Determining rates of virus production in aquatic systems by the virus reduction approach,

The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells due to the decreased abundance of free virus particles. This reoccurrence can be quantified and used to assess production and cell lysis rates. Several modifications of the method are presented and compared. The approaches have great potential for elucidating trends in virus production rates as well as for making generalized estimates of the quantitative effects of viruses on marine microbial communities

Effects of Sodium Azide on the Abundance of Prokaryotes and Viruses in Marine Samples

Flow cytometry is set to become the standard method for enumerating prokaryotes and viruses in marine samples. However, the samples need to be flash-frozen in liquid nitrogen directly after aldehyde fixation. Because liquid nitrogen may not always be available, we tested the potential of sodium azide as a preservative for prokaryotes and viruses in marine samples as a possible alternative. For that we conducted incubation experiments with untreated and sodium azide treated marine water samples at 4°C and room temperature. The data indicate that sodium azide cannot be used to maintain marine samples used for the enumeration of prokaryotes and viruses

Animal community dynamics at senescent and active vents at the 9° N East Pacific Rise after a volcanic eruption

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gollner, S., Govenar, B., Arbizu, P. M., Mullineaux, L. S., Mills, S., Le Bris, N., Weinbauer, M., Shank, T. M., & Bright, M. Animal community dynamics at senescent and active vents at the 9° N East Pacific Rise after a volcanic eruption. Frontiers in Marine Science, 6, (2020): 832, doi:10.3389/fmars.2019.00832.In 2005/2006, a major volcanic eruption buried faunal communities over a large area of the 9°N East Pacific Rise (EPR) vent field. In late 2006, we initiated colonization studies at several types of post eruption vent communities including those that either survived the eruption, re-established after the eruption, or arisen at new sites. Some of these vents were active whereas others appeared senescent. Although the spatial scale of non-paved (surviving) vent communities was small (several m2 compared to several km2 of total paved area), the remnant individuals at surviving active and senescent vent sites may be important for recolonization. A total of 46 meio- and macrofauna species were encountered at non-paved areas with 33 of those species detected were also present at new sites in 2006. The animals living at non-paved areas represent refuge populations that could act as source populations for new vent sites directly after disturbance. Remnants may be especially important for the meiofauna, where many taxa have limited or no larval dispersal. Meiofauna may reach new vent sites predominantly via migration from local refuge areas, where a reproductive and abundant meiofauna is thriving. These findings are important to consider in any potential future deep-sea mining scenario at deep-sea hydrothermal vents. Within our 4-year study period, we regularly observed vent habitats with tubeworm assemblages that became senescent and died, as vent fluid emissions locally stopped at patches within active vent sites. Senescent vents harbored a species rich mix of typical vent species as well as rare yet undescribed species. The senescent vents contributed significantly to diversity at the 9°N EPR with 55 macrofaunal species (11 singletons) and 74 meiofaunal species (19 singletons). Of these 129 species associated with senescent vents, 60 have not been reported from active vents. Tubeworms and other vent megafauna not only act as foundation species when alive but provide habitat also when dead, sustaining abundant and diverse small sized fauna.We received funding from the Austrian FWF (GrantP20190-B17; MB), the U.S. National Science Foundation (OCE-0424953; to LM, D. McGillicuddy, A. Thurnherr, J. Ledwell, and W. Lavelle; and OCE-1356738 to LM), and the European Union Seventh Framework Programme (FP7/2007-2013) under the MIDAS project, Grant Agreement No. 603418. Ifremer and CNRS (France) supported NL cruise participation and sensor developments. BG was supported by a postdoctoral fellowship from the Deep Ocean Exploration Institute at WHOI (United States). TS was supported by the U.S. National Science Foundation (OCE-0327261 to TS and OCE-0937395 to TS and BG)

Comparison of Deep-Water Viromes from the Atlantic Ocean and the Mediterranean Sea

The aim of this study was to compare the composition of two deep-sea viral communities obtained from the RomancheFracture Zone in the Atlantic Ocean (collected at 5200 m depth) and the southwest Mediterranean Sea (from 2400 m depth)using a pyro-sequencing approach. The results are based on 18.7% and 6.9% of the sequences obtained from the AtlanticOcean and the Mediterranean Sea, respectively, with hits to genomes in the non-redundant viral RefSeq database. Theidentifiable richness and relative abundance in both viromes were dominated by archaeal and bacterial viruses accountingfor 92.3% of the relative abundance in the Atlantic Ocean and for 83.6% in the Mediterranean Sea. Despite characteristicdifferences in hydrographic features between the sampling sites in the Atlantic Ocean and the Mediterranean Sea, 440 virusgenomes were found in both viromes. An additional 431 virus genomes were identified in the Atlantic Ocean and 75 virusgenomes were only found in the Mediterranean Sea. The results indicate that the rather contrasting deep-sea environmentsof the Atlantic Ocean and the Mediterranean Sea share a common core set of virus types constituting the majority of bothvirus communities in terms of relative abundance (Atlantic Ocean: 81.4%; Mediterranean Sea: 88.7%)

Response to Interpreting the results of oceanic mesoscale enrichment experiments: Caveats and lessons from limnology and coastal ecology

Peer Reviewe

Response of bacterioplankton community structure to an artificial gradient of pCO2 in the Arctic Ocean

In order to test the influences of ocean acidification on the ocean pelagic ecosystem, so far the largest CO2 manipulation mesocosm study (European Project on Ocean Acidification, EPOCA) was performed in Kings Bay (Kongsfjorden), Spitsbergen. During a 30 day incubation, bacterial diversity was investigated using DNA fingerprinting and clone library analysis of bacterioplankton samples. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the PCR amplicons of the 16S rRNA genes revealed that general bacterial diversity, taxonomic richness and community structure were influenced by the variation of productivity during the time of incubation, but not the degree of ocean acidification. A BIOENV analysis suggested a complex control of bacterial community structure by various biological and chemical environmental parameters. The maximum apparent diversity of bacterioplankton (i.e., the number of T-RFs) in high and low pCO2 treatments differed significantly. A negative relationship between the relative abundance of Bacteroidetes and pCO2 levels was observed for samples at the end of the experiment by the combination of T-RFLP and clone library analysis. Our study suggests that ocean acidification affects the development of bacterial assemblages and potentially impacts the ecological function of the bacterioplankton in the marine ecosystem

Dynamics of nutrients, total organic carbon, prokaryotes and viruses in onboard incubations of cold-water corals

The potential influence of the cold-water corals (CWCs) Lophelia pertusa and Madrepora oculata on the dynamics of inorganic nutrient and total organic carbon (TOC) concentrations and the abundances of prokaryotes and viruses in bottom water was assessed in onboard incubation experiments. Ammonium, nitrite, dissolved inorganic nitrogen (DIN), dissolved inorganic phosphorus (DIP) and TOC concentrations and N:P ratios were typically higher in incubation water with corals than in controls, whereas nitrate concentrations did not reveal a clear trend. Mucus release (normalized to coral surface) was estimated by the net increase rate of TOC concentrations and averaged 23 +/- 6 mg C m(-2) h(-1) for L. pertusa and 21 +/- 8 mg C m(-2) h(-1) for M. oculata. Prokaryotic and viral abundance and turnover rates were typically stimulated in incubation water with corals. This estimated prokaryotic stimulation averaged 6.0 +/- 3.0x10(9) cells m(-2) h(-1) for L. pertusa and 8.4 +/- 2.9x10(9) cells m(-2) h(-1) for M. oculata, whereas the estimated viral stimulation averaged 15.6 +/- 12.7x10(9) particles m(-2) h(-1) for L. pertusa and 4.3 +/- 0.4x10(9) particles m(-2) h(-1) M. oculata. Our data suggest that prokaryotes and viruses are released from corals and that nutrient and mucus release enhanced prokaryotic and viral production. The result of this stimulation could be a fuelling of bottom water in CWC reefs with nutrients and organic matter and consequently an enhancement of microbe-mediated processes

Production of individual marine organic aggregates using paramagnetic microspheres : a new tool for examining microbial associations with aggregates

We describe a new method to produce marine aggregates from natural organic material based on the sticking properties of transparent exopolymeric particles. Seawater samples were prescreened and ultrafiltered to concentrate the 30 kDa to 10 mu m size fraction. First, we produced small magnetizable aggregates by combining glass microfibers and paramagnetic 1-mu m beads with the organic matter present in the concentrated solution. The second step involved clustering the small aggregates into a single macro-aggregate, using a small ring-shaped magnet as an aggregation nucleus. Viral and bacterial densities, determined after dissolution of the newly formed aggregates with methanol, averaged 13.8 x 10(6) +/- 3.6 x 10(6) vir. agg.(-1) and 4.1 x 10(6) +/- 1.1 x10(6) bact. agg.(-1). Bacterial respiration and production measurements of single aggregates averaged 8.47 +/- 1.72 nmol O-2 agg.(-1) h(-1) and 1.54 +/- 0.45 ng C agg.(-1) h(-1), respectively. Particulate organic carbon and nitrogen content of the newly formed macro-aggregates averaged 31.92 +/- 2.67 mu g C agg.(-1) and 3.44 +/- 0.43 mu g N agg.(-1), respectively. This approach allows the concentration and isolation of the organic matter precursors that compose natural aggregates and provides a simple protocol for recombining those precursors into single newly formed macro-aggregates, which can then be easily manipulated for further investigation. This method is a new tool for investigations into the interactions between microorganisms and marine aggregates and their implications at the ecosystem level, but also into the interactions between aggregates and dissolved organic or inorganic substances

Changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir

Bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (80% of the total bacteria by the end of the experiment. Once again, BCC changed strongly and a significant fraction of the large filaments was detected using a FISH probe targeted to members of the Flectobacillus lineage. Shifts of BCC were also reflected in DGGE patterns and in the increases in the relative importance of both beta proteobacteria and members of the Cytophaga-Flavobacterium cluster, which consistently formed different parts of the bacterial flocs. Viral concentrations and frequencies of infected cells were highly significantly correlated with grazing rates, suggesting that protistan grazing may stimulate viral activity