Growth rate effects on fundamental transport properties of bacterial populations

In many natural environments, bacterial populations experience suboptimal growth due to the competition with other microorganisms for limited resources. The chemotactic response provides a mechanism by which bacterial populations can improve their situation by migrating toward more favorable growth conditions. For bacteria cultured under suboptimal growth conditions, evidence for an enhanced chemotactic response has been observed previously. In this article, for the first time, we have quantitatively characterized this behavior in terms of two macroscopic transport coefficients, the random motility and chemotactic sensitivity coefficients, measured in the stopped-flow diffusion chamber assay. Escherichia coli cultured over a range of growth rates in a chemostat exhibits a dramatic increase in the chemotactic sensitivity coefficient for D-fucose at low growth rates, while the random motility coefficient remains relatively constant by comparison. The change in the chemotactic sensitivity coefficient is accounted for by an independently measured increase in the number of galactose-binding proteins which mediate the chemotactic signal. This result is consistent with the relationship between macroscopic and microscopic parameters for chemotaxis, which was proposed in the mathematical model of Rivero and co-workers. (c) 1993 John Wiley & Sons, Inc.     

Isolation and characterization of an atrazine-degrading Rhodococcus sp. strain MB-P1 from contaminated soil

Aims:  The aim of this study is to isolate and characterize organisms capable of utilizing high concentration atrazine from the contaminated sites.
Methods and Results:  A selective enrichment was used for isolating atrazine-degrading organisms from the contaminated sites resulting in isolation of an efficient atrazine-degrading organism designated as strain MB-P1. On the basis of 16S rRNA gene sequencing, total cellular fatty acid analysis and physiological and biochemical tests, strain MB-P1 was identified as a member of genus Rhodococcus . High performance liquid chromatography was performed to identify the atrazine degradation intermediates demonstrating that the degradation proceeds via formation of 'de-ethylatrazine' and 'de-isopropylatrazine'. Further, plasmid curing by SDS method showed atrazine-degrading gene(s) to be plasmid-encoded.
Conclusions:  We have successfully isolated a Rhodococcus sp. strain MB-P1 which is capable of utilizing atrazine as sole source of carbon and energy at very high concentrations of 1000 ppm. The pathway for degradation of atrazine has also been determined. The metabolic gene(s) responsible for atrazine degradation was found to be plasmid-encoded.
Significance and Impact of the Study:  Rhodococcus sp. strain MB-P1 could be used as an ideal model system for in-situ degradation and restoration of ecological niches which are heavily contaminated with atrazine.     

Characterization and functional analysis of a novel gene cluster involved in biphenyl degradation in Rhodococcus sp. strain R04

AIMS: Isolation of the genes relative to PCB biodegradation and identification of the bph gene function in Rhodococcus sp. R04. METHODS AND RESULTS: A 8.7-kb fragment carrying the biphenyl catabolic genes bphABCD was isolated from the gene library in Rhodococcus sp. R04. Based on the deduced amino acid sequence homology, seven bph genes, bphA1A2A3A4, bphB, bphC and bphD, were thought to be responsible for the initial four steps of biphenyl degradation. In Escherichia coli, BphA exhibited poor activity for biphenyl transformation, and BphB, BphC and BphD were found to be catalytically active towards 2,3-dihydro-2,3-dihydroxybiphenyl, 2,3-dihydroxybiphenyl and 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate, respectively (activities of 50, 8.1 and 2.4 micromol l(-1) min(-1) mg(-1)). SDS-PAGE analysis indicated that the sizes of bphA1A2A3A4, bphB, bphC and bphD gene products were 49, 19, 14, 47, 32, 30 and 31 kDa, respectively. After disruption of bph genes, the bphA1 mutants lost the ability to grow on biphenyl, the bphB and bphD mutants were able to transform a little of biphenyl, but hardly grew on biphenyl. CONCLUSION: The cloned bph genes indeed play an important role in the biphenyl catabolism in this strain. SIGNIFICANCE AND IMPACT OF THE STUDY: This bph gene organization in Rhodococcus sp. R04 differs from that of other biphenyl degraders reported previously, indicating it is a novel type of bph gene cluster. Analysis of the phylogenetic tree suggested that BphA1 and BphA2 in Rhodococcus sp. R04 had a different evolutionary relationship with those in the other PCB degraders.     

The survival of the pentachlorophenol-degrading Rhodococcus chlorophenolicus PCP-1 and Flavobacterium sp. in natural soil

The survival of two different pentachlorophenol (PCP)-degrading bacteria were studied in natural soil. The PCP-degraders Rhodococcus chlorophenolicus and Flavobacterium sp., both able to mineralize PCP into CO₂ and chloride in axenic culture, were tested for the capacity to survive and degrade PCP in natural soil. These bacteria were immobilized on polyurethane (PUR) foam and introduced into natural peaty soil to give about 10⁹ cells g^-1 of soil (dry weight). R. chlorophenolicus induced PCP-degrading activity in soil remained detectable for 200 days whether or not a carbon source was added (distillery waste or wood chips). Electron microscopic investigation performed almost a year after inoculation, revealed the presence of R. chlorophenolicus-like cells in the PUR foam particles. PCP-degrading activity of Flavobacterium sp. declined within 60 days of burial in the soil without enhancing the PCP removal. R. chlorophenolicus degraded PCP in soil at a mean rate of 3.7 mg of PCP day^-1 kg^-1 of soil, which corresponds to ca. 5×10^-3 pg of PCP degraded per inoculated R. chlorophenolicus cell day^-1. The solvent extractable organic chlorine contents of the soil decreased stoichiometrically (>95%) with that of PCP indicating that PCP was essentially mineralized.Abbreviations ATCC American type culture collection - DSM Deutsche Sammlung für Mikroorganismen - DW distillery waste - EM electron microscopy - EOX extractable organic halogen - GC/ECD gas chromatograph/electron capture detector - GC/MS gas chromatograph/mass spectrometer - PCP pentachlorophenol - WC wood chips - d.wt. dry weight - w.wt. wet weight - d.s. dry soil - d.H₂O distilled water - PCA polychlorinated aromatics     

NH4 + transport system of a psychrophilic marine bacterium, Vibrio sp. strain ABE-1

NH₄ ⁺ transport system of a psychrophilic marine bacterium Vibrio sp. strain ABE-1 (Vibrio ABE-1) was examined by measuring the uptake of [¹⁴C]methylammonium ion (¹⁴CH₃NH^{3 +}) into the intact cells. ¹⁴CH₃NH₃ ⁺ uptake was detected in cells grown in medium containing glutamate as the sole nitrogen source, but not in those grown in medium containing NH₄Cl instead of glutamate. Vibrio ABE-1 did not utilize CH₃NH₃ ⁺ as a carbon or nitrogen source. NH₄Cl and nonradiolabeled CH₃NH₃ ⁺ completely inhibited ¹⁴CH₃NH₃ ⁺ uptake. These results indicate that ¹⁴CH₃NH₃ ⁺ uptake in this bacterium is mediated via an NH₄ ⁺ transport system and not by a specific carrier for CH₃NH₃ ⁺. The respiratory substrate succinate was required to drive ¹⁴CH₃NH₃ ⁺ uptake and the uptake was completely inhibited by KCN, indicating that the uptake was energy dependent. The electrochemical potentials of H⁺ and/or Na⁺ across membranes were suggested to be the driving forces for the transport system because the ionophores carbonylcyanide m-chlorophenylhydrazone and monensin strongly inhibited uptake activities at pH 6.5 and 8.5, respectively. Furthermore, KCl activated ¹⁴CH₃NH₃ ⁺ uptake. The ¹⁴CH₃NH₃ ⁺ uptake activity of Vibrio ABE-1 was markedly high at temperatures between 0° and 15°C, and the apparent K _m value for CH₃NH₃ ⁺ of the uptake did not change significantly over the temperature range from 0° to 25°C. Thus, the NH₄ ⁺ transport system of this bacterium was highly active at low temperatures. Received: August 1, 1998 / Accepted: October 8, 1998     

Degradation of 1,3-dichloropropene by a soil bacterial consortium and Rhodococcus sp. AS2C isolated from the consortium

A bacterial consortium capable of degrading the fumigant 1,3-D ((Z)- and (E)-1,3-dichloropropene) was enriched from an enhanced soil. This mixedculture degraded (Z)- and (E)-1,3-D only in the presence of a suitable biodegradable organic substrate, such as tryptone, tryptophan, or alanine. After 8 months of subculturing at 2- to 3-week intervals, a strain of Rhodococcus sp. (AS2C) that was capable of degrading 1,3-D cometabolically in the presenceof a suitable second substrate was isolated. (Z)-3-chloroallyl alcohol (3-CAA) and (Z)-3-chloroacrylic acid (3-CAAC), and (E)-3-CAA and (E)-3-CAAC were the metabolites of (Z)- and (E)-1,3-D, respectively. (E)-1,3-D was degraded faster than (Z)-1,3-D by the strain AS2C and the consortium. AS2C also degraded (E)-3-CAA faster than (Z)-3-CAA. Isomerization of (E)-1,3-D to (Z)-1,3-D orthe (Z) form to the (E) form did not occur.     

Light adaptation of cyclic electron transport through Photosystem I in the cyanobacterium Synechococcus sp. PCC 7942

Photosystem I-driven cyclic electron transport was measured in intact cells of Synechococcus sp PCC 7942 grown under different light intensities using photoacoustic and spectroscopic methods. The light-saturated capacity for PS I cyclic electron transport increased relative to chlorophyll concentration, PS I concentration, and linear electron transport capacity as growth light intensity was raised. In cells grown under moderate to high light intensity, PS I cyclic electron transport was nearly insensitive to methyl viologen, indicating that the cyclic electron supply to PS I derived almost exclusively from a thylakoid dehydrogenase. In cells grown under low light intensity, PS I cyclic electron transport was partially inhibited by methyl viologen, indicating that part of the cyclic electron supply to PS I derived directly from ferredoxin. It is proposed that the increased PSI cyclic electron transport observed in cells grown under high light intensity is a response to chronic photoinhibition.Abbreviations DBMIB 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - ES energy storage - MV methyl viologen - PA_m photoacoustic thermal signal with strong non-modulated background light added - PA_s photoacoustic thermal signal without background light addedCIW/DPB Publication No. 1205.     

Influence of nutrient availability on phytoplankton growth and community structure in the Port Adelaide River,Australia: [2pt] bioassay assessment of potential nutrient limitation

We investigated the influence of nutrient availability, specifically nitrogen, phosphorus and silicon on growth and community structure of phytoplankton from the Port Adelaide River estuary, South Australia. Two bioassay experiments were conducted. The first, Nutrich1, involved addition of nutrients in vitro to samples of the natural phytoplankton community from a single location in the upper estuary. The second, Nutrich2, involved nutrient addition and incubation of water from five locations in the estuary following inoculation with a `standardised' phytoplankton assemblage derived from laboratory cultures. In Nutrich1, enrichment with silicon led to greatly enhanced phytoplankton biomass due to increased growth of diatoms. Addition of nitrogen or phosphorus had little effect on phytoplankton growth. In Nutrich2, addition of nitrogen resulted in enhanced growth of phytoplankton in water collected from near the mouth the estuary, but there were no differences in growth among nutrient treatments for the remaining locations. Comparison of phytoplankton growth rate among locations revealed a trend of decreasing growth in moving towards the mouth of the estuary. This trend was unaffected by enrichment with nitrate, phosphate or silicate. We suggest that spatial variation in growth potential within the Port Adelaide River estuary may relate to variation in the concentration of nitrogen as ammonium.     

Identification of the Streptococcus gordonii glmM gene encoding phosphoglucosamine mutase and its role in bacterial cell morphology, biofilm formation, and sensitivity to antibiotics

Phosphoglucosamine mutase (EC 5.4.2.10) catalyzes the interconversion of glucosamine-6-phosphate into glucosamine-1-phosphate, an essential step in the biosynthetic pathway leading to the formation of peptidoglycan precursor uridine 5'-diphospho-N-acetylglucosamine. The gene (glmM) of Escherichia coli encoding the enzyme has been identified previously. We have now identified a glmM homolog in Streptococcus gordonii, an early colonizer on the human tooth and an important cause of infective endocarditis, and have confirmed that the gene encodes phosphoglucosamine mutase by assaying the enzymatic activity of the recombinant GlmM protein. Insertional glmM mutant of S. gordonii did not produce GlmM, and had a growth rate that was approximately half that of the wild type. Morphological analyses clearly indicated that the glmM mutation causes marked elongation of the streptococcal chains, enlargement of bacterial cells, and increased roughness of the bacterial cell surface. Furthermore, the glmM mutation reduces biofilm formation and increases sensitivity to penicillins relative to wild type. All of these phenotypic changes were also observed in a glmM deletion mutant, and were restored by the complementation with plasmid-borne glmM. These results suggest that, in S. gordonii, mutations in glmM appear to influence bacterial cell growth and morphology, biofilm formation, and sensitivity to penicillins.     

Preferential attack of the (S)-configured ether-linked carbons in bis-(1-chloro-2-propyl) ether by Rhodococcus sp. strain DTB

Rhodococcus sp. strain DTB (DSM 44534) was grown on a mixture of (R,R)-, (S,S)- and meso-bis-(1-chloro-2-propyl) ether (BCPE) as the sole source of carbon and energy. During BCPE degradation 1'-chloro-2'-propyl-3-chloro-2-prop-1-enyl-ether (DVE), 1-chloro-2-propanol and chloroacetone intermediates were formed. The BCPE or DVE stereoisomers were metabolized in consecutive order via scission of the ether bond, with discrimination against the (R) configuration. Resting cell suspensions of Rhodococcus pregrown on BCPE showed a preferential attack of the (S)-configured ether-linked carbons, resulting in an enantioselective enrichment of (R,R)-BCPE. Microbial discrimination of BCPE or DVE isomers and chemical conversion of the intermediates to 1-chloro-2-propanol allowed the identification of the configuration of all BCPE isomers and the DVE enantiomers. Elucidation of the absolute configuration of the 1-chloro-2-propanol isomers was achieved by enantioselective chemical synthesis.     

Effect of carbon and nitrogen growth limitation upon nutrient uptake and metabolism in batch cultures of Catharanthus roseus (L) G. Don

Cell suspension cultures of the Madagascan Periwinkle, Catharanthus roseus (L). G. Don were grown as batch cultures in two different types of media; in one medium the limiting nutrient was inorganic nitrogen, and in the other it was carbon. The response of the cells to these growth-limiting conditions was monitored by measuring cellular fresh weight, dry weight and protein accumulation, cell viability, medium sugar and nitrate levels, and the activities of certain intracellular enzymes throughout growth in batch culture. The enzymes investigated were glucose-6-phosphate dehydrogenase (EC 1.1.1.49), 6-phosphogluconate dehydrogenase (EC 1.1.1.44), hexokinase (EC 2.7.1.40), phosphofructokinase (EC 2.7.1.11), nitrate reductase (EC 1.6.6.1), glutamate dehydrogenase (EC 1.4.1.2) and glutamine synthetase (EC 6.3.1.2). The effect of culturing the cells under different nutritional regimes was apparent in all aspects of growth; only some enzyme activities were unaffected. Cell viability remained at a high level for several days after growth limitation in both types of culture. The possibility that protein degradation in nitrogen-limited batch cultures is under very stringent control is discussed.     

Growth and age determination of the tropical Australian cubozoan Chiropsalmus sp.

Chiropsalmus sp. medusae collected in this study ranged from 3 to 71 mm diagonal bell width and displayed growth best described by the following equation size (mm) = 74.9 × exp (−exp(0.041 (time since metamorphosis (day) −35.6674))). Growth rates of up to 7 mm week⁻¹ increase in diagonal bell width are theoretically possible, with animals able to reach sexual maturity in approximately 70 days. Correlation of the number of rings on the statoliths with the predicted age of the individual from the field produced a relationship that indicates the growth rings are laid down daily and as such could be used to infer age of the medusae. Over the 1998–1999 season, there were four influxes of juvenile cohorts, each occurring approximately 14 days after a major rainfall event.     

悬浮培养红豆杉细胞活力及存活率与生长周期的关系

用TTC法制定红豆杉细胞活力,用中性红测细胞存活率,探讨生长周期中细胞活力及存活率的变化规律。结果显示延迟期细胞活力最强,对数生长期活力较低,稳定期活力最低;而细胞存活率在整个周期中基本保持在70%-80%。     

Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synechococcus sp. PCC7942

Summary The nrtA gene, which has been proposed to be involved in nitrate transport of Synechococcus sp. PCC7942 (Anacystis nidulans R2), was mapped at 3.9 kb upstream of the nitrate reductase gene, narB. Three closely linked genes (designated nrtB, nrtC, and nrtD), which encode proteins of 279, 659, and 274 amino acids, respectively, were found between the nrtA and narB genes. NrtB is a hydrophobic protein having structural similarity to the integral membrane components of bacterial transport systems that are dependent on periplasmic substrate-binding proteins. The N-terminal portion of NrtC (amino acid residues 1–254) and NrtD are 58% identical to each other in their amino acid sequences, and resemble the ATP-binding components of binding protein-dependent transport systems. The C-terminal portion of NrtC is 30% identical to NrtA. Mutants constructed by interrupting each of nrtB and nrtC were unable to grow on nitrate, and the nrtD mutant required high concentration of nitrate for growth. The rate of nitrate-dependent O₂ evolution (photosynthetic O₂ evolution coupled to nitrate reduction) in wild-type cells measured in the presence of l-methionine d,l-sulfoximine and glycolaldehyde showed a dual-phase relationship with nitrate concentration. It followed saturation kinetics up to 10 mM nitrate (the concentration required for half-saturation = 1 M), and the reaction rate then increased above the saturation level of the first phase as the nitrate concentration increased. The high-affinity phase of nitrate-dependent O₂ evolution was absent in the nrtD mutant. The results suggest that there are two independent mechanisms of nitrate uptake and that the nrtB-nrtC-nrtD cluster encodes a high-affinity nitrate transport system.     

Growth temperature influences the underlying components of relative growth rate: an investigation using inherently fast- and slow-growing plant species

We examined the effect of growth temperature on the underlying components of growth in a range of inherently fast‐ and slow‐growing plant species. Plants were grown hydroponically at constant 18, 23 and 28 °C. Growth analysis was conducted on 16 contrasting plant species, with whole plant gas exchange being performed on six of the 16 species. Inter‐specific variations in specific leaf area (SLA) were important in determining variations in relative growth rate (RGR) amongst the species at 23 and 28 °C but were not related to variations in RGR at 18 °C. When grown at 18 °C, net assimilation rate (NAR) became more important than SLA for explaining variations in RGR. Variations in whole shoot photosynthesis and carbon concentration could not explain the importance of NAR in determining RGR at the lower temperatures. Rather, variations in the degree to which whole plant respiration per unit leaf area acclimated to the different growth temperatures were responsible. Plants grown at 28 °C used a greater proportion of their daily fixed carbon in respiration than did the 18 and 23 °C‐grown plants. It is concluded that the relative importance of the underlying components of growth are influenced by growth temperature, and the degree of acclimation of respiration is of central importance to the greater role played by NAR in determining variations in RGR at declining growth temperatures.     

Role of a serine-type d-alanyl-d-alanine carboxypeptidase on the survival of Ochrobactrum sp. 11a under ionic and hyperosmotic stress

The plant growth-promoting rhizobacterium, Ochrobactrum sp. 11a displays a high intrinsic salinity tolerance and has been used in this work to study the molecular basis of bacterial responses to high concentrations of NaCl. A collection of Ochrobactrum sp. 11a mutants was generated by Tn 5 -B21 mutagenesis and screened for sensitivity to salinity. One clone, designated PBP and unable to grow on glutamate mannitol salt agar medium supplemented with 300 mM NaCl was selected and further characterized. The PBP mutant carries a single transposon insertion in a gene showing a high degree of identity to the serine-type d -alanyl- d -alanine carboxypeptidase gene of Ochrobactrum anthropi . Interestingly, the expression of this gene was shown to be upregulated by salt in the PBP mutant. Moreover, evidence is presented for the requirement of the gene product for adaptation to high-salt conditions as well as to overcome the toxicity of LiCl, KCl, sucrose, polyethylene glycol (PEG), AlCl₃, CuSO₄, and ZnSO₄. In addition to the altered tolerance to both ionic and osmotic stresses, the PBP mutant exhibited changes in colony and cell morphology, exopolysaccharide production, and an increased sensitivity to detergents.