Low-substrate regulated microaerophilic behavior as a stress response of aquatic and soil bacteria

Expression of stress-related proteins in Sediminibacterium sp. growing under planktonic conditions

Aggregation is a common trait of bacteria in natural and engineered biological systems. Microbial aggregates, such as flocs, granules, and biofilms, are spatially heterogeneous environments. It is generally observed that by growing under aggregated conditions bacteria respond and adapt to environmental stress better than free-swimming bacteria of the same species. We performed a proteomic analysis of a strain of Sediminibacterium, isolated from activated sludge, which grew planktonically in diluted culture media and in an aggregated form in media containing a high concentration of organic substrate. Auto-aggregation was also observed in the presence of pyruvate in dilute media. Expression of a number of stress-related proteins significantly increased under planktonic growth in comparison to aggregate growth. The upregulated proteins, identified by MALDI-TOF mass spectrometry, were two isoforms of a protein belonging to the universal stress family (UspA), a thioredoxin-disulfide reductase, the Campylobacter jejuni orthologue transcriptional regulator (Cj1172c), and the CocE/NonD hydrolase. We conclude that Sediminibaterium sp. C3 growth is stressed under planktonic conditions and that aggregation induced by pyruvate protects the bacteria against oxidative stress.

Bacterioplankton community diversity in a maritime Antarctic lake, determined by culture-dependent and culture-independent techniques

Abstract The biodiversity of the pelagic bacterioplankton community of a maritime Antarctic freshwater lake was examined by cultivation-dependent and cultivation-independent techniques to determine predominant bacterioplankton populations present. The culture-dependent techniques used were direct culture and observation, polymerase chain reaction amplification of 16S rRNA gene fragments, restriction fragment length polymorphism (RFLP) analysis followed by selective sequencing and fatty acid methyl ester analysis. The culture-independent techniques used were 16S ribosomal DNA gene cloning, RFLP analysis and sequencing, in situ hybridisation with group-specific, fluorescently labelled oligonucleotide probes and cloning and sequencing of dominant denaturing gradient gel electrophoresis products. Significant differences occurred between the results obtained with each method. However, sufficient overlap existed between the different methods to identify potentially significant groups. At least six different bacterial divisions including 24 genera were identified using culture-dependent techniques, and eight different bacterial divisions, including 23 genera, were identified using culture-independent techniques. Only five genera, Corynebacterium, Cytophaga, Flavobacterium, Janthinobacterium and Pseudomonas, could be identified using both sets of techniques, which represented four different bacterial divisions. Significantly for Antarctic freshwater lakes, pigment production is found within members of each of these genera. This work illustrates the importance of a comprehensive polyphasic approach in the analysis of lake bacterioplankton, and supports the ecological relevance of results obtained in earlier entirely culture-based studies.

Environmental modification and niche construction: developing O2 gradients drive the evolution of the Wrinkly Spreader

The evolutionary success of the novel Wrinkly Spreader (WS) genotypes in diversifying Pseudomonas fluorescens SBW25 populations in static liquid microcosms has been attributed to the greater availability of O(2) at the air-liquid (A-L) interface where the WS produces a physically cohesive-class biofilm. However, the importance of O(2) gradients in SBW25 adaptation has never been examined. We have explicitly tested the role of O(2) in evolving populations using microsensor profiling and experiments conducted under high and low O(2) conditions. Initial colonists of static microcosms were found to establish O(2) gradients before significant population growth had occurred, converting a previously homogenous environment into one containing a resource continuum with high and low O(2) regions. These gradients were found to persist for long periods by which time significant numbers of WS had appeared colonising the high O(2) niches. Growth was O(2) limited in static microcosms, but high O(2) conditions like those found near the A-L interface supported greater growth and favoured the emergence of WS-like genotypes. A fitness advantage to biofilm formation was seen under high but not low O(2) conditions, suggesting that the cost of biofilm production could only be offset when O(2) levels above the A-L interface were high. Profiling of mature WS biofilms showed that they also contained high and low O(2) regions. Niches within these may support further diversification and succession of the developing biofilm population. O(2) availability has been found to be a major factor underlying the evolutionary success of the WS genotype in static microcosms and illustrates the importance of this resource continuum in microbial diversification and adaptation.

Utilization of capsaicin and vanillylamine as growth substrates by Capsicum (hot pepper)-associated bacteria

Capsaicin contributes to the organoleptic attributes of hot peppers. Here, we show that capsaicin is utilized as a growth nutrient by certain bacteria. Enrichment cultures utilizing capsaicin were successfully initiated using Capsicum-derived plant material or leaves of tomato (a related Solanaceae) as inocula. No other sources of inoculum examined yielded positive enrichments. Of 25 isolates obtained from enrichments: all utilized 8-methylnonanoic acid; nine were found capable of degrading capsaicin as sole carbon and energy source; 11 were found capable of utilizing vanillylamine; but only two strains could use either of these latter two compounds as sole nitrogen source. Phylogenetic analysis of capsaicin degraders revealed them to be strains of Variovorax and Ralstonia, whereas the vanillylamine degraders were strains of Pseudomonas and Variovorax. Neither of the two strains isolated from one enrichment culture originally inoculated with dried pepper fruit was capable of using capsaicin as sole carbon and nitrogen source. However, good growth was achieved under such conditions when the two isolates, a strain of Variovorax paradoxusThat degraded capsaicin when provided with ammonium, and a vanillylamine degrading strain of Pseudomonas putida, were cultured together. A cross-feeding of capsaicin-derived carbon and nitrogen between members of pepper-associated consortia is proposed.

Physiology and microbial community structure in soil at extreme water content

A sandy loam soil was brought to 6 water contents (13-100% WHC) to study the effects of extreme soil moistures on the physiological status of microbiota (represented by biomass characteristics, specific respiration, bacterial growth, and phospholipid fatty acid, PLFA, stress indicators) and microbial community structure (assessed using PLFA fingerprints). In dry soils, microbial biomass and activity declined as a consequence of water and/or nutrient deficiency (indicated by PLFA stress indicators). These microbial communities were dominated by G+ bacteria and actinomycetes. Oxygen deficits in water-saturated soils did not eliminate microbial activity but the enormous accumulation of poly-3-hydroxybutyrate by bacteria showed the unbalanced growth in excess carbon conditions. High soil water content favored G bacteria.