Nitrogenase gene diversity and microbial community structure: a cross-system comparison

Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland)

The nitrogen cycling of Lake Cadagno was investigated by using a combination of biogeochemical and molecular ecological techniques. In the upper oxic freshwater zone inorganic nitrogen concentrations were low (up to approximately 3.4 microM nitrate at the base of the oxic zone), while in the lower anoxic zone there were high concentrations of ammonium (up to 40 microM). Between these zones, a narrow zone was characterized by no measurable inorganic nitrogen, but high microbial biomass (up to 4 x 10(7) cells ml(-1)). Incubation experiments with (15)N-nitrite revealed nitrogen loss occurring in the chemocline through denitrification (approximately 3 nM N h(-1)). At the same depth, incubations experiments with (15)N(2)- and (13)C(DIC)-labelled bicarbonate, indicated substantial N(2) fixation (31.7-42.1 pM h(-1)) and inorganic carbon assimilation (40-85 nM h(-1)). Catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and sequencing of 16S rRNA genes showed that the microbial community at the chemocline was dominated by the phototrophic green sulfur bacterium Chlorobium clathratiforme. Phylogenetic analyses of the nifH genes expressed as mRNA revealed a high diversity of N(2) fixers, with the highest expression levels right at the chemocline. The majority of N(2) fixers were related to Chlorobium tepidum/C. phaeobacteroides. By using Halogen In Situ Hybridization-Secondary Ion Mass Spectroscopy (HISH-SIMS), we could for the first time directly link Chlorobium to N(2) fixation in the environment. Moreover, our results show that N(2) fixation could partly compensate for the N loss and that both processes occur at the same locale at the same time as suggested for the ancient Ocean.

Identity and dynamics of putative N2 -fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation

Heterocystous filamentous cyanobacteria are regarded as the main N2 -fixing organisms (diazotrophs) in the Baltic Sea. However, some studies indicate that picoplankton may also be important. The aim of this study was to examine the composition of putative diazotrophs in the picoplankton (< 3 µm) and to identify links to environmental factors. Nitrogenase (nifH) genes were amplified from community DNA by nested PCR, followed by cloning and sequencing. Clone libraries from nine environmental samples collected from the central Baltic Sea (April-October 2003, 3 m depth) and a negative control yielded a total of 433 sequences with an average clone library coverage of 92%. The sequences fell within nifH Clusters I, II and III and formed 15 distinct groups (> 96% amino acid similarity). Most of the sequences (77%) fell into nifH Cluster I (cyanobacteria and α-, β- and γ-Proteobacteria). However, only 26 sequences were related to cyanobacteria (e.g. Pseudanabaena) and among these no unicellular phylotypes were found. Sequences clustering with alternative nitrogenases (anfH) and Archaea were found in one sample while sequences related to anaerobic phylotypes were found in six samples distributed throughout the season. The identified phylogenetic groups showed covariance with several environmental factors but no strong links could be established. This suggests a variable and complex regulation of diazotrophic groups within Baltic Sea picoplankton.

Fluorescence in situ hybridization for intracellular localization of nifH mRNA

Few reports on in situ mRNA detection in bacteria have been published, even though a major aim in environmental microbiology is to link function/activity to the identity of the organisms. This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. Thus, the approach enabled us specifically to link in situ the information from the dinitrogen fixation activity of an organism to its identity. Unexpectedly, the signals derived from nifH mRNA hybridization showed a distinct uneven pattern within the cells. This indicated that the method used could even give insights about the localization of the detected mRNA within the cell, which is a potential use of mRNA fluorescence in situ hybridization (FISH) that has not been reported up to now for bacterial cells.

Prevalence of betaproteobacterial sequences in nifH gene pools associated with roots of modern rice cultivars

The diversity and function of nitrogen-fixing bacteria colonizing rice roots are not well understood. A field experiment was conducted to determine the diversity of diazotrophic communities associated with roots of modern rice cultivars using culture-independent molecular analyses of nitrogenase gene (nifH) fragments. Experimental treatments included four modern rice cultivars (Oryza sativa, one Indica, one Japonica and two hybrid rice varieties) and three levels (0, 50, and 100 kg N ha(-1)) of N (urea) fertilizer application. Cloning and sequencing of 103 partial nifH genes showed that a diverse community of diazotrophs was associated with rice roots. However, the nifH gene fragments belonging to betaproteobacteria were dominant, accounting for nearly half of nifH sequences analyzed across the clone libraries. Most of them were similar to nifH fragments retrieved from wild rice and Kallar grass, with Azoarcus spp. being the closest cultured relatives. Alphaproteobacteria were also detected, but their relative abundance in the nifH gene pools was dramatically decreased with N fertilizer application. In addition, a high fraction of nifH gene pools was affiliated with methylotrophs and methane oxidizers. The sequence analysis was consistent with the terminal restriction fragment-length polymorphism (T-RFLP) fingerprinting of the nifH gene fragments, which showed three of four dominant terminal restriction fragments were mainly related to betaproteobacteria based on in silico digestion of nifH sequences. T-RFLP analyses also revealed that the effects of N fertilizer on the nifH gene diversity retrieved from roots varied according to rice cultivars. In summary, the present study revealed the prevalence of betaproteobacterial sequences among the proteobacteria associated with roots of modern rice cultivars. This group of diazotrophs appeared less sensitive to N fertilizer application than diazotrophic alphaproteobacteria. Furthermore, methylotrophs may also play a role in nitrogen fixation on rice roots. However, it must be noted that due to the potential bias of polymerase chain reaction protocol, the significance of non-proteobacterial diazotrophs such as Firmicutes and anaerobic bacteria is possibly underestimated.

High diversity of diazotrophs in the forefield of a receding alpine glacier

Forefields of receding glaciers are unique and sensitive environments representing natural chronosequences. In such habitats, microbial nitrogen fixation is of particular interest since the low concentration of bioavailable nitrogen is one of the key limitations for growth of plants and soil microorganisms. Asymbiotic nitrogen fixation in the Damma glacier (Swiss Central Alps) forefield soils was assessed using the acetylene reduction assay. Free-living diazotrophic diversity and population structure were resolved by assembling four NifH sequence libraries for bulk and rhizosphere soils at two soil age classes (8- and 70-year ice-free forefield). A total of 318 NifH sequences were analyzed and grouped into 45 unique phylotypes. Phylogenetic analyses revealed a higher diversity as well as a broader distribution of NifH sequences among phylogenetic clusters than formerly observed in other environments. This illustrates the importance of free-living diazotrophs and their potential contribution to the global nitrogen input in this nutrient-poor environment. NifH diversity in bulk soils was higher than in rhizosphere soils. Moreover, the four libraries displayed low similarity values. This indicated that both soil age and the presence of pioneer plants influence diversification and population structure of free-living diazotrophs.

Bacterial diversity of the broadbalk 'classical' winter wheat experiment in relation to long-term fertilizer inputs

With more than 160 years of contrasting fertilizer regimes, the Broadbalk winter wheat experiment represents a unique experimental resource for studying the effects of long-term fertilizer application on microbial population diversity. Using DGGE and clone library analysis, we report here on eubacterial species diversity (16S rRNA gene) and diversity within two sets of gene products associated with microbial N acquisition: NifH (nitrogen fixation) and AmtB (ammonium transport). Comparisons were made within and between soils treated with mineral N fertilizer, farmyard manure or receiving no fertilizer. Analysis of 16S rRNA gene DGGE profiles showed no clear patterns to qualitatively distinguish bacterial community structure between the three different treatments (P > 0.05), with all samples containing a range of eubacterial taxa similar to those that are characteristic of soil bacteria reported elsewhere. Intra-plot heterogeneity was high and of a similar magnitude to that between treatments. This lack of qualitative between plot differences was echoed in the representative sequences of 16S rRNA, nifH, and amtB genes in the various samples. Taken together, both phylogenetic and functional gene analyses showed bacterial communities in the Broadbalk-trial soil were very stable and relatively non-responsive to long-term management of balanced fertilizer inputs.

Phylogenetic diversity of cyanobacterial narB genes from various marine habitats

Nitrate, the most abundant combined, dissolved form of inorganic nitrogen in global oceans, is a common source of nitrogen (N) for phytoplankton including cyanobacteria. Using a nested polymerase chain reaction (PCR) method, the diversity of the cyanobacterial nitrate reductase gene, narB, was examined in plankton samples from a variety of marine habitats. A total of 480 narB gene fragment sequences were obtained from a coastal coral reef (Heron Island, Australia), open-ocean tropical and subtropical oceanic waters (Atlantic and Pacific Oceans) and a temperate N. Pacific Ocean site (34 degrees N, 129 degrees W). Phylogenetic analyses distinguished eight picocyanobacterial narB clades comprised of DNA sequences derived from the nutrient-replete coastal, nutrient-deplete pelagic and tidally influenced coral reef habitats. The phylogeny of recovered narB gene sequences was consistent with 16S rRNA and ITS sequence phylogenies, suggesting minimal horizontal gene transfer of the narB gene. Depending on sampled habitat, environmental narB sequence types segregated into three divisions: non-picocyanobacterial, coastal picocyanobacterial and open-ocean picocyanobacterial sequences. Using a reverse transcription PCR method, narB mRNA sequences were amplified from Heron Island samples, indicating that narB expression can be detected in environmental samples.

Light dependency of nitrogen fixation in a coastal cyanobacterial mat

The fixation of nitrogen in cyanobacterial mats situated along the littoral gradient on a Dutch barrier island was investigated by using a high-resolution online, near-real-time acetylene reduction assay. Light-response curves of nitrogenase activity yielded a variety of physiological parameters that changed during a day-night cycle. The fitted parameters were used to calculate nitrogen fixation from the incident natural irradiance over several days in two different mat types. Mats occurring in the higher regions of the littoral were composed of a diverse community of cyanobacteria, consisting of both heterocystous and non-heterocystous filamentous species, whereas closer to the low water mark the mats contained mainly non-heterocystous filamentous cyanobacteria. Although the daily cycles of nitrogenase activity differed considerably between the two types of mats, the daily integrated rates of nitrogen fixation were the same. Moreover, the daily integrated nitrogen fixation seemed to be independent from the daily incident photon flux. The measurements further suggest that different types of diazotrophic cyanobacteria become active at different times of the day and that the composition of the mat community affects maximal and daily patterns of nitrogenase activity. Notwithstanding the apparent light independence of nitrogen fixation, the light-response curves as well as light action spectra unequivocally showed that cyanobacteria were the predominant nitrogen-fixing organisms in these mats. It is concluded that the diversity of nitrogen-fixing cyanobacteria leads to an optimization of this process.

Molecular characterization of the diversity and distribution of a thermal spring microbial community by using rRNA and metabolic genes

The diversity and distribution of a bacterial community from Coffee Pots Hot Spring, a thermal spring in Yellowstone National Park with a temperature range of 39.3 to 74.1 degrees C and pH range of 5.75 to 6.91, were investigated by sequencing cloned PCR products and quantitative PCR (qPCR) of 16S rRNA and metabolic genes. The spring was inhabited by three Aquificae genera--Thermocrinis, Hydrogenobaculum, and Sulfurihydrogenibium--and members of the Alpha-, Beta-, and Gammaproteobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, and candidate division OP5. The in situ chemical affinities were calculated for 41 potential metabolic reactions using measured environmental parameters and a range of hydrogen and oxygen concentrations. Reactions that use oxygen, ferric iron, sulfur, and nitrate as electron acceptors were predicted to be the most energetically favorable, while reactions using sulfate were expected to be less favorable. Samples were screened for genes used in ammonia oxidation (amoA, bacterial gene only), the reductive tricarboxylic acid (rTCA) cycle (aclB), the Calvin cycle (cbbM), sulfate reduction (dsrAB), nitrogen fixation (nifH), nitrite reduction (nirK), and sulfide oxidation (soxEF1) by PCR. Genes for carbon fixation by the rTCA cycle and nitrogen fixation were detected. All aclB sequences were phylogenetically related and spatially correlated to Sulfurihydrogenibium 16S rRNA gene sequences using qPCR (R(2) = 0.99). This result supports the recent finding of citrate cleavage by enzymes other than ATP citrate lyase in the rTCA cycle of the Aquificaceae family. We briefly consider potential biochemical mechanisms that may allow Sulfurihydrogenibium and Thermocrinis to codominate some hydrothermal environments.

Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon

The spatial heterogeneity of diversity and abundance of diazotrophs were investigated off the Vietnamese coast in the South China Sea (SCS). The study area extended from the Mekong River plume to the shelf region and beyond to stations extending to 1700 m depth. The SCS diazotroph community, based on nifH gene diversity, had components closely related to sequences from open ocean, estuarine, saltmarsh and microbial mat communities. Rarefaction analysis suggested that by using a 97% similarity operational taxonomic unit definition, the majority of nifH sequence diversity in the samples was covered by the 384 nifH clones obtained. The majority of the nifH sequences recovered fell into two clusters: one comprised of Trichodesmium sequences and the other an alpha-proteobacterial group. Unicellular cyanobacterial groups A and B, and symbiotic filamentous cyanobacterial diazotrophs were detected sporadically. Trichodesmium was by far the most abundant diazotroph, with up to 6 x 10(5) nifH gene copies per liter. Quantitative PCR probe-primer sets were designed and used to quantify two proteobacterial groups, revealing abundances up to 10(3)-10(4) nifH gene copies per liter, with the highest abundances in the photic zone. Major components of the clone library were also revealed by a nifH microarray and multidimensional scaling (MDS) analysis. MDS showed that samples from the >10 microm size fraction from 0- to 5-m depths clustered separately from the rest of the samples, primarily due to the abundance of Trichodesmium sequences. The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

Spatial-temporal variability in diazotroph assemblages in Chesapeake Bay using an oligonucleotide nifH microarray

The distribution of nitrogen-fixing microorganisms in the Chesapeake Bay was investigated using fingerprints from a nifH microarray comprised of 706 60-mer oligonucleotide nifH probes representing cultivated organisms and environmental clones from different nifH clusters. Diverse nifH targets, amplified from samples using degenerate nifH primers, were detected in water column and sediment samples collected in April and October, 2001-2002. Total nifH richness and diversity (Simpson's and Shannon indices) were highest at the most riverine, oligohaline North Bay station. In most samples, the highest diversity was in nifH Cluster 3, which includes many anaerobes, while Cluster 1 (alpha-, beta- gamma- Proteobacteria, Cyanobacteria) targets had the greatest microarray signal intensities. In a multidimensional scaling analysis, deep water communities from April and October were similar within each of the sampling sites, while the surface communities had more variability. Diazotroph communities in the water column in the North Bay were distinct from the Mid- and South Bay communities, and there was a gradual change in sediment diazotroph assemblages from the North to the South Bay. Diazotrophic assemblages from the majority of the water column samples from the Mid- and South Bay clustered with the sediment assemblage in Mid-Bay. Dissolved inorganic nitrogen, salinity, dissolved organic carbon and dissolved organic phosphorus had a significant relationship with the diazotrophic bacterioplankton community. Higher diversity in the freshwater end of the system may reflect variability in disturbance rates and environmental conditions such as forms and concentrations of organic matter, nutrients and oxygen.

Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts

New techniques to explore microbial diversity have led to resurgent interest in prospecting for natural products (bioprospecting or biodiscovery). Although many bioprospecting projects may share little in common at first glance, the vast majority share one particular challenge. Their targets are rare to very rare members of complex natural assemblages. Despite the advances made in bringing new organisms into cultivation and application of culture-independent techniques to isolation of novel genes there remain systematic biases against relatively rare organisms with specific growth requirements. These can frequently be overcome by application of multidisciplinary approaches that take into account principles of evolutionary ecology. Our experiences with prospecting for soluble di-iron monooxygenases (SDIMO) indicate that conventional approaches to organism isolation and metagenomic cloning systematically under-sample diversity in this enzyme family. This reflects that SDIMO-containing organisms are typically relatively low-abundance members of natural assemblages (thus biased against by direct cloning) and SDIMOs have discrete physiological roles in each organism (thus are not amenable to generic enrichment culture strategies). We have sought to overcome this by a PCR-based survey of gene diversity to guide evaluation of subsequent culture or cloning studies. A surprising outcome of this survey was that conventional PCR approaches using degenerate primers also systematically under-sampled diversity, but nested PCR strategies revealed unprecedented diversity. We conclude that many PCR-based gene-prospecting studies are likely to have under-estimated the impact of target:competitor ratios on their success.

Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean

Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.

Abundances and distributions of the dominant nifH phylotypes in the Northern Atlantic Ocean

Understanding the factors that influence the distribution and abundance of marine diazotrophs is important in order to assess their role in the oceanic nitrogen cycle. Environmental DNA samples from four cruises to the North Atlantic Ocean, covering a sampling area of 0 degrees N to 42 degrees N and 67 degrees W to 13 degrees W, were analyzed for the presence and amount of seven nifH phylotypes using real-time quantitative PCR and TaqMan probes. The cyanobacterial phylotypes dominated in abundance (94% of all nifH copies detected) and were the most widely distributed. The filamentous cyanobacterial type, which included both Trichodesmium and Katagnymene, was the most abundant (51%), followed by group A, an uncultured unicellular cyanobacterium (33%), and gamma A, an uncultured gammaproteobacterium (6%). Group B, unicellular cyanobacterium Crocosphaera, and group C Cyanothece-like phylotypes were not often detected (6.9% and 2.3%, respectively), but where present, could reach high concentrations. Gamma P, another uncultured gammaproteobacterium, was seldom detected (0.5%). Water temperature appeared to influence the distribution of many nifH phylotypes. Very high (up to 1 x 10(6) copies liter(-1)) nifH concentrations of group A were detected in the eastern basin (25 to 17 degrees N, 27 to 30 degrees W), where the temperature ranged from 20 to 23 degrees C. The highest concentrations of filamentous phylotypes were measured between 25 and 30 degrees C. The uncultured cluster III phylotype was uncommon (0.4%) and was associated with mean water temperatures of 18 degrees C. Diazotroph abundance was highest in regions where modeled average dust deposition was between 1 and 2 g/m(2)/year.

Diazotrophic bacterioplankton in a coral reef lagoon: phylogeny, diel nitrogenase expression and response to phosphate enrichment

We investigated diazotrophic bacterioplankton assemblage composition in the Heron Reef lagoon (Great Barrier Reef, Australia) using culture-independent techniques targeting the nifH fragment of the nitrogenase gene. Seawater was collected at 3 h intervals over a period of 72 h (i.e. over diel as well as tidal cycles). An incubation experiment was also conducted to assess the impact of phosphate (PO(4)3*) availability on nifH expression patterns. DNA-based nifH libraries contained primarily sequences that were most similar to nifH from sediment, microbial mat and surface-associated microorganisms, with a few sequences that clustered with typical open ocean phylotypes. In contrast to genomic DNA sequences, libraries prepared from gene transcripts (mRNA amplified by reverse transcription-polymerase chain reaction) were entirely cyanobacterial and contained phylotypes similar to those observed in open ocean plankton. The abundance of Trichodesmium and two uncultured cyanobacterial phylotypes from previous studies (group A and group B) were studied by quantitative-polymerase chain reaction in the lagoon samples. These were detected as transcripts, but were not detected in genomic DNA. The gene transcript abundance of these phylotypes demonstrated variability over several diel cycles. The PO(4)3* enrichment experiment had a clearer pattern of gene expression over diel cycles than the lagoon sampling, however PO(4)3* additions did not result in enhanced transcript abundance relative to control incubations. The results suggest that a number of diazotrophs in bacterioplankton of the reef lagoon may originate from sediment, coral or beachrock surfaces, sloughing into plankton with the flooding tide. The presence of typical open ocean phylotype transcripts in lagoon bacterioplankton may indicate that they are an important component of the N cycle of the coral reef.

Analysis of nitrogen-fixing members of the epsilon subclass of Proteobacteria in salt marsh sediments

Based on phylogenetic analysis of clones retrieved from two nifH gene clone libraries that were created using cDNA from suboxic sediment samples obtained from areas densely vegetated with the high-salt marsh plant Spartina patens, a primer set was designed to target nitrogen-fixing bacteria with sequence similarities to members of the epsilon subclass of Proteobacteria. Nested PCR, denaturing gel electrophoresis, and subsequent sequence analysis of reamplified fragments confirmed the specificity of the primer set by retrieving nifH sequences of only putative members of the epsilon subclass of Proteobacteria, all of which were characterized by a highly divergent 27- or 36-bp insertion in both DNA and cDNA.

Evolutionary trend of phylogenetic diversity of nitrogen fixation genes in the gut community of wood-feeding termites

Nitrogen fixation by gut microorganisms is one of the crucial aspects of symbiosis in wood-feeding termites since these termites thrive on a nitrogen-poor diet. In order to understand the evolution of this symbiosis, we analysed the nitrogenase structural gene nifH in the gut microbial communities. In conjunction with the published sequences, we compared approximately 320 putatively functional NifH protein sequences obtained from a total of 19 termite samples that represent all the major branches of their currently proposed phylogeny, and from one species of the cockroach Cryptocercus that shares a common ancestor with termites. Using multivariate techniques for clustering and ordination, a phylogeny of NifH protein sequences was created and plotted variously with host termite families, genera, and species. Close concordance was observed between NifH communities and the host termites at genus level, but family level relationships were not always congruent with accepted termite clade structure. Host groups examined included basal families (Mastotermitidae, Termopsidae, Kalotermitidae, as well as Cryptocercus), the most derived lower termite family Rhinotermitidae, and subfamilies representing the advanced and highly diverse apical family Termitidae (Macrotermitinae, Termitinae, and Nasutitermitinae). This selection encompassed the major nesting and feeding styles recognized in termites, and it was evident that NifH phylogenetic divergence, as well as the occurrence of alternative nitrogenase-type NifH, was to some extent dependent on host lifestyle as well as phylogenetic position.

Molecular characterization of diazotrophic and denitrifying bacteria associated with mangrove roots

An analysis of the molecular diversity of N(2) fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N(2) fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.

Low genomic diversity in tropical oceanic N2-fixing cyanobacteria

High levels of genomic and allelic microvariation have been found in major marine planktonic microbial species, including the ubiquitous open ocean cyanobacterium, Prochlorococcus marinus. Crocosphaera watsonii is a unicellular cyanobacterium that has recently been shown to be important in oceanic N2 fixation and has been reported from the Atlantic and Pacific oceans in both hemispheres, and the Arabian Sea. In direct contrast to the current observations of genomic variability in marine non-N2-fixing planktonic cyanobacteria, which can range up to >15% nucleotide sequence divergence, we discovered that the marine planktonic nitrogen-fixing cyanobacterial genus Crocosphaera has remarkably low genomic diversity, with <1% nucleotide sequence divergence in several genes among widely distributed populations and strains. The cultivated C. watsonii WH8501 genome sequence was virtually identical to DNA sequences of large metagenomic fragments cloned from the subtropical North Pacific Ocean with <1% sequence divergence even in intergenic regions. Thus, there appears to be multiple strategies for evolution, adaptation, and diversification in oceanic microbial populations. The C. watsonii genome contains multiple copies of several families of transposases that may be involved in maintaining genetic diversity through genome rearrangements. Although genomic diversity seems to be the rule in many, if not most, marine microbial lineages, different forces may control the evolution and diversification in low abundance microorganisms, such as the nitrogen-fixing cyanobacteria.

Molecular ecology of nifH genes and transcripts in the eastern Mediterranean Sea

The eastern Mediterranean Sea is one of the most extreme oligotrophic oceanic regions on earth in terms of nutrient concentrations and primary productivity. Nitrogen fixation has been suggested to contribute to the high N : P molar ratios of approximately 28:1 found in this region. Surprisingly, no molecular biological work has been performed in situ to assess whether N(2) fixation genes actually occur in the eastern Mediterranean Sea, or to determine which organisms are responsible for this process. In this study, we examined the presence and expression of nitrogenase genes (nifH) in the upper water layer of the eastern Mediterranean. Clone libraries constructed from both DNA and reverse-transcribed PCR-amplified mRNA were examined and compared. We observed different nifH genes from diverse microbial groups, such as Cyanobacteria, Proteobacteria and methanogenic Archaea. Interestingly, numerous phylotypes were observed in coastal stations at the DNA level but none were active. However, in far offshore stations, the phylotypes observed at the DNA level were the ones that were actually active. Our preliminary study revealed diverse diazotrophs that possess and express nifH genes, which may support N(2) fixation in the eastern Mediterranean Sea.

No evidence of an impact on the rhizosphere diazotroph community by the expression of Bacillus thuringiensis Cry1Ab toxin by Bt white spruce

Nitrogen fixation is one of the most important roles played by soil bacterial communities, as fixation supplies nitrogen to many ecosystems which are often N limited. As impacts on this functional group of bacteria might harm the ecosystem's health and reduce productivity, monitoring that particular group is important. Recently, a field trial with Bt white spruce, which constitutively expresses the Cry1Ab insecticidal toxin of Bacillus thuringiensis, was established. The Bt white spruce was shown to be resistant to spruce budworm. We investigated the possible impact of these genetically modified trees on soil nitrogen-fixing bacterial communities. The trial consisted of untransformed controls, GUS white spruce (transformed with the beta-glucuronidase gene), and Bt/GUS white spruce (which constitutively expresses both the Cry1Ab toxin and beta-glucuronidase) in a random design. Four years after planting, soil samples from the control and the two treatments from plantation as well as from two natural stands of white spruce were collected. Diazotroph diversity was assessed by extracting soil genomic DNA and amplifying a region of the nitrogenase reductase (nifH) gene, followed by cloning and sequencing. Analysis revealed that nitrogen-fixing communities did not differ significantly among the untransformed control, GUS white spruce, and Bt/GUS white spruce. Nevertheless, differences in diazotroph diversity were observed between white spruce trees from the plantation site and those from two natural stands, one of which grew only a few meters away from the plantation. We therefore conclude, in the absence of evidence that the presence of the B. thuringiensis cry1Ab gene had an effect on diazotroph communities, that either site and/or field preparation prior to planting seems to be more important in determining diazotroph community structure than the presence of Bt white spruce.

Isolation and gene quantification of heterotrophic N2-fixing bacterioplankton in the Baltic Sea

Cyanobacteria are regarded as the main N(2)-fixing organisms in marine waters. However, recent clone libraries from various oceans show a wide distribution of the dinitrogenase reductase gene (nifH) originating from heterotrophic bacterioplankton. We isolated heterotrophic N(2)-fixing bacteria from Baltic Sea bacterioplankton using low-nitrogen plates and semi-solid diazotroph medium (SSDM) tubes. Isolates were analysed for the nitrogenase (nifH) gene and active N(2) fixation by nested polymerase chain reaction (PCR) and acetylene reduction respectively. A primer-probe set targeting the nifH gene from a gamma-proteobacterial isolate, 97% 16S rDNA similarity to Pseudomonas stutzeri, was designed for measuring in situ dynamics using quantitative real-time PCR. This nifH gene sequence was detected at two of 11 stations in a Baltic Proper transect at abundances of 3 x 10(4) and 0.8 x 10(3) copies per litre seawater respectively. Oxygen requirements of isolates were examined by cultivation in SSDM tubes where oxygen gradients were determined with microelectrodes. Growth, and thereby N(2) fixation, was observed as horizontal bands formed at oxygen levels of 0-6% air saturation. The apparent microaerophilic or facultative anaerobic nature of the isolates explains why the SSDM approach is the most appropriate isolation method. Our study illustrates how combined isolation, functional analyses and in situ quantification yielded insights into the oxygen requirements of heterotrophic N(2)-fixing bacterioplankton isolates, which were confirmed to be present in situ.

Identification of diazotrophs in the culturable bacterial community associated with roots of Lasiurus sindicus, a perennial grass of Thar Desert, India

Lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the Thar Desert of Rajasthan, India. Analysis of 16S rRNA coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of L. sindicus, showed predominance of Gram-negative over Gram-positive bacteria. According to comparative sequence analysis of 16S rDNA sequence data, Gram-positive bacteria with low GC content (Staphylococcus warneri and Bacillus sp.) and high GC content (Micrococcus luteus, Microbacterium sp.) were identified. Gram-negative bacteria included Azospirillum sp., Rhizobium sp., Agrobacterium tumefaciens, and Inquilinus limosus (alpha-proteobacteria); Ralstonia sp., Variovorax paradoxus, and Bordetella petrii (beta-proteobacteria); and Pseudomonas pseudoalcaligenes, Stenotrophomonas sp. (gamma-proteobacteria). The occurrence of nifH sequences in Azospirillum sp., Rhizobium sp., and P. pseudoalcaligenes showed the possibility of supplying biologically fixed nitrogen by the root-associated diazotrophs to the host plant.

Development of a PCR for the detection and identification of cyanobacterial nifD genes

In this study we have designed degenerate primers after comparative analysis of nifD gene sequences from public databases, and developed a PCR protocol for the amplification of nifD sequences from cyanobacteria. The primers were tested on a variety of nitrogenase-containing and nitrogenase-lacking bacteria. By using this protocol, we amplified nifD sequences from DNA that was isolated from three phototrophic microbial communities. Denaturing gradient gel electrophoresis (DGGE) and clone library analysis of the nifD amplicons showed the presence of distinct groups of diazotrophic cyanobacteria in each of the investigated microbial communities. Phylogenetic trees constructed from the sequences of nifD gene fragments are congruent with those based on ribosomal RNA gene sequences.

On the issue of limiting nutrient and predictions of cyanobacteria in aquatic systems

This study aims at bridging the gap between freshwater and marine eutrophication studies by presenting (1) a cross-system analysis of the relationship between chlorophyll and the total nitrogen (TN) to total phosphorus (TP) ratio (2) a general model to predict concentrations of cyanobacteria from data on TP, the TN/TP ratio, salinity and temperature, and (3) a general trophic level classification for aquatic systems based on chlorophyll classes (for oligo-, meso-, eu- and hypertrophic systems). The data compiled in this study concerns more than 500 lakes and coastal areas covering a very wide domain in terms of nutrient concentrations and salinity. There was no simple relationship between the TN/TP ratio and empirical chlorophyll concentrations or concentrations of cyanobacteria. Variations in TP rather than TN generally seem to be more important to predict variations among systems in chlorophyll-a and cyanobacteria. Different "bioavailable" forms of the nutrients (DIN, DIP, phosphate, nitrate, etc.) have been shown to have very high coefficients of variation (CV), which means that many samples are needed to obtain reliable empirical data which are necessary in models aiming for high predictive power and practical usefulness.

Nitrogenase gene expression in the Chesapeake Bay Estuary

Like many estuaries, the Chesapeake Bay has pronounced gradients in salinity and nutrients. Previous studies have shown that there is a high diversity of nitrogenase (nifH) genes in the estuary, and that there are specific distributions of individual nifH phylotypes. In contrast to previous work that revealed the remarkable diversity of nifH phylotypes in the Chesapeake estuary, in this study of nifH expression we only detected two phylotypes, and both were phylogenetically related to cyanobacterial nifH genes. One of the phylotypes was closely related to a nifH sequence from the filamentous, heterocystous cyanobacterium Anabaena cylindrica, and was found at the head of the estuary. The other phylotype was found in a sample collected near the mouth of the estuary and was closely related to nifH sequences from Group A unicellular cyanobacteria, which has previously been reported in oceanic waters only. These nifH phylotypes had distinct patterns of expression that were restricted to different regions of the Chesapeake Bay. This study provides the first evidence of nifH expression in the Chesapeake Bay, and suggests that diazotrophic unicellular cyanobacteria have a broader distribution and activity than previously recognized.

Nitrogen fixation by reductively dechlorinating bacteria

Significant advances in the ecology, physiology and genetics of reductively dechlorinating bacteria have revealed their important environmental roles in bioremediation and in the global chlorine cycle. N2 fixation has been widely observed in symbiotic, associative and free-living bacteria. Here we show physiological and molecular evidence that reductively dechlorinating bacteria are capable of fixing atmospheric nitrogen. Furthermore, N2 fixation in some of these dechlorinating bacteria stimulated reductive dechlorination, which should help predict and regulate the environmental function of dechlorinating bacteria in in situ bioremediation of chlorinated pollutants. These results imply that N2 fixation in dechlorinating bacteria interacts with other biogeochemical cycles to control the nitrogen status of the anaerobic ecosystem.

A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms

Nitrogen fixation is an important process in biogeochemical cycles exclusively carried out by prokaryotes, mostly by an evolutionarily conserved nitrogenase protein complex, of which one of the structural genes (nifH) is highly valuable for phylogenetic and diversity analyses. We developed a nifH-based short oligonucleotide microarray (nifH diagnostic microarray) as a rapid tool to effectively monitor nitrogen-fixing diazotrophic populations in a wide range of environments. Taking account of the overwhelming predominance of environmental nifH fragments from uncultivated microorganisms in public databases, our nifH microarray is mainly based on nifH sequences from as yet unidentified prokaryotes. Standard conditions for microarray performance were determined, and criteria for the design of specific oligonucleotides were defined. A primary set of 56 oligonucleotides was validated with fluorescence-labeled single-stranded nifH targets from five reference strains, 26 environmental clones, and artificial mixtures of reference strains. The nifH microarray was applied to analyze the diversity (based on DNA) and activity (based on mRNA) of diazotrophs in roots of wild rice samples from Namibia. Results demonstrated that only a small subset of diazotrophs being present in the sample were actually fixing nitrogen actively. Our data suggest that the developed nifH microarray is a highly reproducible and semiquantitative method for mapping the variability of diazotrophic diversity, allowing rapid comparisons of the relative abundance and activity of diazotrophic prokaryotes in the environment. A further refined nifH microarray comprising of 194 oligonucleotide probes now covers more than 90% of sequences in our nifH database.

Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil

Biological nitrogen fixation is a fundamental component of the nitrogen cycle and is the dominant natural process through which fixed nitrogen is made available to the biosphere. While the process of nitrogen fixation has been studied extensively with a limited set of cultivated isolates, examinations of nifH gene diversity in natural systems reveal the existence of a wide range of noncultivated diazotrophs. These noncultivated diazotrophs remain uncharacterized, as do their contributions to nitrogen fixation in natural systems. We have employed a novel 15N2-DNA stable isotope probing (5N2-DNA-SIP) method to identify free-living diazotrophs in soil that are responsible for nitrogen fixation in situ. Analyses of 16S rRNA genes from 15N-labeled DNA provide evidence for nitrogen fixation by three microbial groups, one of which belongs to the Rhizobiales while the other two represent deeply divergent lineages of noncultivated bacteria within the Betaproteobacteria and Actinobacteria, respectively. Analysis of nifH genes from 15N-labeled DNA also revealed three microbial groups, one of which was associated with Alphaproteobacteria while the others were associated with two noncultivated groups that are deeply divergent within nifH cluster I. These results reveal that noncultivated free-living diazotrophs can mediate nitrogen fixation in soils and that 15N2-DNA-SIP can be used to gain access to DNA from these organisms. In addition, this research provides the first evidence for nitrogen fixation by Actinobacteria outside of the order Actinomycetales.

Prokaryotic life in a potash-polluted marsh with emphasis on N-metabolizing microorganisms

Prokaryotic life along the salt gradient of the potash marsh resulting from mining waste at Schreyahn, Northern Germany, was screened for the distribution of total prokaryote (assessed by the 16S rRNA gene) and of N2-fixing (nifH gene), denitrifying (nosZ) and nitrifying (amoA) microorganisms. Information on prokaryotes was retrieved from the different soil sites (a) by culturing in conventional media, (b) by isolating the DNA, amplifying the target genes by PCR followed by sequencing, (c) by employing the recently developed computer program (TReFID [Rösch, C., Bothe, H., 2005. Improved assessment of denitrifying, N2-fixing, and total-community bacteria by terminal restriction fragment length polymorphism analysis using multiple restriction enzymes. Applied and Environmental Microbiology 71, 2026-2035]) based on tRFLP data. New sequences were obtained as well as ones that were almost identical to those found at far distant locations. Whereas the distribution of plants strictly follows the salt gradient, this is apparently not the case with prokaryotes. Bacteria of hypersaline areas coexist with salt-non-tolerant species. The recently developed TReFID program is successfully applied to characterize a prokaryote community structure.

Rhizosphere-bacterial community in Eperua falcata (Caesalpiniaceae) a putative nitrogen-fixing tree from French Guiana rainforest

The rainforest of French Guiana is still largely unaffected by human activity. Various pristine sites like the Paracou Research Station are devoted to study this tropical ecosystem. We used culture-independent techniques, like polymerase chain reaction-temperature gradient gel electrophoresis, and construction of clone libraries of partial 16S rRNA and nifH genes, to analyze the composition of the bacterial community in the rhizosphere of mature trees of Eperua falcata and Dicorynia guianensis, both species within the Caesalpiniaceae family. E. falcata is one of the more abundant pioneer tree species in this ecosystem and so far, no root nodules have ever been found. However, its nitrogen-fixing status is regarded as "uncertain", whereas D. guianensis is clearly considered a non-nitrogen-fixing plant. The rhizospheres of these mature trees contain specific bacterial communities, including several currently found uncultured microorganisms. In these communities, there are putative nitrogen-fixing bacteria specifically associated to each tree: D. guianensis harbors several Rhizobium spp. and E. falcata members of the genera Burkholderia and Bradyrhizobium. In addition, nifH sequences in the rhizosphere of the latter tree were very diverse. Retrieved sequences were related to bacteria belonging to the alpha-, beta-, and gamma-Proteobacteria in the E. falcata rhizoplane, whereas only two sequences related to gamma-Proteobacteria were found in D. guianensis. Differences in the bacterial communities and the abundance and diversity of nifH sequences in E. falcata rhizosphere suggest that this tree could obtain nitrogen through a nonnodulating bacterial interaction.

Diversity and expression of nitrogenase genes (nifH) from ectomycorrhizas of Corsican pine (Pinus nigra)

The diversity of bacterial nitrogenase genes (nifH) and their mRNA transcription in ectomycorrhizas of Corsican pine (Pinus nigra) were examined. DNA and RNA were extracted from surface-sterilized and non-sterilized Corsican pine roots colonized by the ectomycorrhizal (ECM) fungi, Suillus variegatus and Tomentellopsis submollis. DNA-derived nifH polymerase chain reaction (PCR) products were obtained from all samples, but only a few reverse transcription PCRs for nifH mRNA were successful, suggesting that nitrogenase genes were not always transcribed. Several different nifH sequences were detected and the bacteria actively transcribing nifH were different from those whose genes were detected through DNA-based PCR. Putative nitrogenase amino acid sequences revealed that more than half of the nifH products were derived from methylotrophic bacteria, such as Methylocella spp. The next most frequent sequence types were similar to those from Burkholderia.

Toxic effects of acetochlor, methamidophos and their combination on nifH gene in soil

Toxic effects of two agrochemicals on nifH gene in agricultural black soil were investigated using denaturing gradient gel electrophoresis (DGGE) and sequencing approaches in a microcosm experiment. Changes of soil nifH gene diversity and composition were examined following the application of acetochlor, methamidophos and their combination. Acetochlor reduced the nifH gene diversity (both in gene richness and diversity index values) and caused changes in the nifH gene composition. The effects of acetochlor on nifH gene were strengthened as the concentration of acetochlor increased. Cluster analysis of DGGE banding patterns showed that nifH gene composition which had been affected by low concentration of acetochlor (50 mg/kg) recovered firstly. Methamidophos reduced nifH gene richness that except at 4 weeks. The medium concentration of methamidophos (150 mg/kg) caused the most apparent changes in nifH gene diversity at the first week while the high concentration of methamidophos (250 mg/kg) produced prominent effects on nifH gene diversity in the following weeks. Cluster analysis showed that minimal changes of nifH gene composition were found at 1 week and maximal changes at 4 weeks. Toxic effects of acetochlor and methamidophos combination on nifH gene were also apparent. Different nifH genes (bands) responded differently to the impact of agrochemicals: four individual bands were eliminated by the application of the agrochemicals, five bands became predominant by the stimulation of the agrochemicals, and four bands showed strong resistance to the influence of the agrochemicals. Fifteen prominent bands were partially sequenced, yielding 15 different nifH sequences, which were used for phylogenetic reconstructions. All sequences were affiliated with the alpha- and beta-proteobacteria, showing higher similarity to eight different diazotrophic genera.

Archaeal diversity and community structure in a Swedish barley field: Specificity of the EK510R/(EURY498) 16S rDNA primer

The aim of this study was to analyze a total euryarchaeal community at DNA and RNA levels in a Swedish barley field with relation to soil depth (0-10 and 20-30 cm layers), soil fraction (bulk soil and rhizosphere) and time (August and November sample collection). Amplification of 16S rRNA gene using the archaeal universal A2F and Euryarchaea specific EK510R/(EURY498) primer pair, combined with denaturing gradient gel electrophoresis (DGGE), revealed distinct differences between rDNA and rRNA DGGE profiles. The soil depth, time, or rhizosphere effects did not significantly influence Archaeal community structure. Surprisingly, sequence analysis of DGGE-derived amplicons revealed the presence of Euryarchaea as well as uncultured soil Crenarchaea affiliated with group 1. In agreement, sequence comparison analyses showed that the majority of uncultured Crenarchaea group 1 had almost 100% sequence complementarity to the 3' end of the EK510R/(EURY498) primer. Therefore, we propose that EK510R/(EURY498R) is a universal archaeal primer rather than a Euryarchaea specific SSUrRNA primer. Hence, considerable care should be taken during application of this primer in studies of euryarchaeal biodiversity in soil environments.

Genotypic and phenotypic diversity of cyanobacteria assigned to the genus Phormidium (Oscillatoriales) from different habitats and geographical sites

In this study, 30 strains of filamentous, non-heterocystous cyanobacteria from different habitats and different geographical regions assigned to diverse oscillatorian genera but here collectively referred to as members of the Phormidium group have been characterized using a polyphasic approach by comparing phenotypic and molecular characteristics. The phenotypic analysis dealt with cell and filament morphology, ultrastructure, phycoerythrin content, and complementary chromatic adaptation. The molecular phylogenetic analyses were based on sequences of the 16S rRNA gene and the adjacent intergenic transcribed spacer (ITS). The sequences were located on multiple branches of the inferred cyanobacterial 16S rRNA tree. For some, but not all, strains with identical 16S rDNA sequences, a higher level of discrimination was achieved by analyses of the less conserved ITS sequences. As shown for other cyanobacteria, no correlation was found between position of the strains in the phylogenetic tree and their geographic origin. Genetically similar strains originated from distant sites while other strains isolated from the same sampling site were in different phylogenetic clusters. Also the presence of phycoerythrin was not correlated with the strains' position in the phylogenetic trees. In contrast, there was some correlation among inferred phylogenetic relationship, original environmental habitat, and morphology. Closely related strains came from similar ecosystems and shared the same morphological and ultrastructural features. Nevertheless, structural properties are insufficient in themselves for identification at the genus or species level since some phylogenetically distant members also showed similar morphological traits. Our results reconfirm that the Phormidium group is not phylogenetically coherent and requires revision.

Characterization of diatom-cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences

Richelia intracellularis is a symbiotic heterocystous cyanobacterium that is capable of forming associations with several genera of diatoms. nifH, 16S rRNA and hetR sequences were amplified and cloned from field populations of Richelia associated with Hemiaulus hauckii (N. Atlantic), with Rhizosolenia clevei (N. Pacific), and from a cultivated isolate of Calothrix associated with Chaetoceros from station ALOHA (N. Pacific). Sequence identity was highest (98.2%) among the 16S rRNA sequences, and more divergent for the hetR (83.8%) and nifH (91.1%) sequences. The hetR and nifH DNA and amino acid sequences obtained from the symbionts associated with the three different diatom genera diverged into three separate lineages supported by high bootstrap values. The data indicate that symbionts in the different hosts are distinct species or strains. Furthermore, three previously unidentified heterocystous-like nifH sequence groups recently reported from station ALOHA in the subtropical Pacific, het-1, het-2 and het-3, were linked to Richelia associated with R. clevei, H. hauckii and the Calothrix symbiont of Chaetoceros sp. respectively.

Study of nitrogen fixation in microbial communities of oil-contaminated marine sediment microcosms

Aerobic microbial degradation of pollutant oil (petroleum) in aquatic environments is often severely limited by the availability of combined nitrogen. We therefore studied whether the microbial community enriched in marine sediment microcosms with an added oil layer and exposure to light harboured nitrogenase activity. The acetylene reduction (AR) assay indeed indicated active nitrogenase; however, similar activity was observed in oil-free control microcosms. In both microcosms, the AR rate was significantly reduced upon a dark shift, indicating that enriched cyanobacteria were the dominant diazotrophs. Analysis of structural dinitrogenase reductase genes (nifH) amplified from both microcosms indeed revealed NifH sequences related mostly to those of heterocystous cyanobacteria. NifH sequences typically affiliating with those of heterotrophic bacteria were more frequently retrieved from the oil-containing sediment. Expression analyses showed that mainly nifH genes similar to those of heterocystous cyanobacteria were expressed in the light. Upon a dark shift, nifH genes related to those of non-heterocystous cyanobacteria were expressed. Expression of nifH assignable to heterotrophs was apparently not significant. It is concluded that cyanobacteria are the main contributors of fixed nitrogen to oil-contaminated and pristine sediments if nitrogen is a limiting factor and if light is available. Hence, also the oil-degrading heterotrophic community may thus receive a significant part of combined nitrogen from cyanobacteria, even though oil vice versa apparently does not stimulate an additional nitrogen fixation in the enriched community.

Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats

Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety-six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7-month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.

The rice field cyanobacteria Anabaena azotica and Anabaena sp. CH1 express vanadium-dependent nitrogenase

Anabaena azotica FACHB-118 and Anabaena sp. CH1, heterocystous cyanobacteria isolated from Chinese and Taiwanese rice fields, expressed vanadium-containing nitrogenase when under molybdenum deficiency. This is the second direct observation of an alternative nitrogenase in cyanobacteria. The vanadium nitrogenase-specific genes vnfDG are fused and clustered in a phylogenetic tree next to the corresponding genes of Methanosarcina. The expression of vnfH in cells cultured in Mo-free medium and of nifH in Mo-grown cells was shown for the first time by sequencing cDNA derived from cultures of A. azotica and Anabaena sp. CH1. The vnfH sequences clustered with that of Anabaena variabilis. The vnf genes were strongly transcribed only in cultures grown either in Mo-free medium, or in W-containing medium, but also weakly in Mo-containing medium. NifH was transcribed in all media. On-line measurements of acetylene reduction by Mo-free A. azotica cultures demonstrated that the V-nitrogenase was active. Ethane was formed continuously at a rate of 2.1% of that of ethylene. Acetylene reduction of cultures grown either with or without Mo had a high temperature optimum of 42.5 degrees C. The uptake hydrogenase gene hupL was expressed in Mo-free medium concomitantly with vnfDG in A. azotica, Anabaena sp. CH1, and A. variabilis.