported from the deep-sea fungi during 2012-2016 that have displayed anticancer activities in various cell lines. ...
Article
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Metabolites from marine fungi have hogged the limelight in drug discovery because of their promise as therapeutic agents. A number of metabolites related to marine fungi have been discovered from various sources which are known to possess a range of activities as antibacterial, antiviral and anticancer agents. Although, over a thousand marine fungi based metabolites have already been reported, none of them have reached the market yet which could partly be related to non-comprehensive screening approaches and lack of sustained lead optimization. The origin of these marine fungal metabolites is varied as their habitats have been reported from various sources such as sponge, algae, mangrove derived fungi, and fungi from bottom sediments. The importance of these natural compounds is based on their cytotoxicity and related activities that emanate from the diversity in their chemical structures and functional groups present on them. This review covers the majority of anticancer compounds isolated from marine fungi during 2012–2016 against specific cancer cell lines.
... The definition of marine fungi has changed as the study of marine mycology has advanced. Past definitions of marine fungi were based on their ability to grow at seawater salinity concentrations (Johnson and Sparrow, 1961), to grow and sporulate in situ in marine or estuarine habitats (Kohlmeyer and Kohlmeyer, 1979), or to be metabolically active in the marine environment (Mahé et al., 2014). These definitions are fundamentally physiological and ecological in aspect. ...
... However, they also reported that sequences related to Mimiviruses were present in the Loki sample [14], suggesting the presence of DNA from their eukaryotic hosts. In fact, several analyses have detected various types of eukaryotes, especially fungi, in the deep subseafloor sedimentary biosphere [43][44][45][46][47][48]. The possible contamination hypothesis would also be compatible with the fact that in the Loki Castle environmental sample, up to 9% of the relative abundance of archaeal 16S reads correspond to Thaumarchaeota (Thaumarchaea, Bathyarchaea) [14]. ...
Article
Author summary Two scenarios have been proposed to describe the history of cellular life on our planet. For some authors, two lineages emerged from the last universal cellular ancestor, one leading to Bacteria, the other one leading to a common ancestor of Archaea and Eukarya (Woese’s hypothesis), while others suggest that Eukaryotes emerged from within an archaeal subgroup (eocyte hypothesis). This latter hypothesis has been boosted by the reconstruction of new archaeal genomes from environmental DNA. These analyses have suggested that eukaryotes originated from complex archaea, called Lokiarchaeota, the first described members of the recently proposed Asgard superphylum. Considering the importance of this question, we performed new analyses of the universal proteins from Lokiarchaea and realized that their affiliation to Eukaryotes was most probably due to different biases, including chimeric sequences and unequal rate of protein evolution. From our results, we suggest here that Lokiarchaea and close relatives are sister group to Euryarchaeota, not to Eukarya. Notably, we also show that the choices of the universal markers to include in one’s analysis will critically impact the scenario supported and that some markers as the RNA polymerase support the traditional Woese’s tree.
Chapter
Fungi display an extraordinary level of structural and functional diversity with an estimated 1.5–5.1 million extant species. But, only 100,000 fungal species have so far been described. Fungi are one of the most important groups of eukaryotic organisms that are exploited for metabolites of potential therapeutic value as well as applications in diverse industries; by the way, fungal metabolites have a long history of both adverse and beneficial effects. Fungal biomolecules are an indispensable tool planned to accelerate the pace of the current research regarding the diverse roles of fungal biomolecules. The chapter encompasses a wide range of topics related to biomolecules synthesized and secreted by various fungal ecological groups useful in industrial, pharmaceutical, agricultural, and biotechnology sectors. Topics related to fungal enzymes have highlighted the significance of such enzymes in textile industries and environmental cleanup programs through the absorption of toxic heavy metals from soil, sludge, and industrial wastes.
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Chapter
Marine fungi have long been considered as exotic microorganisms fascinating only a few scientists. However, during the last two decades there has been an increasing interest in marine fungal communities resulting in a considerable advance in our knowledge of marine fungi. Marine fungi have been retrieved from various marine habitats, ranging from coastal waters to the deep sub-seafloor, and their ecologically important roles have been demonstrated. The purpose of this chapter is to review the increasing amount of culture-based and molecular-based data along with metabolomics and to summarize our current knowledge of the diversity, adaptive capabilities, functions, ecological roles and biotechnological potential of marine fungi. The availability of this amount of complementary data allows a revision of the consensual but likely out-of-date definition of marine fungi. Since the field of marine fungal natural products continues to expand rapidly, another aim of this chapter is to provide some innovative approaches to optimize the search for novel bioactive compounds using genomics and metabolomics.
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The Mid-Cayman spreading centre is an ultraslow-spreading ridge in the Caribbean Sea. Its extreme depth and geographic isolation from other mid-ocean ridges offer insights into the effects of pressure on hydrothermal venting, and the biogeography of vent fauna. Here we report the discovery of two hydrothermal vent fields on the Mid-Cayman spreading centre. The Von Damm Vent Field is located on the upper slopes of an oceanic core complex at a depth of 2,300?m. High-temperature venting in this off-axis setting suggests that the global incidence of vent fields may be underestimated. At a depth of 4,960?m on the Mid-Cayman spreading centre axis, the Beebe Vent Field emits copper-enriched fluids and a buoyant plume that rises 1,100?m, consistent with >400?°C venting from the world's deepest known hydrothermal system. At both sites, a new morphospecies of alvinocaridid shrimp dominates faunal assemblages, which exhibit similarities to those of Mid-Atlantic vents.
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The relationship between growth rate and rRNA content in a marine Synechococcus strain was examined. A combination of flow cytometry and whole- cell hybridization with fluorescently labeled 16S rRNA-targeted oligonucleotide probes was used to measure the rRNA content of Synechococcus strain WH8101 cells grown at a range of light-limited growth rates. The sensitivity of this approach was sufficient for the analysis of rRNA even in very slowly growing Synechococcus cells (μ = 0.15 day-1). The relationship between growth rate and cellular rRNA content comprised three phases: (i) at low growth rates (<~0.7 day-1), rRNA cell-1 remained approximately constant; (ii) at intermediate rates (~0.7 - 1.6 day-1), rRNA cell-1 increased proportionally with growth rate; and (iii) at the highest, light- saturated rates (>~1.6 day-1), rRNA cell-1 dropped abruptly. Total cellular RNA (as measured with the nucleic acid stain SYBR Green II) was well correlated with the probe-based measure of rRNA and varied in a similar manner with growth rate. Mean cell volume and rRNA concentration (amount of rRNA per cubic micrometer) were related to growth rate in a manner similar to rRNA cell-1, although the overall magnitude of change in both cases was reduced. These patterns are hypothesized to reflect an approximately linear increase in ribosome efficiency with increasing growth rate, which is consistent with the prevailing prokaryotic model at low growth rates. Taken together, these results support the notion that measurements of cellular rRNA content might be useful for estimating in situ growth rates in natural Synechococcus populations.
Chapter
The most concentrated and widespread occurrences of organisms are generally in “moderate” environments with approximately neutral pH, temperatures around 20°37°C, pressures near 0.1 MPa, and adequate concentrations of nutrients and saline. In contrast, the deep-sea is an extreme environment with especially high hydrostatic pressure and low temperature. Microorganisms living there presumably have developed particular characteristics that allow them to thrive in such an environment. Bacteria have been isolated from deep-sea mud and from benthic organisms such as amphipods and sea cucumbers in the bathypelagic zone (Yayanos 1979; Yayanos et al. 1981). However, little information is available on bacterial diversity in sediments of the deep-sea floor because most marine biologists have focused on barophilic and psychrophilic inhabitants of the deep-sea environment (Yayanos 1995).
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The frequent discrepancy between direct microscopic counts and numbers of culturable bacteria from environmental samples is just one of several indications that we currently know only a minor part of the diversity of microorganisms in nature. A combination of direct retrieval of rRNA sequences and whole-cell oligonucleotide probing can be used to detect specific rRNA sequences of uncultured bacteria in natural samples and to microscopically identify individual cells. Studies have been performed with microbial assemblages of various complexities ranging from simple two-component bacterial endosymbiotic associations to multispecies enrichments containing magnetotactic bacteria to highly complex marine and soil communities. Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts. For the analysis of complex communities such as multispecies biofilms and activated-sludge flocs, a different approach has proven advantageous. Sets of probes specific to different taxonomic levels are applied consecutively beginning with the more general and ending with the more specific (a hierarchical top-to-bottom approach), thereby generating increasingly precise information on the structure of the community. Not only do rRNA-targeted whole-cell hybridizations yield data on cell morphology, specific cell counts, and in situ distributions of defined phylogenetic groups, but also the strength of the hybridization signal reflects the cellular rRNA content of individual cells. From the signal strength conferred by a specific probe, in situ growth rates and activities of individual cells might be estimated for known species. In many ecosystems, low cellular rRNA content and/or limited cell permeability, combined with background fluorescence, hinders in situ identification of autochthonous populations. Approaches to circumvent these problems are discussed in detail.
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A new method is presented for the separation of cells from a marine sediment matrix. Different methods and reagents were tested for detaching microbial cells from sediment particles; the highest yields were achieved in a solution of EDTA, Tween 80, sodium-pyrophosphate, and methanol plus gentle ultrasonic treatment, followed by density centrifugation through a cushion of Nycodenz. If present, carbonates were dissolved before extraction. Comparison with untreated sediments and pure cultures verified that this technique minimizes cell lysis. The new procedure was tested on seafloor sediment from several locations and water depths (<1 to >4000 m) and subseafloor sediment from the Arctic Ocean (IODP Expedition 302). Cell extraction efficiency was relatively high (65% to 100%) and consistent for each sediment type, with significantly (P < 0.01) lower variability of counts of separated cells compared with conventional counts on slurried sediments. Concentrating cells before enumeration allows for a much lower minimum detection limit and lower uncertainty than the conventional approach of simply slurrying sediment. Resolving relatively small differences in the distribution of microorganisms will allow for comparisons to other parameters (porewater chemistry, lithology, etc). Additionally, this method has potential for the use of molecular techniques that were previously difficult owing to coelution of interfering compounds from the sediment matrix.
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Eight Fusarium strains were isolated from five prawns showing black gills at a farm in Kagoshima Prefecture, Japan in December 2001. On the other hand, no fungi were isolated from five prawns without black gills. Two out of the eight strains were morphologically identified as F. oxysporum and the other six strains as F. solani. Morphological characteristics of F. oxysporum were described and illustrated. The fungus showed pathogenicity when injected to juvenile kuruma prawns. This is the first case of F. oxysporum infection of kuruma prawn in Japan.
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In the last few years several comprehensive reviews of the biology of hydrothermal vent organisms and communities have been published. In this contribution I will not attempt to exhaustively review the literature, list the fauna, or the known sites, but rather present a conceptual basis for understanding the relation between the dominant metazoan "primary producers" in hydrothermal vent communities and their environment. In addition to the other chapters in this volume, interested readers are encouraged to consult the following reviews for a more detailed discussion of particular aspects of vent biology. The community ecology of hydrothermal vents is reviewed by Grassle [1986], Tunnicliffe [1991], and Lutz and Kennish [1993]. Tunnicliffe [1991] contains the most complete species lists and general site descriptions currently available. Fisher [1990] reviews the literature on chemoautotrophic symbioses and presents species lists of the hosts to chemoautotrophic symbionts known at that time. Those lists are updated in Nelson and Fisher [1995] and the physiology of the associations reviewed from a distinctly bacterial (symbiont) viewpoint. The 1992 review by Childress and Fisher takes a detailed look at the physiology of vent fauna, with a full coverage of subjects such as rate processes, blood function, and chemical composition, which are not covered in depth in the other reviews, but are of special relevance to this contribution. Uses (and abuses) of stable isotopes are discussed in several of the above reviews, and are also reviewed specifically by Conway et al. [1994], Fiala-Médioni et al. [1993], and Kennicutt et al. [1992].
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[1] The InterRidge Vents Database is available online as the authoritative reference for locations of active submarine hydrothermal vent fields. Here we describe the revision of the database to an open source content management system and conduct a meta-analysis of the global distribution of known active vent fields. The number of known active vent fields has almost doubled in the past decade (521 as of year 2009), with about half visually confirmed and others inferred active from physical and chemical clues. Although previously known mainly from mid-ocean ridges (MORs), active vent fields at MORs now comprise only half of the total known, with about a quarter each now known at volcanic arcs and back-arc spreading centers. Discoveries in arc and back-arc settings resulted in an increase in known vent fields within exclusive economic zones, consequently reducing the proportion known in high seas to one third. The increase in known vent fields reflects a number of factors, including increased national and commercial interests in seafloor hydrothermal deposits as mineral resources. The purpose of the database now extends beyond academic research and education and into marine policy and management, with at least 18% of known vent fields in areas granted or pending applications for mineral prospecting and 8% in marine protected areas.
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The deep-sea is one of the most mysterious and unexplored extreme environments, holding great potential and interest for science. Despite extensive studies on deep-sea prokaryotes, the diversity of fungi, one of the most ecologically important groups of eukaryotic micro-organisms, remains largely unknown. However, the presence of fungi in these ecosystems is starting to be recognised. Many fungi have been isolated by culture-dependent methods from various deep-sea environments, with the majority showing similarity to terrestrial species. However, culture-independent methods have revealed many novel fungal phylotypes, including novel fungal lineages recently described as Cryptomycota, which are suspected to lack typical fungal chitin-rich cell walls. Although true fungal diversity and its role in deep-sea environments is still unclear, the intention of this review is to assess current knowledge of the diversity of fungi in these ecosystems and to suggest future direction for deep-sea fungal research.
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We used stable isotopes of carbon and nitrogen to examine the diversity of microbial populations consumed as foods at deep-sea hydrothermal vents. Invertebrate consumers at Gorda and Juan de Fuca Ridge vent sites had variable carbon isotope compositions, implying the use of more than one microbial food resource. 6'C values for consumer invertebrates at Gorda ranged between - 13.2% (polynoid polychaete) and -43.7% (limpet); within Gorda microhabitats, fi13C compositions of invertebrate species were also not uniform, differing by as much as 8-19%. At the Juan de Fuca site, 6'C values showed a wide range (- 14.6 to - 33.9%) for nine invertebrate species collected from a dense community colonizing the surface of a sulfide flange. Carbon isotope differences between tubeworm symbioses and consumer invcrtebratcs within microhabitats suggest that these symbioses may play a minor role as nutritional resources in vent food webs. Nitrogen isotope compositions of consumer spccics from vents were con- sistently depicted in 15N relative to animals collected away from vents. 615N compositions of some vent individuals are among the lowest measured in any organism (< - 10%) and likely reflect relatively abun- dant supplies of inorganic nitrogen compounds used by microbial populations at vents.
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The marine subseafloor biosphere is estimated to be up to 1/3rd of all life on Earth or 50-80% of the Earth's microbial biomass. These estimates are based on theoretical calculations and cell counts from ODP sites located in areas of high primary productivity. The cell counts range from 108 to 1010 cells- cm-3 in surface sediments and rapidly decrease to 1029 cells-cm-3 within 10 to 100 m of the seafloor. In contrast, recent cell counts from the low primary productivity region of the South Pacific Gyre are four orders of magnitude lower with an even more rapid decrease in cell count with depth. Based on these new observations, the previous estimates of subseafloor biosphere are likely exaggerated upper limits. To obtain a more accurate measure of subseafloor biosphere, we combined well-correlated cell count and depth relationships with the global distribution parameters of sea-surface chlorophyll, organic carbon burial rates, and distance to land. Specifically, we performed linear regressions for a compilation of published subseafloor cell counts plotted as a function of depth in log-log space. The y-intercept (i.e., cell count at 1 m depth) and slope (i.e., log-rate of cell count decrease with depth) for all correlations with R-square values greater than 0.5 were then compared to each of the three global distribution parameters at corresponding geographic locations. The relationship between each global distribution parameter and the remaining y- intercepts and slopes were then used to create a global grid of predicted y-intercept and slope. These grids were integrated as a function of depth to the corresponding sediment thickness (maximum sediment thickness of 4 km) and then integrated spatially to obtain an estimate of global cell counts. The resulting total cell counts are surprisingly similar for each of the global parameters (e.g., 4.2 x 1029 for sea- surface chlorophyll, 5.9 x 1029 for organic carbon burial rates, and 3.8 x 1029 for distance from land) and suggest cell counts that are 10-20% of the previous estimate of 3.5 x 1030. These results imply a significantly smaller marine subseafloor biosphere that only comprises 1/20th of all life on Earth or 5-15% of the Earth's microbial biomass.
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Rates of carbon dioxide assimilation and methane oxidation were determined in various zones of the Rainbow Hydrothermal Field (36°N) of the Mid-Atlantic Ridge. In the plume above the hydrothermal field, anomalously high methane content was recorded, the microbial population density (up to 105 cells/ml) was an order of magnitude higher than the background values, and the CO2 assimilation rate varied from 0.01 to 1.1 µg C/(l day). Based on the data on CO2 assimilation, the production of organic carbon due to bacterial chemosynthesis in the plume was calculated to be 930 kg/day or 340 tons/year (about 29% of the organic carbon production in the photic zone). In the black smoke above active smokers, the microbial population density was as high as 106 cells/ml, the rate of CO2 assimilation made up 5–10 µg C/(l day), the methane oxidation rate varied from 0.15 to 12.7 µl/(l day), and the methane concentration ranged from 1.05 to 70.6 µl/l. In bottom sediments enriched with sulfides, the rate of CO2 assimilation was at least an order of magnitude higher than in oxidized metal-bearing sediments. At the base of an active construction, whitish sediment was found, which was characterized by a high methane content (92 µl/dm3) and a high rate of methane oxidation (1.7 µl/(dm3 day)).
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Besides temperature, hydrostatic pressure has been used as a physical-chemical parameter for studying the energetics and phase behavior of membrane systems. First we review some theoretical aspects of lipid self-assembly. Then, the temperature and pressure dependent structure and phase behavior of lipid bilayers, differing in chain configuration, headgroup structure and composition as revealed by using thermodynamic, spectroscopic and scattering experiments is discussed. We also report on the lateral organization of phase-separated lipid membranes and model raft mixtures as well as the influence of peptide and protein incorporation on membrane structure and dynamics upon pressurization. Also the effect of other additives, such as ions, cholesterol, and anaesthetics is discussed. Furthermore, we introduce pressure as a kinetic variable. Applying the pressure-jump relaxation technique in combination with time-resolved synchrotron X-ray diffraction, the kinetics of various lipid phase transformations was investigated. Finally, also new data on pressure effects on membrane mimetics, such as surfactants and microemulsions, are presented.
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Diversity of fungi from deep biosphere is recently gaining an increasing attention. We investigated fungal diversity in two sediment cores similar to 40 cmbsf (cm below seafloor) at a depth of similar to 5 000 m in the Central Indian Basin (CIB), by culture-dependent as well as culture-independent approaches. This resulted in recovering a total of 19 culturable fungi and 46 operational taxonomic units (OTUs) respectively. Two of the cultured fungi showed similarity to Hortaea werneckii and Aspergillus versicolor, and 11 OTUs from environmental libraries showed high divergence (86-97 %) from the existing sequences in the GenBank (NCBI database). Some of the fungi, such as Cerrena, Hortaea and Aspergillus sp., were recovered by culture-dependent as well as culture-independent approaches. Together, culture-dependent and culture-independent approaches detected a total of 12 distinct fungal genera and 42 OTUs respectively from two sediment cores indicating presence of a high fungal diversity in deep-sea sediments.
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Ecology Letters (2010) 13: 776–791AbstractEnvironmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.
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A new genus of a deep-sea ascomycete with one new species, Alisea longicolla, is described based on analyses of 18S and 28S rDNA sequences and morphological characters. A. longicolla was found together with Oceanitis scuticella, on small twigs and sugar cane debris trawled from the bottom of the Pacific Ocean off Vanuatu Islands. Molecular and morphological characters indicate that both fungi are members of Halosphaeriaceae. Within this family, O. scuticella is phylogenetically related to Ascosalsum and shares similar ascospore morphology and appendage ontogeny. The genus Ascosalsum is considered congeneric with Oceanitis and Ascosalsum cincinnatulum, Ascosalsum unicaudatum and Ascosalsum viscidulum are transferred to Oceanitis, an earlier generic name.
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Deep-sea endemic fungi are one component of an under-sampled invisible biosphere whose contribution to benthic ecosystems is not yet understood. In the last decade, molecular techniques have facilitated the discovery of several new deep-sea fungal groups, especially in habitats such as hydrothermal vents and methane seeps. We assessed fungal diversity at a methane seep in the Gulf of Mexico by sequencing partial ITS and LSU gene regions from environmental DNA recovered from microoxic and anoxic sediment. While most phylotypes were closely allied with common fungal species, the dominant phylotype did not match any known terrestrial species and aligned with an uncultured deep-sea fungus found in oxygen-depleted sediment at multiple sites in the Pacific Ocean. Despite its apparently broad distribution and frequent occurrence in oxygen-depleted sediment, the ecological role of this phylotype is not yet known.
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In an attempt to characterize the microbial flora on the deepest sea floor, we isolated thousands of microbes from a mud sample collected from the Mariana Trench. The microbial flora found at a depth of 10 897 m was composed of actinomycetes, fungi, non-extremophilic bacteria, and various extremophilic bacteria such as alkaliphiles, thermophiles, and psychrophiles. Phylogenetic analysis of Mariana isolates based on 16S rDNA sequences revealed that a wide range of taxa were represented.
Article
We examined sediments collected at Ocean Drilling Program (ODP) Leg 201 Site 1229 on the Peru Margin for microbial populations throughout the sediment column. Heterotrophic cultivation from these sediments yielded numerous colonies from various depths, including 49 bacterial isolates. At ODP Site 1229, there are significant interfaces of sulfate and methane, across which microbial cell numbers increase substantially. At these sulfate/methane transition zones (SMTZs), however, we observed a decrease in the success rate for the cultivation of bacterial colonies. Utilizing both direct plating and enrichment in different media, we cultivated isolates from the upper SMTZ around 30 m below seafloor (mbsf); however, similar attempts yielded no colonies from within the lower zone at 85 mbsf. The phylogenetic relationships of the 16S rRNA gene sequences for the isolates were determined and most were related to other organisms and sequences previously found in the subsurface belonging to the γ-Proteobacteria, cytophaga–flavobacterium–bacteroides, high G + C Gram-positives, and Firmicutes groups. The most diverse group of isolates from Site 1229 was found between the SMTZs at 50 mbsf. ODP Leg 201 Site 1228 was examined for comparison and yielded an additional 18 isolates from 16 to 179 mbsf that were similar to those found at Site 1229. Direct plating at Site 1228 also showed decreased colony formation in the area of sulfate/methane transition. Our results suggest that heterotrophic bacterial populations are affected by SMTZs in deeply buried sediment.
Article
Marine fungi are an ecological rather than a taxonomic group and comprise an estimated 1500 species, excluding those that form lichens. They occur in most marine habitats and generally have a pantropical or pantemperate distribution. Marine fungi are major decomposers of woody and herbaceous substrates in marine ecosystems. Their importance lies in their ability to aggressively degrade lignocellulose. They may be important in the degradation of dead animals and animal parts. Marine fungi are important pathogens of plants and animals and also form symbiotic relationships with other organisms. The effect of disturbances on marine fungi is poorly investigated. Keystone marine species may exist, especially in mutualistic symbioses. However, as many saprophytes appear to carry out the same function simultaneously, they may be functionally redundant. The need for a concerted effort to investigate the biodiversity and role of marine fungi globally and on as many substrata as possible is presented.
Chapter
In marine sediments, methane is present in dissolved form in the pore water, as free gas, or trapped within gas hydrate. As an extremely large reservoir of reduced carbon, methane hydrates represent an enormous carbon and energy source in many low-temperature deep marine sediments. In this chapter, fungal communities of methane hydrate-bearing deep sea sediments are presented and possible interactions among Fungi, Bacteria, and Archaea are discussed.
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Marine fungi have been widely studied over the past millennium and considerable progress has been made in documenting their phylogeny, biodiversity, ultrastructure, ecology, physiology and their ability to cause decay of lignocellulosic compounds. These studies have generated a wealth of publications and this review will focus primarily on research undertaken since 1995. During this period new topics have attracted marine mycologists especially: algicolous and manglicolous fungi, deep sea fungi, planktonic fungi, endophytes of marine plants, and the screening of taxa for new chemical structures and bioactive compounds. This review will also highlight areas that warrant further investigation, including surveys for marine fungi in Africa, artic waters and south America, more detailed studies of their physiology and biochemistry, and to determine the marine origin of so called “marine derived” fungi. KeywordsBiodiversity–Bioactive metabolites–Taxonomy and phylogeny–Substrata–Ultrastructure
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Measured rates of sediment oxygen consumption are extrapolated throughout the Atlantic and Pacific Ocean basins from 61° N to 61° S latitude. Because benthic respiration must be supported predominantly by the rain of organic matter from surface waters, the pattern of oxygen consumption in the surface sediments reveals the distribution of particle fluxes in the deep ocean. Benthic oxygen consumption in the Atlantic and Pacific basins appears to account for the remineralization of 1 to 2& of global oceanic primary production and 4 to 10% of global new production. These values are minimum estimates of the role of the sea floor in global cycles because the contributions from the Arctic, Antarctic and Indian Oceans are not included. Comparison of total respiration estimated for the deep Atlantic from AOU and 14C relationships and from benthic respiration indicates that sea floor processes account for 33 to 40% of the organic matter remineralization occurring below 1000 m. Introduction