Deep-Sea pH

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

Recent advances in deep-sea natural products

Covering: 2009 to 2013. This review covers the 188 novel marine natural products described since 2008, from deep-water (50->5000 m) marine fauna including bryozoa, chordata, cnidaria, echinodermata, microorganisms, mollusca and porifera. The structures of the new compounds and details of the source organism, depth of collection and country of origin are presented, along with any relevant biological activities of the metabolites. Where reported, synthetic studies on the deep-sea natural products have also been included. Most strikingly, 75% of the compounds were reported to possess bioactivity, with almost half exhibiting low micromolar cytotoxicity towards a range of human cancer cell lines, along with a significant increase in the number of microbial deep-sea natural products reported.

Recent advances in deep-sea natural products

Review of deep-sea natural products covering the five-year period 2009–2013.

Concept of Biogenic Ferromanganese Crust Formation: Coccoliths as Bio-seeds in Crusts from Central Atlantic Ocean (Senghor Seamount/Cape Verde)

At depths of 2,000 to 3,000 m, seamounts from the Cape Verde archipelago (Central Atlantic Ocean) are largely covered with ferromanganese crusts. Here we studied 60 to 150 mm thick crusts from the Senghor Seamount (depth: 2257.4 m). The crusts have a non lamellated texture and are covered with spherical nodules. The chemical composition shows a dominance of MnO2 (26.1%) and Fe2O3 (38.8%) with considerable amounts of Co (0.74%) and TiO2 (2.1%). Analysis by scanning electron probe microanalyzer (EPMA) revealed a well defined compositional zonation of micro-layers; the distribution pattern of Mn does not match that of Fe. Analysis by high resolution scanning electron microscopy (SEM) revealed that coccospheres/coccoliths exist in the crust material as microfossils; most of the coccospheres/coccoliths are not intact. The almost circular coccoliths belong to the type of heterococcoliths and are taxonomically related to species of the family Calcidiscaceae. By energy dispersive X-ray spectroscopic analysis an accumulation of the coccoliths in the Mn- and Fe rich micronodules was detected. Focused ion beam assisted SEM mapping highlighted that the coccoliths in the crust are Mn rich, suggesting that the calcareous material of the algal skeleton has been replaced by Mn-minerals. We conclude that a biologically induced mechanism has been involved in the formation of the crusts, collected from the Cape Verde archipelago from depths of 2,000 to 3,000 m in the mixing region between the oxygen-minimum surface zone and the oxygen-rich deep waters; the deposition process might have been triggered by chemical reactions during the dissolution of the Ca-carbonate skeletons of the coccoliths allowing Mn(II) to oxidize to Mn(IV) and in turn to deposit this element in the crust material.

Effects of seawater acidification on early development of the intertidal sea urchin Paracentrotus lividus (Lamarck 1816)

The effect of pH ranging from 8.0 to 6.8 (total scale - pH(T)) on fertilization, cleavage and larval development until pluteus stage was assessed in an intertidal temperate sea urchin. Gametes were obtained from adults collected in two contrasting tide pools, one showing a significant nocturnal pH decrease (lowest pH(T)=7.4) and another where pH was more stable (lowest pH(T)=7.8). The highest pH(T) at which significant effects on fertilization and cleavage were recorded was 7.6. On the contrary, larval development was only affected below pH(T) 7.4, a value equal or lower than that reported for several subtidal species. This suggests that sea urchins inhabiting stressful intertidal environments produce offspring that may better resist future ocean acidification. Moreover, at pH(T) 7.4, the fertilization rate of gametes whose progenitors came from the tide pool with higher pH decrease was significantly higher, indicating a possible acclimatization or adaptation of gametes to pH stress.

Deep-sea natural products

This review covers the 390 novel marine natural products described to date from deep-water (>50 m) marine fauna, with details on the source organism, its depth and country of origin, along with any reported biological activity of the metabolites. Relevant synthetic studies on the deep-sea natural products have also been included.

Seawater Hydrogen-Ion Concentration: Vertical Distribution

Two major processes that affect the vertical distribution of hydrogen-ion concentration in the sub-Arctic region of the northeastern Pacific Ocean are the apparent oxygen utilization by marine organisms and, to a lesser extent, carbonate dissolution.

Marine Thiobacilli. I. Isolation and distribution

Bacterial colonies were isolated from Caribbean and Atlantic Ocean seawaters by the membrane filter technique and enrichment cultures in which thiosulfate was the only added source of energy. Although colonies were never abundant (0–275 per 100 ml), they have been recovered from the open ocean. The colonies were translucent to pale yellow on thiosulfate marine agar. The cells were Gram-negative motile rods (1–3 μ in length) requiring seawater for growth. The pH of the culture flasks dropped to 2.1 – 2.3 in some cases, and to 5.6 in others. On the basis of these observations, the colonies have been classified as marine thiobacilli.In seawater samples examined, the total reduced sulfur compounds ranged from 0 to 0.101 milliequivalents per liter.