深海真菌多样性及其代谢产物生物活性的研究进展

深海环境复杂多样,深海微生物逐渐进化以适应其生存环境。真菌作为深海环境中的重要微生物类群,是开发海洋生物的新兴资源。综述了近年来深海真菌的物种多样性、活性代谢产物的多样性及其生物学功能等的研究进展,并对未来深海真菌的应用进行了展望。     

Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance

Deep-sea vents support productive ecosystems driven primarily by chemoautotrophs. Chemoautotrophs are organisms that are able to fix inorganic carbon using a chemical energy obtained through the oxidation of reduced compounds. Following the discovery of deep-sea vent ecosystems in 1977, there has been an increasing knowledge that deep-sea vent chemoautotrophs display remarkable physiological and phylogenetic diversity. Cultivation-dependent and -independent studies have led to an emerging view that the majority of deep-sea vent chemoautotrophs have the ability to derive energy from a variety of redox couples other than the conventional sulfur-oxygen couple, and fix inorganic carbon via the reductive tricarboxylic acid cycle. In addition, recent genomic, metagenomic and postgenomic studies have considerably accelerated the comprehensive understanding of molecular mechanisms of deep-sea vent chemoautotrophy, even in yet uncultivable endosymbionts of vent fauna. Genomic analysis also suggested that there are previously unrecognized evolutionary links between deep-sea vent chemoautotrophs and important human/animal pathogens. This review summarizes chemoautotrophy in deep-sea vents, highlighting recent biochemical and genomic discoveries.     

Frequency and characteristics of plasmids in bacteria isolated from deep-sea amphipods

Bacterial strains isolated from deep-sea amphipods were identified, classified, and screened for plasmid content. Plasmids were common, with 11 of 16 isolates carrying one or more plasmids; these ranged in size from 2.9 to 63 megadaltons. Several of the strains demonstrated distinctly different phenotypic traits yet contained plasmids of the same molecular weight. Results of agarose gel electrophoresis, DNA hybridization, and restriction analysis indicate that the plasmids detected in these deep-sea isolates are identical, suggesting that transmission may occur in the deep-sea environment and that plasmids are common in some deep-sea habitats.     

First glimpse into Lower Jurassic deep-sea biodiversity: in situ diversification and resilience against extinction

Owing to the assumed lack of deep-sea macrofossils older than the Late Cretaceous, very little is known about the geological history of deep-sea communities, and most inference-based hypotheses argue for repeated recolonizations of the deep sea from shelf habitats following major palaeoceanographic perturbations. We present a fossil deep-sea assemblage of echinoderms, gastropods, brachiopods and ostracods, from the Early Jurassic of the Glasenbach Gorge, Austria, which includes the oldest known representatives of a number of extant deep-sea groups, and thus implies that in situ diversification, in contrast to immigration from shelf habitats, played a much greater role in shaping modern deep-sea biodiversity than previously thought. A comparison with coeval shelf assemblages reveals that, at least in some of the analysed groups, significantly more extant families/superfamilies have endured in the deep sea since the Early Jurassic than in the shelf seas, which suggests that deep-sea biota are more resilient against extinction than shallow-water ones. In addition, a number of extant deep-sea families/superfamilies found in the Glasenbach assemblage lack post-Jurassic shelf occurrences, implying that if there was a complete extinction of the deep-sea fauna followed by replacement from the shelf, it must have happened before the Late Jurassic.     

Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms]

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".     

The Effects of Hydrostatic Pressure on Living Aquatic Organisms IV. Recovery and Pressure Experimentation on Deep-sea Animals

Capture of living deep-sea animals is reviewed. The conditions for the successful recovery of living animals from the deep-sea are elaborated with examples. Control of pressure, temperature, or both, appears to be a prerequisite for the capture of living deep-sea animals. Deep-sea animals (archibenthal) show a loss of the R₁ response in comparison with their shallow-water counterparts. Genuine deep-sea animals have now been recovered in a living state suitable for experimentation from the High Arctic.     

Antibacterial and antilarval activity of deep-sea bacteria from sediments of the West Pacific Ocean

Deep-sea microorganisms are a new source of bioactive compounds. In this study, crude ethyl acetate extracts of 176 strains of deep-sea bacteria, isolated from sediments of the West Pacific Ocean, were screened for their antibacterial activity against four test bacterial strains isolated from marine biofilms. Of these, 28 deep-sea bacterial strains exhibited antibacterial activity against one or more of the bacteria tested. Active deep-sea bacterial strains belonged mainly to the genera of Pseudomonas, Psychrobacter and Halomonas. Additionally, antilarval activity of 56 deep-sea bacterial strains was screened using Balanus amphitrite larvae. Seven bacterial strains produced metabolites that had strong inhibitive effects on larval settlement. None of these metabolites showed significant toxicity. The crude extract of one deep-sea Streptomyces strain could completely inhibit larval settlement at a concentration of 25 microg ml(-1).     

Fungi and Macroaggregation in Deep-Sea Sediments

Whereas fungi in terrestrial soils have been well studied, little is known of them in deep-sea sediments. Recent studies have demonstrated the presence of fungal hyphae in such sediments but in low abundance. We present evidence in this study that one of the apparent reasons for the poor detection of fungi in deep-sea sediments is their cryptic presence in macroaggregates. Fungal biomass carbon from different core sections of deep-sea sediments from approximately 5000 m depth in the Central Indian Ocean was estimated based on direct microscopic detection of fungal mycelia. Treatment of sediment samples with ethylenediamine tetra-acetic acid (EDTA) enabled more frequent detection and significantly higher biomass than in samples without such treatment. Treatment with EDTA resulted in detecting various stages of breakdown of aggregates in the sediments, gradually revealing the presence of fungal hyphae within them. Experimental studies of a deep-sea, as well as three terrestrial isolates of fungi, showed that all could grow at 200 bar and 5 degrees C in a nutrient medium and in deep-sea sediment extract. Hyphae of fungi grown in sediment extract under the above conditions showed various stages of accretion of particles around them, leading to the formation of aggregates. Such aggregates showed the presence of humic material, carbohydrate, and proteins. We suggest that fungi in deep-sea sediments may be involved in humic aggregate formation by processes very similar to those in terrestrial sediments. The importance of such a process in carbon sequestration and food web in the deep sea needs to be examined.     

Yeast forms dominate fungal diversity in the deep oceans

Fungi are the principal degraders of biomass in most terrestrial ecosystems. In contrast to surface environments, deep-sea environmental gene libraries have suggested that fungi are rare and non-diverse in high-pressure marine environments. Here, we report the diversity of fungi from 11 deep-sea samples from around the world representing depths from 1,500 to 4,000 m (146-388 atm) and two shallower water column samples (250 and 500m). We sequenced 239 clones from 10 fungal-specific 18S rRNA gene libraries constructed from these samples, from which we detected only 18 fungal 18S-types in deep-sea samples. Our phylogenetic analyses show that a total of only 32 fungal 18S-types have so far been recovered from deep-sea habitats, and our results suggest that fungi, in general, are relatively rare in the deep-sea habitats we sampled. The fungal diversity detected suggests that deep-sea environments host an evolutionarily diverse array of fungi dominated by groups of distantly related yeasts, although four putative filamentous fungal 18S-types were detected. The majority of our new sequences branch close to known fungi found in surface environments. This pattern contradicts the proposal that deep-sea and hydrothermal vent habitats represent ancient ecosystems, and demonstrates a history of frequent dispersal between terrestrial and deep-sea habitats.     

Ancient Origin of the Modern Deep-Sea Fauna

The origin and possible antiquity of the spectacularly diverse modern deep-sea fauna has been debated since the beginning of deep-sea research in the mid-nineteenth century. Recent hypotheses, based on biogeographic patterns and molecular clock estimates, support a latest Mesozoic or early Cenozoic date for the origin of key groups of the present deep-sea fauna (echinoids, octopods). This relatively young age is consistent with hypotheses that argue for extensive extinction during Jurassic and Cretaceous Oceanic Anoxic Events (OAEs) and the mid-Cenozoic cooling of deep-water masses, implying repeated re-colonization by immigration of taxa from shallow-water habitats. Here we report on a well-preserved echinoderm assemblage from deep-sea (1000–1500 m paleodepth) sediments of the NE-Atlantic of Early Cretaceous age (114 Ma). The assemblage is strikingly similar to that of extant bathyal echinoderm communities in composition, including families and genera found exclusively in modern deep-sea habitats. A number of taxa found in the assemblage have no fossil record at shelf depths postdating the assemblage, which precludes the possibility of deep-sea recolonization from shallow habitats following episodic extinction at least for those groups. Our discovery provides the first key fossil evidence that a significant part of the modern deep-sea fauna is considerably older than previously assumed. As a consequence, most major paleoceanographic events had far less impact on the diversity of deep-sea faunas than has been implied. It also suggests that deep-sea biota are more resilient to extinction events than shallow-water forms, and that the unusual deep-sea environment, indeed, provides evolutionary stability which is very rarely punctuated on macroevolutionary time scales.     

Cell biology of deep-sea multicellular organisms

Establishing tissue cultures derived from deep-sea multicellular organisms has been extremely difficult because of the serious damage they sustain upon decompression and exposure to the high temperature of surface seawater. We developed a novel pressure-stat aquarium system for the study of living deep-sea multicellular organisms under pressure. Using this system, we have succeeded in maintaining a variety of deep-sea multicellular organisms under pressure and atmospheric conditions after gradual, slow decompression. Furthermore, we successfully cultivated and freeze-stocked pectoral fin cells of the deep-sea eel Simenchelys parasiticus collected at a depth of 1,162 m under atmospheric pressure conditions. This review describes novel capture and maintenance devices for deep-sea organisms and cell culture studies of the organisms under atmospheric and pressure conditions.     

Gazing into the abyss: A glimpse into the diversity,distribution, and behaviour of heterotrophic protists from the deep-sea floor

The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.     

Identification and Diversity of Putative Aminoglycoside-Biosynthetic Aminotransferase Genes from Deep-Sea Environmental DNA

We obtained DNA fragments encoding putative aminotransferases possibly involved in the biosynthesis of aminoglycoside antibiotics from deep-sea sediments of the northwest Pacific Ocean by nested PCR, and 34 individual genes (total 89 clones) were identified. About half of the deep-sea sequences showed similarity with genes of known aminoglycoside-producers, but others were deep-sea specific genes. Furthermore, we found that temperature-gradient gel electrophoresis (TGGE) can be an effective tool in the analysis of these DNA fragments.     

Identification and diversity of putative aminoglycoside-biosynthetic aminotransferase genes from deep-sea environmental DNA

We obtained DNA fragments encoding putative aminotransferases possibly involved in the biosynthesis of aminoglycoside antibiotics from deep-sea sediments of the northwest Pacific Ocean by nested PCR, and 34 individual genes (total 89 clones) were identified. About half of the deep-sea sequences showed similarity with genes of known aminoglycoside-producers, but others were deep-sea specific genes. Furthermore, we found that temperature-gradient gel electrophoresis (TGGE) can be an effective tool in the analysis of these DNA fragments.     

Low endemism,continued deep-shallow interchanges,and evidence for cosmopolitan distributions in free-living marine nematodes (order Enoplida)

Background  

Nematodes represent the most abundant benthic metazoa in one of the largest habitats on earth, the deep sea. Characterizing major patterns of biodiversity within this dominant group is a critical step towards understanding evolutionary patterns across this vast ecosystem. The present study has aimed to place deep-sea nematode species into a phylogenetic framework, investigate relationships between shallow water and deep-sea taxa, and elucidate phylogeographic patterns amongst the deep-sea fauna.     

Exponential decline of deep-sea ecosystem functioning linked to benthic biodiversity loss

BACKGROUND: Recent investigations suggest that biodiversity loss might impair the functioning and sustainability of ecosystems. Although deep-sea ecosystems are the most extensive on Earth, represent the largest reservoir of biomass, and host a large proportion of undiscovered biodiversity, the data needed to evaluate the consequences of biodiversity loss on the ocean floor are completely lacking. RESULTS: Here, we present a global-scale study based on 116 deep-sea sites that relates benthic biodiversity to several independent indicators of ecosystem functioning and efficiency. We show that deep-sea ecosystem functioning is exponentially related to deep-sea biodiversity and that ecosystem efficiency is also exponentially linked to functional biodiversity. These results suggest that a higher biodiversity supports higher rates of ecosystem processes and an increased efficiency with which these processes are performed. The exponential relationships presented here, being consistent across a wide range of deep-sea ecosystems, suggest that mutually positive functional interactions (ecological facilitation) can be common in the largest biome of our biosphere. CONCLUSIONS: Our results suggest that a biodiversity loss in deep-sea ecosystems might be associated with exponential reductions of their functions. Because the deep sea plays a key role in ecological and biogeochemical processes at a global scale, this study provides scientific evidence that the conservation of deep-sea biodiversity is a priority for a sustainable functioning of the worlds' oceans.     

The red and the black: bioluminescence and the color of animals in the deep sea

The colors of deep-sea species are generally assumed to be cryptic,but it is not known how cryptic they are and under what conditions.This study measured the color of approximately 70 deep-sea species,both pelagic and benthic, and compared the results with twosets of predictions: 1) optimal crypsis under ambient light,2) optimal crypsis when viewed by bioluminescent "searchlights."The reflectances of the pelagic species at the blue-green wavelengthsimportant for deep-sea vision were far lower than the predictedreflectances for crypsis under ambient light and closer to thezero reflectance prediction for crypsis under searchlights.This suggests that bioluminescence is more important than ambientlight for the visual detection of pelagic species at mesopelagicdepths. The reflectances of the benthic species were highlyvariable and a relatively poor match to the substrates on whichthey were found. However, estimates of the contrast sensitivityof deep-sea visual systems suggest that even approximate matchesmay be sufficient for crypsis in visually complex benthic habitats.Body coloration was generally uniform, but many crabs had strikingpatterns that may serve to disrupt the outlines of their bodies.     

Antibacterial and antilarval activity of deep-sea bacteria from sediments of the West Pacific Ocean

Abstract

Deep-sea microorganisms are a new source of bioactive compounds. In this study, crude ethyl acetate extracts of 176 strains of deep-sea bacteria, isolated from sediments of the West Pacific Ocean, were screened for their antibacterial activity against four test bacterial strains isolated from marine biofilms. Of these, 28 deep-sea bacterial strains exhibited antibacterial activity against one or more of the bacteria tested. Active deep-sea bacterial strains belonged mainly to the genera of Pseudomonas, Psychrobacter and Halomonas. Additionally, antilarval activity of 56 deep-sea bacterial strains was screened using Balanus amphitrite larvae. Seven bacterial strains produced metabolites that had strong inhibitive effects on larval settlement. None of these metabolites showed significant toxicity. The crude extract of one deep-sea Streptomyces strain could completely inhibit larval settlement at a concentration of 25 μg ml^?1.     

Piezotolerance of the cytoskeletal structure in cultured deep-sea fish cells using DNA transfection and protein introduction techniques

We used DNA transfection and protein introduction techniques to investigate the pressure tolerance of cytoskeletal structures in pectoral fin cells derived from the deep-sea fish Simenchelys parasiticus (habitat depth, 366–2,630 m). The deep-sea fish cells have G418 resistance. The cell number increased until day 6 of cultivation and all cells had died by day 35 when cultured in 35-mm Petri dishes in medium containing G418. Enhanced yellow fluorescent protein-tagged human β-actin (EYFP-actin) was stably expressed by 1 in 100,000 deep-sea fish cells. Because almost none of the EYFP-actin was incorporated into actin filaments of the cells, we replaced the relatively large EYFP tag with a chemical fluorescent compound and succeeded in incorporating fluorescently labeled rabbit actins into the deep-sea fish actin filaments. Most of the filament structure in the cells with rabbit actin inserted underwent depolymerization when subjected to pressure of 100 MPa for 20 min, in contrast to control cells. There were no differences in the tubulin filament structure between control cells and deep-sea fish cells with fluorescein-labeled bovine tubulin inserted after the application of pressure ranging from 40 to 100 MPa for 20 min.     

Insights into Deep-Sea Sediment Fungal Communities from the East Indian Ocean Using Targeted Environmental Sequencing Combined with Traditional Cultivation

The fungal diversity in deep-sea environments has recently gained an increasing amount attention. Our knowledge and understanding of the true fungal diversity and the role it plays in deep-sea environments, however, is still limited. We investigated the fungal community structure in five sediments from a depth of ∼4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation. This approach resulted in the recovery of a total of 45 fungal operational taxonomic units (OTUs) and 20 culturable fungal phylotypes. This finding indicates that there is a great amount of fungal diversity in the deep-sea sediments collected in the East Indian Ocean. Three fungal OTUs and one culturable phylotype demonstrated high divergence (89%–97%) from the existing sequences in the GenBank. Moreover, 44.4% fungal OTUs and 30% culturable fungal phylotypes are new reports for deep-sea sediments. These results suggest that the deep-sea sediments from the East India Ocean can serve as habitats for new fungal communities compared with other deep-sea environments. In addition, different fungal community could be detected when using targeted environmental sequencing compared with traditional cultivation in this study, which suggests that a combination of targeted environmental sequencing and traditional cultivation will generate a more diverse fungal community in deep-sea environments than using either targeted environmental sequencing or traditional cultivation alone. This study is the first to report new insights into the fungal communities in deep-sea sediments from the East Indian Ocean, which increases our knowledge and understanding of the fungal diversity in deep-sea environments.