Identification of a Novel Subgroup of Koala Retrovirus from Koalas in Japanese Zoos

We identified a new subgroup of koala retrovirus (KoRV), named KoRV-J, which utilizes thiamine transport protein 1 as a receptor instead of the Pit-1 receptor used by KoRV (KoRV-A). By subgroup-specific PCR, KoRV-J and KoRV-A were detected in 67.5 and 100% of koalas originating from koalas from northern Australia, respectively. Altogether, our results indicate that the invasion of the koala population by KoRV-J may have occurred more recently than invasion by KoRV-A.     

A guideline for ecological risk management procedures

A practical guideline for community-level ecological risk management is proposed, with particular emphasis on the mutual interdependencies of the scientific analysis, public consensus building, and an adaptive management. The procedure we recommend spans the screening of potential ecological risks, the involvement of related stakeholders, the conceptual development from the undesired event over assessment endpoints to measures of effect and stress factors, the risk assessment for the no-action case, the planning phase from the public decision to become active and the setting of goals over a specification of monitoring and control methods to an assessment of feasibility and a public approval of the management plan and finally the adaptive management from initiation over continued monitoring to revisions of the plan, if required. The procedure contains several checkpoints, alternative routes, and possibilities to correct previous decisions.     

Heterogeneity of koala retrovirus isolates

Koala retrovirus (KoRV) is a gammaretrovirus which may induce immune suppression, leukemia and lymphoma in koalas. Currently three KoRV subgroups (A, B, and J) have been reported. Our phylogenetic analysis suggests that KoRV-B and KoRV-J should be classified as the same subgroup. In long terminal repeat (LTR), a KoRV-B isolate has four 17 bp tandem repeats named direct repeat (DR)-1, while a KoRV-J isolate (strain OJ-4) has three 37 bp tandem repeats named DR-2. We also found that the promoter activity of the KoRV-J strain OJ-4 is stronger than that of original KoRV-A, suggesting that KoRV-J may replicate more efficiently than KoRV-A.     

Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of vertical migration and cell division

To better understand the mechanism underlying the bloom outbreaks of dinoflagellates, Ceratium furca, and Ceratium fusus in the temperate coastal area of Sagami Bay, we investigated the diel changes of vertical migration, swimming speed, cell volume, and cell division. Our results from both the field and laboratory indicate that C. furca and C. fusus can migrate vertically between surface and sub-surface layers to avoid strong sunlight (>1000 μmol m⁻² s⁻¹). Diel vertical migration (DVM) of C. furca was observed in the laboratory, while that of C. fusus was not observed. C. furca demonstrated a constant DVM rhythm, i.e., their cells began to descend from the surface before the light was extinguished, and ascended into the surface before the light was turned on. The downward and upward migrations of the cells occurred at every 3 h before turning on and off the light, suggesting that the DVM pattern was independent of nutrient concentration. The swimming speeds of C. furca (avg. 250 μm s⁻¹) were always faster than those of C. fusus (avg. 75 μm s⁻¹). In addition, the speeds of C. furca during light periods were faster than those during dark periods, whereas the speeds of C. fusus remained relatively constant. A higher proportion of dividing cells was recorded near dawn (05:00–07:00 h). Cell volumes of C. furca and C. fusus did not markedly change between 12:00 and 21:00 h, but gradually increased until 03:00 h and then sharply decreased. Furthermore, the cell volume of the two Ceratium species was significantly shifted to the temporal pattern of cell division. Combined with the DVM manner of two Ceratium and cell division timing, only C. furca divided at the bottom, and then moved toward the surface shortly before the dark to light transition. Based on our observations, C. furca has an ecological advantage due to their DVM activity, since nutrients can be obtained well in the near bottom layers, while during the daytime, light present in nutrient-depleted surface water can be obtained using their high swimming speed. On the other hand, C. fusus stimulated by low salinity conditions, might be dependent on external environmental conditions such as additional nutrients following freshwater discharge by heavy rainfall because they may not perform active DVM due to a slow swimming ability. Our findings support that specific characteristics, including the DVM behavior in C. furca, yield a competitive advantage over C. fusus in Sagami Bay.     

Ryocalanus spinifrons,a new species of Ryocalanidae (Copepoda: Calanoida), from the southwestern part of Sagami Bay,Japan

A new Ryocalanoid copepod, Ryocalanus spinifrons, collected by the MTD net system at a depth of 1400 m from the southwestern part of Sagami Bay, Japan, is described. The new species is morphologically very close to R. infelix Tanaka, 1956 (female unknown) from the Izu region of Sagami Bay. It is distinguished from other species by the presence of 12 long spinules on the ventral inner side of the fifth pedigerous somite, nine setae on the coxal epipodite of the maxillule and nine large robust spinules on the coxal segment of the fourth leg. The row of five robust spines on the paragnath distinguishes R. spinifrons.     

Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of temperature, light intensity and photoperiod

Seasonal changes of field populations and growth rates of two dinoflagellates, Ceratium furca and Ceratium fusus, were examined in the temperate coastal water of Sagami Bay, Japan. Weekly field sampling was conducted from August 2002 to August 2003, and laboratory experiments were also carried out to investigate effects of temperature, irradiance and photoperiod on the growth rates of these two Ceratium species. In the field, the abundances of both species increased significantly from April to August 2003, were gradually decreased from November 2002 and were not observed in January 2003. C. fusus was able to increase at lower temperatures in February 2003 compared to C. furca. In the laboratory, the two species did not grow at <10 °C or >32 °C. The highest specific growth rate of C. furca was 0.72 d⁻¹ at 24 °C and 600 μmol m⁻² s⁻¹. Optimum growth rates (>0.4 d⁻¹) of C. furca were observed at temperatures from 18 to 28 °C and at irradiances from 216 to 796 μmol m⁻² s⁻¹. The highest growth rate of C. fusus was 0.56 d⁻¹ at 26 °C and 216 μmol m⁻² s⁻¹. Optimum growth rates of C. fusus were observed at the same irradiance rage of C. furca, whereas optimum temperature range was narrower (26–28 °C). The growth curves of both species indicated saturation of the growth rates when light intensity was above 216 μmol m⁻² s⁻¹, and did not show photoinhibition at irradiances up to 796 μmol m⁻² s⁻¹. The specific growth rates of both Ceratium species were clearly decreased at L:D = 10:14 relative to those at L:D = 14:10 and L:D = 12:12. The present study indicates the two Ceratium species can adapt to a wide range of temperature and irradiance.     

Growth of dinoflagellates, Ceratium furca and Ceratium fusus in Sagami Bay, Japan: The role of nutrients

In order to study the influence of nutrients on the growth characteristics of the dominant dinoflagellates, Ceratium furca and Ceratium fusus, in the temperate coastal area of Sagami Bay, Japan, we conducted field monitoring from January 2000 to December 2005 and performed laboratory culture experiments. In the field study, population densities of C. furca and C. fusus were high, even in low nutrient concentrations (N: 1.58 μM, P: 0.17 μM). Both species were more abundant in the surface and sub-surface layers than in the bottom layers during the stratification periods. In the laboratory study, the specific growth rates of C. furca and C. fusus increased gradually along with increasing nutrients up to the T₅ (N: 5 μM, P: 0.5 μM) and T₁₀ (N: 10 μM, P: 1 μM) concentration levels, after which the growth rate plateaued at the T₅₀ (N: 50 μM, P: 5 μM) concentration level. In contrast, the nutrient uptake rates of both species continuously increased, indicating “luxury consumption”, i.e., excessive cellular storage not related to growth rate. The half-saturation constants (K_s) of C. furca for nitrate (0.49 μM) and phosphate (0.05 μM) were slightly higher than C. fusus (0.32 and 0.03 μM, respectively). We offer two reasons why the two Ceratium population densities were maintained at high levels in low nutrient conditions. First, these two species have a competitive advantage over other algal species because of low K_s values and specific characteristics for nutrient uptake such as luxury consumption. Their ability to obtain nutrients through alternative methods, such as phagotrophy, might contribute to bloom formation and population persistence. Second, the cell densities of both Ceratium species increased along with nitrate concentrations in the media even when phosphorus was held constant. In particular, the growth of C. furca was directly supported by various nitrogen sources such as nitrate, ammonium, and urea, although the highest growth rates were observed only in the nitrate-enriched cultures. Our field and laboratory results revealed that the growth rates of the two Ceratium species increased readily in high N:P nutrient conditions (i.e., conditions of P limitation) indicating an advantage over other algal species in phosphorus-limited environments such as Sagami Bay.     

DNA metabarcoding focused on difficult-to-culture protists: An effective approach to clarify biological interactions

DNA metabarcoding on a single organism is a promising approach to clarify the biological interactions (e.g., predator–prey relationships and symbiosis, including parasitism) of difficult-to-culture protists. To evaluate the effectiveness of this method, Radiolaria and Phaeodaria, which are ecologically important protistan groups, were chosen as target taxa. DNA metabarcoding on a single organism focused on the V9 region of the 18S rRNA gene revealed potential symbionts, parasites and food sources of Radiolaria and Phaeodaria. Previously reported hosts and symbionts (parasites) were detected, and newly recognized combinations were also identified. The contained organisms largely differed between Radiolaria and Phaeodaria. In Radiolaria, members of the same order tended to contain similar organisms, and the taxonomic composition of possible symbionts, parasites, and food sources was fixed at the species level. Members of the same phaeodarian family, however, did not contain similar organisms, and body part (i.e., the central capsule or the phaeodium) was the most important factor that divided the taxonomic composition of detected organisms, implying that the selection of appropriate body part is important when trying to ascertain contained organisms, even for unicellular zooplankton. Our results show that DNA metabarcoding on a single organism is effective in revealing the biological interactions of difficult-to-culture protists.