Salinispora pacifica sp. nov., an actinomycete from marine sediments

A polyphasic analysis was carried out to clarify the taxonomic status of four marine actinomycete strains that share a phylogenetic relationship and phenotypic characteristics with the genus Salinispora. These strains formed a distinct lineage within the Salinispora 16S rRNA and gyrB trees and were found to possess a range of phenotypic properties and DNA:DNA hybridization values that distinguished them from the type strains of the two validly named species in this genus, Salinispora tropica (CNB-440^T, ATCC BAA-916^T) and Salinispora arenicola (CNH-643^T, ATCC BAA-917^T). The combined genotypic and phenotypic data support this conclusion. It is proposed that the strains be designated as Salinispora pacifica sp. nov., the type strain of which is CNR-114^T (DSMZ YYYYT = KACC 17160^T).     

Multilocus Sequence Typing Reveals Evidence of Homologous Recombination Linked to Antibiotic Resistance in the Genus Salinispora

The three closely related species that currently comprise the genus Salinispora were analyzed using a multilocus sequence typing approach targeting 48 strains derived from four geographic locations. Phylogenetic congruence and a well-supported concatenated tree provide strong support for the delineation of the three species as currently described and the basal relationship of Salinispora arenicola to the more recently diverged sister taxa S. tropica and S. pacifica. The phylogeny of the initial region of the rpoB gene sequenced was atypical, placing the related genera Micromonospora and Verrucosispora within the Salinispora clade. This phylogenetic incongruence was subsequently ascribed to a homologous-recombination event in a portion of the gene associated with resistance to compounds in the rifamycin class, which target RpoB. All S. arenicola strains produced compounds in this class and possessed resistance-conferring amino acid changes in RpoB. The phylogeny of a region of the rpoB gene that is not associated with rifamycin resistance was congruent with the other housekeeping genes. The link between antibiotic resistance and homologous recombination suggests that incongruent phylogenies provide opportunities to identify the molecular targets of secondary metabolites, an observation with potential relevance for drug discovery efforts. Low ratios of interspecies recombination to mutation, even among cooccurring strains, coupled with high levels of within-species recombination suggest that the three species have been described in accordance with natural barriers to recombination.     

Diversity and distribution of the bioactive actinobacterial genus Salinispora from sponges along the Great Barrier Reef

Isolates from the marine actinobacterial genus Salinispora were cultured from marine sponges collected from along the length of the Great Barrier Reef (GBR), Queensland, Australia. Strains of two species of Salinispora, Salinispora arenicola and “Salinispora pacifica”, were isolated from GBR sponges Dercitus xanthus, Cinachyrella australiensis and Hyattella intestinalis. Phylogenetic analysis of the 16S rRNA gene sequences of representative strains, selected via BOX-PCR screening, identified previously unreported phylotypes of the species “S. pacifica”. The classification of these microdiverse 16S rRNA groups was further confirmed by analysis of the ribonuclease P RNA (RNase P RNA) gene through both phylogenetic and secondary structure analysis. The use of RNase P RNA sequences combined with 16S rRNA sequences allowed distinction of six new intraspecies phylotypes of “S. pacifica” within the geographical area of the GBR alone. One of these new phylotypes possessed a localised regional distribution within the GBR.     

The effects of cations upon the action potentials recorded from neurohaemal tissue of the stick insect

Summary The ionic requirement for the action potentials recorded from the neurohaemal tissue on the lateral branch of the median nerve inCarausius morosus has been studied using extracellular electrodes. Sodium-free, magnesium-free, or calcium-free salines produce irreversible block of the action potentials following prolonged exposure to the nerves. Reducing the sodium concentration to 4 mM has little effect on the amplitude of the action potentials, whilst increasing the sodium concentration to 100 mM reduces the amplitude by 50%. Neither tetrodotoxin nor procaine has any effect on these action potentials.Reducing the magnesium concentration to 1 mM increases the amplitude of the action potentials, whilst increasing the concentration of magnesium reduces the amplitude.The amplitude of the action potentials is linearly related to the log of the external calcium concentration, and the action potentials are blocked by both cobalt ions and lanthanum ions.It is concluded that calcium is the major charge carrier of the inward current in these neurosecretory axons which is the first report of calcium dependent action potentials in a nerve axon. Furthermore, small amounts of sodium and magnesium are necessary to maintain electrical activity. Magnesium is a competitive inhibitor of the calcium currents.We are grateful to the Science Research Council for financial support, and to Mrs. J. Birch for the printing of the electron micrographs.     

Competitive strategies differentiate closely related species of marine actinobacteria

Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.     

CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense,microdiversity and biogeography

Background

Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus.

Results

CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense.

Conclusions

This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-936) contains supplementary material, which is available to authorized users.     

A low-sodium-salt formulation for the fermentation of salinosporamides by <Emphasis Type="Italic">Salinispora tropica</Emphasis> strain NPS21184

In this paper, we described the development of a potassium-chloride-based-salt formulation containing low sodium concentrations (5.0 to 11 mM) to support the growth of Salinispora tropica strain NPS21184 and its production of salinosporamide A (NPI-0052). The sodium present in the media was essentially derived from the complex nitrogen sources Hy Soy, yeast extract, and peptone used in the media. We demonstrated that good growth rate and yield of S. tropica strain NPS21184 were detected in both agar and liquid media containing the potassium-chloride-based-salt formulation with sodium concentration as low as 5.0 mM, significantly less than the critical seawater-growth requirement concentration of 50 mM sodium for a marine microorganism. We also observed good production of NPI-0052 (176 to 243 mg/l) by S. tropica strain NPS21184 grown in production media containing the potassium chloride-based-salt formulation. The production of deschloro analog, salinosporamide B (NPI-0047), was significantly lower in the low-sodium-salt-formulation medium than in the high-sodium-salt-formulation media. We demonstrated that while S. tropica strain NPS21184 is a novel marine actinomycete that requires high salt content for growth, it does not require sodium-chloride-based seawater-type media for growth and production of NPI-0052.     

CALCULATIONS OF BIOELECTRIC POTENTIALS : VI. SOME EFFECTS OF GUAIACOL ON NITELLA

Values have been calculated for apparent mobilities and partition coefficients in the outer non-aqueous layer of the protoplasm of Nitella. Among the alkali metals (with the exception of cesium) the order of mobilities resembles that in water and the partition coefficients (except for cesium) follow the rule of Shedlovsky and Uhlig, according to which the partition coefficient increases with the ionic radius. Taking the mobility of the chloride ion as unity, we obtain the following: lithium 2.04, sodium 2.33, potassium 8.76, rubidium 8.76, cesium 1.72, ammonium 4.05, ½ magnesium 20.7, and ½ calcium 7.52. After exposure to guaiacol these values become: lithium 5.83, sodium 7.30, potassium 8.76, rubidium 8,76, cesium 3.38, ammonium 4.91, ½ magnesium 20.7, and ½ calcium 14.46. The partition coefficients of the chlorides are as follows, when that of potassium chloride is taken as unity: lithium 0.0133, sodium 0.0263, rubidium 1.0, cesium 0.0152, ammonium 0.0182, magnesium 0.0017, and calcium 0.02. These are raised by guaiacol to the following: lithium 0.149, sodium 0.426, rubidium 1.0, cesium 0.82, ammonium 0.935, magnesium 0.0263, and calcium 0.323 (that of potassium is not changed). The effect of guaiacol on the mobilities of the sodium and potassium ions resembles that seen in Halicystis but differs from that found in Valonia where guaiacol increases the mobility of the sodium ion but decreases that of the potassium ion.     

<Emphasis Type="Italic">Salinispora</Emphasis><Emphasis Type="Italic">arenicola</Emphasis> from temperate marine sediments: new intra-species variations and atypical distribution of secondary metabolic genes

The obligate marine actinobacterium Salinispora arenicola was successfully cultured from temperate sediments of the Pacific Ocean (Tosa Bay, offshore Kochi Prefecture, Japan) with the highest latitude of 33°N ever reported for this genus. Based on 16S rRNA gene sequence analysis, the Tosa Bay strains are of the same phylotype as the type strain S. arenicola NBRC105043. However, sequence analysis of their 16S-23S rRNA intergenic spacer (ITS) revealed novel sequence variations. In total, five new ITS sequences were discovered and further phylogenetic analyses using gyrase B and rifamycin ketosynthase (KS) domain sequences supported the phylogenetic diversity of the novel Salinispora isolates. Screening of secondary metabolite genes in these strains revealed the presence of KS1 domain sequences previously reported in S. arenicola strains isolated from the Sea of Cortez, the Bahamas and the Red Sea. Moreover, salinosporamide biosynthetic genes, which are highly homologous to those of Bahamas-endemic S. tropica, were detected in several Tosa Bay isolates, making this report the first detection of salinosporamide genes in S. arenicola. The results of this study provide evidence of a much wider geographical distribution and secondary metabolism diversity in this genus than previously projected.     

INFLUENCE OF IONIC CONDITIONS ON CELL DIFFERENTIATION AND MORPHOGENESIS OF THE CELLULAR SLIME MOLDS

Effects of various ionic conditions on the development of the cellular slime molds D. discoideum and D. mucoroides were studied. A certain concentration of lithium ions (7 mM) promoted differentiation of the stalk cells and conversely inhibited formation of the spores. The presence of calcium and magnesium ions was needed for Li to manifest its specific effect. A high concentration of Ca (100-120 mM) also facilitated differentiation of the stalk cells. On the other hand, fluoride ions stimulated considerable formation of spores at 15 mM. In the absence of divalent cations, sodium ions inhibited morphogenesis and cell differentiation proportionately with its concentration, and complete inhibition was obtained at 20 mM. The inhibitory effect of Na was nullified by addition of small amounts of Ca. Possible mechanisms by which these ions exert their influences on development of this organism were discussed.     

Coordinated cations in dipicolinato complexes of divalent metal ions

Several salts of alkali, alkaline earth metal and organic ammonium cations of a complex anion [ML₂]²⁻ {Where L = dipicolinato dianion, M = copper(II), nickel(II) and zinc(II)} are prepared. The coordination effect of [ML₂]²⁻ with the cations such as sodium, potassium, calcium, magnesium, and organic cations namely diammonium cation of 1,5-pentanediamine, diammonium cation of 1,8-octyldiamine, mono ammonium cation of 4-aminobenzylamine are studied by determining their X-ray crystal structures. Depending on the nature of cations, four different types of structures are obtained. When calcium is the cation a polymeric structure with calcium ions bridging the [ML₂]²⁻ is observed. The salts having sodium and potassium cations form polymeric chain like structures by oxo and aqua bridges. In the case of magnesium, the hydrated form of magnesium cations coordinates to [ML₂]²⁻. The organic ammonium salts of [ML₂]²⁻ have the structural features of conventional ionic complexes. These salts easily exchange cations. The organic ammonium salts of [ML₂]²⁻ decomposes to give the corresponding metal oxides at relatively low temperature range 300-450 °C.     

Adenosine triphosphate-lead histochemical reactions in ependymal epithelia of murine brains do not represent calcium transport adenosine triphosphatase

Summary The strong enzyme histochemical reactions for adenosine triphosphatase (ATPase) seen in ependymal tanycytes after incubation in calcium-containing media have previously been reported as calcium transport ATPase. Investigation of these reactions showed that: (1) any nucleoside triphosphate can serve as a substrate; (2) diphosphates and monophosphates cannot replace triphosphates; this includes p-nitrophenyl phosphate which is readily hydrolysed by plasma membrane transport ATPases; (3) strong localization occurs in the presence of millimolar concentrations of either calcium or magnesium ions; there is no absolute requirement for calcium ions; (4) they are not inhibited by sulphydryl inhibitors or calmodulin antagonists; (5) lead phosphate precipitates are localized almost entirely on the external face of tanycyte plasma membranes. In addition, the technique gives strong localization to vessels in the choroid plexus but not to the choroidal epithelium. Immunohistochemistry with a primary antibody raised against Ca²⁺,Mg²⁺-ATPase stains the choroidal epithelium but not the vessels or the ependymal tanycytes. These results are inconsistent with identification of the reaction as calcium transport ATPase but support characterization as an ecto-ATPase.     

ELEMENTAL DISTRIBUTION IN SEEDS OF THE HALOPHYTES SALICORNIA PACIFICA VAR. UTAHENSIS AND ATRIPLEX CANESCENS

Little information is available on the distribution of ions in seeds of halophytes. Seeds of two halophytes, Salicornia pacifica var. utahensis (Tidestrom) Munz, a desert salt playa type, and Atriplex canescens (Pursh) Nutt., a desert shrub, were analyzed by energy dispersive X-ray microanalysis. The relative ion concentration in three regions, the seed coat, endosperm, and embryo, were determined. The total relative concentration of elements was higher in seeds of S. pacifica var. utahensis as compared to A. canescens. The seed coats of S. pacifica var. utahensis contained the highest counts of sodium, chlorine, potassium, and calcium, whereas the embryo and endorsperm were both high in phosophorus. In A. canescens, sodium and chlorine were very low in all three tissues. The embryo contained the major amount of phosphorus, although potassium was high in both the seed coat and the embryo. These results support the concept of ion compartmentalization in the seeds of these two halophytes.     

Genetic variation,breeding system evolution,and conservation of the narrow sand dune endemic Stellaria arenicola and the widespread S. longipes (Caryophyllaceae)

Genetic variation was examined by electrophoresis in 14 populations of Stellaria arenicola, an endemic of the Athabasca sand dunes in northern Saskatchewan, Canada, and seven populations of S. longipes, its progenitor. Three of the 5. longipes populations were sympatric with the endemic. Populations of the endemic were found to have fewer alleles per polymorphic locus (2.21 vs. 2.37), fewer polymorphic loci (29.9 vs. 33.8), and lower genetic diversity (0.087 vs. 0.107) than populations of the progenitor. Genetic identities for all pairs of populations were high (0.932 to 1.000). The endemic had one novel allele and shared ten alleles with progenitor populations from the sand dunes that were not found in other populations of S. longipes. Populations of both species were found to partition most of their genetic variation within populations. An investigation of the multilocus outcrossing rates revealed that S. arenicola had higher rates of selling and biparental inbreeding than S. longipes. This study suggests that partial genetic isolation through a shift in the breeding system, in addition to previously reported strong directional selection, has been important in the sympatric evolution of the endemic S. arenicola. The close genetic relationship between populations of S. arenicola and S. longipes found on the Athabasca sand dunes supports the suggestion that the endemic evolved while sympatric to the gene pool of the progenitor species that is found presently in the region.     

THE COMPOSITION OF FLUIDS AND SERA OF SOME MARINE ANIMALS AND OF THE SEA WATER IN WHICH THEY LIVE

1. The electrolyte composition, the pH, and freezing points of the fluids of several invertebrates and one primitive chordate are reported. 2. Fluids of the worms, echinoderms, and the clam Venus were isotonic with sea water; fluids of the Arthropoda were hypertonic to sea water. 3. The pH of all fluids was below that of sea water. In the Arthropoda and Myxine less individual variation in pH appeared than in the echinoderms and worms. 4. Ratios of ionic concentrations in the fluid to those in the sea water indicated (1) uniform distribution of ions between the internal and external media for the echinoderms and Venus, (2) differential distribution of potassium and magnesium in the worms; (3) differential distribution of sulfate, magnesium, potassium, and calcium in the Arthropoda; and (4) differential distribution of calcium, magnesium, and sulfate in Myxine. 5. The unequal distribution of ions implies the expenditure of energy against a concentration gradient across the absorbing or excreting membranes, a capacity frequently overlooked in the invertebrates. 6. The sera of the Arthropoda from diluted sea water showed higher concentrations of sodium, potassium, calcium, and chloride ions relative to the respective concentrations in the external medium than in normal sea water, and also showed different orders for those ions. 7. The increase in osmotic pressure of the sera of the animals moving into brackish water is caused by unequal accumulation of sodium, potassium, calcium, and chloride ions. Sulfate and magnesium ionic ratios do not change.     

Studies on the Germination of Pine Pollen (Pinus mugo) in vitro. II. Effects of Different Ions

Studies on the initial germination of pollen of Pinus mugo showed no significant influence of ions on O₂ uptake and uptake of ³²P-labelled phosphate. At the onset of tube growth O₂ uptake decreased in the absence of calcium. In inorganic media tube growth and ³²P uptake were reduced in the absence of calcium or boric acid. In the absence of calcium a requirement for magnesium was observed. When the medium was deprived of polyvalent ions with EDTA, growth and ³²P uptake ceased. The presence of calcium in the medium was found to be essential for the maintenance of the structural and functional integrity of the cell membranne. — The ion requirement was more pronounced when tube growth was stimulated with sucrose. Calcium, magnesium, boric acid, and nitrate (as nitrogen source) were essential constitutents of the medium. The stimulation due to calcium required either magnesium or boric acid. — A density effect was observed which can be related to diffusible substances from the pollen into the medium. This was not observed when calcium and magnesium were present in the medium. The phenomenon is explained as an enrichment of the medium with diffusible substances from non-germinated dead pollen. — Germination and the tube growth were found to be greatly dependent on a short period of equilibration of pollen at room temperature before sowing.     

Influence of Potassium in the Agar Medium on the Growth Pattern of the Filamentous Fungus Fusarium solani

A decrease in the concentration of K⁺ ions below 3 mM in agar medium which also contained starch, casein hydrolysate, MgSO₄, and K₂HPO₄ changed the growth pattern of Fusarium solani illuminated in diurnal 12-h light/12-h dark cycles from zonation to a feathery growth mode. Rubidium or cesium ions could replace potassium, but lithium, sodium, and the bivalent alkaline earth ions could not.     

Effect of cations,including heavy metals,on cadmium uptake by Lemna polyrhiza L.

Cations, including calcium, magnesium, potassium, sodium, copper, iron, nickel and zinc, inhibited (up to 40%) extracellular binding and intracellular uptake of cadmium by Lemna polyrhiza in solution culture. Test plants showed a high capacity of extracellular cadmium binding which was competitively inhibited by copper, nickel and zinc; however, calcium, magnesium and potassium caused non-competitive inhibition. Iron and sodium increased K _m and decreased V _max, thereby causing mixed inhibition of extracellular binding. Intracellular cadmium uptake displayed Michaelis-Menten kinetics. It was competitively inhibited by calcium, magnesium, iron, nickel and zinc. Monovalent cations (sodium and potassium) caused non-competitive and copper caused mixed inhibition of intracellular cadmium uptake. Thus, high levels of cations and metals in the external environment should be expected to lower the cadmium accumulation efficiency of L. polyrhiza.     

The karyotype of Axarus festivus (Say) and a comparison with species of Lipiniella (Chironomidae: Diptera)

Larvae of Axarus andLipiniella share several apparantly apomorphic features of the mouth-part structure, however adults ofLipiniella show possible relationships toDemeijerea andChironomus. In order to assist in refining the relationships ofAxarus toLipiniella the karyotype ofAxarus festivus was determined and compared to the karyotypes ofLipiniella arenicola andL. moderata. Larvae ofA. festivus from a population in Kansas were monomorphous, with 2n=8, the Ist, IInd and IIIrd chromosomes metacentric, and IVth acrocentric.Axarus festivus therefore differs fromL. arenicola in chromosome number (2n=6), however homologous sections of all chromosomes were identified. Inversions were detected in the Ist, IInd and IIIrd chromosomes ofA. festivus relative toL. arenicola. It was determined that both species have high functional activity, as indicated by the presence of three Balbiani rings, and more than one nucleolus per genome. Differing degrees of polyteny, a feature previously described forL. arenicola, were observed in the salivary glands, with highest degrees of polyteny in cells near the salivary duct. These similarities of chromosome structure indicate close genetic relationships betweenA. festivus andL. arenicola. However, we did not find evidence for similarity ofA. festivus toL. moderata, which supports the previous conclusions byKiknadze et al. (1989) regardingL. arenicola andL. moderata.     

Further Investigations on the Nature of the Heat Resistance of Thermophilic Bacteria

When cells of Bacillus stearothermophilus, strain NCA 1503, were grown in tryptone starch broth and subsequently transferred to tris buffer, a fraction of the cells: rapidly died in ttie buffer. This fraction increased with increasing content of calcium chloride in the growth medium. The' addition of sodium, potassium or magnesium chloride to the growth medium had no such effect. The rapid dying of the cells in tris buffer was associated with a leakage of organic material and calcium ions from the cells. The results obtained are probably caused by a damage to the osmotic barrier of the cells during their contact with the buffer. Observations: made during the present investigation and a previous one (Ljunger 1970) indicate that the heat resistance of thermophilic bacteria depends on the maintenance of a high intracellular concentration of free calcium ions.