Removal of a complex VOC mixture by potted plants-effects on soil microorganisms

Microorganisms in the soil of potted plants are important for removal of volatile organic compounds (VOCs) from indoor air, but little is known about the subject. The aim of this study was therefore to obtain a better understanding of the effect of VOCs on the microbial community in potted plants. Hedera helix was exposed to gasoline vapors under dynamic chamber conditions for 21 days and three main parameters were investigated. These were (1) removal of the target compounds heptane, 3-methylhexane, benzene, toluene, ethylbenzene, m,p-xylene, and naphthalene from the gasoline mixture; (2) toluene mineralization; and (3) bacterial abundance and bacterial community structure. H. helix was able to reduce the concentration of the target compounds in the continuously emitted gasoline by 25-32%, except for naphthalene, which was too low in concentration. The soil microcosm of gasoline exposed plants had for an initial 66 h increased toluene mineralization rate compared to the soil microcosm in the soil of plants exposed to clean air. Bacterial abundance was decreased in response to gasoline exposure while bacterial community structure was changed. The change in bacterial community structure was, however, different between the two experiments indicating that several taxonomic units can degrade gasoline components. Especially the genera Rhodanobacter and Pseudonorcardia significantly increased in abundance in response to gasoline vapors. Bauldia, Devosia, and Bradyrhizobium, on the other hand, decreased.

The cytokinin-producing plant beneficial bacterium Pseudomonas fluorescens G20-18 primes tomato (Solanum lycopersicum) for enhanced drought stress responses

Plant growth-promoting rhizobacteria (PGPR) are known for exerting beneficial effects on plant growth and tolerance to plant pathogens. However, their specific role in mediating protection against abiotic stress remains underexplored. The aim of this study was to characterise the ability of the cytokinin-producing beneficial bacterium Pseudomonas fluorescens G20-18 to enhance tomato growth and boost tolerance to drought stress. Tomato seedlings were root inoculated and their growth and physiological and molecular responses assessed under well-watered conditions and also in response to progressive drought stress and a subsequent recovery period. Root inoculation with G20-18 had a significant positive impact on tomato growth. Furthermore, G20-18 inoculated and drought-stressed plants showed higher leaf chlorophyll and abscisic acid (ABA) content and stomatal closure than non-inoculated controls. Root inoculation also increased the activity of different carbohydrate metabolism enzymes, which are important for root and leaf growth and development in drought stressed plants. A significant increase in the activity of different antioxidant enzymes and total antioxidant capacity correlated with elevated levels of relevant secondary metabolites, such as phenolics, anthocyanins and flavonoids. RNA sequencing revealed distinct qualitative and quantitative differences in gene regulation in response to G20-18. Notably, the number of genes differentially regulated in response to G20-18 was approximately sevenfold higher during drought stress, indicating that root inoculation with the bacteria primed the plants for a much stronger transcriptionally regulated systemic drought stress response. The regulated genes are related to phenylalanine metabolism and other key processes linked to plant growth, development and drought stress resilience. A role of the ability of G20-18 to produce the plant hormone cytokinin for interaction with tomato was established by the cytokinin-deficient biosynthesis mutants CNT1 and CNT2. In comparison with G20-18, the inoculation of plants with CNT1 resulted in a reduced number of differentially regulated genes. The relative change was most prominent under well-watered conditions with a 85 % reduction, corresponding to 462 genes. However, under drought conditions the absolute number of differentially regulated genes was reduced by even 2219 in response to the CNT1 mutant. The relevance of the ability of G20-18 to produce cytokinins for interaction with plants was also evident from differences in growth and specific cell and ecophysiological parameters in response to CNT1 and CNT2. These findings provide novel insights about G20-18's ability to improve drought stress responses and the role of interkingdom signalling by bacterial-derived cytokinins, and contribute to enhance the robustness of the practical application of these microorganisms to improve crop resilience in agricultural production.

OUP accepted manuscript

During germination, the seed releases nutrient-rich exudates into the spermosphere, thereby fostering competition between resident microorganisms. However, insight into the composition and temporal dynamics of seed-associated bacterial communities under field conditions is currently lacking. This field study determined the temporal changes from 11 to 31 days after sowing in the composition of seed-associated bacterial communities of winter wheat as affected by long-term soil fertilization history, and by introduction of the plant growth-promoting microbial inoculants Penicillium bilaiae and Bacillus simplex. The temporal dynamics were the most important factor affecting the composition of the seed-associated communities. An increase in the relative abundance of genes involved in organic nitrogen metabolism (ureC and gdhA), and in ammonium oxidation (amoA), suggested increased mineralization of plant-derived nitrogen compounds over time. Dynamics of the phosphorus cycling genes ppt, ppx and cphy indicated inorganic phosphorus and polyphosphate cycling, as well as phytate hydrolysis by the seed-associated bacteria early after germination. Later, an increase in genes for utilization of organic phosphorus sources (phoD, phoX and phnK) indicated phosphorus limitation. The results indicate that community temporal dynamics are partly driven by changed availability of major nutrients, and reveal no functional consequences of the added inoculants during seed germination.

Phosphate-solubilising microorganisms for improved crop productivity: a critical assessment

Phosphate-solubilising microorganisms (PSM) are often reported to have positive effects on crop productivity through enhanced phosphorus (P) nutrition. Our aim was to evaluate the validity of this concept. Most studies that report 'positive effects' of PSM on plant growth have been conducted under controlled conditions, whereas field experiments more frequently fail to demonstrate a positive response. Many studies have indicated that the mechanisms seen in vitro do not translate into improved crop P nutrition in complex soil-plant systems. Furthermore, associated mechanisms are often not rigorously assessed. We suggest that PSM do not mobilise sufficient P to change the crops' nutritional environment under field conditions. The current concept, in which PSM solubilise P 'for the plant' should thus be revised. Although PSM have the capacity to solubilise P to meet their own needs, it is the turnover of the microbial biomass that subsequently provides P to plants over a longer time. Therefore, the existing concept of PSM function is unlikely to deliver a reliable strategy for increasing crop P nutrition. A further mechanistic understanding is needed to determine how P mobilisation by PSM as a component of the whole soil community can be manipulated to become more effective for plant P nutrition.

Identification of Root-Associated Bacteria That Influence Plant Physiology, Increase Seed Germination, or Promote Growth of the Christmas Tree Species Abies nordmanniana

Abies nordmanniana is used for Christmas tree production but poor seed germination and slow growth represent challenges for the growers. We addressed the plant growth promoting potential of root-associated bacteria isolated from A. nordmanniana. Laboratory screenings of a bacterial strain collection yielded several Bacillus and Paenibacillus strains that improved seed germination and produced indole-3-acetic acid. The impact of three of these strains on seed germination, plant growth and growth-related physiological parameters was then determined in greenhouse and field trials after seed inoculation, and their persistence was assessed by 16S rRNA gene-targeted bacterial community analysis. Two strains showed distinct and significant effects. Bacillus sp. s50 enhanced seed germination in the greenhouse but did not promote shoot or root growth. In accordance, this strain did not increase the level of soluble hexoses needed for plant growth but increased the level of storage carbohydrates. Moreover, strain s50 increased glutathione reductase and glutathione-S-transferase activities in the plant, which may indicate induction of systemic resistance during the early phase of plant development, as the strain showed poor persistence in the root samples (rhizosphere soil plus root tissue). Paenibacillus sp. s37 increased plant root growth, especially by inducing secondary root formation, under in greenhouse conditions, where it showed high persistence in the root samples. Under these conditions, it further it increased the level of soluble carbohydrates in shoots, and the levels of starch and non-structural carbohydrates in roots, stem and shoots. Moreover, it increased the chlorophyll level in the field trial. These findings indicate that this strain improves plant growth and vigor through effects on photosynthesis and plant carbohydrate reservoirs. The current results show that the two strains s37 and s50 could be considered for growth promotion programs of A. nordmanniana in greenhouse nurseries, and even under field conditions.

Effects of Intra- and Interspecific Plant Density on Rhizosphere Bacterial Communities

There have been very few studies on the effects of plant competition on the rhizosphere bacterial community. To investigate the impacts of intra- and interspecific plant competition, we analyzed the responses of rhizosphere bacterial communities to plant density as determined by 16S rRNA gene targeted sequencing. We included five weedy plant species growing in field soil in monocultures and mixed cultures at three densities in a greenhouse experiment. The rhizosphere bacterial community of each species changed more with density in a mixture of all five plant species than in monocultures, so intra- and interspecific plant competition had different effects on the bacterial community. For the dominant plant competitor, Centaurea cyanus, neither intra- nor interspecific competition had major effects on the composition of its rhizosphere bacterial communities. In contrast, the bacterial communities of the weakest competitor, Trifolium repens, were affected differently by intra- and interspecific competition. During increasing intraspecific competition T. repens maintained a highly specialized bacterial community dominated by Rhizobium; while during interspecific competition, the relative abundance of Rhizobium declined while other nitrogen fixing and potentially plant growth promoting taxa became more abundant. Contrary to previous observations made for soil microbial communities, the bacterial rhizosphere community of the weakest competitor did not become more similar to that of the dominant species. Thus, the process of competition, as well as the plant species themselves, determined the rhizosphere bacterial community. Our results emphasize the role of plant-plant interactions for rhizosphere bacterial communities. These effects may feedback to affect plant-plant interactions, and this is an important hypothesis for future research.

Preferential flow paths shape the structure of bacterial communities in a clayey till depth profile

Preferential flow paths in subsurface soils serve as transport routes for water, dissolved organic matter and oxygen. Little is known about bacterial communities in flow paths or in subsoils below ∼4 m. We compared communities from preferential flow paths (biopores, fractures and sand lenses) with those in adjacent matrix sediments of clayey till from the plough layer to a depth of 6 m. 16S rRNA gene-targeted community analysis showed bacterial communities of greater abundance and diversity in flow paths than in matrix sediments at all depths. Deep fracture communities contained a higher relative abundance of aerobes and plant material decomposers like Nitrospirae, Acidobacteria and Planctomycetes than adjacent matrix sediments. Similarly, analyses of the relative abundances of archaeal amoA, nirK and dsrB genes indicated transition from aerobic to anaerobic nitrogen and sulphur cycling at greater depth in preferential flow paths than in matrix sediments. Preferential flow paths in the top 260 cm contained more indicator operational taxonomic units from the plough layer community than the matrix sediments. This study indicates that the availability of oxygen and organic matter and downward transport of bacteria shape bacterial communities in preferential flow paths, and suggests that their lifestyles differ from those of bacteria in matrix communities.

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin

Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.

Identification of Root-Associated Bacteria That Influence Plant Physiology, Increase Seed Germination, or Promote Growth of the Christmas Tree Species Abies nordmanniana

Abies nordmanniana is used for Christmas tree production but poor seed germination and slow growth represent challenges for the growers. We addressed the plant growth promoting potential of root-associated bacteria isolated from A. nordmanniana. Laboratory screenings of a bacterial strain collection yielded several Bacillus and Paenibacillus strains that improved seed germination and produced indole-3-acetic acid. The impact of three of these strains on seed germination, plant growth and growth-related physiological parameters was then determined in greenhouse and field trials after seed inoculation, and their persistence was assessed by 16S rRNA gene-targeted bacterial community analysis. Two strains showed distinct and significant effects. Bacillus sp. s50 enhanced seed germination in the greenhouse but did not promote shoot or root growth. In accordance, this strain did not increase the level of soluble hexoses needed for plant growth but increased the level of storage carbohydrates. Moreover, strain s50 increased glutathione reductase and glutathione-S-transferase activities in the plant, which may indicate induction of systemic resistance during the early phase of plant development, as the strain showed poor persistence in the root samples (rhizosphere soil plus root tissue). Paenibacillus sp. s37 increased plant root growth, especially by inducing secondary root formation, under in greenhouse conditions, where it showed high persistence in the root samples. Under these conditions, it further it increased the level of soluble carbohydrates in shoots, and the levels of starch and non-structural carbohydrates in roots, stem and shoots. Moreover, it increased the chlorophyll level in the field trial. These findings indicate that this strain improves plant growth and vigor through effects on photosynthesis and plant carbohydrate reservoirs. The current results show that the two strains s37 and s50 could be considered for growth promotion programs of A. nordmanniana in greenhouse nurseries, and even under field conditions.

Root-Associated Microbial Communities of Abies nordmanniana: Insights Into Interactions of Microbial Communities With Antioxidative Enzymes and Plant Growth

Abies nordmanniana is a major Christmas tree species in Europe, but their uneven and prolonged growth slows down their production. By a 16S and 18S rRNA gene amplicon sequencing approach, we performed a characterization of root-associated bacterial and fungal communities for three-year-old A. nordmanniana plants collected from two nurseries in Denmark and Germany and displaying different growth patterns (small versus tall plants). Proteobacteria had the highest relative abundance at both sampling sites and plant sizes, and Ascomycota was the most abundant fungal phylum. At the order level, Acidobacteriales, Actinomycetales, Burkholderiales, Rhizobiales, and Xanthomonadales represented the bacterial core microbiome of A. nordmanniana, independently of the sampling site or plant size, while the fungal core microbiome included members of the Agaricales, Hypocreales, and Pezizales. Principal Coordinate Analysis indicated that both bacterial and fungal communities clustered according to the sampling site pointing to the significance of soil characteristics and climatic conditions for the composition of root-associated microbial communities. Major differences between communities from tall and small plants were a dominance of the potential pathogen Fusarium (Hypocreales) in the small plants from Germany, while Agaricales, that includes reported beneficial ectomycorrhizal fungi, dominated in the tall plants. An evaluation of plant root antioxidative enzyme profiles showed higher levels of the antioxidative enzymes ascorbate peroxidase, peroxidase, and superoxide dismutase in small plants compared to tall plants. We suggest that the higher antioxidative enzyme activities combined with the growth arrest phenotype indicate higher oxidative stress levels in the small plants. Additionally, the correlations between the relative abundances of specific taxa of the microbiome with the plant antioxidative enzyme profiles were established. The main result was that many more bacterial taxa correlated positively than negatively with one or more antioxidative enzyme activity. This may suggest that the ability of bacteria to increase plant antioxidative enzyme defenses is widespread.

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota

Arbuscular mycorrhizal fungi (AMF) colonise roots of most plants; their extra-radical mycelium (ERM) extends into the soil and acquires nutrients for the plant. The ERM coexists with soil microbial communities and it is unresolved whether these communities stimulate or suppress the ERM activity. This work studied the prevalence of suppressed ERM activity and identified main components behind the suppression. ERM activity was determined by quantifying ERM-mediated P uptake from radioisotope-labelled unsterile soil into plants, and compared to soil physicochemical characteristics and soil microbiome composition. ERM activity varied considerably and was greatly suppressed in 4 of 21 soils. Suppression was mitigated by soil pasteurisation and had a dominating biotic component. AMF-suppressive soils had high abundances of Acidobacteria, and other bacterial taxa being putative fungal antagonists. Suppression was also associated with low soil pH, but this effect was likely indirect, as the relative abundance of, e.g., Acidobacteria decreased after liming. Suppression could not be transferred by adding small amounts of suppressive soil to conducive soil, and thus appeared to involve the common action of several taxa. The presence of AMF antagonists resembles the phenomenon of disease-suppressive soils and implies that ecosystem services of AMF will depend strongly on the specific soil microbiome.

Cupriavidus pinatubonensis AEO106 deals with copper-induced oxidative stress before engaging in biodegradation of the herbicide 4-chloro-2-methylphenoxyacetic acid

BACKGROUND

Microbial degradation of phenoxy acid (PA) herbicides in agricultural soils is important to minimize herbicide leaching to groundwater reservoirs. Degradation may, however, be hampered by exposure of the degrader bacteria to toxic metals as copper (Cu) in the soil environment. Exposure to Cu leads to accumulation of intracellular reactive oxygen species (ROS) in some bacteria, but it is not known how Cu-derived ROS and an ensuing oxidative stress affect the degradation of PA herbicides. Based on the previously proposed paradigm that bacteria deal with environmental stress before they engage in biodegradation, we studied how the degradation of the PA herbicide 2-methyl-4-chlorophenoxyacetic acid (MCPA) by the model PA degrader Cupriavidus pinatubonensis AEO106 was affected by Cu exposure.

RESULTS

Exposure of C. pinatubonensis in batch culture to sublethal concentrations of Cu increased accumulation of ROS measured by the oxidant sensing probe 2,7-dichlorodihydrofluorescein diacetate and flow cytometry, and resulted in upregulation of a gene encoding a protein belong to the Ohr/OsmC protein family. The ohr/osmC gene was also highly induced by H₂O₂ exposure suggesting that it is involved in the oxidative stress response in C. pinatubonensis. The increased ROS accumulation and increased expression of the oxidative stress defense coincided with a delay in the catabolic performance, since both expression of the catabolic tfdA gene and MCPA mineralization were delayed compared to unexposed control cells.

CONCLUSIONS

The current study suggests that Cu-induced ROS accumulation in C. pinatubonensis activates a stress response involving the product of the ohr/osmC gene. Further, the stress response is launched before induction of the catabolic tfdA gene and mineralization occurs.

A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil

It is important to identify and recover bacteria associating with fungi under natural soil conditions to enable eco-physiological studies, and to facilitate the use of bacterial-fungal consortia in environmental biotechnology. We have developed a novel type of baiting microcosm, where fungal hyphae interact with bacteria under close-to-natural soil conditions; an advantage compared to model systems that determine fungal influences on bacterial communities in laboratory media. In the current approach, the hyphae are placed on a solid support, which enables the recovery of hyphae with associated bacteria in contrast to model systems that compare bulk soil and mycosphere soil. We used the baiting microcosm approach to determine, for the first time, the composition of the bacterial community associating in the soil with hyphae of the phosphate-solubilizer, Penicillium bilaii. By applying a cultivation-independent 16S rRNA gene-targeted amplicon sequencing approach, we found a hypha-associated bacterial community with low diversity compared to the bulk soil community and exhibiting massive dominance of Burkholderia OTUs. Burkholderia is known be abundant in soil environments affected by fungi, but the discovery of this massive dominance among bacteria firmly associating with hyphae in soil is novel and made possible by the current bait approach.

Nitrogen regulation of the xyl genes of Pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil

The nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by Pseudomonas putida. Nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m‐xylene in soil, the natural habitat of this bacterium. To address this issue, we have developed a test‐tube‐to‐soil model system that exposes the end‐effects of remediation practices influencing gene expression of P. putida mt‐2. We found that NO₃⁻ compared with NH₄⁺ had a stimulating effect on xyl gene expression in pure culture as well as in soil, and that this stimulation was translated into increased m‐xylene mineralization in soil. Furthermore, expression analysis of the nitrogen‐regulated genes amtB and gdhA allowed us to monitor nitrogen sensing status in both experimental systems. Hence, for nitrogen sources, regulatory patterns that emerge in soil reflect those observed in liquid cultures. The current study shows how distinct regulatory traits can lead to discrete environmental consequences; and it underpins that attempts to improve bioremediation by nitrogen amendment should integrate knowledge on their effects on growth and on catabolic gene regulation under natural conditions.

Pseudomonas putida mt-2 tolerates reactive oxygen species generated during matric stress by inducing a major oxidative defense response

Background

Soil bacteria typically thrive in water-limited habitats that cause an inherent matric stress to the cognate cells. Matric stress gives rise to accumulation of intracellular reactive oxygen species (ROS), which in turn may induce oxidative stress, and even promote mutagenesis. However, little is known about the impact of ROS induced by water limitation on bacteria performing important processes as pollutant biodegradation in the environment. We have rigorously examined the physiological consequences of the rise of intracellular ROS caused by matric stress for the toluene- and xylene-degrading soil bacterium Pseudomonas putida mt-2.

Methods

For the current experiments, controlled matric potential stress was delivered to P. putida cells by addition of polyethylene glycol to liquid cultures, and ROS formation in individual cells monitored by a specific dye. The physiological response to ROS was then quantified by both RT-qPCR of RNA transcripts from genes accredited as proxies of oxidative stress and the SOS response along with cognate transcriptional GFP fusions to the promoters of the same genes.

Results

Extensive matric stress at −1.5 MPa clearly increased intracellular accumulation of ROS. The expression of the two major oxidative defense genes katA and ahpC, as well as the hydroperoxide resistance gene osmC, was induced under matric stress. Different induction profiles of the reporters were related to the severity of the stress. To determine if matric stress lead to induction of the SOS-response, we constructed a DNA damage-inducible bioreporter based on the LexA-controlled phage promoter P_PP3901. According to bioreporter analysis, this gene was expressed during extensive matric stress. Despite this DNA-damage mediated gene induction, we observed no increase in the mutation frequency as monitored by emergence of rifampicin-resistant colonies.

Conclusions

Under conditions of extensive matric stress, we observed a direct link between matric stress, ROS formation, induction of ROS-detoxifying functions and (partial) activation of the SOS system. However, such a stress-response regime did not translate into a general DNA mutagenesis status. Taken together, the data suggest that P. putida mt-2 can cope with this archetypal environmental stress while preserving genome stability, a quality that strengthens the status of this bacterium for biotechnological purposes.

Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms

Pseudomonads produce several lipopeptide biosurfactants that have antimicrobial properties but that also facilitate surface motility and influence biofilm formation. Detailed studies addressing the significance of lipopeptides for biofilm formation and architecture are rare. Hence, the present study sets out to determine the specific role of the lipopeptide viscosin in Pseudomonas fluorescens SBW25 biofilm formation, architecture and dispersal, and to relate viscA gene expression to viscosin production and effect. Initially, we compared biofilm formation of SBW25 and the viscosin-deficient mutant strain SBW25ΔviscA in static microtitre assays. These experiments demonstrated that viscosin had little influence on the amount of biofilm formed by SBW25 during the early stages of biofilm development. Later, however, SBW25 formed significantly less biofilm than SBW25ΔviscA. The indication that viscosin is involved in biofilm dispersal was confirmed by chemical complementation of the mutant biofilm. Furthermore, a fluorescent bioreporter showed that viscA expression was induced in biofilms 4 h prior to dispersal. Subsequent detailed studies of biofilms formed in flow cells for up to 5 days revealed that SBW25 and SBW25ΔviscA developed comparable biofilms dominated by well-defined, mushroom-shaped structures. Carbon starvation was required to obtain biofilm dispersal in this system. Dispersal of SBW25 biofilms was significantly greater than of SBW25ΔviscA biofilms after 3 h and, importantly, carbon starvation strongly induced viscA expression, in particular for cells that were apparently leaving the biofilm. Thus, the present study points to a role for viscosin-facilitated motility in dispersal of SBW25 biofilms.

Evaluation of the leucine incorporation technique for detection of pollution-induced community tolerance to copper in a long-term agricultural field trial with urban waste fertilizers

Copper (Cu) is known to accumulate in agricultural soils receiving urban waste products as fertilizers. We here report the use of the leucine incorporation technique to determine pollution-induced community tolerance (Leu-PICT) to Cu in a long-term agricultural field trial. A significantly increased bacterial community tolerance to Cu was observed for soils amended with organic waste fertilizers and was positively correlated with total soil Cu. However, metal speciation and whole-cell bacterial biosensor analysis demonstrated that the observed PICT responses could be explained entirely by Cu speciation and bioavailability artifacts during Leu-PICT detection. Hence, the agricultural application of urban wastes (sewage sludge or composted municipal waste) simulating more than 100 years of use did not result in sufficient accumulation of Cu to select for Cu resistance. Our findings also have implications for previously published PICT field studies and demonstrate that stringent PICT detection criteria are needed for field identification of specific toxicants.

The biosurfactant viscosin transiently stimulates n-hexadecane mineralization by a bacterial consortium

Pseudomonas produces powerful lipopeptide biosurfactants including viscosin, massetolide A, putisolvin, and amphisin, but their ability to stimulate alkane mineralization and their utility for bioremediation have received limited attention. The four Pseudomonas lipopeptides yielded emulsification indices on hexadecane of 20–31 % at 90 mg/l, which is comparable to values for the synthetic surfactant Tween 80. Viscosin was the optimal emulsifier and significantly stimulated n-hexadecane mineralization by diesel-degrading bacterial consortia but exclusively during the first 2 days of batch culture experiments. Growth of the consortia, as determined by OD₆₀₀ measurements and quantification of the alkB marker gene for alkane degradation, was arrested after the first day of the experiment. In contrast, the control consortia continued to grow and reached higher OD₆₀₀ values and higher alkB copy numbers during the next days. Due to the short-lived stimulation of n-hexadecane mineralization, the stability of viscosin was analyzed, and it was observed that added viscosin was degraded by the bacterial consortium during the first 2 days. Hence, viscosin has a potential as stimulator of alkane degradation, but its utility in bioremediation may be limited by its rapid degradation and growth-inhibiting properties.

Low concentration of copper inhibits colonization of soil by the arbuscular mycorrhizal fungus Glomus intraradices and changes the microbial community structure

Common agricultural practices result in accumulation of copper in agricultural soils worldwide. The effect of bioavailable copper ([Cu](bio)) on colonization of soil by the AM fungus Glomus intraradices and other soil microorganisms was investigated in microcosms containing copper-amended soil. To avoid indirect effects through the plant, copper was only added to root-free microcosm compartments. [Cu](bio) was measured using a Pseudomonas fluorescens biosensor strain. In the range of 0-1.5 μg g(-1) [Cu](bio), a log-log linear relationship between added copper and [Cu](bio) was found. Microbial colonization of the root-free compartment was evaluated by whole-cell fatty acid analysis (WCFA) and amplified rDNA restriction analysis (ARDRA). The WCFA analysis showed that the AM fungus soil colonization was severely inhibited by Cu with a 50% reduction of mycorrhizal growth at 0.26 μg g(-1) [Cu](bio). The growth of other main microbial groups was not significantly affected by copper. However, ARDRA analysis showed a very strong effect of copper on the bacterial community composition probably caused by an increased proportion of Cu-resistant bacteria. Our results suggest that problems with plant yield may arise when converting slightly copper-contaminated soils to land uses such as low-input and sustainable agriculture that are dependent on AM fungal symbiosis.

2,6-Dichlorobenzamide (BAM) herbicide mineralisation by Aminobacter sp. MSH1 during starvation depends on a subpopulation of intact cells maintaining vital membrane functions

Mineralisation capability was studied in the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 under growth-arrested conditions. Cells were starved in mineral salts (MS) solution or groundwater before (14)C-labelled BAM (0.1mM) was added. Cell physiology was monitored with a panel of vitality stains combined with flow cytometry to differentiate intact, depolarised and dead cells. Cells starved for up to 3 weeks in MS solution showed immediate growth-linked mineralisation after BAM amendment while a lag-phase was seen after 8 weeks of starvation. In contrast, cells amended with BAM in natural groundwater showed BAM mineralisation but no growth. The cell-specific mineralisation rate was always comparable (10(-16)molCintact cell(-1)day(-1)) independent of media, growth, or starvation period after BAM amendment; lower rates were only observed as BAM concentration decreased. MSH1 seems useful for bioremediation and should be optimised to maintain an intact cell subpopulation as this seems to be the key parameter for successful mineralisation.

Cu exposure under field conditions coselects for antibiotic resistance as determined by a novel cultivation-independent bacterial community tolerance assay

Environmental reservoirs of antibiotic resistance are important to human health, and recent evidence indicates that terrestrial resistance reservoirs have expanded during the antibiotic era. Our aim was to study the impact of Cu pollution as a selective driver for the spread of antibiotic resistance in soil. Bacteria were extracted from a well-characterized soil site solely contaminated with CuSO₄ more than 80 years ago and from a corresponding control soil. Pollution-induced bacterial community tolerance (PICT) to Cu and a panel of antibiotics was determined by a novel cultivation-independent approach based on [³H]bromodeoxyuridine (BrdU) incorporation into DNA and by resistance profiling of soil bacterial isolates on solid media. High Cu exposure selected for Cu-tolerant bacterial communities but also coselected for increased community-level tolerance to tetracycline and vancomycin. Cu-resistant isolates showed significantly higher incidence of resistance to five out of seven tested antibiotics (tetracycline, olaquindox, nalidixic acid, chloramphenicol, and ampicillin) than Cu-sensitive isolates. Our BrdU-PICT data demonstrate for the first time that soil Cu exposure coselects for resistance to clinically important antibiotics (e.g., vancomycin) at the bacterial community-level. Our study further indicates that Cu exposure provides a strong selection pressure for the expansion of the soil bacterial resistome.

Degrader density determines spatial variability of 2,6-dichlorobenzamide mineralisation in soil

The metabolite 2,6-dichlorobenzamide (BAM) is a frequent groundwater pollutant produced during degradation of the herbicide 2,6-dichlorobenzonitrile (dichlobenile). Spatial variability of BAM mineralisation is uncharacterized in surface soil, however, and factors controlling the heterogeneity remain unknown. We addressed these issues by sample-to-sample comparisons of BAM mineralisation rates and a range of soil characteristics at spatial scales ranging from meters to centimetres. For mineralisation assays nano-molar concentrations of labelled BAM were added to determine mineralisation rates under realistic conditions. We found a significant variability of BAM mineralisation which increased with decreasing spatial scale. BAM mineralisation rates were correlated to the density of BAM-degrading bacteria but not to water content, TOC, NH(4)(+), NO(3)(-), or pH. The genus Aminobacter, which contains the only BAM degraders known, was detected in MPN samples of BAM degraders by a specific PCR assay targeting the 16S rRNA gene, confirming a role of Aminobacter in BAM mineralisation.

Occurrence and degradation of peptidoglycan in aquatic environments

Mechanisms controlling microbial degradation of dissolved organic matter (DOM) in aquatic environments are poorly understood, although microbes are crucial to global nutrient cycling. Bacterial cell wall components may be one of the keys in understanding the presence of slowly degrading DOM in nature. We found that dominant components of bacterial cell walls (D-amino acids (D-AA), glucosamine (GluA) and diaminopimelic acid (DAPA)) comprised up to 11.4% of the dissolved organic nitrogen in 50 diverse rivers entering the Baltic Sea. Occurrence of DAPA, a characteristic component of Gram-negative (G(-)) bacteria, in the rivers suggests that G(-) bacteria rather than Gram-positive (G(+)) were the major source of the cell wall material. In laboratory studies, the degradation of whole bacterial cells, cell wall material and purified peptidoglycan was studied to characterize degradation of cell wall material by natural aquatic bacteria. Addition of whole killed G(-) and G(+) bacteria to cultures of estuarine bacteria demonstrated fragmentation and loss of cell structure of the G(+) bacteria, while the G(-) bacteria maintained an intact cell shape during the entire 69-day period. In another experiment, estuarine bacteria degraded 39-69% of GluA, D-AA and DAPA in added cell wall material of a representative G(-) bacterial species during 8 days, as compared to a 72-89% degradation of GluA, D-AA and DAPA in cell material of a G(+) bacterial species. When cultures of estuarine bacteria were enriched with purified G(-) and G(+) peptidoglycan (1 mg l(-1)), at least 49% (G(-)) and 58% (G(+)) of D-AA in the peptidoglycan was degraded. No major changes in GluA were obvious. Interpretation of the results was difficult as a portion of the purified peptidoglycan was of similar size to the bacteria and could not be differentiated from cells growing in the cultures. Addition of the purified peptidoglycan stimulated the bacterial growth, and after 6 days the cell density in the enriched cultures was 4-fold higher than in the controls. A regrowth of bacteria after addition of L-broth at 105 days caused a 50- to 75-fold increase in dissolved D-AA and GluA. Most of the D-AA and GluA were taken up during the following 10 days, indicating that cell wall constituents are dynamic compounds. Our results show that a variable portion of peptidoglycan in G(-) and G(+) bacteria can be degraded by natural bacteria, and that peptidoglycan in G(-) bacteria is more resistant to bacterial attack than that in G(+) bacteria. Thus, the presence of cell wall constituents in natural DOM may reflect the recalcitrant nature of especially G(-) peptidoglycan.

Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water

A novel, non-pigmented, rod-shaped, Gram-negative strain was isolated from mesotrophic lake water in Zealand, Denmark. Phylogenetic analysis of the 16S rRNA gene sequence of the bacterium, designated strain 389(T), indicated that the strain belonged to the genus Vogesella and formed a monophyletic group with Vogesella perlucida DS-28(T) (99.1 % nucleotide similarity); it was less related to Vogesella indigofera ATCC 19706(T) (96.9 % similarity) and Vogesella lacus LMG 24504(T) (96.8 % similarity). Hybridization of DNA from strain 389(T) and V. perlucida demonstrated a reassociation of 50.6 ± 9.6 %. The DNA G+C content of strain 389(T) was 61.2 mol%. The fatty acid profile of the strain differed from those of the other strains representing the genus Vogesella by a high content of C₁₆:₁ω7c and/or iso-C₁₅:₀ 2-OH (71.6 %) and a lower content of C₁₆: ₀. Strain 389(T) was capable of degrading peptidoglycan and had chitinase and lysozyme activities, possibly associated with the degradation of peptidoglycan, and had capacity for degradation of several other polymer compounds. Based on phenotypic and genotypic characteristics, strain 389(T) represents a novel species, for which we propose the name Vogesella mureinivorans sp. nov. The type strain is 389(T) (=DSM 21247(T) =LMG 25302(T)).

Increased pollution-induced bacterial community tolerance to sulfadiazine in soil hotspots amended with artificial root exudates

Sulfadiazine (SDZ) residues constitute an important pollutant in soils that may increase environmental reservoirs of antibiotic resistance. Our primary aim was to compare the development of pollution-induced community tolerance (PICT) to SDZ concentration levels in bulk soil and nutrient amended soil hotspots. Agricultural soil microcosms were amended with different concentrations of SDZ with or without weekly additions of artificial root exudates corresponding to realistic rhizodeposition rates. Bacterial community tolerance to SDZ residues, as determined by the [3H]leucine incorporation technique, increased progressively with elevated SDZ exposure, and was significantly increased in soil hotspots (LOEC of 1microg kg(-1)). An alternative PICT approach based on single-cell esterase probing by flow cytometry failed to demonstrate SDZ impacts. Bacterial growth rates ([3H]leucine incorporation) were significantly reduced in both bulk soil and hotspots 24 h after amendment with environmentally relevant concentrations of SDZ, while soil respiration remained unaffected even at 100 microg SDZ g(-1). Our study for the first time demonstrates a drastically increased PICT response of a soil bacterial community due to increased carbon substrate amendment per se. Hence, hotspot soil environments such as rhizosphere and manure-soil interfaces may comprise key sites for proliferation of bacteria that are resistant or tolerant to antibiotics.

Bacterial feeders, the nematode Caenorhabditis elegans and the flagellate Cercomonas longicauda, have different effects on outcome of competition among the Pseudomonas biocontrol strains CHA0 and DSS73

How bacterial feeding fauna affects colonization and survival of bacteria in soil is not well understood, which constrains the applicability of bacterial inoculants in agriculture. This study aimed to unravel how food quality of bacteria and bacterial feeders with different feeding habits (the selective feeding flagellate Cercomonas longicauda versus the non-selective feeding nematode Caenorhabditis elegans) influence the abundance of two bacteria that compete for resources in simple model communities. Microcosms consisted of either one gfp-tagged bacterial strain (Pseudomonas fluorescens DSM50090 or one of two biocontrol strains P. fluorescens CHA0 or Pseudomonas sp. DSS73) or combinations of two bacterial strains. DSM50090 is a suitable food bacterium, DSS73 is of intermediate food quality, and CHA0 is inedible to the bacterial feeders. Bacterial and protozoan cell numbers were measured by flow cytometry. In the presence of flagellates, CHA0 increased its abundance as compared to the other biocontrol strain DSS73 or to DSM50090, which were both eaten by the flagellates. In contrast, the number of CHA0 declined as compared to DSS73 when the model community was subjected to nematode predation pressure. Hence, the results suggested that the outcome of competition among bacteria depended on their ability to cope with the prevailing bacterial predator.

Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties

Genetic, structural and physiological differences between strains of the marine bacterium Cellulophaga baltica MM#3 (Flavobacteriaceae) developing in response to the activity of two virulent bacteriophages, Phi S(M) and Phi S(T), was investigated during 3 weeks incubation in chemostat cultures. A distinct strain succession towards increased phage resistance and a diversification of the metabolic properties was observed. During the incubation the bacterial population diversified from a single strain, which was sensitive to 24 tested Cellulophaga phages, into a multistrain and multiresistant population, where the dominant strains had lost susceptibility to up to 22 of the tested phages. By the end of the experiment the cultures reached a quasi steady state dominated by Phi S(T)-resistant and Phi S(M) + Phi S(T)-resistant strains coexisting with small populations of phage-sensitive strains sustaining both phages at densities of > 10(6) plaque forming units (pfu) ml(-1). Loss of susceptibility to phage infection was associated with a reduction in the strains' ability to metabolize various carbon sources as demonstrated by BIOLOG assays. This suggested a cost of resistance in terms of reduced physiological capacity. However, there was no direct correlation between the degree of resistance and the loss of metabolic properties, suggesting either the occurrence of compensatory mutations in successful strains or that the cost of resistance in some strains was associated with properties not resolved by the BIOLOG assay. The study represents the first direct demonstration of phage-driven generation of functional diversity within a marine bacterial host population with significant implications for both phage susceptibility and physiological properties. We propose, therefore, that phage-mediated selection for resistant strains contributes significantly to the extensive microdiversity observed within specific bacterial species in marine environments.

Effect of availability of nitrogen compounds on community structure of aquatic bacteria in model systems

To test if the quality and concentration of dissolved nitrogen (N) species could be a selective force in shaping bacterioplankton community structure, competition for various N compounds among five heterotrophic marine bacteria (Pseudomonas strains B, B25, and AX; Bacillus strain A6; Erythrobacter strain F19) was examined. Two of the five strains (AX and B25) were capable of utilizing urea for growth. The five strains were inoculated into dilute (1/1,000 strength) ZoBell medium enriched with various N sources (free amino acids, casein, ammonium, nitrate, or urea). Regardless of the added N source, the communities were either dominated by strain B (at 50 microM N) or strain AX (at 250 microM N). Without any addition of N, strain F19 dominated. If F19 was not included in the community, strain B25 dominated. Despite these differences in community structure, consumption of the added N compounds was surprisingly similar and no advantages of urea for the urea-utilizing bacterium B25 were obvious. To examine if urea could be of selective advantage to the urea-degrading strains B25 and AX, communities with and without B25 were amended with urea N. As expected, strain B25 became dominant when present, but without this strain the non-urea-utilizing strain B outcompeted the urea-utilizing strain AX. Possibly, strain B benefited from N released during catabolism of urea by strain AX. Changes in community composition did not result in major changes in the nitrogen dynamics. The results indicate that dissolved N species can be a selective force in shaping microbial communities. Relative to nutrient generalists, nutrient specialists may either have competitive advantages or stimulate growth of other species by synergetic interactions. Results from the model communities suggest that there may be a large degree of unpredictability in the making of microbial communities, whereas major ecosystem functions such as N cycling appear relatively stable.

Differential bioavailability of copper complexes to bioluminescent Pseudomonas fluorescens reporter strains

Increased levels of Cu in agricultural soils are of concern, because Cu toxicity may adversely affect important soil microorganisms, including pseudomonads. Because total metal concentrations correlate poorly with bioavailability and toxicity, a need exists for more information linking Cu speciation, bioavailability, and toxicity. The objective of the present study was to determine the bioavailability of different Cu complexes to Pseudomonas spp. A Cu-specific bioluminescent Pseudomonas fluorescens reporter strain was used to determine bioavailable Cu, which was operationally defined as those Cu species that induced expression of bioluminescence. Another strain of P. fluorescens, which continuously expressed bioluminescence, was used as a toxicity reporter. Experiments were performed in a defined aqueous medium containing 0.04 microM Cu, which was amended with ethylenediaminetetraacetic acid (EDTA), citrate, or a well-characterized pool of dissolved organic matter (DOM). Bioluminescence emitted by the biosensors was related to data for Cu speciation obtained by geochemical modeling. Changes in Cu bioavailability in the presence of EDTA coincided with modeled changes in Cu2+ activity, indicating that Cu-EDTA complexes were not bioavailable to the Cu-specific reporter. In contrast, changes of Cu bioavailability in the presence of citrate did not correspond to changes in Cu2+, indicating that Cu-citrate complexes were fully bioavailable to the reporter strain. Finally, the response of the Cu-reporter strain to Cu in the presence of DOM indicated that Cu formed bioavailable as well as unavailable complexes with DOM. We conclude that free Cu2+ activity is a poor predictor of Cu bioavailability to Pseudomonas spp. in samples containing organic ligands.

Evidence for bioavailable copper-dissolved organic matter complexes and transiently increased copper bioavailability in manure-amended soils as determined by bioluminescent bacterial biosensors

The short-term (3 months) dynamics of bioavailable copper (Cu) species was determined in soils amended with various amounts of manure and Cu. Bioavailable Cu species were operationally defined as those species that were able to induce gene expression in a Cu-specific Pseudomonas fluorescens biosensor. Biosensor measurements were backed by analysis of total Cu in soil and of total Cu and free Cu2+ ion activity in solution. Cu bioavailability relative to the total Cu concentration increased dramatically with increasing Cu loading of manure and with increasing manure amendment to soil. In both cases, the immediate increase in bioavailability could be explained in part by increased Cu concentration in solution and in part by an increased bioavailability of dissolved Cu species. In contrast to Cu bioavailability, Cu2+ ion activity decreased progressively with increasing manure loading. Cu bioavailability declined rapidly during the weeks after manure amendment concomitant with a marked slow-down of C mineralization indicating a shift from initially bioavailable Cu-dissolved organic matter (Cu-DOM) complexes to nonavailable Cu-DOM complexes over time. Our data do not support the conventional view of metal bioavailability being primarily related to the free metal ion activity and strongly suggest differential bioavailability of Cu-DOM complexes in manure-amended soils.

Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts

Phages are a main mortality factor for marine bacterioplankton and are thought to regulate bacterial community composition through host-specific infection and lysis. In the present study we demonstrate for a marine phage-host assemblage that interactions are complex and that specificity and efficiency of infection and lysis are highly variable among phages infectious to strains of the same bacterial species. Twenty-three Bacteroidetes strains and 46 phages from Swedish and Danish coastal waters were analyzed. Based on genotypic and phenotypic analyses, 21 of the isolates could be considered strains of Cellulophaga baltica (Flavobacteriaceae). Nevertheless, all bacterial strains showed unique phage susceptibility patterns and differed by up to 6 orders of magnitude in sensitivity to the same titer of phage. The isolated phages showed pronounced variations in genome size (8 to >242 kb) and host range (infecting 1 to 20 bacterial strains). Our data indicate that marine bacterioplankton are susceptible to multiple co-occurring phages and that sensitivity towards phage infection is strain specific and exists as a continuum between highly sensitive and resistant, implying an extremely complex web of phage-host interactions. Hence, effects of phages on bacterioplankton community composition and dynamics may go undetected in studies where strain identity is not resolvable, i.e., in studies based on the phylogenetic resolution provided by 16S rRNA gene or internal transcribed spacer sequences.

Initial characterization of a bolA homologue from Pseudomonas fluorescens indicates different roles for BolA-like proteins in P. fluorescens and Escherichia coli

The RpoS-regulated bolA gene in Escherichia coli is important for the decrease in cell size during stationary phase or sudden carbon starvation. A Pseudomonas fluorescens strain mutated in a gene with homology to bolA reduced its cell size upon carbon starvation, and RpoS had little effect on bolA expression. The mutant grew slower than the wild-type strain in minimal medium with L-serine as the sole nitrogen source, while growth rates were similar on a mixture of L-serine and L-cysteine. Reverse transcriptase polymerase chain reaction analysis indicated that the bolA homologue is the second gene in an operon where the two next ORFs encode putative proteins with homology to sulphurtransferases and protein disulphide isomerases. Complementation of the mutant phenotypes was only obtained by plasmids encoding BolA as well as the above two proteins. Growth phenotypes and gene homologies suggest that BolA-like proteins have different functions in E. coli and Pseudomonas.

Bioavailability and toxicity of soil particle-associated copper as determined by two bioluminescent Pseudomonas fluorescens biosensor strains

We report the development and application of a novel, solid phase-contact bioassay based on two whole-cell bacterial biosensor strains. Our data indicate that a significant fraction of particle-associated Cu may be available to bacteria in dilute soil suspensions but also support the conventional view that mainly the soluble fraction of Cu is directly available to bacteria under more realistic soil conditions.

Decreased abundance and diversity of culturable Pseudomonas spp. populations with increasing copper exposure in the sugar beet rhizosphere

Recent studies have indicated that culturable bacteria constitute highly sensitive bioindicators of metal-induced stress in soil. We report the impact of different copper exposure levels characteristic of contaminated agricultural soils on culturable Pseudomonas spp. in the rhizosphere of sugar beet. We observed that the abundance of Pseudomonas spp. was much more severely affected than that of the general population of culturable heterotrophic bacteria by copper. For diversity assessment, Pseudomonas isolates were divided into operational taxonomic units based on amplified ribosomal DNA restriction analysis and genomic PCR fingerprinting by universally primed PCR. Copper significantly decreased the diversity of Pseudomonas spp. in the rhizosphere and significantly increased the frequency of copper-resistant isolates. Concomitant chemical and biological analysis of copper in the rhizosphere and in bulk soil extracts indicated no rhizosphere effect and a relatively low copper bioavailability in the studied soil, suggesting that the observed effects of copper may occur at lower total concentrations in other soils. We conclude that culturable Pseudomonas sensu stricto constitutes a highly sensitive and relevant bioindicator group for the impact of copper in the rhizosphere habitat, and suggest that continued application of copper to agricultural soils poses a significant risk to successful rhizosphere colonization by Pseudomonas spp.

Genes involved in cyclic lipopeptide production are important for seed and straw colonization by Pseudomonas sp. strain DSS73

Survival in natural bulk soil and colonization of sugar beet seeds and barley straw residues were determined for Pseudomonas sp. strain DSS73 and Tn5 mutants in amsY (encoding a peptide synthetase involved in production of the cyclic lipopeptide amphisin) and gacS (encoding the sensory kinase of the two-component GacA/GacS regulatory system). No differences in survival or growth in response to carbon amendment (citrate) were observed in bulk soil. However, both mutants were impaired in their colonization of sugar beet seeds and barley straw residues by an inoculum established in the bulk soil. The two mutants had comparable colonization phenotypes, suggesting that amphisin production is more important for colonization than other gacS-controlled traits.

Copper amendment of agricultural soil selects for bacterial antibiotic resistance in the field

AIMS

The objective of this study was to determine whether Cu-amendment of field plots affects the frequency of Cu resistance, and antibiotic resistance patterns in indigenous soil bacteria.

METHODS AND RESULTS

Soil bacteria were isolated from untreated and Cu-amended field plots. Cu-amendment significantly increased the frequency of Cu-resistant isolates. A panel of isolates were characterized by Gram-reaction, amplified ribosomal DNA restriction analysis and resistance profiling against seven antibiotics. More than 95% of the Cu-resistant isolates were Gram-negative. Cu-resistant Gram-negative isolates had significantly higher incidence of resistance to ampicillin, sulphanilamide and multiple (> or =3) antibiotics than Cu-sensitive Gram-negative isolates. Furthermore, Cu-resistant Gram-negative isolates from Cu-contaminated plots had significantly higher incidence of resistance to chloramphenicol and multiple (> or =2) antibiotics than corresponding isolates from control plots.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this field experiment show that introduction of Cu to agricultural soil selects for Cu resistance, but also indirectly selects for antibiotic resistance in the Cu-resistant bacteria. Hence, the widespread accumulation of Cu in agricultural soils worldwide could have a significant effect on the environmental selection of antibiotic resistance.

Functional characteristics of culturable bacterioplankton from marine and estuarine environments

Information on the structure of bacterioplankton communities is continuously increasing, while knowledge of their metabolic capabilities remains limited. In this study, the metabolic capacity of bacterioplankton was investigated, as such information is necessary to fully understand carbon cycling and other biogeochemical processes. The diversity of dominant culturable chemoorganotrophic bacteria from one estuarine and three marine environments was analyzed by random isolation of colony-forming units on solid media, taxonomical identification by partial 16S rRNA gene sequence analysis, and functional characterization of the isolates. A total of 76 16S rRNA gene sequences, representing 19 different genotypes, were obtained from the four sampling localities, including Bacillus, Pseudomonas, Pseudoalteromonas, Vibrio, and Erythrobacter as the most frequently isolated genera. The range of metabolic functions possessed by the cultured bacterial assemblages differed significantly between sites. Similarly, the percentage at each sampling station of bacteria capable of performing a specific function was significantly different for 18 of the 25 investigated metabolic functions. At two localities, the bacterial assemblages were dominated by a single genus (Pseudoalteromonas or Erythrobacter) and appeared to be functionally specialized. More than 95% of the isolates were capable of utilizing dissolved free amino acids and protein as their sole nitrogen sources, and all isolates of the specialized assemblages expressed beta-glucosidase. Furthermore, only some of the isolates were able to utilize NH4+, while up to two thirds of the isolates of the two marine sites were able to grow on NO3-.