A new group of bacteriophages is revealed

Researchers, Bischoff et al. (2019), were able to isolate and sequence viruses found within bacterial samples collected from the North Sea. Over 5,000 marine metagenomes from across the globe, including data from TARA ocean and Malaspina expeditions, were then screened for their presence. Through this, three genera of Rhodobacteraceae were revealed to host a newly found group of phages – called Cobaviruses. These bacteriophages appear to be relatively ubiquitous within tropical and temperate regions. Phylogenetic analysis suggests that the group may even warrant placement within a newly proposed subfamily and genus, within the Podoviridae family.

Cobaviruses could regulate dynamics within Rhodobacteraceae populations. As Rhodobacteraceae represent one of the most abundant and diverse groups of bacteria within the ocean, viruses may have more influence on our oceans than previously thought. Future research aiming to understand this relationship could shed light on the complex microbial interactions occurring here.

Whilst several genomes within the study remain incomplete, likely due to difficulties they had with sequencing, this study remains an insightful first glimpse at this new bacteriophage. Phages, and the lysin enzymes they produce, can also be studied and used as an alternative to antibiotic treatments, potentially opening new avenues for medical research.

Bischoff, V., Bunk, B., Meier-Kolthoff, J.P., Spröer, C., Poehlein, A., Dogs, M., Nguyen, M., Petersen, J., Daniel, R., Overmann, J., Göker, M., Simon, M., Thorsten Brinkhoff, T., & Moraru, C. (2019). Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems. ISME Journal, 13, 1404–1421.

Can clams clean up aquaculture?

Aquaculture is a rapidly growing industry, but suffers from high levels of waste. Using shellfish as part of a bioremediation system has been proposed and is becoming more popular in China. This is thought to reduce nutrient outflow into the environment by increasing microbial activity within the wastewater treatment through bioturbuation. Lukwambe et al (2018) seeks to demonstrate this is the case. They used a simple experimental design; there were two treatments, one with the clam Sinovacula constricta and the other without, as a control. Both treatments pumped water from an intensive shrimp farm for 35 days, then had a total of 3 sediment samples taken from each. These were then split into the top (0-4cm) middle (4-8cm) and bottom (8-12cm) of the sediment. Then community structure was determined using high throughput sequencing and grouping into OTUs of 97%. Enzyme activity was determined and organic matter (in the form of total organic carbon, total organic nitrogen and total phosphorus) was measured. In the clam treatment enzyme activity increased and microbial diversity increased and favoured keystone denitrifying & nitrifying taxa. Total organic carbon and nitrogen levels were lower in the experimental treatment however, whilst total phosphorus showed no significant difference overall, in the 8-12cm and 0-4cm sample there was a significant decrease. Overall this paper concludes that there was a significant difference brought about by the clams and that they appear to be a fairly effective bioremediation tool.

Sponges play host to viruses

Marine sponges play host to a complex range of microorganisms which vary in abundance and diversity among species. While the current understanding of sponge-microbe interaction has dramatically increased recently, very little is known about how sponges and their microbiota interact with viruses. Many studies in the past have only alluded to the potential importance of viruses in areas such as sponge disease. Pascelli et al., 2018, aimed to bridge this gap in knowledge using three transmission electron microscopy preparation methods to provide the first-ever comprehensive morphological evaluation of sponge-associated viruses. Overall, across sponge cells  50 unique morphologies of viral-like particles (VLPs), with the frequent detection of multiple viral morphotypes highlighting a large number of potential hosts. Non-enveloped, non-tailed icosahedral VLPs were the most abundant morphology found. The study lacked a quantitative method, so future directions of this study would aim to include a quantitative method to count the number of VLPs per given area of tissue. In conclusion, the use of TEM confirmed that sponges are hosts to not only a diverse community of microorganisms but also a diverse community of viruses which allows for future research into characterising the taxonomy and function of viral sponge communities.

Pascelli, C., Laffy, P., Kupresanin, M., Ravasi, T. and Webster, N. (2018). Morphological characterisation of virus-like particles in coral reef sponges. PeerJ, 6, p.e5625.

Peanut worms: a sulphate reducing bacteria repellent!

Sedimental bacterial communities play an important ecological and biogeochemical role in tidal flat ecosystems for nutrient recycling and pollutant degradation. Bioturbation by benthic organisms can reshape the biological and physiochemical properties of the sediment, manipulating the distribution and composition of bacterial communities. The ecological role of sipunculid worms in reshaping bacterial community composition and biogeochemical cycles in intertidal zones is not currently well understood. Li et al. (2019) used high-throughput sequencing to investigate the microbial communities and their response to bioturbation by Sipunculus nudus at different depths in a sandy tidal flat.

This study demonstrates that bioturbation by S. nudus plays and important role in reshaping the bacterial community composition in intertidal regions, from the bottom to the surface layer. Interestingly, sulphate-reducing bacteria (SRB) were the most abundant taxa, indicating that sulphate reduction is the main process in the sandy tidal flat. The abundances of Desulfococcus and LCP-6 in the non-burrow sediment were greater than in the burrow sediment, suggesting that anoxic conditions are more suitable for Desulfococcus and LCP-6 when the activity of S. nudusis absent. In previous research, the accumulation of sulphide has been linked to the low biodiversity of S. nudus and reduced growth rates; and so, sulphate metabolism in the sediment and burrows require further study to understand the interaction between SRB and the presence of peanut worms further.

Li, J., Hu, R., Guo, Y., Chen, S., Xie, X., Qin, J.G., Ma, Z., Zhu, C. and Pei, S., 2019. Bioturbation of peanut worms Sipunculus nudus on the composition of prokaryotic communities in a tidal flat as revealed by 16S rRNA gene sequences. MicrobiologyOpen, p.e802.

Oceanic distribution of single-celled protosists

Single-celled protosists are key players in the world’s largest ecosystem through global biogeochemical cycling of energy and nutrients. Currently, there is a good understanding of their roles as primary producers and grazers yet in other aspects such as their life histories remain an overlooked area due to the challenges faced through culturing and sequencing. Seeleuthner et al., 2018, integrated single-celled genomics with metagenomics and metatranscriptomic sequence data to analyse the genome content and oceanic distribution of seven lineages of uncultured heterotrophic stramenopiles. Due to being highly abundant in temperate and tropical oceans the authors selected Marine stramenopile group 4 (MAST-4). Fundamentally the study found that each genome had a specific oceanic distribution linked to water temperature and depth. The conclusions of the study were limited by the data harvested from the TARA oceans project which used a singular time point per sample area resulting in a relatively low resolution of results. Despite this these findings provide the basis for a hypothesis of specialisation of niche species based on motility, nutrient range and trophic stages, in turn demonstrating the notion that heterotrophic marine protosists perform a diverse function in ocean ecology.

Seeleuthner, Y., Mondy, S., Lombard, V., Carradec, Q., Pelletier, E., Wessner, M., Leconte, J., Mangot, J., Poulain, J., Labadie, K., Logares, R., Sunagawa, S., de Berardinis, V., Salanoubat, M., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Pesant, S., Poulton, N., Stepanauskas, R., Bork, P., Bowler, C., Hingamp, P., Sullivan, M., Iudicone, D., Massana, R., Aury, J., Henrissat, B., Karsenti, E., Jaillon, O., Sieracki, M., de Vargas, C. and Wincker, P. (2018). Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans: Nature Communications, 9(1).

Time Space and Hydrothermal Vents

There are global patterns in microbial communities of hydrothermal vents, but variations in local geochemistry may play a more significant role in structuring the microbiome. The volatility of hydrothermal vents causes a variation in geochemistry over time, especially after eruptions. Investigations into the organisms that thrive within these environments has captured the imagination of the scientific community and public. To understand how these environments function and influence the global ocean a working knowledge of the microbiome’s role and structure is required.  

Researchers performed metagenome and metatranscriptome analyses of samples from 3 geochemically distinct vents at Axle sea mount over 3 years. The main findings were that each vent hosted distinct populations of microbes with different metabolic functions that changed vent geochemistry. A high proportion of methanotrophs at two sites was linked to increased hydrogen drawdown.  These populations were stable through time even after an eruption event in 2015.

The fluid chemistry, fluid dynamics, energetics and physical structure of the vents were seen to all play roles in the structuring of these microbial communities. The paper seems to overlook the role of microbial interactions which could be key to a better understanding of the big picture.

Fortunato, C. S., Larson, B., Butterfield, D. A., & Huber, J. A. (2018). Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids. Environmental microbiology, 20(2), 769-784.

The multifaceted lifestyle of ocean plants

The ecology of mixotrophs, i.e. organisms that combine autotrophy and heterotrophy, is not adequately understood, which is why these organisms are often misrepresented in biogeochemical models. Wilken et al. (2019) provide evidence for variation in the mixotrophic lifestyle of marine chrysophytes (genus Ochromonas) from coastal and pelagic ecosystems. The two eukaryotes were cultured under varying light and prey (Vibrio fischeri) availability. Subsequently, growth rate, ingestion rate and carbon fixation were quantified. While prey-depletion reduced growth in both organisms, the coastal chrysophyte maintained similar photosynthetic rates in the absence of prey. In contrast, primary production of the oceanic strain halved. Ingestion rates emulated photosynthetic rates in the oceanic chrysophyte, while they displayed an opposite trend in the coastal type. 

This study highlights the stark contrasts in mixotrophic metabolism found among congeners. While the coastal chrysophyte has the ability to switch effortlessly between photoautotrophy and heterotrophy, both metabolic pathways are coupled in the pelagic strain. The authors thus define the former as a facultative and the latter as an obligate mixotroph. The observed functional diversity can be interpreted as an adaptation to a fluctuating and stable environment, respectively. Nevertheless, it remains unclear how widespread these energy-acquisition strategies are in their respective habitat.

Wilken, S., Choi, C. J., & Worden, A. Z. (2019). Contrasting mixotrophic lifestyles reveal different ecological niches in two closely related marine protists. Journal of Phycology, 0(0), 0-0.