The response of benthic bacterial community composition, diversity, and biomass to phytoplankton deposition was investigated in 2 different sediment horizons at 2 contrasting sites in the southern North Sea. Differences in bacterial community composition between stations were observed. Seasonal differences in bacterial community composition were significant and were stronger in fine sediments, probably related to stronger fluctuations in food availability. Variation in community composition over the vertical sediment profile was different for both stations. In coarser sediment, the difference was mostly due to the absence of certain operational taxonomic units (OTUs) at the surface, while in fine sediment, 2 distinct communities were present. A RELATE test revealed that bacterial community composition was influenced by the amount of labile organic matter (estimated through chl a concentration in the sediment). Diversity in terms of OTU richness and ShannonWeaver diversity index was higher in finer grained sediments. In coarser sediments, diversity at the surface layer was lower, which might be related to stronger hydrodynamic pressure at this station. These differences were not observed at the other station. Seasonal changes in diversity were not detected at either station. Bacterial biomass was slightly higher in finer sediments and was not correlated with either chl a or temperature. Seasonal differences in bacterial biomass followed those observed for community composition, while no vertical differences were detected.

The type III secretion system (T3SS) is an important virulence factor of pathogenic bacteria, but the natural occurrence of variants of bacterial plant pathogens with deficiencies in their T3SS raises questions about the significance of the T3SS for fitness. Previous work on T3SS-deficient plant pathogenic bacteria has focused on strains from plants or plant debris. Here we have characterized T3SS-deficient strains of Pseudomonas syringae from plant and nonplant substrates in pristine nonagricultural contexts, many of which represent recently described clades not yet found associated with crop plants. Strains incapable of inducing a hypersensitive reaction (HR À ) in tobacco were detected in 65% of 126 samples from headwaters of rivers (mountain creeks and lakes), snowpack, epilithic biofilms, wild plants and leaf litter and constituted 2 to 100% of the P. syringae population associated with each sample. All HR À strains lacked at least one gene in the canonical hrp/hrc locus or the associated conserved effector locus, but most lacked all six of the genes tested (hrcC, hrpL, hrpK1, avrE1 and hrpW1) and represented several disparate phylogenetic clades. Although most HR À strains were incapable of causing symptoms on cantaloupe seedlings as expected, strains in the recently described TA-002 clade caused severe symptoms in spite of the absence of any of the six conserved genes of the canonical T3SS according to PCR and Southern blot assays. The phylogenetic context of the T3SS variants we observed provides insight into the evolutionary history of P. syringae as a pathogen and as an environmental saprophyte.

Denaturing gradient gel electrophoresis (DGGE) of amplified nifH gene fragments was used to study the diazotrophic community of soil samples under Acacia tortilis ssp. raddiana (legume tree) and Balanites aegyptiaca (non-legume tree), two dominant plant species growing naturally in the dryland part of Senegal. Samples were taken along transects from the stem up to 10 m distance from it, at depths of 0-0.25 m and 0.25-0.50 m. Sampling was done in the dry season (25 June 1999) and in the rainy season (28 August 1999). The community structure and diversity of the bacterial groups from the different samples was analysed further using different techniques, such as statistical analysis and diversity index evaluation of the band patterns. Diazotrophic diversity was lower under B. aegyptiaca than under A. tortilis ssp. raddiana. Multidimensional scaling (MDS) analysis and ANOSIM tests showed a significant effect of the tree on the diazotroph assemblages. SIMPER analysis showed that the major elements responsible for the dissimilarity are a member of the genus Sinorhizobium, which is characteristic of the samples taken under A. tortilis ssp. raddiana and a member of the cluster Bradyrhizobium for the samples taken under B. aegyptiaca. Forty-four major bands were partially sequenced, yielding 33 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were affiliated with the alpha- beta- and gamma-proteobacteria. Five nifH sequences were identical to those of Pseudomonas stutzeri, and one sequence showed 100% similarity to that of Azotobacter vinelandii. Four bands were affiliated with the Cyanobacteria and a single one with the Firmicutes. For both trees, there were also clear differences between the samples taken in the dry and rainy seasons. Only for the samples taken under A. tortilis ssp. raddiana was a significant difference found between the two sampling depths.

The bias of widely used degenerate nifH-specific primer sets was first tested using denaturing gradient gel electrophoresis (DGGE), and their application for profiling of complex communities assessed for roots of Oryza longistaminata. When primers (P) with mismatches at nondegenerate positions were used on genomic DNA of Azotobacter vinelandii, which harbors three single divergent nifH genes, template-to-product ratios were highly skewed. In contrast, we obtained no evidence for a large PCR bias when we used highly degenerate primers with no mismatches (Z). Similar results were obtained for reverse transcription (RT)-PCR amplifications from root RNA from O. longistaminata grown at the river bed of the Okavango, where Z-primers detected a more complex nifH pool, corroborating that the P-primers are quite biased in the nifH sequences they amplify. In microcosms of O. longistaminata grown in the phytotron in the presence or absence of constant low nitrogen input (25 kg NH4NO3 ha(-1) year(-1)), roots of nitrogen-treated plants showed similar, slightly higher levels of nifH-mRNA. However, nitrogen treatment had a strong effect on the composition and diversity of expressed nifH pools that shifted towards methylotroph-related nitrogenases. Thus the active population of diazotrophs was not resistant towards low rates of nitrogen input and decreased significantly in richness, as also observed for plant species richness in grasslands by others.

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