Carbon isotopic composition of Trichodesmium spp. colonies off Bermuda: effects of colony mass and season

Colonies of Trichodesmium spp. are conspicuous, macroscopiccomponents of the life in tropical and subtropical oceans. Thelarge size and the morphology of the colony raise questionsregarding the mechanism of carbon supply for photosynthesis.Constraints on these mechanisms may be indicated by the stablecarbon isotopic composition (¹³C) that reflects the balancebetween carbon supply and speciation, as well as the growthrate and colony size. The ¹³C of Trichodesmium off Bermuda measuredhere revealed a strong correlation between size of individualcolonies and season. The smallest colonies, 2–7 µgC colony^–1, showed the lightest ¹³C composition (–19),increasing to asymptotic values of –12 above 7 µgC colony^–1. The average ¹³C of the colonies was lightestimmediately after the onset of stratification in the SargassoSea, gradually increasing by 4 to heavier values during thesummer. We propose that the mass effect is due to increaseduse of HCO₃^– by the larger colonies, whereas the seasonalinfluence may be related to changes in irradiance and pCO₂ affectingthe internal carbon cycling.     

Glutamine synthetase and nitrogen cycling in colonies of the marine diazotrophic cyanobacteria Trichodesmium spp.

We examined freshly collected samples of the colonial planktonic cyanobacterium Trichodesmium thiebautii to determine the pathways of recently fixed N within and among trichomes. High concentrations of glutamate and glutamine were found in colonies. Glutamate and glutamine uptake rates and concentrations in cells were low in the early morning and increased in the late morning to reach maxima near midday; then uptake and concentration again fell to low values. This pattern followed that previously observed for T. thiebautii nitrogenase activity. Our results suggest that recently fixed nitrogen is incorporated into glutamine in the N2-fixing trichomes and may be passed as glutamate to non-N2-fixing trichomes. The high transport rates and concentrations of glutamate may explain the previously observed absence of appreciable uptake of NH4+, NO3-, or urea by Trichodesmium spp. Immunolocalization, Western blots (immunoblots), and enzymatic assays indicated that glutamine synthetase (GS) was present in all cells during both day and night. GS appeared to be primarily contained in cells of T. thiebautii rather than in associated bacteria or cyanobacteria. Double immunolabeling showed that cells with nitrogenase (Fe protein) contained levels of the GS protein that were twofold higher than those in cells with little or no nitrogenase. GS activity and the uptake of glutamine and glutamate dramatically decreased in the presence of the GS inhibitor methionine sulfoximine. Since no glutamate dehydrogenase activity was detected in this species, GS appears to be the primary enzyme responsible for NH3 incorporation.     

Glutamine synthetase and nitrogen cycling in colonies of the marine diazotrophic cyanobacteria Trichodesmium spp.

We examined freshly collected samples of the colonial planktonic cyanobacterium Trichodesmium thiebautii to determine the pathways of recently fixed N within and among trichomes. High concentrations of glutamate and glutamine were found in colonies. Glutamate and glutamine uptake rates and concentrations in cells were low in the early morning and increased in the late morning to reach maxima near midday; then uptake and concentration again fell to low values. This pattern followed that previously observed for T. thiebautii nitrogenase activity. Our results suggest that recently fixed nitrogen is incorporated into glutamine in the N2-fixing trichomes and may be passed as glutamate to non-N2-fixing trichomes. The high transport rates and concentrations of glutamate may explain the previously observed absence of appreciable uptake of NH4+, NO3-, or urea by Trichodesmium spp. Immunolocalization, Western blots (immunoblots), and enzymatic assays indicated that glutamine synthetase (GS) was present in all cells during both day and night. GS appeared to be primarily contained in cells of T. thiebautii rather than in associated bacteria or cyanobacteria. Double immunolabeling showed that cells with nitrogenase (Fe protein) contained levels of the GS protein that were twofold higher than those in cells with little or no nitrogenase. GS activity and the uptake of glutamine and glutamate dramatically decreased in the presence of the GS inhibitor methionine sulfoximine. Since no glutamate dehydrogenase activity was detected in this species, GS appears to be the primary enzyme responsible for NH3 incorporation.     

Characterization of Trichodesmium spp. by genetic techniques

The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus TRICHODESMIUM: The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of KATAGNYMENE: Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.     

Characterization of Trichodesmium spp. by Genetic Techniques

The genetic diversity of Trichodesmium spp. from natural populations (off Bermuda in the Sargasso Sea and off North Australia in the Arafura and Coral Seas) and of culture isolates from two regions (Sargasso Sea and Indian Ocean) was investigated. Three independent techniques were used, including a DNA fingerprinting method based on a highly iterated palindrome (HIP1), denaturing gradient gel electrophoresis of a hetR fragment, and sequencing of the internal transcribed spacer (ITS) of the 16S-23S rDNA region. Low genetic diversity was observed in natural populations of Trichodesmium spp. from the two hemispheres. Culture isolates of Trichodesmium thiebautii, Trichodesmium hildebrandtii, Trichodesmium tenue, and Katagnymene spiralis displayed remarkable similarity when these techniques were used, suggesting that K. spiralis is very closely related to the genus Trichodesmium. The largest genetic variation was found between Trichodesmium erythraeum and all other species of Trichodesmium, including a species of Katagnymene. Our data obtained with all three techniques suggest that there are two major clades of Trichodesmium spp. The HIP1 fingerprinting and ITS sequence analyses allowed the closely related species to be distinguished. This is the first report of the presence of HIP1 in marine cyanobacteria.     

Experimental design and quantitative analysis of microbial community multiomics

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.     

Large-scale latitudinal distribution of Trichodesmium spp. in the Atlantic Ocean

The Atlantic Meridional Transect (AMT) programme is a seriesof bi-annual cruises between the Falkland Islands (50°S)and the UK (50°N). Measurements of the abundance of theN₂-fixing, colonial cyanobacterium Trichodesmium along thistransect in the years 1995–1999 reveal that it is especiallyabundant between 0 and 15°N, but by contrast almost completelyabsent between 5 and 30°S. The cruise path between 0 and15°N lies close to 20°W, on the African (eastern) sideof the Atlantic. The maximum colony abundances we observed (     

Organization of a parasitoid community associated with a complex of galls on Atriplex spp. in southern California

Abstract. 1. Atriplex canescens (Pursh) Nuttall and A.polycarpa (Torrey) Watson (Chenopodiaceae) support twelve morphologically distinct gall types in southern California. Thirty-seven common species of parasitoids, predators and inquilines are associated with these galls. 2. The galls incited by eight members of the Asphondylia atriplicis Cockerell (Diptera: Cecidomyiidae) species complex are linked into a single, interacting community through shared hymenopterous parasitoids and inquilines. 3. Cluster analysis (UPGMA) grouped the fifteen most common species of Chalcidoidea into three host guilds of five species each: (1) specialists in tumour stem and blister leaf galls on A.canescens, (2) specialists in woolly stem galls on A.poiycarpa, and (3) generalists that attack all galls. Guild 1 dominated the galls with which it was primarily associated, while guild 3 dominated the remainder. 4. The abundances of the parasitoids of the tumour stem and blister leaf galls were negatively correlated with the abundances of two organizer species, a gall-forming inquiline, Tetrastichus cecidobroter Gordh and Hawkins, and an internal, larval—pupal parasitoid, Tetrastichus sp. B. The abundances of nine of the twelve most common chalcidoids were not correlated with the abundances of all coaccurring species in six other galls. 5. Host seasonality partly determines parasitoid population dynamics and guild structure. Parasitoid dominance increased with gall duration, suggesting that parasitoid competition depends on resource stability. The two continuously available galls were dominated by their specialist guild, while all seasonal galls were dominated by generalists. The subdominant specialists of woolly stem galls may represent competitively inferior species that utilize those galls opportunistically, because of the gall's widespread distribution and 9–10 month yearly availability. 6. Sites in the Colorado Desert and chaparral that supported several gall types showed stable relative abundances of the major parasitoid species, whereas sites in the Mojave Desert that supported only woolly stem galls had unpredictable parasitoid species assemblages. 7. The competitive success of Atriplex gall parasitoids may depend primarily on voltinism (multivoltine species dominated univoltine species) and mode of feeding (phytophagous, mixed entomophagous—phytophagous and facultatively hyperparasitic species in general dominated strict primary parasitoids).     

Molecular analysis of the phosphorus starvation response in Trichodesmium spp.

The marine diazotroph Trichodesmium is a major contributor to primary production and nitrogen fixation in the tropical and subtropical oceans. These regions are often characterized by low phosphorus (P) concentrations, and P starvation of Trichodesmium could limit growth, and potentially constrain nitrogen fixation. To better understand how this genus responds to P starvation we examined four genes involved in P acquisition: two copies of a high-affinity phosphate binding protein ( pstS and sphX ) and two putative alkaline phosphatases ( phoA and phoX ). Sequence analysis of these genes among cultured species of Trichodesmium ( T. tenue, T. erythraeum, T. thiebautii and T. spiralis ) showed that they all are present and conserved within the genus. In T. erythraeum IMS101, the expression of sphX , phoA and phoX were sensitive to P supply whereas pstS was not. The induction of alkaline phosphatase activity corresponded with phoA and phoX expression, but enzyme activity persisted after the expression of these genes returned to basal levels. Additionally, nifH (nitrogenase reductase; involved in nitrogen fixation) expression was downregulated under P starvation conditions. These data highlight molecular level responses to low P and lay a foundation for better understanding the dynamics of Trichodesmium P physiology in low-P environments.     

The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession

Soluble microbial products (SMP) are organic compounds produced by activated sludge microorganisms as they degrade substrates. They include by-products of microbial activity, death and lysis. The available literature does not reveal how SMP influence microbial community composition. In this regard, we microscopically studied changes in composition of microbial communities, especially protozoa and metazoa, under the influence of increased as well as reduced levels of SMP. The presence of SMP at high level significantly caused changes in microbial community composition. Microbial species shifted from attached ciliates (12-175 microm) to free-swimming and crawling ciliates (35-330 microm) and then invertebrates, which included rotifers (0.2-1 mm) and nematodes (1-50 mm). The shift of small-size microorganisms to large ones was observed as one of the most significant influences of SMP. Attached ciliates reappeared when we removed the SMP that had accumulated in the bioreactors - we have called this as the resurrection phenomenon of microorganisms. Such rapid changes in microbial community composition were not observed in the experiment with low concentration of SMP. Overall, the results suggest that accumulation of SMP is one of the intrinsic regulatory mechanisms that control viability and dormancy of microbial communities in activated sludge.     

The nitrogen physiology of the marine N2-fixing cyanobacteria Trichodesmium spp

Trichodesmium spp. have proved to be enigmatic organisms, and their ecology and physiology are unusual among diazotrophs. Recent research shows that they can simultaneously fix N2 and take up combined nitrogen. The co-occurrence of these two processes is thought to be incompatible, but they could be obligatory in Trichodesmium spp. if only a small fraction of cells within a colony or along a filament are capable of N2 fixation. Combined nitrogen is released from cells during periods of active growth and N2 fixation, and concomitantly taken up by Trichodesmium spp. or cells living in association with colonies. Although the nitrogenase of Trichodesmium spp. is affected by high concentrations of combined nitrogen, it might be relatively less sensitive to low concentrations of combined nitrogen typical of the oligotrophic ocean and culture conditions. Nitrogenase activity and synthesis exhibits an endogenous rhythm in Trichodesmium spp. cultures, which is affected by the addition of nitrogen.     

Epidemiological survey of Giardia spp. and Blastocystis hominis in an Argentinian rural community

The aim of this study was to relate personal data, socio-cultural and environmental characteristics, and the presence of symptoms/signs with the frequencies of Giardia spp. and Blastocystis hominis among a rural population in Buenos Aires Province, Argentina. Of the surveyed population (350), 3.7% were infected with only Giardia spp. or 22.9% with B. hominis, and 2.3% were infected with both protozoa. The frequency of infection according to sex; 6.1% of males were infected and 1.6% of females by Giardia spp., 26.7% and 19.5% by B. hominis, and 2.4% and 2.2% by both parasites, respectively. Giardia spp. was detected in only three adults (over 14 years), but B. hominis was more frequent in adults than in children. The prevalences of these protozoa in this community are lower than those reported by other Argentinean studies, which is probably associated with the low density of the studied population (5.95 inhab/km2). Statistical analysis revealed that a male sex, flooding of the home, the use of a latrine, and an abdominal pain were correlated with the presence of these parasites, which indicate the importance of these factors in rural communities.     

Whole-Cell Immunolocalization of Nitrogenase in Marine Diazotrophic Cyanobacteria, Trichodesmium spp.

The mechanism by which planktonic marine cyanobacteria of the genus Trichodesmium fix N₂ aerobically during photosynthesis without heterocysts is unknown. As an aid in understanding how these species protect nitrogenase, we have developed an immunofluorescence technique coupled to light microscopy (IF-LM) with which intact cyanobacteria can be immunolabeled and the distribution patterns of nitrogenase and other proteins can be described and semiquantified. Chilled ethanol was used to fix the cells, which were subsequently made permeable to antibodies by using dimethyl sulfoxide. Use of this technique demonstrated that about 3 to 20 cells (mean ± standard deviation, 9 ± 4) consecutively arranged in a Trichodesmium trichome were labeled with the nitrogenase antibody. The nitrogenase-containing cells were distributed more frequently around the center of the trichome and were rarely found at the ends. On average 15% of over 300 randomly encountered cells examined contained nitrogenase. The percentage of nitrogenase-containing cells (nitrogenase index [NI]) in an exponential culture was higher early in the light period than during the rest of the light-dark cycle, while that for a stationary culture was somewhat constant at a lower level throughout the light-dark cycle. The NI was not affected by treatment of the cultures with the photosynthetic inhibitor dichloro 1,3′-dimethyl urea or with low concentrations of ammonium (NH₄Cl). However, incubation of cultures with 0.5 μM NH₄Cl over 2 days reduced the NI. The IF technique combined with ¹⁴C autoradiography showed that the CO₂ fixation rate was lower in nitrogenase-containing cells. The results of the present study suggest that (i) the IF-LM technique may be a useful tool for in situ protein localization in cyanobacteria, (ii) cell differentiation occurs in Trichodesmium and only a small fraction of cells in a colony have the potential to fix nitrogen, (iii) the photosynthetic activity (CO₂ uptake) is reduced if not absent in N₂-fixing cells, and (iv) variation in the NI may be a modulator of nitrogen-fixing activity.     

Analysis of a microbial community associated with polychlorinated biphenyl degradation in anaerobic batch reactors

The degradation of polychlorinated biphenyls (PCBs) was investigated under fermentative-methanogenic conditions for up to 60 days in the presence of anaerobic biomass from a full-scale UASB reactor. The low methane yields in the PCBs-spiked batch reactors suggested that the biomass had an inhibitory effect on the methanogenic community. Reactors containing PCBs and co-substrates (ethanol/sodium formate) exhibited substantial PCB reductions from 0.7 to 0.2 mg mL^?1. For the Bacteria domain, the PCBs-spiked reactors were grouped with the PCB-free reactors with a similarity of 55 %, which suggested the selection of a specific population in the presence of PCBs. Three genera of bacteria were found exclusively in the PCB-spiked reactors and were identified using pyrosequencing analysis, Sedimentibacter, Tissierela and Fusibacter. Interestingly, the Sedimentibacter, which was previously correlated with the reductive dechlorination of PCBs, had the highest relative abundance in the R_CS-PCB (7.4 %) and R_CS-PCB-PF (12.4 %) reactors. Thus, the anaerobic sludge from the UASB reactor contains bacteria from the Firmicutes phylum that are capable of degrading PCBs.     

Ultrastructural characterisation of cells specialised for nitrogen fixation in a non-heterocystous cyanobacterium,Trichodesmium spp.

Summary Trichodesmium is the first described example of a filamentous cyanobacterium without heterocysts that contains cells specialised for nitrogen fixation. The ultrastructure of cells with and without nitrogenase were compared using primarilyTrichodesmium tenue Wille, but alsoT. thiebautii Gomont andT. erythraeum Ehrenberg et Gomont. Immunohistochemistry demonstrated that the cytoplasm of certain cells was densely labelled with antibodies against Fe-protein (dinitrogenase reductase). Comparative TEM-image analysis revealed that these cells were also distinguished by a denser thylakoid network, dividing the vacuole-like space into smaller units. The nitrogenase-containing cells also exhibited less extensive gas vacuoles as well as fewer and smaller cyanophycin granules compared to cells which lacked nitrogenase. Carboxysomes were present in both cell types in equal proportion. Longitudinal sections showed that cells with nitrogenase were arranged adjacent to each other, and that groups of cells with and without nitrogenase may coexist in the same trichome. The correlation between modifications in ultrastructure and the presence of nitrogenase suggests a new type of cyanobacterial cell specialisation related to nitrogen fixation. The results obtained also question the systematic affiliation of the genusTrichodesmium.     

Evidence for seafloor microbial mats and associated metazoan lifestyles in Lower Cambrian phosphorites of Southwest China

The increase in the depth and intensity of bioturbation through the Proterozoic-­Phanerozoic transition changed the substrates on which marine benthos lived from being relatively firm with a sharp sediment-water interface to having a high water content and blurry sediment-water interface. Additionally, microbial mats, once dominant on normal marine Proterozoic seafloors, were relegated to stressed settings lacking intense metazoan activity. This change in substrates has been termed the 'agronomic revolution', and its impact on benthic metazoans has been termed the 'Cambrian substrate revolution'. The shallow marine phosphorites of the Lower Cambrian Meishucun Formation of southwest China contain evidence suggestive of the presence of seafloor microbial mats. This evidence includes abundant and distinctive red-colored bedding planes enriched in heavy iron minerals and mica, interpreted as resulting from mat-decay mineralization and mica trapping by microbial mats. The radular grazing trace fossil Radulichnus is also found in this formation, indicating a firm, microbial mat-bound substrate. These radular scratches are always preserved with circular impressions around 10 cm in diameter, possibly the fossils of soft-bodied organisms. The first relatively intense bioturbation in this region is found in this formation and is dominated by horizontal Thalassinoides burrows, which could represent undermat mining behavior. The evidence for the presence of microbial mats in the Lower Cambrian Meishucun Formation, and for metazoan lifestyles associated with such mat-bound seafloors, reveals that normal marine environments dominated by typical Proterozoic-style soft substrates still existed during the Cambrian substrate revolution.     

Dynamics of a microbial community associated with manure hot spots as revealed by phospholipid fatty acid analyses.

Microbial community dynamics associated with manure hot spots were studied by using a model system consisting of a gel-stabilized mixture of soil and manure, placed between layers of soil, during a 3-week incubation period. The microbial biomass, measured as the total amount of phospholipid fatty acids (PLFA), had doubled within a 2-mm distance from the soil-manure interface after 3 days. Principal-component analyses demonstrated that this increase was accompanied by reproducible changes in the composition of PLFA, indicating changes in the microbial community structure. The effect of the manure was strongest in the 2-mm-thick soil layer closest to the interface, in which the PLFA composition was statistically significantly different (P < 0.05) from that of the unaffected soil layers throughout the incubation period. An effect was also observed in the soil layer 2 to 4 mm from the interface. The changes in microbial biomass and community structure were mainly attributed to the diffusion of dissolved organic carbon from the manure. During the initial period of microbial growth, PLFA, which were already more abundant in the manure than in the soil, increased in the manure core and in the 2-mm soil layer closest to the interface. After day 3, the PLFA composition of these layers gradually became more similar to that of the soil. The dynamics of individual PLFA suggested that both taxonomic and physiological changes occurred during growth. Examples of the latter were decreases in the ratios of 16:1 omega 7t to 16:1 omega 7c and of cyclopropyl fatty acids to their respective precursors, indicating a more active bacterial community. An inverse relationship between bacterial PLFA and the eucaryotic 20:4 PLFA (arachidonic acid) suggested that grazing was important.     

Size structure of the metazoan community in a Piedmont stream

We characterized the size structure of virtually the entire metazoan community in a fourth order, sandybottomed Piedmont stream during late summer. Our study, the first to sample across all habitat types and sizes of metazoans in an aquatic ecosystem, indicates that at the community level, stream size spectra may be bimodal for the benthos or trimodal when fish are included. Animals spanning 10 orders of magnitude in dry mass (from gastrotrichs to fish) were quantitatively collected from nine habitat types. The bimodal benthic size spectrum was characterized by a meiofaunal component (mostly oligochaetes and micro-crustacea) and a macrobenthic component (mostly the introduced asiatic clam, Corbicula fluminea). Insects contributed little to overall standing crop. Size-specific contribution to whole-community metabolism was assessed using allometric equations for respiration, and we found a distinctly bimodal distribution across the entire metazoan size range, with peaks in the meiofaunal and benthic macrofaunal size ranges. Our bimodal benthic size spectrum is similar to that observed for marine benthos but not to other freshwater benthic systems, possibly because the entire range of habitat types and/or animal sizes were not sampled in the latter. Numerous factors may influence size spectra in stream ecosystems, including local geomorphic (habitat) conditions, water level fluctuations, species introductions, and predation processes.     

Metagenomic analysis of the microbial community associated with the coral Porites astreoides

The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific; coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide diversity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.