Evaluation of Marine Bacterial Lysogens for Development of a Marine Prophage Induction Assay

The demonstrated relationship between carcinogenicity of a chemical compound in mammals and its tendency to cause prophage induction in bacteria provides a method for biologically based carcinogen screening. Because of the need for this type of screening and the abundance of lysogens in the marine environment, 14 isolates were evaluated for the degree of prophage induction in exponentially growing cultures in the presence of a known mutagen (0.5 μg/ml mitomycin C). Assays were performed both in liquid culture and in microtiter plates. Virus-like particles were enumerated by epifluorescence microscopy after staining with SYBR-Gold. Two isolates designated P94-4B3 (identified as Halomonas aquamarina) and P94-4S3 (identified as Pseudomonas aeruginosa) were further evaluated for potential use. Because of the rapid growth, larger size of its virus-like particles, and linear response to increasing dose of mitomycin C, the P. aeruginosa st. P94-4S3 was determined a better candidate for the marine prophage induction assay (MPIA). The Pseudomonas isolate was then used in several experiments for the development and optimization of the MPIA procedure. Initial screenings of the MPIA were also performed with selected environmental pollutants. Received March 12, 2001; accepted April 9, 2001.     

Sunscreen Products Increase Virus Production Through Prophage Induction in Marine Bacterioplankton

Classical pollutants (e.g., hydrocarbon, pesticides) have been recently recognized to induce lytic cycle in lysogenic bacteria, but information on micro-pollutants is almost completely lacking. We investigated the effects of cosmetic sun products (sunscreen and solar oil) on viral abundance and bacterial activity. We found that both sunscreen and solar oil acted as pollutants, inducing viral development and controlling bacterial abundance and production, thus leading to an increase of the virus to bacterium ratio. Short-term experiments revealed that sunscreen supplementation induced the lytic cycle in a large fraction of total bacterial abundance (13–24% of bacteria, at low and high concentrations, respectively), whereas solar oil had a lower impact (6–9%). A synchronized development of the phage–host system was observed only after sunscreen addition. The addition of sunscreen, even at low concentrations, had a significant impact on all enzymatic activities (aminopeptidase, glucosidase, and phosphatase), which increased significantly. However, when enzymatic activities were normalized per cell, a selective enhancement was observed for certain enzymes (e.g., aminopeptidase) and inhibition for others (e.g., glucosidase). These results indicate that sunscreen products can modify C, N, and P biogeochemical cycling in seawater and increase virus abundance through prophage induction in marine bacterioplankton.     

Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host''s genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains.     

Nutrient Requirement and Growth of a Synechococcus Species Isolated from Lake Balaton

A pico sized Synechococcus species isolated from Lake Balaton was studied in batch and continuous cultures. This picocyanobacterium had a pH optimum at 8.5 and a temperature optimum at 28-30°C. The I_k value for growth was 52 μEinstein m⁻² S⁻¹, the maximum growth rate 2.27 d⁻¹, the half saturation Constant of growth 1.2 μg PO₄-P I⁻¹ and the minimal cell quota 1.74 nig P g dry weight⁻¹. The dry weight of cells showed a minimum, the chlorophyll-a/biomass ratio a maximum as a function of growth rate. Above the quota of 3.4 fg P Cell⁻¹ significant amounts of non-reactive dissolved Phosphorous were released.     

Effect of Temperature on Photosynthesis and Growth in Marine Synechococcus spp.

In this study, we develop a mechanistic understanding of how temperature affects growth and photosynthesis in 10 geographically and physiologically diverse strains of Synechococcus spp. We found that Synechococcus spp. are able to regulate photochemistry over a range of temperatures by using state transitions and altering the abundance of photosynthetic proteins. These strategies minimize photosystem II (PSII) photodamage by keeping the photosynthetic electron transport chain (ETC), and hence PSII reaction centers, more oxidized. At temperatures that approach the optimal growth temperature of each strain when cellular demand for reduced nicotinamide adenine dinucleotide phosphate (NADPH) is greatest, the phycobilisome (PBS) antenna associates with PSII, increasing the flux of electrons into the ETC. By contrast, under low temperature, when slow growth lowers the demand for NADPH and linear ETC declines, the PBS associates with photosystem I. This favors oxidation of PSII and potential increase in cyclic electron flow. For Synechococcus sp. WH8102, growth at higher temperatures led to an increase in the abundance of PBS pigment proteins, as well as higher abundance of subunits of the PSII, photosystem I, and cytochrome b6f complexes. This would allow cells to increase photosynthetic electron flux to meet the metabolic requirement for NADPH during rapid growth. These PBS-based temperature acclimation strategies may underlie the larger geographic range of this group relative to Prochlorococcus spp., which lack a PBS.Marine picocyanobacteria are the most abundant phytoplankton, inhabiting nearly every area of the surface ocean and dominating in tropical and subtropical waters. The smallest and most abundant marine picocyanobacteria belong to the genera Synechococcus and Prochlorococcus, which together account for one-third of the total primary production on Earth (Partensky et al., 1999b). Marine Synechococcus spp. are genetically diverse (Scanlan et al., 2009; Mazard et al., 2012), play an important role in the biogeochemical cycling of carbon (Grob et al., 2007), and are found from the equator to the polar circle, though they are less abundant at higher latitudes (Agusti, 2004; Scanlan et al., 2009; Huang et al., 2012). Temperature is a major factor that controls photosynthetic rates, and the biogeography of Synechococcus spp. strains in the modern ocean has been linked to temperature (Zwirglmaier et al., 2008). In this study, we explore the effect of temperature on growth and photosynthesis in several Synechococcus spp. strains.Photosynthetic electron transport in cyanobacteria, including Synechococcus spp., shares similarities with that of plants and green algae (Fig. 1). Photosynthetic organisms are commonly able to perform photosynthesis efficiently over a range of temperatures bracketing the optimal growth temperature (T_opt). However, decreased metabolic rates at temperatures too far below T_opt can cause an imbalance between photochemistry and metabolism, leading to photodamage (Huner et al., 1996). By contrast, elevated temperatures may affect membrane fluidity and denature proteins, which can also lead to a decline in photosynthetic efficiency (Falk et al., 1996). A range of diverse acclimation strategies have evolved among algae and plants to balance electron flow through the electron transport chain (ETC) during temperature fluctuations (Maxwell et al., 1994; Krol et al., 1997; Gray et al., 1998; Miśkiewicz et al., 2000).Open in a separate windowFigure 1.PBS structure and linear photosynthetic electron flow in cyanobacteria. In this schematic, the PBS is in “state 1,” indicating it is associated with a PSII dimer. Photosynthetic electron flow pathways are indicated by black arrows, and chemical reactions are indicated by blue arrows. Major ETC components include PSII, PSI, PQ/plastoquinol (PQH₂), cytochrome b6f (Cyt b6f), plastocyanin (PLC), ferredoxin (FX), flavodoxin (FL), and ferredoxin/flavodoxin NADP reductase (FNR). Other proteins depicted include the phycobiliproteins APC, PC, two forms of PE (PE I and PE II), PSII chlorophyll-binding proteins CP47 and CP43, the PSII core polypeptides D1 and D2, the PSI chlorophyll-binding core proteins PsaA and PsaB, and the PSI reaction center subunit PsaD. [See online article for color version of this figure.]Less is known about mechanisms marine cyanobacteria use to acclimate to temperature. Cyanobacteria differ from plants and green algae in that photosynthesis and respiration occur in the same membrane. In addition, the ratios of PSII:PSI are more variable in cyanobacteria (Campbell et al., 1998; Bailey et al., 2008), which can impact the flow of electrons through the ETC. Cells must prevent overreduction of the ETC because this can lead to damage of the D1 polypeptide of PSII in a process called photoinhibition; to sustain PSII activity, replacement of the damaged D1 by de novo protein synthesis is required (Aro et al., 1993). Cyanobacteria have evolved a suite of strategies to balance electron flow in the thylakoid membrane when the cells are exposed to high light; important strategies include nonphotochemical quenching (El Bissati et al., 2000; Bailey and Grossman, 2008) and alternative electron flow pathways (Asada, 1999; Bailey et al., 2008; Mackey et al., 2008). Cyanobacteria may also selectively funnel light energy to PSII or PSI to regulate the amount of electrons entering and exiting the ETC (Campbell et al., 1998).In cyanobacteria, including Synechococcus spp., the main light-harvesting antennae are water-soluble pigment-protein complexes called phycobilisomes (PBSs; Grossman et al., 1993; Six et al., 2007). Unlike the antenna of plants and algae that are embedded within the thylakoid membrane, PBSs are located on the cytoplasmic surface of the membrane (Fig. 1). Structurally, the PBS consists of phycobiliproteins, including the PBS core allophycocyanin (APC) and lateral rods of phycocyanin (PC) and phycoerythrin (PE; Fig. 1). The PBS core has evolved together with the core genome of Synechococcus spp., whereas the rod components appear to have evolved separately through gene duplication, DNA exchange between cells, and possibly virally mediated lateral gene transfer (Six et al., 2007). Each phycobiliprotein binds chromophores called phycobilins (linear tetrapyrroles) that selectively absorb different wavelengths of green-red light, thereby extending the range of photosynthetically active radiation the cell can use beyond that of chlorophyll (Campbell et al., 1998). The PBS is capable of rapid diffusion over the thylakoid membrane surface (Mullineaux et al., 1997), where it can associate with either PSI or PSII. The PBS is a mobile antenna element that does not bind chlorophyll and that likely associates with reaction centers by weak interactions with lipid head groups (Sarcina et al., 2001).State transitions, the movements of PBS or other antenna pigments between reaction centers, allow the cells to avoid PSII photodamage by balancing electron flow such that electrons do not accumulate within the ETC. Whether the PBS associates with PSI or PSII is determined by the redox poise of the plastoquinone (PQ) pool (Fig. 1), which serves as an indicator of electron flow through the ETC. When the PQ pool is oxidized, the PBS becomes associated with PSII (state 1) such that the rate of linear electron flow increases. By contrast, a reduced PQ pool elicits affiliation of the PBS with PSI (state 2), which could increase the withdrawal of electrons from the ETC. In the dark, the PQ pool tends to be reduced due to respiratory electron flow, and the PBS affiliates primarily with PSI.Recent ocean basin scale research has shed light on the role of temperature on the global distributions of Synechococcus spp. in the ocean. Collectively, these studies have shown that marine Synechococcus spp. tolerate a broad range of temperatures, likely due to high genetic diversity among strains. For example, of the four clades that dominate in natural communities, clades I and IV typically inhabit cooler waters north of 30°N and south of 30°S (Brown et al., 2005; Zwirglmaier et al., 2007, 2008), while clades II and III generally inhabit warmer tropical and subtropical waters (Fuller et al., 2006; Zwirglmaier et al., 2008). Other Synechococcus spp. sequences have been recently identified from colder waters in the northern Bering Sea and Chukchi Sea, suggesting that a possible cold adaptation could exist in some strains present at high latitudes (Huang et al., 2012). Still, other studies have found no relationship between Synechococcus spp. abundance and temperature (Zinser et al., 2007), suggesting that additional factors (e.g. nutrient availability) may be responsible for shaping Synechococcus spp. community structure (Palenik et al., 2003, 2006; Scanlan et al., 2009).While field surveys have made great strides in understanding the role of temperature in controlling picocyanobacteria distributions, much remains to be learned about the range of growth responses to temperature that can occur in marine Synechococcus spp. To date, characterization of individual Synechococcus spp. strains includes work with two isolates from the Sargasso Sea, showing variable responses to temperature (Moore et al., 1995; Fu et al., 2007). These studies demonstrate the potential for changing sea surface temperature (SST) to influence the biogeochemical role of Synechococcus spp. in the Sargasso Sea; however, little is known about whether these responses can be generalized to other strains or environments. Changes in growth rate and photosynthetic efficiency, if they occur, could alter global Synechococcus spp. distributions, affect ecosystem structure, and ultimately impact marine biogeochemical cycles and Earth’s climate, and thus could have important implications for the earth system.A mechanistic understanding of how temperature affects growth and photosynthesis in geographically and physiologically diverse strains of Synechococcus spp. is needed to clarify how temperature influences Synechococcus spp. biogeography, as well as to provide insights into how populations are likely to respond to increased SST in the future. The goal of this study is to characterize the growth, photosynthetic efficiency, and light-harvesting characteristics of 10 diverse Synechococcus spp. isolates over a range of temperatures. Using chlorophyll fluorescence analysis, we show that regulation of light harvesting via state transitions is an important acclimation process that allows cells to increase photosynthetic electron flow under high temperature conditions. This effect is enhanced for strains with higher proportions of phycoerythrobilin and phycouribilin. We use global proteome data from Synechococcus sp. WH8102 to show that this temperature-dependent enhancement is brought about in part by an increase in the abundance of PBS proteins, as well as proteins from PSII, PSI, and other ETC components. The results are discussed in the context of Synechococcus spp. biogeography in the modern ocean, and potential implications for how cells could respond to future increases in SST are considered.     

Dynamics and Distribution of Cyanophages and Their Effect on Marine Synechococcus spp

Cyanophages infecting marine Synechococcus cells were frequently very abundant and were found in every seawater sample along a transect in the western Gulf of Mexico and during a 28-month period in Aransas Pass, Tex. In Aransas Pass their abundance varied seasonally, with the lowest concentrations coincident with cooler water and lower salinity. Along the transect, viruses infecting Synechococcus strains DC2 and SYN48 ranged in concentration from a few hundred per milliliter at 97 m deep and 83 km offshore to ca. 4 x 10 ml near the surface at stations within 18 km of the coast. The highest concentrations occurred at the surface, where salinity decreased from ca. 35.5 to 34 ppt and Synechococcus concentrations were greatest. Viruses infecting strains SNC1, SNC2, and 838BG were distributed in a similar manner but were much less abundant (<10 to >5 x 10 ml). When Synechococcus concentrations exceeded ca. 10 ml, cyanophage concentrations increased markedly (ca. 10 to > 10 ml), suggesting that a minimum host density was required for efficient viral propagation. Data on the decay rate of viral infectivity d (per day), as a function of solar irradiance I (millimoles of quanta per square meter per second), were used to develop a relationship (d = 0.2610I - 0.00718; r = 0.69) for conservatively estimating the destruction of infectious viruses in the mixed layer of two offshore stations. Assuming that virus production balances losses and that the burst size is 250, ca. 5 to 7% of Synechococcus cells would be infected daily by viruses. Calculations based on contact rates between Synechococcus cells and infectious viruses produce similar results (5 to 14%). Moreover, balancing estimates of viral production with contact rates for the farthest offshore station required that most Synechococcus cells be susceptible to infection, that most contacts result in infection, and that the burst size be about 324 viruses per lytic event. In contrast, in nearshore waters, where ca. 80% of Synechococcus cells would be contacted daily by infectious cyanophages, only ca. 1% of the contacts would have to result in infection to balance the estimated virus removal rates. These results indicate that cyanophages are an abundant and dynamic component of marine planktonic communities and are probably responsible for lysing a small but significant portion of the Synechococcus population on a daily basis.     

Factors Influencing the Effect of Segregation Distortion in Natural Populations of DROSOPHILA MELANOGASTER

The major components of the SD system have been examined in two natural populations of D. melanogaster to investigate how SD behaves and is maintained in nature and to estimate its impact and efficiency. A twofold approach was used: (1) direct measurements of segregation distortion in wild males and (2) measurement of sensitivity of wild SD (+) chromosomes to SD action. Characterization of newly isolated SD chromosomes and of a large number of SD( +) chromosomes from nature demonstrated that (1) SD can operate efficiently in the wild genome: 45% of SD/SD(+) males collected from nature had k values larger than 0.70. (2) Forty-three of 44 newly recovered SD chromosomes are of the SD-72 type, having a small pericentric inversion that maintains tight linkage among the Sd, E(SD) and Rsp loci in the SD complex. In 1956, most SD chromosomes in Madison lacked this inversion. (3) Only 12 of the 44 SD chromosomes carried a recessive lethal (compared with five of six in 1956), and many of the viable SD chromosomes were fertile as homozygotes, indicating that SD homozygotes need not have obvious reductions in fitness. (4) Among more than 500 wild chromosomes assayed for response to distortion by a strong SD, at least 40-50% were sensitive, about 33% were partially sensitive and 17% were insensitive. This frequency of sensitives is higher than in reports from some other populations. An estimated 12% of the wild chromosomes were classified as true Rsp(i) by their constellation of effects, including a special test of ability to cause self-distortion of a "suicide" chromosome, R(cn)-10. In a direct assay with R(cn)-10, an independent sample of 99 chromosomes from nature gave 30% putative Rsp(i). Thus, these populations contain in the range of 12-30% Rsp(i). (5) Chromosomes supersensitive to SD, previously described for certain laboratory stocks, were also found to coexist in nature with SD. (6) Profiles of wild chromosomes with a panel of three or four different SD testers suggest a series of allelic alternatives at the Rsp locus including supersensitive, sensitive, semisensitive and insensitive, and that loci other than Rsp may also be important in determining the effect of SD in nature.     

Dynamics and Distribution of Cyanophages and Their Effect on Marine Synechococcus spp.

Cyanophages infecting marine Synechococcus cells were frequently very abundant and were found in every seawater sample along a transect in the western Gulf of Mexico and during a 28-month period in Aransas Pass, Tex. In Aransas Pass their abundance varied seasonally, with the lowest concentrations coincident with cooler water and lower salinity. Along the transect, viruses infecting Synechococcus strains DC2 and SYN48 ranged in concentration from a few hundred per milliliter at 97 m deep and 83 km offshore to ca. 4 × 10⁵ ml^-1 near the surface at stations within 18 km of the coast. The highest concentrations occurred at the surface, where salinity decreased from ca. 35.5 to 34 ppt and Synechococcus concentrations were greatest. Viruses infecting strains SNC1, SNC2, and 838BG were distributed in a similar manner but were much less abundant (<10 to >5 × 10³ ml^-1). When Synechococcus concentrations exceeded ca. 10³ ml^-1, cyanophage concentrations increased markedly (ca. 10² to > 10⁵ ml^-1), suggesting that a minimum host density was required for efficient viral propagation. Data on the decay rate of viral infectivity d (per day), as a function of solar irradiance I (millimoles of quanta per square meter per second), were used to develop a relationship (d = 0.2610I - 0.00718; r² = 0.69) for conservatively estimating the destruction of infectious viruses in the mixed layer of two offshore stations. Assuming that virus production balances losses and that the burst size is 250, ca. 5 to 7% of Synechococcus cells would be infected daily by viruses. Calculations based on contact rates between Synechococcus cells and infectious viruses produce similar results (5 to 14%). Moreover, balancing estimates of viral production with contact rates for the farthest offshore station required that most Synechococcus cells be susceptible to infection, that most contacts result in infection, and that the burst size be about 324 viruses per lytic event. In contrast, in nearshore waters, where ca. 80% of Synechococcus cells would be contacted daily by infectious cyanophages, only ca. 1% of the contacts would have to result in infection to balance the estimated virus removal rates. These results indicate that cyanophages are an abundant and dynamic component of marine planktonic communities and are probably responsible for lysing a small but significant portion of the Synechococcus population on a daily basis.     

Uptake of Cyclic AMP by Natural Populations of Marine Bacteria

The major objective of this study was to describe the mechanism(s) of cyclic AMP uptake by natural populations of marine bacteria. A second objective was to determine whether this uptake could contribute to the intracellular regulatory pool of cyclic AMP. Using high-specific-activity ³²P-labeled cyclic AMP, we found several high-affinity uptake systems. The highest-affinity system had a half-saturation constant of <10 pM. This system was extremely specific for cyclic nucleotides, particularly cyclic AMP. It appeared to meet the criteria for active transport. Uptake of cyclic AMP over a wide concentration range (up to 2 μM) showed multiphasic kinetics, with half-saturation constants of 1 nM and greater. These lower-affinity systems were much less specific for cyclic nucleotides. Although much of the labeled cyclic AMP taken up by the high-affinity systems was metabolized, some remained as intact cyclic AMP within the cells during 1 h of incubation. This suggests that at least some of the bacteria use cyclic AMP dissolved in seawater to augment their intracellular pools.     

Variable Incidence of Spiroplasma Infections in Natural Populations of Drosophila Species

Spiroplasma is widespread as a heritable bacterial symbiont in insects and some other invertebrates, in which it sometimes acts as a male-killer and causes female-biased sex ratios in hosts. Besides Wolbachia, it is the only heritable bacterium known from Drosophila, having been found in 16 of over 200 Drosophila species screened, based on samples of one or few individuals per species. To assess the extent to which Spiroplasma infection varies within and among species of Drosophila, intensive sampling consisting of 50–281 individuals per species was conducted for natural populations of 19 Drosophila species. Infection rates varied among species and among populations of the same species, and 12 of 19 species tested negative for all individuals. Spiroplasma infection never was fixed, and the highest infection rates were 60% in certain populations of D. hydei and 85% in certain populations of D. mojavensis. In infected species, infection rates were similar for males and females, indicating that these Spiroplasma infections do not confer a strong male-killing effect. These findings suggest that Spiroplasma has other effects on hosts that allow it to persist, and that environmental or host variation affects transmission or persistence leading to differences among populations in infection frequencies.     

Effect of Light on the Cell Cycle of a Marine Synechococcus Strain

Light-dependent regulation of cell cycle progression in the marine cyanobacterium Synechococcus strain WH-8101 was demonstrated through the use of flow cytometry. Our results show that, similar to eucaryotic cells, marine Synechococcus spp. display two gaps in DNA synthesis, at the beginning and at the end of the cell cycle. Progression through each of these gaps requires light, and their durations lengthen under light limitation.     

Apparent Mutagenic Effect of Induction of Lambda Prophage Inserted Between lysA and thyA

Induction of a heat-inducible abnormal lambda prophage inserted between lysA and thyA in Escherichia coli resulted in a number of auxotrophic mutants in the surviving cured-cell populations. These mutants could not be accounted for by deletions arising on formation of lambda hybrid particles carrying regions adjacent to the insertion site. The properties of these mutants, which were almost all spontaneously revertable, have been described and mapped by F′ episome complementation. Tentatively, it was suggested that induction of the lambda lysogen leads to a mutagenic state.     

麻雀种群数量与环境因素关系研究的某些进展

本文主要对1986年以来国外的麻雀种群数量与环境因素的关系研究作一综述。①[树]麻雀和家麻雀间存在巢穴竞争和重叠,家麻雀有更多的防御行为和数量上占优势。[树]麻雀群体繁殖第一次比单独繁殖产更多的卵,孵出更多的雏鸟,第二：、三次则相反。②农药的使用对[树]麻雀繁殖成功有一定的影响。③麻雀可以作为环境污染的指示种：家麻雀体内非正常金属元素有铝、汞、镉和铅。当铅的积累超过2μg／g干重,病、死雏鸟的比例就会增加。④在发达国家,交通可以引起麻雀死亡。     

Relationship Between Prophage Induction and Transformation in Haemophilus influenzae

The interaction between transformation and prophages of HP1c1, S2, and a defective phage of Haemophilus influenzae has been investigated by measurement of (i) the effect of prophage on transformation frequency and (ii) the effect of transformation on phage induction. The presence of any of the prophages does not appreciably alter transformation frequencies in various Rec(+) and Rec(-) strains. However, exposure of competent lysogens to transforming deoxyribonucleic acid (DNA) may induce phage but only in Rec(+) strains, which are able to integrate transforming DNA into their genome. Transformation of Rec(+) lysogens with DNA irradiated with ultraviolet (UV) light causes the production of even more phage than results from unirradiated DNA, but this indirect UV induction is not as effective as direct induction by UV irradiation of lysogens. Both types of UV induction are influenced by the repair capacity of the host. Wild-type cells contain a prophage and can be induced by transformation to produce a defective phage, which kills a small fraction of the cells. Defective phage in wild-type cells are also induced by H. parainfluenzae DNA, and a much larger fraction of the cells is killed. Strain BC200, which is highly transformable but is not inducible for defective phage, is not killed by H. parainfluenzae DNA, suggesting that wild-type cells are killed by killed by this DNA because of phage induction. A minicell-producing mutant, LB11, has been isolated. Some phage induction occurs in this strain when the cells are made competent, unlike the wild type. A large majority of LB11 cells surviving the competence regime are killed by exposure to transforming DNA.     

Factors Affecting Variability in Time between Addition of Nutrient Germinants and Rapid Dipicolinic Acid Release during Germination of Spores of Bacillus Species

The simultaneous nutrient germination of hundreds of individual wild-type spores of three Bacillus species and a number of Bacillus subtilis strains has been measured by two new methods, and rates of release of the great majority of the large pool of dipicolinic acid (DPA) from individual spores of B. subtilis strains has been measured by Raman spectroscopy with laser tweezers. The results from these analyses and published data have allowed a number of significant conclusions about the germination of spores of Bacillus species as follows. (i) The time needed for release of the great majority of a Bacillus spore''s DPA once rapid DPA release had begun (ΔT_release) during nutrient germination was independent of the concentration of nutrient germinant used, the level of the germinant receptors (GRs) that recognize nutrient germinants used and heat activation prior to germination. Values for ΔT_release were generally 0.5 to 3 min at 25 to 37°C for individual wild-type spores. (ii) Despite the conclusion above, germination of individual spores in populations was very heterogeneous, with some spores in wild-type populations completing germination ≥15-fold slower than others. (iii) The major factor in the heterogeneity in germination of individual spores in populations was the highly variable lag time, T_lag, between mixing spores with nutrient germinants and the beginning of ΔT_release. (iv) A number of factors decrease spores'' T_lag values including heat activation, increased levels of GRs/spore, and higher levels of nutrient germinants. These latter factors appear to affect the level of activated GRs/spore during nutrient germination. (v) The conclusions above lead to the simple prediction that a major factor causing heterogeneity in Bacillus spore germination is the number of functional GRs in individual spores, a number that presumably varies significantly between spores in populations.Spores of various Bacillus species are metabolically dormant and can survive for years in this state (30). However, spores constantly sense their environment, and if appropriate small molecules termed germinants are present, spores can rapidly return to life in the process of germination followed by outgrowth (25, 29, 30). The germinants that most likely trigger spore germination in the environment are low-molecular-weight nutrient molecules, the identities of which are strain and species specific, including amino acids, sugars, and purine nucleosides. Metabolism of these nutrient germinants is not needed for the triggering of spore germination. Rather, these germinants are recognized by germinant receptors (GRs) located in the spore''s inner membrane that recognize their cognate germinants in a stereospecific manner (17, 24, 25, 29). Spores have a number of such GRs, with three functional GRs in Bacillus subtilis spores and even more in Bacillus anthracis, Bacillus cereus, and Bacillus megaterium spores (6, 29, 30). Binding of nutrient germinants to some single GRs is sufficient to trigger spore germination, for example the triggering of B. subtilis spore germination by binding of l-alanine or l-valine to the GerA GR. However, many GRs cooperate such that binding of germinants by ≥2 different GRs is needed to trigger germination (2, 29): for example, the triggering of B. subtilis spore germination by the binding of components of a mixture of l-asparagine, d-glucose, d-fructose, and K⁺ ions (AGFK) to the GerB and GerK GRs. The binding of nutrient germinants to GRs triggers subsequent events in germination, although how this is accomplished is not known.The first readily measured biochemical event after addition of nutrient germinants to Bacillus spores is the rapid release of the spore''s large depot (∼10% of spore dry weight) of pyridine-2,6-dicarboxylic acid (dipicolinic acid [DPA]) plus its chelated divalent cations, predominantly Ca²⁺ (Ca-DPA), from the spore core (25, 29). Ca-DPA release then results in the activation of two redundant cortex-lytic enzymes (CLEs), CwlJ and SleB, which hydrolyze the spore''s peptidoglycan cortex layer (16, 22, 27, 29). CwlJ is activated by Ca-DPA as it is released from the spore while SleB is activated only after most DPA is released (17, 20, 22, 26, 27). Cortex hydrolysis ultimately allows the spore core to expand and take up more water, raising the core water content from the 35 to 45% of wet weight in the dormant spore to the 80% of wet weight characteristic of growing cells. Full hydration of the spore core then allows enzyme action, metabolism, and macromolecular synthesis to resume in the now fully germinated spore.Germination of spores in populations is very heterogeneous, with some spores germinating rapidly and some extremely slowly (4, 5, 9, 11, 13-15, 19, 26, 31, 32). Where it has been studied, the reason for this heterogeneity has been suggested to be due to a variable lag period (T_lag) between the time of mixing spores with a germinant and the time at which rapid DPA release begins, since once rapid DPA release begins, the time required for release of almost all DPA as well as for subsequent cortex hydrolysis is generally rather short compared to T_lag values in individual spores (5, 11, 13-15, 19, 26, 31, 32). The times required for DPA release and cortex hydrolysis are also similar in wild-type spores with both very short and long T_lag values (5, 15, 19, 27). The reasons for the variability in T_lag times between individual spores in populations are not known, although there are reports that both activation of spores for germination by a sublethal heat treatment (heat activation) as well as increasing concentrations of nutrient germinants can shorten T_lag values (12, 14, 15, 18, 32). However, there has been no detailed study of the causes of the variability in T_lag values between very large numbers of individual spores in populations.In order to study the heterogeneity in spore germination thoroughly, methods are needed to follow the germination of hundreds of individual spores over several hours. Initial studies of the germination of individual spores examined a single spore in a phase-contrast microscope and followed the germination of this spore by changes in the core''s refractive index due to DPA release and core swelling (14, 15, 32, 34). However, this method is labor-intensive for gathering data with hundreds of individual spores. More recently, confocal microscopy and then surface adsorption and optical tweezers have been used to capture single spores, and germination events have been followed by methods such as Raman spectroscopy to directly measure DPA release, as well as phase-contrast microscopy and elastic light scattering (3, 5, 9, 10, 19, 26). While the latter recent advances have allowed accumulation of much information about germination, collection of this type of data for large numbers of individual spores is still labor-intensive, although use of dual optical traps (35) and perhaps multiple traps in the future may alleviate this problem. However, phase-contrast microscopy plus appropriate computer software has recently allowed the monitoring of many hundreds of individual spores for several hours, with automated assessment of various changes in the cells during the period of observation (19). In the present work, we have used both phase-contrast and differential interference contrast (DIC) microscopy to monitor the germination of many hundreds of individual spores of three Bacillus species adhered on either an agarose pad or a glass coverslip for 1 to 2 h. This work, as well as examination of times needed for release of most DPA once rapid DPA release has begun during germination of individual spores under a variety of conditions, has allowed detailed examination of the effects of heat activation, nutrient germinant concentration, GR numbers per spore, and individual CLEs on spore germination heterogeneity and on values of T_lag for individual spores.     

Seasonal Variations in Virus-Host Populations in Norwegian Coastal Waters: Focusing on the Cyanophage Community Infecting Marine Synechococcus spp.

Viruses are ubiquitous components of the marine ecosystem. In the current study we investigated seasonal variations in the viral community in Norwegian coastal waters by pulsed-field gel electrophoresis (PFGE). The results demonstrated that the viral community was diverse, displaying dynamic seasonal variation, and that viral populations of 29 different sizes in the range from 26 to 500 kb were present. Virus populations from 260 to 500 kb and dominating autotrophic pico- and nanoeukaryotes showed similar dynamic variations. Using flow cytometry and real-time PCR, we focused in particular on one host-virus system: Synechococcus spp. and cyanophages. The two groups covaried throughout the year and were found in the highest amounts in fall with concentrations of 7.3 × 10⁴ Synechococcus cells ml⁻¹ and 7.2 × 10³ cyanophage ml⁻¹. By using primers targeting the g20 gene in PCRs on DNA extracted from PFGE bands, we demonstrated that cyanophages were found in a genomic size range of 26 to 380 kb. The genetic richness of the cyanophage community, determined by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified g20 gene fragments, revealed seasonal shifts in the populations, with one community dominating in spring and summer and a different one dominating in fall. Phylogenetic analysis of the sequences originating from PFGE and DGGE bands grouped the sequences into three groups, all with homology to cyanomyoviruses present in cultures. Our results show that the cyanophage community in Norwegian coastal waters is dynamic and genetically diverse and has a surprisingly wide genomic size range.     

Mitochondrial DNA Polymorphism in Natural Populations of the Drosophila virilis Species Group

Restriction fragment length polymorphism (RFLP) analysis has been used to evaluate mitochondrial DNA (mtDNA) variation in 12 sibling species forming the Drosophila virilis species group. The variation thresholds corresponding to the interspecific and interstrain levels have been determined. The results indicate that interspecific hybridization has significantly contributed to the evolutionary history of the virilis species group.     

Species Diversity of Uncultured and Cultured Populations of Soil and Marine Ammonia Oxidizing Bacteria

Although molecular techniques are considered to provide a more comprehensive view of species diversity of natural microbial populations, few studies have compared diversity assessed by molecular and cultivation-based approaches using the same samples. To achieve this, the diversity of natural populations of ammonia oxidising bacteria in arable soil and marine sediments was determined by analysis of 16S rDNA sequences from enrichment cultures, prepared using standard methods for this group, and from 16S rDNA cloned from DNA extracted directly from the same environmental samples. Soil and marine samples yielded 31 and 18 enrichment cultures, respectively, which were compared with 50 and 40 environmental clones. There was no evidence for selection for particular ammonia oxidizer clusters by different procedures employed for enrichment from soil samples, although no culture was obtained in medium at acid pH. In soil enrichment cultures, Nitrosospira cluster 3 sequences were most abundant, whereas clones were distributed more evenly between Nitrosospira clusters 2, 3, and 4. In marine samples, the majority of enrichment cultures contained Nitrosomonas, whereas Nitrosospira sequences were most abundant among environmental clones. Soil enrichments contained a higher proportion of identical sequences than clones, suggesting laboratory selection for particular strains, but the converse was found in marine samples. In addition, 16% of soil enrichment culture sequences were identical to those in environmental clones, but only 1 of 40 marine enrichments was found among clones, indicating poorer culturability of marine strains represented in the clone library, under the conditions employed. The study demonstrates significant differences in species composition assessed by molecular and culture-based approaches but indicates also that, employing only a limited range of cultivation conditions, 7% of the observed sequence diversity in clones of ammonia oxidizers from these environments could be obtained in laboratory enrichment culture. Further studies and experimental approaches are required to determine which approach provides better representation of the natural community.     

Ni Uptake and Limitation in Marine Synechococcus Strains

Ni accumulation and utilization were studied in two strains of marine Synechococcus, isolated from both coastal (CC9311; clade I) and open-ocean (WH8102; clade III) environments, for which complete genome sequences are available. Both strains have genes encoding an Ni-containing urease and when grown on urea without Ni become Ni-N colimited. The Ni requirements of these strains also depend upon the genomic complement of genes encoding superoxide dismutase (SOD). WH8102, with a gene encoding only an Ni-SOD, has a novel obligate requirement for Ni, regardless of the N source. Reduced SOD activity in Ni-depleted cultures of WH8102 supports the link of this strain's Ni requirement to Ni-SOD. The genome of CC9311 contains a gene for a Cu/Zn-SOD in addition to a predicted pair of Ni-SODs, yet this strain cannot grow without Ni on NO₃⁻ and can grow only slowly on NH₄⁺ without Ni, implying that the Cu/Zn-SOD cannot completely replace Ni-SOD in marine cyanobacteria. CC9311 does have a greater tolerance for Ni starvation. Both strains increase their Ni uptake capabilities and actively bioconcentrate Ni in response to decreasing extracellular and intracellular Ni. The changes in Ni uptake rates were more pronounced in WH8102 than in CC9311 and for growth on urea or nitrate than for growth on ammonia. These results, combined with an analysis of fully sequenced marine cyanobacterial genomes, suggest that the growth of many marine Synechococcus and all Prochlorococcus strains is dependent upon Ni.