Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses

BACKGROUND

Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes.

METHODS

Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation.

RESULTS

Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.).

CONCLUSIONS

The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.

Vertical distribution and acoustic characteristics of deep water micronektonic crustacean in the Bay of Biscay

Vertical distribution of meso- and bathypelagic crustacean are scarcely known. The logistics involved in their studies hinder an adequate assessment of their role in the deep ecosystems. As a result, the literature on zooplankton scattering models is mainly focused on epipelagic organisms, particularly krill species. This study analyses data of the plankton community classified by family from the surface down to 2000 m taken in the Bay of Biscay, but focusses on the meso- and bathypelagic zone. Photographic data was employed to obtain a micronektonic crustacean shape catalogue. The Distorted Wave Born Approximation (DWBA) model was employed to estimate target strength. Pasiphaeidae, Euphausiidae and Acanthephyridae were mainly distributed above 500 m depth, while Benthesicymidae, Sergestidae and Mysidae were concentrated in the lower mesopelagic to upper bathypelagic area. The most abundant species were Euphausiidae and Benthesicymidae with up to 30 and 40 individuals per cubic meter respectively. Standard length ranged from 8 to 85 mm and was significantly related with height but not with depth. The Pasiphaeidae family presented the largest individuals followed by Acanthephyridae and Sergestidae while Euphausiidae, Benthesicymidae, and Mysidae were shorter. An smooth fluid-like response was estimated for shorter organisms, while individuals of 60 mm or higher present TS oscillations from around 60 kHz. Pasiphaeidae present an almost 10 dB higher TS than Sergestidae, Acanthephyridae and Benthesicymidae while Mysidae followed by Euphausiidae produce the lower TS. Simple models of TS values at broadside versus the logarithm of standard length (SL) that can be employed as an approximation of their scattering are provided for four common frequencies (TS = 58.5*log₁₀(SL)-188.7, TS = 57.03*log₁₀(SL)-174.1, TS = 22.48*log₁₀(SL)-157.14, TS = 17.55*log₁₀(SL)-135 and TS = 10.53*log₁₀(SL)-109 at 18, 38, 70, 120 and 200 kHz respectively). Changes in body density and sound speed contrast may increase by 10 or 2 dB the resulting TS respectively but are constant in phase, while orientation can decrease the TS by up to 20 dB at the higher frequencies and alter the spectra to an almost flat trend. This study provides further insight into the vertical distribution and physical characteristics of the micronektonic crustacean families inhabiting the Bay of Biscay down to 2000 m depth. It also estimates their echo from a real-shape catalogue that can be employed to infer knowledge from acoustic recordings, particularly of the lower mesopelagic and the bathypelagic zones.

Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome

The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.

A bathypelagic ostracod Conchoecissa nigromaculatus sp. nov. (Myodocopa, Halocyprididae) from the South China Sea

Pelagic ostracods are one of the main groups of zooplankton and are abundant in marine ecosystems worldwide. The record of marine planktonic ostracod species in the central and southern part of the South China Sea accounts over for one-third of the total recorded marine planktonic ostracods in seas around China. In this study, we examined and compared the specimens from a recent cruise in this region that appeared to be different from previously described species of genus Conchoecissa, and then confirmed them as a new bathypelagic species Conchoecissa nigromaculatus. These specimens clearly differed from the other species of genus Conchoecissa with differences observed in the size, carapace, locations of glands, mandible, maxilla, sixth limb, and furca. In this species, mandibular coxal endite has no ventral finger process, maxilla has prominently large endites and has only two claws on the tip, the sixth limb has very simple endites, and this species has distinctive features not previously observed in the tribe Conchoeciini before. It is therefore necessary to emend the diagnosis of this group.