Mathias Middelboe

Global-scale processes with a nanoscale drive: the role of marine viruses

Viruses, the smallest and most numerous of all biotic agents, represent the planets largest pool of genetic diversity. The sheer abundance of oceanic viruses results in ~1029 viral infections per day, causing the release of 108–109 tonnes of carbon per day from the biological pool (Suttle, 2007). Still, how and to what extent virus-mediated nanoscale processes are linked to global-scale biodiversity and biogeochemistry is poorly defined.

Isolation and Characterization of Bacteriophages Infecting the Fish Pathogen Flavobacterium psychrophilum

ABSTRACT Flavobacterium psychrophilum is a serious pathogen in trout aquaculture, responsible for the diseases rainbow trout fry syndrome (RTFS) and cold water disease (CWD). Bacteriophage control of F. psychrophilum may constitute a realistic approach in the treatment of these diseases; however, a detailed understanding of the phage-host interactions is needed to evaluate the potential of F. psychrophilum bacteriophages for that purpose. Twenty-two F. psychrophilum phages from Danish rainbow trout farms were isolated and characterized. The phage genome sizes differed considerably and fell into three major size classes (8.5 to 12 kb, 48 kb, and 90 kb). The phage host ranges comprised from 5 to 23 of the 28 tested F. psychrophilum strains, and 18 of the phage isolates showed unique host ranges. Each bacterial strain had a unique pattern of susceptibility to the 22 phages, and individual strains also showed large variations (up to 107-fold differences) in susceptibility to specific phages. Phage burst size (7 to 162 phages infected cell−1) and latency period (4 to 6 h) also showed pronounced differences both between phages and, for a specific phage, between host strains. In general, the characterization documented the presence of diverse F. psychrophilum phage communities in Danish trout farms, with highly variable patterns of infectivity. The discovery and characterization of broad-host-range phages with strong lytic potential against numerous pathogenic F. psychrophilum host strains thus provided the foundation for future exploration of the potential of phages in the treatment of RTFS and CWD.

Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties

Genetic, structural and physiological differences between strains of the marine bacterium Cellulophaga baltica MM#3 (Flavobacteriaceae) developing in response to the activity of two virulent bacteriophages, Phi S(M) and Phi S(T), was investigated during 3 weeks incubation in chemostat cultures. A distinct strain succession towards increased phage resistance and a diversification of the metabolic properties was observed. During the incubation the bacterial population diversified from a single strain, which was sensitive to 24 tested Cellulophaga phages, into a multistrain and multiresistant population, where the dominant strains had lost susceptibility to up to 22 of the tested phages. By the end of the experiment the cultures reached a quasi steady state dominated by Phi S(T)-resistant and Phi S(M) + Phi S(T)-resistant strains coexisting with small populations of phage-sensitive strains sustaining both phages at densities of > 10(6) plaque forming units (pfu) ml(-1). Loss of susceptibility to phage infection was associated with a reduction in the strains ability to metabolize various carbon sources as demonstrated by BIOLOG assays. This suggested a cost of resistance in terms of reduced physiological capacity. However, there was no direct correlation between the degree of resistance and the loss of metabolic properties, suggesting either the occurrence of compensatory mutations in successful strains or that the cost of resistance in some strains was associated with properties not resolved by the BIOLOG assay. The study represents the first direct demonstration of phage-driven generation of functional diversity within a marine bacterial host population with significant implications for both phage susceptibility and physiological properties. We propose, therefore, that phage-mediated selection for resistant strains contributes significantly to the extensive microdiversity observed within specific bacterial species in marine environments.

Viral and bacterial production in the North Water: in situ measurements, batch-culture experiments and characterization and distribution of a virus–host system

Abstract Growth and viral lysis of bacterioplankton at subzero temperatures were measured in the North Water polynya in July 1998. In situ measurements of bacterial carbon consumption in surface waters ranged from 15 to 63xa0μgxa0Cxa0l−1xa0d−1 in the eastern and 6 to 7xa0μgxa0Cxa0l−1xa0d−1 in the northern part of the polynya. Both bacterial abundance and activity appeared to increase in response to the decay of the phytoplankton bloom that developed in the North Water. Organic carbon was the limiting substrate for bacteria in the polynya since addition of glucose, but not inorganic nutrients, to batch cultures increased both the carrying capacity of the substrate and the growth rate of the bacteria. Bacterial growth rates ranged from 0.11 to 0.40xa0d−1, corresponding to bacterial generation times of 1.7–6.3xa0d. The in situ viral production rate was estimated both from the frequency of visibly infected cells and from the rate of viral production in batch cultures; it ranged from 0.04 to 0.52xa0d−1 and from 0.25 to 0.47xa0d−1, respectively. From 6% to 28% of bacterial production was found to be lost due to viral lysis. The average virus–bacteria ratio was 5.1±3.1, with the abundance of viruses being correlated positively with bacterial production. A Pseudoalteromonas sp. bacterial host and an infective virus were isolated from the polynya; characteristics and distribution of the virus–host system were examined. The Pseudoalteromonas sp. showed psychrotolerant growth and sustained significant production of viruses at 0°C. The virus–host system was found throughout the polynya. Overall the results suggested that a large amount of organic carbon released during the development and breakdown of the spring phytoplankton bloom was consumed by planktonic bacteria and that the microbial food web was an important and dynamic component of the planktonic food web in the North Water.

Viral lysis of marine bacterioplankton: Implications for organic matter cycling and bacterial clonal composition

Abstract Viruses are responsible for a large part of bacterio-plankton mortality in marine waters. They regulate population dynamics and diversity of the bacterial community and influence carbon dynamics via the release of bacterial cell contents. A large fraction of viral lysates is rapidly consumed by bacteria making the transfer of matter from bacteria via dissolved organic matter (DOM) and back to bacteria (the “Viral loop”) an efficient pathway. Viral infection has extensive and complex effects on bacterial species and clonal composition. The general perception of virus-bacteria interactions as a simple predator — prey interplay between lyric viruses and their specific hosts is a crude simplification. For instance, acquisition of resistance to viral infection is a common defense mechanism. In addition, lysogenic bacteria and broad-host range viruses are occasionally important; illustrating that lytic infection of a specific host is one of many viral effects on the bacterial community. In this minireview, ideas emerging from the most recent literature concerning virus-bacteria dynamics in marine plankton are synthesized. The significance of bioavailable and refractory lysis products for the DOM dynamics in marine waters is discussed along with the potential effects of viruses on bacterioplankton clonal composition (resistant vs. sensitive bacteria), diversity, and distributional patchiness.

Influence of bacterial uptake on deep‐ocean dissolved organic carbon

[1]xa0Particulate organic carbon (POC) sinking out of the sunlit euphotic zone at the surface of the ocean feeds the deep sea and alters the CO2 concentration of the atmosphere. Most of the sinking POC is reoxidized to dissolved inorganic carbon (DIC) before it hits the sea floor, but the mechanism for this is poorly understood. Here we develop a global model of the microbial loop in the aphotic zone based on new measurements of deep ocean bacterial metabolism. These together imply that a significant fraction of the decreasing POC flux with depth is converted to dissolved organic carbon (DOC) rather than directly to DIC as is commonly assumed, thereby providing the substrate for free-living bacteria in the deep ocean. The model suggests the existence of a substantial DOC-pool with a relatively fast turnover time in the deep sea. By implementing the microbial loop in a model of the global ocean circulation, we show that the observed gradient of DOC in the deep North Atlantic can be explained by the temperature dependence of bacterial metabolic activity in conjunction with the formation of deep-water at high latitudes.

Viral activity along a trophic gradient in continental margin sediments off central Chile

Abstract The influence of benthic viruses for bacterial mortality and carbon recycling was investigated in continental margin sediments off central Chile. Virus net production correlated significantly with the total benthic mineralization rate (r2=0.94, nu200a=u200a5) across a coastal–shelf transect. Within anoxic bag incubations, viral production also correlated significantly with bacterial activity (r2=0.86, nu200a=u200a7). The coupling between virus production and independent measurements of bacterial mineralization strongly suggested that benthic viral production was regulated by bacterial metabolic activity. From the rates of viral and bacterial production [2–6×106 virus-like particles (VLP) cm−3 h−1 and 2–7×105 cells cm−3 h−1, respectively], the potential impact of viruses on bacterial mortality and dissolved organic carbon production was estimated. Viral-induced mortality corresponded to 44–138% of bacterial net production, indicating that viruses had substantial impact on bacterial mortality. The estimated release of viral lysates of 0.3–3.5 nmol C cm−3 h−1, however, contributed insignificantly to bacterial carbon respiration (<8%). Compiling data for various sediments using the same incubation approach confirmed that (1) viral activity is coupled to benthic mineralization rates, (2) virus-induced mortality constitutes a significant loss factor for benthic bacteria, whereas (3) viral-mediated recycling of organic carbon plays a minor role in benthic environments.

Viral dynamics in a coastal sediment: seasonal pattern, controlling factors and relations to the pelagic–benthic coupling

Abstract The present study demonstrates for the first time a clear seasonal variability in the abundance of virobenthos that largely followed the variations in bacterial abundance. Following the spring bloom settlement, the benthic metabolic activity intensified and viral and bacterial abundance in the surface sediment increased 4.0- and 2.6-fold while the increase in a deeper anoxic sediment layer (6–10 cm) was 5.0- and 2.5-fold, respectively. The data strongly indicated a relationship between the pelagic–benthic coupling of organic material, the benthic metabolic activity, and the abundance and activity of bacteria and viruses in marine sediments on a seasonal basis. These suggestions were supported by parallel measurements of viral production rates in short-term laboratory incubations of surface and deep sediments: in these, viral production was significantly enhanced by addition of organic carbon and increasing temperature, with maximum values obtained in organic carbon-enriched incubations in July (19.7×106 and 38.4×106 virus-like particles cm−3 h−1 in surface and deep incubations, respectively). However, the relative enhancement was most explicit during periods of low in situ sedimentation. Conservative estimates indicated that viral lysis caused bacterial mortality rates of 2.8–27.4×105 cells cm−3 h−1, corresponding to 2–61% day−1 of bacterial standing stock during incubations (average 12.3±13.9%, n=18). An estimation of virus-generated dissolved organic carbon production using theoretical values of bacterial cell carbon content (20–50 fg cell−1), showed that viral lysates could sustain 2–38% of the measured bacterial respiration. The data suggest that viruses may have considerable impact on benthic microbial mortality and carbon cycling.

High rates of benthic microbial activity at 10.900 meters depth: Results from the Challenger Deep (Mariana Trench)

Microbes regulate the decomposition of organic matter in marine sediments. Measurements at the deepest oceanic site on Earth reveal high rates of microbial activity, potentially fuelled by the deposition of organic matter. Microbes control the decomposition of organic matter inmarine sediments. Decomposition, in turn, contributes to oceanic nutrient regeneration and influences the preservation of organic carbon1. Generally, rates of benthic decomposition decline with increasing water depth, although given the vast extent of the abyss, deep-sea sediments are quantitatively important for the global carbon cycle2,3. However, the deepest regions of the ocean have remained virtually unexplored4. Here, we present observations of microbial activity in sediments at Challenger Deep in the Mariana Trench in the central west Pacific, which at almost 11,000u2009m depth represents the deepest oceanic site on Earth. We used an autonomous micro-profiling system to assess benthic oxygen consumption rates. We show that although the presence of macrofauna is restricted at Challenger Deep, rates of biological consumption of oxygen are high, exceeding rates at a nearby 6,000-m-deep site by a factor of two. Consistently, analyses of sediments collected from the two sites reveal higher concentrations of microbial cells at Challenger Deep. Furthermore, analyses of sediment 210Pb profiles reveal relatively high sediment deposition in the trench. We conclude that the elevated deposition of organic matter at Challenger Deep maintains intensified microbial activity at the extreme pressures that characterize this environment.