The Hadal Amphipod Hirondellea gigas Possessing a Unique Cellulase for Digesting Wooden Debris Buried in the Deepest Seafloor

The Challenger Deep in the Mariana Trench is the deepest point in the ocean (10,994 m). Certain deep-sea animals can withstand the extreme pressure at this great depth. The amphipod Hirondellea gigas is a resident of the Challenger Deep. Amphipods are common inhabitants at great depths and serve as scavengers. However, there is relatively little information available regarding the physiology of H. gigas or this organism's ecological interactions in the hadopelagic zone. To understand the feeding behavior of this scavenger in the deepest oligotrophic hadal zone, we analyzed the digestive enzymes in whole-body extracts. We describe the detection of amylase, cellulase, mannanase, xylanase, and α-glycosidase activities that are capable of digesting plant-derived polysaccharides. Our identification of glucose, maltose, and cellobiose in the H. gigas extracts indicated that these enzymes function under great pressure in situ. In fact, the glucose content of H. gigas averaged 0.4% (w/dry-w). The purified H. gigas cellulase (HGcel) converted cellulose to glucose and cellobiose at an exceptional molar ratio of 2∶1 and efficiently produced glucose from dried wood, a natural cellulosic biomass, at 35°C. The enzyme activity increased under a high hydrostatic pressure of 100 MPa at 2°C, conditions equivalent to those found in the Challenger Deep. An analysis of the amino acid sequence of HGcel supported its classification as a family 31 glycosyl hydrolase. However, none of the enzymes of this family had previously been shown to possess cellulase activity. These results strongly suggested that H. gigas adapted to its extreme oligotrophic hadal oceanic environment by evolving digestive enzymes capable of digesting sunken wooden debris.     

Role of Challenger pesticide and plant extracts on some physiological parameters of the cotton leafworm,Spodoptera littoralis (Boisd.)

Fourth instar larvae of cotton leafworm, Spodoptera littoralis (Boisd.), fed on castor bean leaves treated with sub-lethal concentrations of both alcohol and hexane extracts of Egyptian conyza and Challenger 36% SC insecticide as well to study their effects on mortality, food consumption and utilisation of food. The tested insecticides exhibited relatively high mortality in alcoholic extract of Egyptian conyza (5.0% concentration) followed by Challenger (1.0% concentration). Results showed a slight reduction in the consumption index for larvae treated with both alcoholic extract and Challenger at low concentrations, while hexane extract (5%) recorded significant increase. The approximate digestibility (AD) was reduced in all treatments of alcoholic extract and the relative growth rate insignificantly decreased at 5% concentration, whereas AD increased for larvae fed on Challenger 0.25% concentration. The lower concentration of alcoholic extract of conyza and all treatments of Challenger pesticides induced insignificant decrease in the efficiency of conversion of the ingested food, while hexane extract exhibited insignificant increase. Challenger at all tested concentrations achieved insignificant decrease in the efficiency of the conversion of digested food with respect to the control.     

Geographic limitations in the movement of Deep‐Draft tankers between the Indian and pacific oceans

Abstract

The need to move increasing volumes of petroleum over long distances has stimulated the construction of a large fleet of tankers of unprecedented dimensions. The extraordinarily deep drafts of these ships have necessitated a reevaluation of the extent of navigable ocean. Because some major shipping lanes are closed to their movement, alternative routes have developed. For this study, hydrographic charts of the passages between the Indian and Pacific oceans were examined in detail and special purpose maps were constructed. The patterns illustrate the categories of negative ocean, open ocean, and ocean conditional for the movement of deep‐draft ships. Actual and potential routeways for deep‐draft ships past Southeast Asia are identified and the limitations of the Malacca/Singapore straits are described in greater detail.     

Taxonomic studies of extremely barophilic bacteria isolated from the Mariana Trench and description of Moritella yayanosii sp. nov., a new barophilic bacterial isolate

We have isolated two strains of extremely barophilic bacteria from sediment collected from the world's deepest ocean floor in the Mariana Trench, Challenger Deep, at a depth of 10898m [Kato C, Li L, Nogi Y, Nakamura Y, Tamaoka J, Horikoshi K (1998) Appl Environ Microbiol 64:1510-1513]. One strain, DB21MT-2, was identified as a strain of Shewanella benthica, and the other strain, DB21MT-5, is closely affiliated with members of the genus Moritella on the basis of 16S rDNA sequence analysis. The hybridization values for DNA-DNA relatedness between DB21MT-5 and the Moritella reference strains were significantly lower than that accepted as the phylogenetic definition of a species. Based on this and other taxonomic differences, strain DB21MT-5 appears to represent a novel obligately barophilic deep-sea Moritella species. The name Moritella yaynanosii (JCM 10263) is proposed. This is the first proposed species of obligately barophilic bacteria of the genus Moritella.     

Protist diversity and function in the dark ocean – Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists

The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an “untapped reservoir” of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.     

Effect of Hydrostatic Pressure on Growth and Viability of Vibrio parahaemolyticus

Six strains of marine bacteria, including three strains of Vibrio parahaemolyticus, two Vibrio spp isolated from coastal regions, and the deep ocean isolate Pseudomonas bathycetes, were examined for ability to survive and grow at deep ocean hydrostatic pressures. V. parahaemolyticus and the coastal Vibrio spp. were unable to survive or grow at 200, 400, 600, 800, or 1,000 atm of pressure. In contrast, the deep ocean isolate P. bathycetes was capable of survival and growth at these pressures. The evidence strongly supports the neritic or estuarine origin and habitat for V. parahaemolyticus.     

Dive Europa: a search-for-life initiative.

Liquid water, underwater volcanoes and possibly life forms have been suggested to be present beneath the estimated 10 km-thick ice shell of Europa the Jovian satellite J2. Europa's possible ocean is estimated to be 100-200km deep. Despite the great depth of the Europa's ocean, hydrostatic pressure at the seafloor would be 130-260 MPa, corresponding to 13-26 km depth of a theoretical Earth's ocean. The hydrostatic pressure is not beyond the edge of existing deep-sea technology. Here we propose exploration of Europa's deep-sea by the use of current technologies, taking a symbolic example of a deep submergence vehicle Shinkai 6500 which dives to a depth of 6.5 km deep (50 km depth of Europa's ocean). Shinkai 6500 is embarkable in the payload bay of the Space Shuttles in terms of size and weight for the transportation to a Low Earth Orbit (LEO). Secondary boost is needed for interplanetary flight from the LEO. On-orbit assembly of the secondary booster is a technological challenge. The International Space Station (ISS) and ISS-related technologies will facilitate the secondary boost. Also, ice shell drilling is a challenge and is needed before the dive into Europa's ocean. These challenges should be overcome during a certain leading time for matured experience in the ISS operation.     

Climate change considerations are fundamental to management of deep‐sea resource extraction

Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep‐ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep‐sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep‐seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full‐cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth‐System Model projections of climate‐change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep‐seabed mining. Models that combine climate‐induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep‐seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral‐related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep‐ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.     

Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep‐sea habitats

The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep‐sea habitats due to under‐sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200–1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under‐sampled and/or under‐studied taxa.     

Filter-feeding gelatinous macrozooplankton response to climate change and implications for benthic food supply and global carbon cycle

It is often suggested that gelatinous zooplankton may benefit from anthropogenic pressures of all kinds and in particular from climate change. Large pelagic tunicates, for example, are likely to be favored over other types of macrozooplankton due to their filter-feeding mode, which gives them access to small preys thought to be less affected by climate change than larger preys. In this study, we provide model-based estimate of potential community changes in macrozooplankton composition and estimate for the first time their effects on benthic food supply and on the ocean carbon cycle under two 21st-century climate-change scenarios. Forced with output from an Earth System Model climate projections, our ocean biogeochemical model simulates a large reduction in macrozooplankton biomass in response to anthropogenic climate change, but shows that gelatinous macrozooplankton are less affected than nongelatinous macrozooplankton, with global biomass declines estimated at −2.8% and −3.5%, respectively, for every 1°C of warming. The inclusion of gelatinous macrozooplankon in our ocean biogeochemical model has a limited effect on anthropogenic carbon uptake in the 21st century, but impacts the projected decline in particulate organic matter fluxes in the deep ocean. In subtropical oligotrophic gyres, where gelatinous zooplankton dominate macrozooplankton, the decline in the amount of organic matter reaching the seafloor is reduced by a factor of 2 when gelatinous macrozooplankton are considered (−17.5% vs. −29.7% when gelatinous macrozooplankton are not considered, all for 2100 under RCP8.5). The shift to gelatinous macrozooplankton in the future ocean therefore buffers the decline in deep carbon fluxes and should be taken into account when assessing potential changes in deep carbon storage and the risks that deep ecosystems may face when confronted with a decline in their food source.     

Deep-Sea Bioluminescence Blooms after Dense Water Formation at the Ocean Surface

The deep ocean is the largest and least known ecosystem on Earth. It hosts numerous pelagic organisms, most of which are able to emit light. Here we present a unique data set consisting of a 2.5-year long record of light emission by deep-sea pelagic organisms, measured from December 2007 to June 2010 at the ANTARES underwater neutrino telescope in the deep NW Mediterranean Sea, jointly with synchronous hydrological records. This is the longest continuous time-series of deep-sea bioluminescence ever recorded. Our record reveals several weeks long, seasonal bioluminescence blooms with light intensity up to two orders of magnitude higher than background values, which correlate to changes in the properties of deep waters. Such changes are triggered by the winter cooling and evaporation experienced by the upper ocean layer in the Gulf of Lion that leads to the formation and subsequent sinking of dense water through a process known as “open-sea convection”. It episodically renews the deep water of the study area and conveys fresh organic matter that fuels the deep ecosystems. Luminous bacteria most likely are the main contributors to the observed deep-sea bioluminescence blooms. Our observations demonstrate a consistent and rapid connection between deep open-sea convection and bathypelagic biological activity, as expressed by bioluminescence. In a setting where dense water formation events are likely to decline under global warming scenarios enhancing ocean stratification, in situ observatories become essential as environmental sentinels for the monitoring and understanding of deep-sea ecosystem shifts.     

Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments

Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community—Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.     

The wood preservative chromated copper arsenate is a substrate for trimethylarsine biosynthesis.

The wood preservative chromated copper arsenate (CCA) is a very widely used product. As it contains both copper and arsenic, it is not dissimilar to the pigments Scheele's green and Schweinfurter's green which were found to be biologically convertible to the toxic Gosio gas (B. Gosio, Ber. 30:1024-1026, 1897) later identified by Challenger and co-workers as trimethylarsine (F. Challenger, Adv. Enzymol. 12:429-491, 1951). Thus, it was of interest to determine whether microbiological action on CCA and wood treated with CCA could result in the production of trimethylarsine. We report that the fungus Candida humicola will produce this arsine from dilute solutions of CCA and from wood soaked in CCA.     

The wood preservative chromated copper arsenate is a substrate for trimethylarsine biosynthesis

The wood preservative chromated copper arsenate (CCA) is a very widely used product. As it contains both copper and arsenic, it is not dissimilar to the pigments Scheele's green and Schweinfurter's green which were found to be biologically convertible to the toxic Gosio gas (B. Gosio, Ber. 30:1024-1026, 1897) later identified by Challenger and co-workers as trimethylarsine (F. Challenger, Adv. Enzymol. 12:429-491, 1951). Thus, it was of interest to determine whether microbiological action on CCA and wood treated with CCA could result in the production of trimethylarsine. We report that the fungus Candida humicola will produce this arsine from dilute solutions of CCA and from wood soaked in CCA.     

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%–86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.     

Historic trawl data and recent information infers temporal change in the occurrence of squid in the diet of orange roughy (Hoplostethus atlanticus Collett) in New Zealand

A review of historical trawl data for orange roughy on Chatham Rise and Challenger Plateau, New Zealand, between the years 1984 and 1996 infers a shift in this species’ diet, with a progressive decline in the percentage occurrence of squid being apparent. On Chatham Rise, this decline in the percentage occurrence of squid appears to be compensated for by increases in the percentage occurrence of fish and crustaceans in orange roughy diet, whereas on Challenger Plateau, decreases in all of squid, fish and crustaceans are apparent. New orange roughy dietary data for 2004 from Chatham Rise is consistent with earlier data series, with further declines in the percentage occurrence of squid apparent. Declines in the occurrence of squid in the diet of orange roughy could be attributed to declines in the abundance of squid as a consequence of fisheries activity.     

Abyssal food limitation, ecosystem structure and climate change

The abyssal seafloor covers more than 50% of the Earth and is postulated to be both a reservoir of biodiversity and a source of important ecosystem services. We show that ecosystem structure and function in the abyss are strongly modulated by the quantity and quality of detrital food material sinking from the surface ocean. Climate change and human activities (e.g. successful ocean fertilization) will alter patterns of sinking food flux to the deep ocean, substantially impacting the structure, function and biodiversity of abyssal ecosystems. Abyssal ecosystem response thus must be considered in assessments of the environmental impacts of global warming and ocean fertilization.     

The possible roles of algae in restricting the increase in atmospheric CO2 and global temperature

ABSTRACT

Anthropogenic inputs are increasing the CO₂ content of the atmosphere, and the CO₂ and total inorganic C in the surface ocean and, to a lesser degree, the deep ocean. The greenhouse effect of the increased CO₂ (and, to a lesser extent, other greenhouse gases) is very probably the major cause of present global warming. The warming increases temperature of the atmosphere and the surface ocean to a greater extent than the deep ocean, with shoaling of the thermocline, decreasing nutrient flux to the surface ocean where there is greater mean photosynthetic photon flux density. These global changes influence algae in nature. However, it is clear that algae are important, via the biological pump, in decreasing the steady state atmospheric and ocean surface CO₂, and thus decreasing radiative forcing, a reduction enhanced by algal increases in albedo. As well as these natural processes there are possibilities that algae can, with human intervention, partly offset the increase in atmospheric CO₂. One possibility is to grow algae as sources of fuel for transport, in principle providing an energy source that is close to CO₂-neutral. The other possibility is to increase the role of algae in sequestering CO₂ as organic C over periods of hundreds or more years in the deep ocean and marine sediments and/or increasing albedo and decreasing radiative forcing of temperature. There are problems, currently unresolved, in the economically viable production of algal biofuels without carbon trading subsidies. Enhanced algal CO₂ sequestration also has costs, both in resource input (phosphorus (P) from high P content rocks, a limited resource with a competing use as an agricultural fertilizer) and adverse environmental effects. For example, ocean anoxic zones producing N₂O and increased algal production of short-lived halocarbons by algae that both, through breakdown, destroy O₃ and increase UV flux to the Earth’s surface.     

The metabolic potential of the single cell genomes obtained from the Challenger Deep,Mariana Trench within the candidate superphylum Parcubacteria (OD1)

Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason, we analyzed 12 Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep‐sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra‐deep hadal environment.     

Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump

The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used to understand the significance of heterotrophic microeukaryotes in the transport of particulate organic matter from the surface to the dark ocean. Unlike the sharp vertical decrease of prokaryotic biomass, the LP biomass only slightly decreased with depth and eventually exceeded prokaryotic biomass in the bathypelagic layer. Sequencing identified high diversity of the LP communities with a dominance of Aplanochytrium at all depths. Notably, ASVs that were observed in the surface layer comprised ~20% of ASVs and ~60% of sequences in each of the deeper (including bathypelagic) layers, suggesting potential vertical export of the LP populations to the deep ocean. Further analyses of the vertical patterns of the 50 most abundant ASVs revealed niche partitioning of LP phylotypes in the pelagic ocean, including those that could decompose organic detritus and/or facilitate the formation of fast-sinking particles. Overall, this study presents several lines of evidence that the LP can be an important component of the biological pump through their multiple ecotypes in the pelagic ocean.