Evolutionary relationships among photosynthetic bacteria

To understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within Bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. Recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. Based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria can now be defined in clear molecular terms and their relative branching orders logically deduced. For the 82 presently completed bacterial genomes, the presence or absence of these signatures in various proteins was found to be almost exactly as predicted by the indel model, with only 11 exceptions observed in 1842 observations. The branching order of different bacterial groups as deduced using this approach is as follows: low G+C Gram-positive (Heliobacterium chlorum) ↔ high G+C Gram-positive ↔ Clostridium–Fusobacterium–Thermotoga ↔ Deinococcus–Thermus ↔ green nonsulfur bacteria (Chloroflexus aurantiacus) ↔ Cyanobacteria ↔ Spirochetes ↔ Chlamydia–Cytophaga–Flavobacteria–green sulfur bacteria (Chlorobium tepidum) ↔ Aquifex ↔ Proteobacteria (δ and ∈) ↔ Proteobacteria (α) ↔ Proteobacteria (β) and ↔ Proteobacteria (γ). The Heliobacterium species, which contain an Fe–S type of reaction center (RC 1) and represent the sole photosynthetic phylum from the Gram-positive or monoderm bacteria (i.e., bounded by only a single membrane), is indicated to be the most ancestral of the photosynthetic lineages. Among the Gram-negative or diderm bacteria (containing both inner and outer cell membranes) the green nonsulfur bacteria, which contain a pheophytin-quinone type of reaction center (RC 2), are indicated to have evolved first. The later emerging photosynthetic groups which contain either one or both of these reaction centers could have acquired such genes from the earlier branching lineages by either direct descent or by means of lateral gene transfer. This revised version was published online in August 2006 with corrections to the Cover Date.     

Phylogenetic composition of bacterial communities in small boreal lakes and ombrotrophic bogs of the upper Volga basin

Fluorescent in situ hybridization (FISH) with rRNA-specific oligonucleotide probes was used to assess the numbers and phylogenetic diversity of prokaryotic microorganisms in the water of small boreal lakes and peatland catchments of the swampy upper Volga basin. The abundance of bacterioplankton in lake water was found to vary from 1.6 to 8.7 × 10⁶ cells ml⁻¹, with the highest values detected in neutral eutrophic lakes. The total cell numbers in the peat of ombrotrophic bogs were 3.9–4.3 × 10⁸ cells g⁻¹ of wet peat. The proportion of bacteria identified by the group-specific probes decreased from 79–85% in neutral (pH 6.6–6.9) mesotrophic and eutrophic lakes to 65–69% in acidic (pH 4.4–5.5) dystrophic lakes and to 51–58% in the peat of acidic (pH 3.6–3.9) ombrotrophic bogs. The diversity of bacterial communities was highest in lakes with neutral water. These communities were dominated by members of the phylum Actinobacteria (31–44% of the total bacterial number), while the contribution of Alphaproteobacteria (16–19%), Bacteroidetes (6–16%), Betaproteobacteria (6–7%), Planctomycetes (2–8%), and Gammaproteobacteria (4–5%) was also significant. In acidic dystrophic lakes, Actinobacteria (25–35%) and Betaproteobacteria (25–34%) predominated, while peatland catchments were dominated by the Alphaproteobacteria (20–23%). The presence of acidobacteria and some planctomycetes common for bogs in the water of acidic dystrophic lakes, as well as the high proportion of bacteria (31–49%) that were not identified by the group-specific probes, suggest the impact of microbial processes in peatland catchments on the microbial composition of the receiving waters.     

Effects of Spilled Oil on Bacterial Communities of Mediterranean Coastal Anoxic Sediments Chronically Subjected to Oil Hydrocarbon Contamination

The effects of spilled oil on sedimentary bacterial communities were examined in situ at 20 m water depth in a Mediterranean coastal area. Sediment collected at an experimental site chronically subjected to hydrocarbon inputs was reworked into PVC cores with or without a massive addition of crude Arabian light oil (∼20 g kg⁻¹ dry weight). Cores were reinserted into the sediment and incubated in situ at the sampling site (20 m water depth) for 135 and 503 days. The massive oil contamination induced significant shifts in the structure of the indigenous bacterial communities as shown by ribosomal intergenic spacer analysis (RISA). The vertical heterogeneity of the bacterial communities within the sediment was more pronounced in the oiled sediments particularly after 503 days of incubation. Response to oil of the deeper depth communities (8–10 cm) was slower than that of superficial depth communities (0–1 and 2–4 cm). Analysis of the oil composition by gas chromatography revealed a typical microbial alteration of n-alkanes during the experiment. Predominant RISA bands in oiled sediments were affiliated to hydrocarbonoclastic bacteria sequences. In particular, a 395-bp RISA band, which was the dominant band in all the oiled sediments for both incubation times, was closely related to hydrocarbonoclastic sulfate-reducing bacteria (SRB). These bacteria may have contributed to the main fingerprint changes and to the observed biodegradation of n-alkanes. This study provides useful information on bacterial dynamics in anoxic contaminated infralittoral sediments and highlights the need to assess more precisely the contribution of SRB to bioremediation in oil anoxic contaminated areas.     

Catch Composition on Red Shrimps’ (Aristaeomorpha foliacea and Aristeus antennatus) Grounds in the Eastern Ionian Sea

In the present study, the catch composition and the catch per unit effort (CPUE) by weight and numbers in red shrimps’ (Aristaeomorpha foliacea and Aristeus antennatus) grounds was examined in the southern part of the eastern Ionian Sea, in order to collect important information for the Greek waters, where no deep-water fishery exists. In the depth stratum 500–700 m, the catch of the commercial species represented a high proportion (>70%) of the total catch. Red shrimps and several other commercial species were found in important quantities. The present results suggest the possibility of developing a deep-water fishery in Greece. In such a case, attention should be paid because of the high vulnerability of A. foliacea – the main deep-water fishing resource in the area – to the fishing pressure.     

Regulation of Ethylene Biosynthesis Under Salt Stress in Red Pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) by 1-Aminocyclopropane-1-Carboxylic Acid (ACC) Deaminase-producing Halotolerant Bacteria

The present study was carried out to understand the mechanism of salt stress amelioration in red pepper plants by inoculation of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing halotolerant bacteria. In general, ethylene production, ACC concentration, ACC synthase (ACS), and ACC oxidase (ACO) enzyme activities increased with increasing levels of salt stress. Treatment with halotolerant bacteria reduced ethylene production by 47–64%, ACC concentration by 47–55% and ACO activity by 18–19% in salt-stressed (150 mmol NaCl) red pepper seedlings compared to uninoculated controls. ACS activity was lower in red pepper seedlings treated with Bacillus aryabhattai RS341 but higher in seedlings treated with Brevibacterium epidermidis RS15 (44%) and Micrococcus yunnanensis RS222 (23%) under salt-stressed conditions as compared to uninoculated controls. A significant increase was recorded in red pepper plant growth under salt stress when treated with ACC deaminase-producing halotolerant bacteria as compared to uninoculated controls. The results of this study collectively suggest that salt stress enhanced ethylene production by increasing enzyme activities of the ethylene biosynthetic pathway. Inoculation with ACC deaminase-producing halotolerant bacteria plays an important role in ethylene metabolism, particularly by reducing the ACC concentration, although a direct effect on reducing ACO activity was also observed. It is suggested that growth promotion in inoculated red pepper plants under inhibitory levels of salt stress is due to ACC deaminase activity present in the halotolerant bacteria.     

Haemagglutination Induced by Bordetella pertussis Filamentous Haemagglutinin Adhesin (FHA) Is Inhibited by Antibodies Produced Against FHA430–873 Fragment Expressed in Lactobacillus casei

Filamentous haemagglutinin adhesin (FHA) is an important virulence factor from Bordetella pertussis related to the adhesion and spread of the bacteria through the respiratory tract. Three distinct domains have been characterized in mature FHA, and among them, the FHA_442–863 fragment was suggested to be responsible for the heparin-binding activity. In this study, we cloned the gene encoding the HEP fragment (FHA_430–873) in a Lactobacillus casei–inducible expression vector based on the lactose operon. The recombinant bacteria, transformed with the resulting construct (L. casei-HEP), were able to express the heterologous protein depending on the sugar added to the culture. Subcutaneous inoculation of L. casei-HEP in Balb/C mice, using the cholera toxin B subunit as adjuvant, induced systemic anti-HEP antibodies that were able to inhibit in vitro erythrocyte haemagglutination induced by FHA. This is the first example of a B. pertussis antigen produced in lactic acid bacteria and opens new perspectives for alternative vaccine strategies against whooping cough.     

Methane Release through Resuspension of Littoral Sediment

Sediment in the littoral zone of lakes is frequently disturbed by wave action or bioturbation, resulting in sediment resuspension. In undisturbed sediment, methanotrophic bacteria efficiently reduce the diffusive flux of methane into the water column. In a microcosm study, the resuspension of littoral sediment was simulated in sediment cores for a winter (n = 3) and a summer situation (n = 3). The erosion of surface sediment resulted in a large flux of methane into the overlying water (207 ± 176 μmol h⁻¹ m⁻² in winter and 73 ± 18 μmol h⁻¹ m⁻² in summer). Only a minor part (16 ± 7%) of the methane released was oxidized by methanotrophic bacteria, whereas the major part escaped into the water column. Only 6–16% of the littoral zone has to be resuspended to reach the same flux as from undisturbed littoral sediment. For the daily flux, a sediment resuspension has to last 1–4 h to reach the undisturbed daily flux. The study reveals the important role of sediment resuspension in the littoral methane cycle as an intense but variable source of methane of largely unknown magnitude.     

Expression of the antimicrobial peptide cecropin fused with human lysozyme in Escherichia coli

Lysozyme is an abundant, cationic antimicrobial protein that plays an important role in host defense. It targets the β (1–4) glycosidic bond between N-acetylglucosamine and N-acetylmuramic residues that make up peptidoglycan, making lysozyme highly active against Gram-positive bacteria. However, lysozyme alone is inactive against Gram-negative bacteria because it cannot reach the peptidoglycan layer. Cecropins are cationic molecules with a wide range of antimicrobial activities. The main target for these peptides is the cytoplasmic membrane. We resume that cecopin may disrupt the outer membrane, giving the enzyme access to the peptidoglycan in cell wall. So in the present study, novel hybrid protein combining Musca domestica cecropin (Mdc) with human lysozyme (Hly) was designed. The DNA sequence encoding recombination fusion protein Mdc–hly was cloned into the pET-32a vector for protein expression in Escherichia coli strain BL21 (DE3). The protein was expressed as a His-tagged fusion protein, and the Mdc–hly was released from the fusion by enterokinase cleavage and separated from the carrier thioredoxin. Antimicrobial activity assays showed that the recombinant fusion protein Mdc–hly has improved in vitro antimicrobial activity and action spectrum compared to Mdc and hly. Mdc–hly may have important potential application as a future safely administered human drug and food additive.     

Antimicrobial activity of the extracts from fruits of <Emphasis Type="Italic">Rumex</Emphasis> L. species

This study was designed primarily to investigate the antibacterial and antifungal activity of the extracts from fruits of six Rumex L. species: R. acetosa L., R. acetosella L., R. confertus Willd., R. crispus L., R. hydrolapathum Huds. and R. obtusifolius L. The 7 Grampositive and 7 Gram-negative bacteria strains and 5 fungal ones were tested by agar and broth dilution method. Determination of minimal inhibitory concentration (MIC) revealed that the extracts from R. confertus, R. crispus, R. hydrolapathum and R. obtusifolius exerted differential inhibitory effect on the growth of Gram-positive bacteria — staphylococci (MIC=62.5–125 μg/mL) and Gramnegative bacteria — Escherichia coli ATCC 3521, Proteus mirabilis, Pseudomonas aeruginosa (MIC=125→500 μg/mL); MIC values determined by agar dilution method were somewhat higher. The same extracts inhibited also the growth of fungi — Candida spp. or Trichophyton mentagrophytes ATCC 9533 (MIC=250–500 μg/mL), as found by agar dilution method. The total content of polyphenols (11.66–78.36 mg/g), anthracene derivatives (0.26–12.93 mg/g) and tannins (4.00–11.16%) was also determined.     

Diversity and Activity of PAH-Degrading Bacteria in the Phyllosphere of Ornamental Plants

Phyllosphere bacteria on ornamental plants were characterized based on their diversity and activity towards the removal of polycyclic aromatic hydrocarbons (PAHs), the major air pollutants in urban area. The amounts of PAH-degrading bacteria were about 1–10% of the total heterotrophic phyllosphere populations and consisted of diverse bacterial species such as Acinetobacter, Pseudomonas, Pseudoxanthomonas, Mycobacterium, and uncultured bacteria. Bacterial community structures analyzed by polymerase chain reaction–denaturing gradient gel electrophoresis from each plant species showed distinct band patterns. The uniqueness of these phyllosphere bacterial communities was partly due to the variation in leaf morphology and chemical properties of ornamental plants. The PAH degradation activity of these bacteria was monitored in gas-tight systems containing sterilized or unsterilized leaves. The results indicated that phyllosphere bacteria on unsterilized leaves were able to enhance the activity of leaves for phenanthrene removal. When compared between plant species, phenanthrene removal efficiency corresponded to the size of phenanthrene-degrading bacteria. In addition, phyllosphere bacteria on Wrightia religiosa were able to reduce other PAHs such as acenaphthylene, acenaphthene, and fluorine in 60-ml glass vials and in a 14-l glass chamber. Thus, phyllosphere bacteria on ornamental plants may play an important role in natural attenuation of airborne PAHs in urban areas.     

Metabolism of polyunsaturated fatty acids and their toxicity to the microflora of the rumen

Ruminal microorganisms hydrogenate polyunsaturated fatty acids (PUFA) present in forages and thereby restrict the availability of health-promoting PUFA in meat and milk. The aim of this study was to investigate PUFA metabolism and the influence of PUFA on members of the ruminal microflora. Eleven of 26 predominant species of ruminal bacteria metabolised linoleic acid (LA; cis-9,cis-12–18:2) substantially. The most common product was vaccenic acid (trans-11–18:1), produced by species related to Butyrivibrio fibrisolvens. α-Linolenic acid (LNA; cis-9,cis-12,cis-15–18:3) was metabolised mostly by the same species. The fish oil fatty acids, eicosapentaenoic acid (EPA; 20:5(n − 3)) and docosahexaenoic acid (DHA; 22:6(n − 3)) were not metabolised. Cellulolytic bacteria did not grow in the presence of any PUFA at 50 μg ml⁻¹, nor did some butyrate-producing bacteria, including the stearate producer Clostridium proteoclasticum, Butyrivibrio hungatei and Eubacterium ruminantium. Toxicity to growth was ranked EPA > DHA > LNA > LA. Cell integrity, as measured using propidium iodide, was damaged by LA in all 26 bacteria, but to different extents. Correlations between its effects on growth and apparent effects on cell integrity in different bacteria were low. Combined effects of LA and sodium lactate in E. ruminantium and C. proteoclasticum indicated that LA toxicity is linked to metabolism in butyrate-producing bacteria. PUFA also inhibited the growth of the cellulolytic ruminal fungi, with Neocallimastix frontalis producing small amounts of cis-9,trans-11–18:2 (CLA) from LA. Thus, while dietary PUFA might be useful in suppressing the numbers of biohydrogenating ruminal bacteria, particularly C. proteoclasticum, care should be taken to avoid unwanted effects in suppressing cellulolysis.     

Identification of a Vibrio strain producing antimicrobial agents in the excretory organs of Nautilus pompilius (Cephalopoda: Nautiloidea)

The aim of the present study was to identify and characterize bacteria producing antimicrobial compounds in the excretory organs of Nautilus pompilius. Culture-dependent and culture-independent complementary approaches were used for bacterial identification such as: culture on selective media, Gram staining, CARD-FISH, direct DNA extraction from host tissue, PCR amplification and sequencing of the bacterial 16S rRNA gene. Results show presence of three bacterial groups: γ-Proteobacteria with three clusters (Pseudomonadales, Vibrionales, Alteromonadales), β-Proteobacteria and spirochetes. In order to screen for active strains, antimicrobial activity was tested by diffusion agar assay against Micrococcus luteus, Escherichia coli, Vibrio harveyi, and Candida albicans. Nautilus isolates showed antimicrobial activities against both Gram-positive and Gram-negative reference strains. Most of the active strains were phylogenetically related to environmental Vibrionaceae. These strains were always abundant in N. pompilius PA but were absent from Nautilus macromphalus from other geographical areas. Therefore, we suggest that antimicrobial active Vibrionaceae infect N. pompilius by environmental transmission.     

Bacterial Uptake by the Marine Sponge <Emphasis Type="Italic">Aplysina aerophoba</Emphasis>

Sponges (Porifera) are filter feeders that take up microorganisms from seawater and digest them by phagocytosis. At the same time, many sponges are known to harbor massive consortia of symbiotic microorganisms, which are phylogenetically distinct from those in seawater, within the mesohyl matrix. In the present study, feeding experiments were performed to investigate whether phylogenetically different bacterial isolates, hereafter termed “food bacteria,” microbial seawater consortia, and sponge symbiont consortia are taken up and processed differently by the host sponge. Aplysina aerophoba retained high numbers of bacterial isolates and microbial seawater consortia with rates of up to 2.76 × 10⁶ bacteria (g sponge wet weight)^–1 h^–1, whereas the retention of sponge symbionts was lower by nearly two orders of magnitude [5.37 × 10⁴ bacteria (g sponge wet weight)⁻¹ h^–1]. In order to visualize the processing of a food bacterium within sponge tissues, the green fluorescent protein-labeled Vibrio strain MMW1, which had originally been isolated from A. aerophoba, was constructed. Incubation of this strain with A. aerophoba and subsequent visualization in tissue cryosections showed its presence in the choanocytes and/or endopinacocytes lining the canals but, unlike latex beads, not in deeper regions of the mesohyl, which suggests digestion of the bacteria upon contact with the host. Denaturing gradient gel electrophoresis (DGGE) was performed on the incubation seawater to monitor the changes in phylogenetic composition after incubation of the sponge with either seawater or sponge symbiont consortia. However, the DGGE experiment provided no evidence for selective processing of individual lineages by the host sponge. In conclusion, this study extends early studies by Wilkinson et al. (Proc R Soc London B 220:519–528, 1984) that sponges, here A. aerophoba, are able to differentiate between food bacteria and their own bacterial symbionts.     

Water supply regulates structure, productivity, and water use efficiency of Acacia koa forest in Hawaii

We studied changes in stand structure, productivity, canopy development, growth efficiency, and intrinsic water use efficiency (WUE=photosynthesis/stomatal conductance) of the native tree koa (Acacia koa) across a gradient of decreasing rainfall (2600–700 mm) with increasing elevation (700–2000 m) on the island of Hawaii. The stands were located on organic soils on either smooth (pahoehoe) or rough (aa) lava flows. In the greenhouse, we also examined growth and WUE responses to different water regimes of koa seedlings grown from seeds collected in the study area. We tested the hypotheses that (1) stand basal area, aboveground net primary productivity (ANPP), leaf area index (LAI), and growth per unit leaf area decreased with decreasing rainfall, (2) WUE increased with decreasing rainfall or water supply, and (3) WUE responses were caused by stomatal limitation rather than by nutrient limitations to photosynthesis. The carbon isotope composition of phyllode tissues (δ¹³C) was examined as an integrated measure of WUE. Basal area and LAI of koa stands on both pahoehoe and aa lava flows, and ANPP on aa lava flows decreased with elevation. Basal area, LAI, and ANPP of koa in mixed stands with the exotic tropical ash (Fraxinus udhei) were lower compared to single-species koa stands at similar elevations. Along the gradient, phyllode δ¹³C (and therefore WUE) increased with elevation from –30.2 to –26.8‰. Koa in mixed stands exhibited higher (less negative) δ¹³C than in single-species stands suggesting that koa and tropical ash competed for water. In the greenhouse, we observed the same trend observed in the field, as phyllode δ¹³C increased from –27.7 to –24‰ as water supply decreased. Instantaneous gas exchange measurements in the greenhouse showed an inverse correlation of both maximum (morning) photosynthesis (A) and conductance (g) with δ¹³C values and, also, a good agreement between instantaneous (A/g) and integrated measures of WUE. Phyllode δ¹³C was not correlated with foliar concentrations of N or other nutrients in either the field or the greenhouse, indicating that differences in δ¹³C were caused by stomatal limitation rather than by nutrient-related changes in photosynthetic capacity. This study provided evidence that long-term structural and growth adjustments as well as changes in WUE are important mechanisms of koa response to water limitation.     

Molecular- and cultivation-based analyses of microbial communities in oil field water and in microcosms amended with nitrate to control H2S production

Nitrate injection into oil fields is an alternative to biocide addition for controlling sulfide production (‘souring’) caused by sulfate-reducing bacteria (SRB). This study examined the suitability of several cultivation-dependent and cultivation-independent methods to assess potential microbial activities (sulfidogenesis and nitrate reduction) and the impact of nitrate amendment on oil field microbiota. Microcosms containing produced waters from two Western Canadian oil fields exhibited sulfidogenesis that was inhibited by nitrate amendment. Most probable number (MPN) and fluorescent in situ hybridization (FISH) analyses of uncultivated produced waters showed low cell numbers (≤10³ MPN/ml) dominated by SRB (>95% relative abundance). MPN analysis also detected nitrate-reducing sulfide-oxidizing bacteria (NRSOB) and heterotrophic nitrate-reducing bacteria (HNRB) at numbers too low to be detected by FISH or denaturing gradient gel electrophoresis (DGGE). In microcosms containing produced water fortified with sulfate, near-stoichiometric concentrations of sulfide were produced. FISH analyses of the microcosms after 55 days of incubation revealed that Gammaproteobacteria increased from undetectable levels to 5–20% abundance, resulting in a decreased proportion of Deltaproteobacteria (50–60% abundance). DGGE analysis confirmed the presence of Delta- and Gammaproteobacteria and also detected Bacteroidetes. When sulfate-fortified produced waters were amended with nitrate, sulfidogenesis was inhibited and Deltaproteobacteria decreased to levels undetectable by FISH, with a concomitant increase in Gammaproteobacteria from below detection to 50–60% abundance. DGGE analysis of these microcosms yielded sequences of Gamma- and Epsilonproteobacteria related to presumptive HNRB and NRSOB (Halomonas, Marinobacterium, Marinobacter, Pseudomonas and Arcobacter), thus supporting chemical data indicating that nitrate-reducing bacteria out-compete SRB when nitrate is added.     

Evaluation of haloalkaliphilic sulfur-oxidizing microorganisms with potential application in the effluent treatment of the petroleum industry

Haloalkaliphilic sulfur-oxidizing mixed cultures for the treatment of alkaline–saline effluents containing sulfide were characterized and evaluated. The mixed cultures (IMP-PB, IMP-XO and IMP-TL) were obtained from Mexican alkaline soils collected in Puebla (PB), Xochimilco (XO) and Tlahuac (TL), respectively. The Ribosomal Intergenic Spacer Analysis (RISA) revealed bacteria related to Thioalkalibacterium and Thioalkalivibrio in IMP-XO and IMP-PB mixed cultures. Halomonas strains were detected in IMP-XO and IMP-TL. In addition, an uncultured Bacteroides bacterium was present in IMP-TL. Mixed cultures were evaluated at different pH and NaCl concentrations at 30°C. IMP-PB and IMP-TL expressed thiosulfate-oxidizing activity in the 7.5–10.5 pH range, whereas IMP-XO presented its maximal activity with 19.0 mg O₂ g_protein⁻¹ min⁻¹, at pH 10.6; it was not affected by NaCl concentrations up to 1.7 M. In continuous culture, IMP-XO showed a growth rate of 15 day⁻¹, productivity of 433.4 mg_protein l⁻¹ day⁻¹ and haloalkaliphilic sulfur-oxidizing activity was also detected up to 170 mM by means of N-methyl-diethanolamine (MDEA). Saline–alkaline soil samples are potential sources of haloalkaliphilic sulfur-oxidizing bacteria and the mixed cultures could be applied in the treatment of inorganic sulfur compounds in petroleum industry effluents under alkaline–saline conditions.     

Characterization of ‘Schizokinen’; a dihydroxamate-type siderophore produced by Rhizobium leguminosarum IARI 917

The Rhizobia comprise one of the most important groups of beneficial bacteria, which form nodules on the roots (rarely on the stems) of leguminous plants. They live within the nodules and reduce atmospheric nitrogen to ammonia, which is further assimilated by plants into required nitrogenous compounds. The Rhizobia in return obtain nutrition from the plant. Rhizobia are free-living soil bacteria and have to compete with other microorganisms for the limited available iron in the rhizosphere. In order to acquire iron Rhizobia have been shown to express siderophore-mediated iron transport systems. Rhizobium leguminosarum IARI 917 was investigated for its ability to produce siderophore. It was found to produce a dihydroxamate type siderophore under iron restricted conditions. The siderophore was purified and chemically characterized. The ESMS, MS/MS and NMR analysis indicate the dihydroxamate siderophore to be ‘schizokinen’, a siderophore reported to be produced by Bacillus megaterium that shares a similar structure to ‘rhizobactin 1021’ produced by Sinorhizobium meliloti 1021. This is the first report of production of schizokinen by a strain of R. leguminosarum, therefore it was carefully investigated to confirm that it is indeed ‘schizokinen’ and not a degradation product of ‘rhizobactin 1021’. Since ferric–siderophore complexes are transported across the outer membrane (OM) into the periplasm via an OM receptor protein, R. leguminosarum IARI 917 was investigated for the presence of an OM receptor for ‘ferric–schizokinen’. SDS PAGE analysis of whole cell pellet and extracted OM fractions indicate the presence of a possible iron-repressible OM receptor protein with the molecular weight (MW) of approximately 74 kDa.     

In vitro and in vivo evaluation of the prebiotic activity of water-soluble blueberry extracts

The prebiotic effects of water extracts of two blueberry (BBE) cultivars (‘Centurion’ and ‘Maru’) were studied using pure and mixed cultures of human faecal bacteria. The results demonstrated for the first time that addition of BBE from both cultivars to broth media containing pure cultures of Lactobacillus rhamnosus and Bifidobacterium breve resulted in a significant increase (P < 0.05–0.0001) in the population size of these strains. Batch fermentation system was used to monitor the effect of BBE addition on the mixed faecal bacterial populations (obtained from healthy human donors). Addition of BBE from both cultivars to batch cultures inoculated with mixed human faecal cultures resulted in a significant increase in the number of lactobacilli (P < 0.01–0.0001) and bifidobacteria (P < 0.05–0.0001). Furthermore, a significant influence on the population size of lactobacilli and bifidobacteria was observed after administration of extracts from both cultivars to rats daily for 6 days in comparison with the control group. In rats gavaged orally with 4 ml kg⁻¹ day⁻¹ of BBE for 6 days, the population size of lactobacilli (P < 0.05) and bifidobacteria (P < 0.05–0.01) was increased significantly. We hypothesize that BBE could modify the bacterial profile by increasing the numbers of beneficial bacteria and thereby improving gut health.     

Systematics and distribution of theDiplophos taenia species complex (Gonostomatidae), with a description of a new species

For the systematic study of the gonostomatid fishes of theDiplophos taenia species complex, a total of 698 specimens was obtained from the three oceans. Four valid species were recognized:D. taenia Günther,D. proximus Parr,D. orientalis Matsubara, andD. australis sp. nov. The diagnostic characters are 90–100 total vertebrae (TV) (37–41 abdominal (AV) +52–60 caudal vertebrae (CV)) and 103–115 IC photophores (IC) for D.taenia, 85–90 TV (36–39 AV + 48–52 CV) and 98–104 IC forD. proximus, 83–86 TV (33–35 AV + 49–52 CV) and 92–100 IC for D.orientalis, and 84–91 TV (33–37 AV+ 50–54 CV) and 99–105 IC forD. australis. In addition to the above,D. proximus has larger orbital diameter (the proportion to head length 21–28%) than the other three species (15–23%) beyond 70mm in standard length. Due to wide distribution,D. taenia shows meristic variations: the numbers of TV, IC and anal fin rays (A) are smaller at lower latitudes and larger at higher ones in all oceans, and the number of A is smaller in the Atlantic (56–71) than in the other oceans (59–72) of the same latitude. Because of these variations, identification to species level is possible only area by area. The distribution of each of the four species is also distinct:D. taenia is a cosmopolitan between about 40° N and 30° S exclusive of the eastern tropical Pacific;D. proximus is endemic to the eastern tropical Pacific;D. orientalis is limited to the North Pacific transitional zone between about 30° and 40° N; andD. australis in a transitional zone of the Southern Ocean south of 20° S.     

Transpiration and whole-tree conductance in ponderosa pine trees of different heights

Changes in leaf physiology with tree age and size could alter forest growth, water yield, and carbon fluxes. We measured tree water flux (Q) for 14 ponderosa pine trees in two size classes (12 m tall and ∼40 years old, and 36 m tall and ∼ 290 years old) to determine if transpiration (E) and whole-tree conductance (g _t) differed between the two sizes of trees. For both size classes, E was approximately equal to Q measured 2 m above the ground: Q was most highly correlated with current, not lagged, water vapor pressure deficit, and night Q was <12% of total daily flux. E for days 165–195 and 240–260 averaged 0.97 mmol m^–2 (leaf area, projected) s^–1 for the 12-m trees and 0.57 mmol m^–2 (leaf area) s^–1 for the 36-m trees. When photosynthetically active radiation (I _P) exceeded the light saturation for photosynthesis in ponderosa pine (900 μmol m^–2 (ground) s^–1), differences in E were more pronounced: 2.4 mmol m^–2 (leaf area) s^–1 for the 12-m trees and 1.2 mmol m^–2 s^–1 for the 36-m trees, yielding g _t of 140 mmol m^–2 (leaf area) s^–1 for the 12-m trees and 72 mmol m^–2 s^–1 for the 36-m trees. Extrapolated to forests with leaf area index =1, the 36-m trees would transpire 117 mm between 1 June and 31 August compared to 170 mm for the 12-m trees, a difference of 15% of average annual precipitation. Lower g _t in the taller trees also likely lowers photosynthesis during the growing season. Received: 19 April 1999 / Accepted: 23 March 2000