Contributions of single-cell genomics to our understanding of planktonic marine archaea

Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes—the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue ‘Single cell ecology’.

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group—the marine Thaumarchaeota—has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.

Production of Poly(3-Hydroxybutyrate-Co-3-Hydroxyvalerate) by Marine Archaea Haloferax mediterranei Dsm 1411 with Yeast Extract As Nutrient Source

In many countries, most of household goods are made from polymer or plastic. The polymer manufacturing industry has been relying on fossil fuel-based raw materials which are non-biodegradable. Plastics derived from these non-biodegradable sources will be difficult to degrade in nature, which in turn will pollute the environment and harm the ecosystem. One way to reduce the ecosystem damages caused by petroleum-based plastic is by using biodegradable materials for plastic industry, such as Polyhydroxyalkanoates (PHA). Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) or PHBV is an example of PHA that can be produced by several types of microorganism, one of them is marine archaea Haloferax mediterranei. The objective of this study is to determine the productivity of marine archaea H. mediterranei cultures to produce PHBV with yeast extract as main nutrient sources. Experiments and analysis were conducted in triplicate and batch operating system. During the fermentation process, optical density, glucose levels, phosphorus levels, pH, and dry cell weight (DCW) were observed. The final product was then analysed using GC-MS to determine 3HB (3-hydroxybutyrate) and 3HV (3-hydroxyvalerate) fraction composition in the PHBV. The results showed that the maximum specific growth rate (m) and doubling time (Td) of the H. mediterranei were 0.1258 hours-1 and 5.51 hours, respectively. H. mediterranei biomass increased until it reached stationary phase after 95 hours incubation. The PHBV content, dry biomass and yield of PHBV to substrate were 2.62 g/L, 29.1% and 0.27 g/g, respectively.

Productivity of Marine Archaea Haloferax mediterranei Culture in Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Production with Yeast Extract as Nutrient Source

Currently, most of household goods are made from polymer or plastic. The polymer manufacturing industry has been relying on fossil fuel-based raw materials which is non-biodegradable. Plastics derived from these non-biodegradable sources will be difficult to degrade in nature, which in turn will pollute the environment and harm the ecosystem. One way to reduce the ecosystem damages caused by plastic made from petroleum-based plastic is to use biodegradable materials as plastic industry raw materials, such as Polyhydroxyalkanoates (PHA). Poly (3-hydroxybutyrate-co-3-hydroxyvalerate) or PHBV is an example of PHA that can be produced by several types of microorganisms, such as marine archaea Haloferax mediterranei. This objective of this study is to determine the productivity of marine archaea cultures H. mediterranei to produce PHBV with yeast extract as main nutrient sources. H. mediterranei will produce PHBV at extreme conditions with excess carbon and limited nutrients. Experiments and analysis were conducted in triplicate and batch operating systems. During the fermentation process, Optical Density, glucose levels, phosphorus levels, pH, and Dry Cell Weight (DCW) were observed. The final product then analysed using GC-MS to determine the PHBV content and 3HB (3-hydroxybutyrate) and 3HV (3-hydroxyvalerate) fraction composition in the PHBV. The results show that the maximum specific growth rate and doubling time (Td) of the H. mediterranei were 0.1258 hours-1 and 5.51 hours. H. mediterranei biomass were increasing until it reached stationary phase at 95 hours. The results show PHBV content, dry biomass and yield PHA to substrate were 2.62 g/L, 29.1% and 0.27 g/g.

Marine archaea and archaeal viruses under global change

Global change is altering oceanic temperature, salinity, pH, and oxygen concentration, directly and indirectly influencing marine microbial food web structure and function. As microbes represent >90% of the ocean’s biomass and are major drivers of biogeochemical cycles, understanding their responses to such changes is fundamental for predicting the consequences of global change on ecosystem functioning. Recent findings indicate that marine archaea and archaeal viruses are active and relevant components of marine microbial assemblages, far more abundant and diverse than was previously thought. Further research is urgently needed to better understand the impacts of global change on virus–archaea dynamics and how archaea and their viruses can interactively influence the ocean’s feedbacks on global change.

Tracking natural organic carbon in the River Clyde, UK, using glycerol dialkyl glycerol tetraethers

ABSTRACTSurface sediments from a 100-km stretch of the River Clyde, UK, and its estuary were analysed for glycerol dialkyl glycerol tetraethers (GDGTs) to track the downstream changes in the source of organic matter (OM) and to evaluate the impact of urbanisation. Bacterial membrane lipids, named branched GDGTs (brGDGTs), produced in soils and rivers ranged from 1.6 to 58μgg−1 organic carbon (OC) and the isoprenoid GDGT crenarchaeol, mainly from marine archaea, ranged from 0.01 to 42μgg−1 OC. The highest brGDGT concentrations were in the upper river, in Glasgow city and in the outer estuary, suggesting higher soil-derived OM input. By contrast, crenarchaeol concentrations gradually increased from the tidal weir in Glasgow towards the sea. This spatial distribution of the tetraethers was reflected in the branched and isoprenoid tetraether (BIT) index, a proxy for soil versus marine carbon. The highest BIT values (1.0) occurred upstream, estuarine values ranged from 0.9 to 0.6 and the lowest values (0.4) were found in the outer estuary. An independent proxy for soil-derived OM, stable carbon isotope (δ13C) values, showed a comparable decrease in terrigenous OM contribution towards the sea, but was more variable compared to the BIT. Conversely, carbon/nitrogen (C/N) showed a constant trend, suggesting that it is not a reliable indicator of OM source in the Clyde. Neither BIT, δ13C nor C/N were able to reflect the input of urban effluents from Glasgow.