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Heterotrophic Bacteria (heterotrophic + bacteria)
Selected AbstractsUREASE GENE SEQUENCES FROM ALGAE AND HETEROTROPHIC BACTERIA IN AXENIC AND NONAXENIC PHYTOPLANKTON CULTURES,JOURNAL OF PHYCOLOGY, Issue 3 2009Kristopher M. Baker While urea has long been recognized as an important form of nitrogen in planktonic ecosystems, very little is known about how many or which phytoplankton and bacteria can use urea as a nitrogen source. We developed a method, targeting the gene encoding urease, for the direct detection and identification of ureolytic organisms and tested it on seven axenic phytoplankton cultures (three diatoms, two prymnesiophytes, a eustigmatophyte, and a pelagophyte) and on three nonaxenic Aureococcus anophagefferens Hargraves et Sieburth cultures (CCMP1784 and two CCMP1708 cultures from different laboratories). The urease amplicon sequences from axenic phytoplankton cultures were consistent with genomic data in the three species for which both were available. Seven of 12 phytoplankton species have one or more introns in the amplified region of their urease gene(s). The 63 urease amplicons that were cloned and sequenced from nonaxenic A. anophagefferens cultures grouped into 17 distinct sequence types. Eleven types were related to ,-Proteobacteria, including three types likely belonging to the genus Roseovarius. Four types were related to ,-Proteobacteria, including two likely belonging to the genus Marinobacter, and two types were related to ,-Proteobacteria. Terminal restriction fragment length polymorphism (TRFLP) analyses suggested that the sequenced amplicons represented approximately half of the diversity of bacterial urease genes present in the nonaxenic cultures. While many of the bacterial urease sequence types were apparently lab- or culture-specific, others were found in all three nonaxenic cultures, suggesting the possibility of specific relationships between these bacteria and A. anophagefferens. [source] Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Xavier Mayali Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source] Molecular characterization of early colonizer bacteria from wastes in a steel plantLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2008D.B. Freitas Abstract Aims:, Forty-nine bacteria isolated from four newly-produced waste samples of a steel industry, which had a high content of CaO, MgO, Cr and P2O5, were characterized molecularly and phenotypically by susceptibility testing against heavy metals. Methods and Results:, Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates belonged to nine genera, Pseudomonas, Micrococcus, Acinetobacter, Bacillus, Dietzia, Kocuria, Diaphorobacter, Staphylococcus and Brevibacillus. Besides, some isolates could be affiliated to species: M. luteus, Ac. junii, Ac. schindleri, B. cereus, K. marina, D. nitroreducens and Staph. warneri. The bacteria that were characterized are taxonomically diverse, and Pseudomonas and Micrococcus predominated. Fingerprinting BOX-PCR revealed high genomic heterogeneity among the isolates. Among the heavy metal compounds Zn, Ni, Pb and Cu were least toxic to the bacterial isolates, whereas Ag inhibited all isolates at 0·001 mmol l,1. Conclusions:, Heterotrophic bacteria, affiliated with several phylogentic groups, were able to colonize different wastes of a steel industry. Significance and Impact of the Study:, This study extends our knowledge of the early colonizers bacteria populating siderurgic environments. Some of these bacteria could have potential for recycling siderurgic waste for steel production. [source] The microbiological quality of drinking water sold on the streets in Kumasi, GhanaLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2003K. Obiri-Danso Abstract Aim: The aim of this study was to assess the microbiological quality of Ghanaian bottled and plastic-bagged drinking water sold on the streets of Metropolitan Kumasi, Ghana. Methods and Results: Eight bottled, 88 factory-filled plastic sachet and 40 hand-filled hand-tied polythene-bagged drinking waters were examined for the presence of heterotrophic bacteria total viable counts (TVCs), indicators of faecal contamination (total coliforms, faecal coliforms and enterococci) and for lead, manganese and iron. Heterotrophic bacteria were found in all three types of water with TVCs per millilitre ranging from 1 to 460 for bottled water, 2,6·33 × 105 for factory-bagged sachet water and 2·33 × 103,7·33 × 1012 for hand-filled hand-tied bagged water. None of the microbial indicators of faecal contamination were detected in bottled water, whereas 4·5% of the factory-bagged sachets contained total coliforms and 2·3% faecal coliforms, and 42·5% of the hand-filled hand-tied bags contained total coliforms, 22·5% faecal coliforms and 5% enterococci. Iron was found in all three types of drinking water but at concentrations well within the WHO recommendations. Lead and manganese were not detected. Conclusion: Ghanaian bottled water is of good microbiological quality but some factory-bagged sachet and hand-filled hand-tied polythene-bagged drinking water are of doubtful quality. Significance and Impact of the Study: Factory-bagged sachets and hand-filled hand-tied bags of drinking water sold in Ghana should be monitored for microbiological contamination, with the aim of raising standards in the industry and re-assuring the public. [source] Use of non-limiting substrates to increase size; a generic strategy to simultaneously optimize uptake and minimize predation in pelagic osmotrophs?ECOLOGY LETTERS, Issue 7 2005T. Frede Thingstad Abstract Coexistence of two organisms competing for the same nutrient is possible if one is an ,uptake', and the other a ,predation defence' specialist. In pelagic food webs this principle has been linked to cell size. Small osmotroph cells, with their high surface : volume ratio, have been argued to be uptake specialists, while larger osmotrophs avoiding the intense grazing pressure from small protozoan predators might represent ,predation defence' specialists. This may seem like an obligatory trade-off situation that necessitates a choice of either being small or being large, and thus being potentially dominant in oligotrophic or in eutrophic environments, respectively. However, in a more precise form, the theory for nutrient diffusion states that it is the ,surface : cell requirement of limiting element' ratio, rather than the ,surface : volume' ratio, that is important. The distinction is crucial, since it opens up the possibility of there being life strategies that use a non-limiting element to increase size. Hypothesized to maximize uptake and predator defence simultaneously, such strategies should be particularly successful. We suggest that this strategy is exploited by osmotrophs with different size and physiology, such as heterotrophic bacteria, unicellular cyanobacteria and diatoms. Since the strategy implies a shift in organism stoichiometry, the biogeochemical implications are strong, illustrating the tight relationships between physical micro-scale processes, organism life strategies, biodiversity, food web structure, and biogeochemistry. [source] Nitrogen fixation in seagrass meadows: Regulation, plant,bacteria interactions and significance to primary productivityECOLOGY LETTERS, Issue 1 2000D.T. Welsh The rhizosphere sediments of seagrasses are generally a site of intense nitrogen fixation activity and this can provide a significant source of "new" nitrogen for the growth of the plants. In this paper, I review the data concerning nitrogen fixation in seagrass ecosystems, the transfer of the fixed nitrogen from the bacteria to the plants and its contribution to the overall productivity of seagrasses in different climatic zones. The relationship between the plants and diazotrophic heterotrophic bacteria in the rhizosphere is discussed, particularly focusing on the potentially important role of nitrogen-fixing, sulphate-reducing bacteria. The regulation of nitrogen fixation rates in the rhizosphere by photosynthetically driven oxygen and fixed carbon release by the plant roots and rhizomes, and the availability of ammonium in the porewater, is assessed. Finally, the hypothesis that a mutualistic or symbiotic association exists between the seagrasses and heterotrophic nitrogen fixers in the rhizosphere, based on the mutual exchange of fixed carbon and nitrogen, is discussed. [source] The Dry Limit of Microbial Life in the Atacama Desert Revealed by Calorimetric ApproachesENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 5 2008N. Barros Abstract The Atacama desert in Chile is one of the driest and most lifeless environments on Earth. It rains possibly once a decade. NASA examined these soils as a model for the Martian environment by comparing their degradation activity with Martian soil and looking for "the dry limit of life". The existence of heterotrophic bacteria in Atacama soil was demonstrated by DNA extraction and by the isolation of microorganisms. So far, however, no data have been available about the metabolic activities in these soils due to the limitations of the existing methodologies when applied to desert soils. Calorimetry was used to obtain information on the metabolic and thermal properties of eleven soil samples collected at different sites in the Atacama desert. Differential scanning calorimetry and isothermal calorimetry were employed to determine the pyrolysis properties of the carbon-containing matter and to measure biomass and microbial metabolism. They were compared to other soil properties such as total carbon and nitrogen, carbon to nitrogen ratio and pH. There was measurable organic matter in nine of the eleven samples and the heat of pyrolysis of those soils was correlated to the carbon content. In five of the eleven samples no biomass could be detected and the existence of basal microbial metabolism could not be established because all samples showed endothermic activity, probably from inorganic reactions with water. Six samples showed microbial activation after the addition of glucose. Carbon content, nitrogen content and the microbial activity after glucose amendment were correlated to the altitude and to the average minimum temperature of the sampling sites calculated from meteorological data. The detectable microbial metabolism was more dissipative with increasing altitude and decreasing temperature. [source] Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic OceanENVIRONMENTAL MICROBIOLOGY, Issue 10 2010Krista Longnecker Summary Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of 33P-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub-tropical North Atlantic Ocean was incubated with 33P-phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community-assimilating phosphate. Complementary incubations using 3H-leucine and 3H-thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD-FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga -like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of 3H-leucine or 3H-thymidine. [source] Distribution of microbial populations and their relationship with environmental parameters in the coastal waters of Qingdao, ChinaENVIRONMENTAL MICROBIOLOGY, Issue 7 2010Min Wang Summary In order to understand the large-scale distribution of microbial populations simultaneously and their relationship with environmental parameters, flow cytometry was used to analyse samples collected from 46 stations in the coastal waters of Qingdao in spring, 2007. The distribution of virus was significantly and positively correlated with heterotrophic bacteria. Two groups of picophytoplankton (Synechococcus and picoeukaryotes) were detected; however, Prochlorococcus was not found. Picoeukaryotes and nanophytoplankton were abundant in the near-shore waters, whereas Synechococcus was abundant in the off-shore areas. No variation was found in vertical distribution of virus, heterotrophic bacteria, Synechococcus and nanophytoplankton abundances, except picoeukaryotes abundance in the bottom layer was dramatically lower than that in the upper layers. Correlation analyses indicated that the relationship between abiotic variables and heterotrophic bacteria, pico- and nanophytoplankton was closer than that between abiotic variables and virioplankton. Temperature and nutrients were the synchronous factors controlling the growth of heterotrophic bacteria, pico- and nanophytoplankton in the coastal waters of Qingdao in spring. The results suggested that synergistic and antagonistic effects existed among microbial groups. [source] Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technologyENVIRONMENTAL MICROBIOLOGY, Issue 4 2010Xavier Mayali Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source] Phylogenetic 16S rRNA analysis reveals the presence of complex and partly unknown bacterial communities in Tito Bustillo cave, Spain, and on its Palaeolithic paintingsENVIRONMENTAL MICROBIOLOGY, Issue 7 2002Claudia Schabereiter-Gurtner Summary Tito Bustillo cave (Ribadesella, Spain) contains valuable Palaeolithic paintings, which date back 15 000,20 000 years. Since 1969, the cave has been open to the public. Rock wall surfaces, spelaeothems and soils are covered by apparent biofilms of phototrophic microorganisms, which develop under artificial lighting. In addition, rock surfaces present conspicuous bacterial growth in the form of round colonies of different colours and about 1,2 mm in diameter. Even the famous Paintings Panel shows some evident microbial growth. In the present study, bacterial communities on the paintings and on the rock surfaces near the paintings were analysed by culture-independent techniques, including polymerase chain reaction (PCR) amplification of bacterial 16S rRNA genes (16S rDNA), phylogenetic sequence analyses and genetic community fingerprinting by denaturing gradient gel electrophoresis (DGGE). DGGE fingerprints showed complex bacterial community patterns. Forty-one clones matching DGGE bands of the community fingerprints were sequenced, representing about 39% of DNA fragments in the DGGE patterns. Phylogenetic sequence analyses revealed a high number of phylogenetically novel 16S rDNA sequence types and a high diversity of putatively chemotrophic and heterotrophic bacteria. Sequences were phylogenetically most closely related to the Proteobacteria (20 clones), green non-sulphur bacteria (three clones), Planctomycetales order (one clone), Cytophaga,Flexibacter, Bacteroides division (one clone) and the Actinobacteria (four clones). Furthermore, we report the presence of members of the Acidobacterium division (12 clones) in a karstic hypogean environment. Members of this phylum have not so far been detected in these particular environments. [source] Biochemical and spectroscopic characterization of the bacterial phytochrome of Pseudomonas aeruginosaFEBS JOURNAL, Issue 8 2005Ronja Tasler Phytochromes are photochromic biliproteins found in plants as well as in some cyanotrophic, photoautotrophic and heterotrophic bacteria. In many bacteria, their function is largely unknown. Here we describe the biochemical and spectroscopic characterization of recombinant bacterial phytochrome from the opportunistic pathogen Pseudomonas aeruginosa (PaBphP). The recombinant protein displays all the characteristic features of a bonafide phytochrome. In contrast with cyanobacteria and plants, the chromophore of this bacterial phytochrome is biliverdin IX,, which is produced by the heme oxygenase BphO in P. aeruginosa. This chromophore was shown to be covalently attached via its A-ring endo-vinyl group to a cysteine residue outside the defined bilin lyase domain of plant and cyanobacterial phytochromes. Site-directed mutagenesis identified Cys12 and His247 as being important for chromophore binding and photoreversibility, respectively. PaBphP is synthesized in the dark in the red-light-absorbing Pr form and immediately converted into a far-red-light-absorbing Pfr-enriched form. It shows the characteristic red/far-red-light-induced photoreversibility of phytochromes. A chromophore analog that lacks the C15/16 double bond was used to show that this photoreversibility is due to a 15Z/15E isomerization of the biliverdin chromophore. Autophosphorylation of PaBphP was demonstrated, confirming its role as a sensor kinase of a bacterial two-component signaling system. [source] Diversity and distribution of pigmented heterotrophic bacteria in marine environmentsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006Hailian Du Abstract A systematic investigation of marine pigmented heterotrophic bacteria (PHB) based on the cultivation method and sequencing analysis of 16S rRNA genes was conducted in Chinese coastal and shelf waters and the Pacific Ocean. Both the abundance of PHB and the ratio of PHB to CFU decreased along trophic gradients from coastal to oceanic waters, with the highest values of 9.9 × 103 cell mL,1 and 39.6%, respectively, in the Yangtze River Estuary. In contrast to the total heterotrophic bacteria (TB) and CFU, which were present in the whole water column, PHB were primarily confined to the euphotic zone, with the highest abundance of PHB and ratio of PHB to CFU occurring in surface water. In total, 247 pigmented isolates were obtained during this study, and the phylogenetic analysis showed a wide genetic diversity covering 25 genera of six phylogenetic classes: Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacilli, Flavobacteria and Sphingobacteria. PHB belonging to Alphaproteobacteria, Flavobacteria and Sphingobacteria were obtained mainly from the South China Sea and East China Sea; PHB from the Pacific Ocean water were predominantly affiliated with Gammaproteobacteria, and most isolates from the Yangtze River Estuary fell into the classes Actinobacteria and Bacilli. The isolates exhibited various colours (e.g. golden, yellow, red, pink and orange), with genus or species specificity. Furthermore, the pigment of PHB cells absorbed light mainly in the wavelength range between 450 and 550 nm. In conclusion, our work has revealed that PHB with broad genetic diversity are widely distributed in the marine environment, and may account for up to 39.6% of culturable bacteria, equivalent to 1.4% of the total microbial community. This value might even be underestimated because it is probable that not all pigmented bacteria were isolated. Their abundance and genetic distribution are heavily influenced by environmental properties, such as light and nutrition, suggesting that they have important roles in the marine ecosystem, especially in the absorption of visible light. [source] Effect of petrochemical sludge concentrations on microbial communities during soil bioremediationFEMS MICROBIOLOGY ECOLOGY, Issue 2 2005María T. del Panno Abstract Qualitative and quantitative changes of microbial communities in soil microcosms during bioremediation were determined throughout one year. The soil was contaminated with 0%, 2.5%, 5%, 10% (wt/wt) of petrochemical sludge containing polynuclear aromatic hydrocarbons. We analyzed the hydrocarbon concentration in the microcosms, the number of cultivable bacteria using CFU and most probable number assays, the community structure using denaturing gradient gel electrophoresis, and the metabolic activity of soil using dehydrogenase activity and substrate-induced respiration assays. After one year of treatment, the chemical analysis suggested that the hydrocarbon elimination process was over. The biological analysis, however, showed that the contaminated microcosms suffered under long-term disturbance. The number of heterotrophic bacteria that increased after sludge addition (up to 108,109 cells ml,1) has not returned to the level of the control soil (2,6 × 107 cells ml,1). The community structure in the contaminated soils differed considerably from that in the control. The substrate-induced respiration of the contaminated soils was significantly lower (,10-fold) and the dehydrogenase activity was significantly higher (20,40-fold) compared to the control. Changes in the community structure of soils depended on the amount of added sludge. The species, which were predominant in the sludge community, could not be detected in the contaminated soils. [source] Abundance and production of bacteria, and relationship to phytoplankton production, in a large tropical lake (Lake Tanganyika)FRESHWATER BIOLOGY, Issue 6 2009STEPHANE STENUITE Summary 1. Abundance and bacterial production (BP) of heterotrophic bacteria (HBact) were measured in the north and south basins of Lake Tanganyika, East Africa, during seasonal sampling series between 2002 and 2007. The major objective of the study was to assess whether BP can supplement phytoplankton particulate primary production (particulate PP) in the pelagic waters, and whether BP and particulate PP are related in this large lake. HBact were enumerated in the 0,100 m surface layer by epifluorescence microscopy and flow cytometry; BP was quantified using 3H-thymidine incorporation, usually in three mixolimnion layers (0,40, 40,60 and 60,100 m). 2. Flow cytometry allowed three subpopulations to be distinguished: low nucleic acid content bacteria (LNA), high nucleic acid content bacteria (HNA) and Synechococcus -like picocyanobacteria (PCya). The proportion of HNA was on average 67% of total bacterial abundance, and tended to increase with depth. HBact abundance was between 1.2 × 105 and 4.8 × 106 cells mL,1, and was maximal in the 0,40 m layer (i.e. roughly, the euphotic layer). Using a single conversion factor of 15 fg C cell,1, estimated from biovolume measurements, average HBact biomass (integrated over a 100-m water column depth) was 1.89 ± 1.05 g C m,2. 3. Significant differences in BP appeared between seasons, especially in the south basin. The range of BP integrated over the 0,100 m layer was 93,735 mg C m,2 day,1, and overlapped with the range of particulate PP (150,1687 mg C m,2 day,1) measured in the same period of time at the same sites. 4. Depth-integrated BP was significantly correlated to particulate PP and chlorophyll- a, and BP in the euphotic layer was on average 25% of PP. 5. These results suggest that HBact contribute substantially to the particulate organic carbon available to consumers in Lake Tanganyika, and that BP may be sustained by phytoplankton-derived organic carbon in the pelagic waters. [source] Relationships between picophytoplankton and environmental variables in lakes along a gradient of water colour and nutrient contentFRESHWATER BIOLOGY, Issue 4 2003Stina Drakare SUMMARY 1. Biomass and production of picophytoplankton, phytoplankton and heterotrophic bacterioplankton were measured in seven lakes, exhibiting a broad range in water colour because of humic substances. The aim of the study was to identify environmental variables explaining the absolute and relative importance of picophytoplankton. In addition, two dystrophic lakes were fertilised with inorganic phosphorus and nitrogen, to test eventual nutrient limitation of picophytoplankton in these systems. 2. Picophytoplankton biomass and production were highest in lakes with low concentrations of dissolved organic carbon (DOC), and DOC proved the factor explaining most variation in picophytoplankton biomass and production. The relationship between picophytoplankton and lake trophy was negative, most likely because much P was bound in humic complexes. Picophytoplankton biomass decreased after the additions of P and N. 3. Compared with heterotrophic bacterioplankton, picophytoplankton were most successful at the clearwater end of the lake water colour gradient. Phytoplankton dominated over heterotrophic bacteria in the clearwater systems possibly because heterotrophic bacteria in such lakes are dependent on organic carbon produced by phytoplankton. 4. Compared with other phytoplankton, picophytoplankton did best at intermediate DOC concentrations; flagellates dominated in the humic lakes and large autotrophic phytoplankton in the clearwater lakes. 5. Picophytoplankton were not better competitors than large phytoplankton in situations when heterotrophic bacteria had access to a non-algal carbon source. Neither did their small size lead to picophytoplankton dominance over large phytoplankton in the clearwater lakes. Possible reasons include the ability of larger phytoplankton to float or swim to reduce sedimentation losses and to acquire nutrients by phagotrophy. [source] Unravelling the microbial role in ooid formation , results of an in situ experiment in modern freshwater Lake Geneva in SwitzerlandGEOBIOLOGY, Issue 4 2008K. PLEE ABSTRACT The microbial role in the formation of the cortex of low-Mg calcite freshwater ooids in western part of Lake Geneva in Switzerland has been suggested previously, but not demonstrated conclusively. Early work mostly concentrated in hypersaline milieus, and hence little is known about their genesis in freshwater environments. We designed an in situ experiment to mimic the natural process of low-Mg calcite precipitation. A special device was placed in the ooid-rich bank of the lake. It contained frosted glass (SiO2) slides, while quartz (SiO2) is the most abundant mineral composition of ooid nuclei that acted as artificial substrates to favour microbial colonization. Microscopic inspection of the slides revealed a clear seasonal pattern of carbonate precipitates, which were always closely associated with biofilms that developed on the surface of the frosted slides containing extracellular polymeric substance, coccoid and filamentous cyanobacteria, diatoms and heterotrophic bacteria. Carbonate precipitation peaks during early spring and late summer, and low-Mg calcite crystals mostly occur in close association with filamentous and coccoid cyanobacteria (e.g. Tolypothrix, Oscillatoria and Synechococcus, Anacystis, respectively). Further scanning electron microscope inspection of the samples revealed low-Mg calcite with crystal forms varying from anhedral to euhedral rhombohedra, depending on the seasons. Liquid cultures corroborate the in situ observations and demonstrate that under the same physicochemical conditions the absence of biofilms prevents the precipitation of low-Mg calcite crystals. These results illustrate that biofilms play a substantial role in low-Mg calcite ooid cortex formation. It further demonstrates the involvement of microbes in the early stages of ooid development. Combined with ongoing microbial cultures under laboratory-controlled conditions, the outcome of our investigation favoured the hypothesis of external microbial precipitation of low-Mg calcite as the main mechanism involved in the early stage of ooid formation in freshwater Lake Geneva. [source] Earliest fossil record of bacterial,cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA)GEOBIOLOGY, Issue 2 2008A. M. F. TOMESCU ABSTRACT Cyanobacteria in terrestrial and aquatic habitats are frequently associated with heterotrophic bacteria, and such associations are most often metabolically interactive. Functionally, the members of such bacterial,cyanobacterial consortia benefit from diverse metabolic capabilities of their associates, thus exceeding the sum of their parts. Such associations may have been just as ubiquitous in the past, but the fossil record has not produced any direct evidence for such associations to date. In this paper, we document fossil bacteria associated with a macrophytic cyanobacterial mat in the early Silurian (Llandovery) Massanutten Sandstone of Virginia, USA. Both the bacterial and the cyanobacterial cells are preserved by mineral replacement (pyrite subsequently replaced by iron oxyhydroxides) within an amorphous carbonaceous matrix which represents the common exopolysaccharide investment of the cyanobacterial colony. The bacteria are rod-shaped, over 370 nm long and 100 nm in diameter, and occur both as isolated cells and as short filaments. This occurrence represents the oldest fossil evidence for bacterial,cyanobacterial associations, documenting that such consortia were present 440 Ma ago, and revealing the potential for them to be recognized deeper in the fossil record. [source] Biogeochemistry of microbial mats under Precambrian environmental conditions: a modelling studyGEOBIOLOGY, Issue 2 2005E. K. HERMAN ABSTRACT Microbial mats have arguably been the most important ecosystem on Earth over its 3.5 Gyr inhabitation. Mats have persisted as consortia for billions of years and occupy some of Earth's most hostile environments. With rare exceptions (e.g. microbial mats developed on geothermal springs at Yellowstone National Park, USA), today's mats do not exist under conditions analogous to Precambrian habitats with substantially lower oxygen and sulphate concentrations. This study uses a numerical model of a microbial mat to investigate how mat composition in the past might have differed from modern mats. We present a numerical model of mat biogeochemistry that simulates the growth of cyanobacteria (CYA), colourless sulphur bacteria (CSB), and purple sulphur bacteria (PSB), with sulphate-reducing bacteria (SRB) and heterotrophic bacteria represented by parameterized sulphate reduction rates and heterotrophic consumption rates, respectively. Variations in the availability of light, oxygen, sulphide, and sulphate at the upper boundary of the mat are the driving forces in the model. Mats with remarkably similar biomass and chemical profiles develop in models under oxygen boundary conditions ranging from 2.5 × 10,13 to 0.25 mm and sulphate boundary concentrations ranging from 0.29 to 29 mm, designed to simulate various environments from Archean to modern. The modelled mats show little sensitivity to oxygen boundary conditions because, independent of the overlying oxygen concentrations, cyanobacterial photosynthesis creates similar O2 concentrations of 0.45,0.65 mm in the upper reaches of the mat during the photoperiod. Varying sulphate boundary conditions have more effect on the biological composition of the mat. Sulphide generated from sulphate reduction controls the magnitude and distribution of the PSB population, and plays a part in the distribution of CSB. CSB are the most sensitive species to environmental change, varying with oxygen and sulphide. [source] Utilization of oligo- and polysaccharides at microgram-per-litre levels in freshwater by Flavobacterium johnsoniaeJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010E.L.W. Sack Abstract Aims:, To obtain a bacterial strain that can be used to quantify biodegradable polysaccharides at concentrations of a few micrograms per litre in freshwater. Methods and Results:,Flavobacterium johnsoniae strain A3 was isolated from tap water supplemented with laminarin, pectin or amylopectin at 100 ,g C l,1 and river Rhine water. The organism utilized 14 of 23 oligo- and polysaccharides, and 1 of 9 monosaccharides, but none of the sugar acids, sugar alcohols, carboxylic acids or aromatic acids tested at 10 ,g C l,1. Amino acids promoted growth of strain A3, but not in coculture with assimilable organic carbon (AOC) test strain Pseudomonas fluorescens P17, which utilized these compounds more rapidly than strain A3. Compounds released by strain P17 and AOC test strain Spirillum sp. NOX grown on acetate promoted the growth of strain A3 at Nmax values of , 2 × 105 CFU ml,1 of strain P17 and , 5 × 105 CFU ml,1 of strain NOX. Significant growth of strain A3 was observed in surface water and in tap water in the presence of strain P17 (Nmax P17 < 2 × 105 CFU ml,1). Conclusions:, Strain A3 utilizes oligo- and polysaccharides at microgram-per-litre levels. In surface water and in tap water, the organism was able to utilize compounds that were not utilized by strain P17. These compounds may include oligo- and/or polysaccharides. Significance and Impact of the Study:, Phytoplanktonic and bacterial polysaccharides can constitute an important biodegradable fraction of natural organic matter in water and may promote growth of heterotrophic bacteria during water treatment and drinking water distribution. Strain A3 can be used to quantify a group of compounds that includes oligo- and polysaccharides at microgram-per-litre levels in freshwater. [source] Comparison of the microbial population dynamics and phylogenetic characterization of a CANOXIS reactor and a UASB reactor degrading trichloroetheneJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2005O. Tresse Abstract Aims:, To understand the microbial ecology underlying trichloethene (TCE) degradation in a coupled anaerobic/aerobic single stage (CANOXIS) reactor oxygenated with hydrogen peroxide (H2O2) and in an upflow anaerobic sludge bed (UASB) reactor. Methods and Results:, The molecular study of the microbial population dynamics and a phylogenetic characterization were conducted using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). In both reactors, TCE had a toxic effect on two uncultured bacterial populations whereas oxygen favoured the growth of aerobic species belonging to Rhizobiaceae and Dechloromonas. No methanotrophic bacteria were detected when targeting 16S rRNA gene with universal primers. Alternatively, pmo gene encoding the particulate methane monooxygenase of Methylomonas sp. LW21 could be detected in the coupled reactor when H2O2 was supplied at 0·7 g O2 l day,1. Conclusions:,Methylomonas sp. LW21 that could be responsible for the aerobic degradation of the TCE by-products is not among the predominant bacterial populations in the coupled reactor. It seems to have been outcompeted by heterotrophic bacteria (Rhizobiaceae and Dechloromonas sp.) for oxygen. Significance and Impact of the Study:, The results obtained show the limitations of the coupled reactor examined in this study. Further investigations should focus on the operating conditions of this reactor in order to favour the growth of the methanotrophs. [source] Mediation of arsenic oxidation by Thiomonas sp. in acid-mine drainage (Carnoulès, France)JOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2003O. Bruneel Abstract Aims: To isolate, identify, and characterize heterotrophic bacteria in acid-mine drainage that mediate oxidation of As(III). Methods and Results: Samples of acid-mine drainage were collected over a period of 14 months. Heterotrophic and non-obligatory acidophilic bacteria in the samples were cultured on a solid medium (pH 7·0,7·2), and three strains were isolated. The three different strains belong to the genus Thiomonas, and have more than 99% homology with the group Ynys1. Culturing in mineral media demonstrated that the isolated strains used thiosulphate as an energy source, and oxidized iron in the presence of thiosulphate. However, none of the strains were able to oxidize arsenic in the presence of thiosulphate, nor could they use iron or arsenic alone as an energy source. In vitro experiments demonstrated that two of the Thiomonas strains were able to oxidize more than 90% of the As(III) present in the acid-mine drainage, whereas no abiotic oxidation of arsenic occurred. Conclusions: Two strains of newly identified Thiomonas sp. found in acid-mine drainage are capable of oxidizing arsenic. Significance and Impact of Study: These results represent the first reported oxidation of arsenic by Thiomonas sp. Biologically mediated oxidation and subsequent immobilization of arsenic is of great interest for the remediation of contaminated mine sites. [source] The fate of stormwater-associated bacteria in constructed wetland and water pollution control pond systemsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2000C.M. Davies The performances of a constructed wetland and a water pollution control pond were compared in terms of their abilities to reduce stormwater bacterial loads to recreational waters. Concentrations of thermotolerant coliforms, enterococci and heterotrophic bacteria were determined in inflow and outflow samples collected from each system over a 6-month period. Bacterial removal was significantly less effective in the water pollution control pond than in the constructed wetland. This was attributed to the inability of the pond system to retain the fine clay particles (< 2 µm) to which the bacteria were predominantly adsorbed. Sediment microcosm survival studies showed that the persistence of thermotolerant coliforms was greater in the pond sediments than in the wetland sediments, and that predation was a major factor influencing bacterial survival. The key to greater bacterial longevity in the pond sediments appeared to be the adsorption of bacteria to fine particles, which protected them from predators. These observations may significantly affect the choice of treatment system for effective stormwater management. [source] Use of probiotics to control furunculosis in rainbow trout, Oncorhynchus mykiss (Walbaum)JOURNAL OF FISH DISEASES, Issue 6 2002A Irianto Aerobic heterotrophic bacteria were isolated from the intestinal contents of Atlantic salmon, Salmo salar, rainbow trout, Oncorhynchus mykiss, and turbot, Scophthalmus maximus, on tryptone soya agar and De Man Rogosa and Sharpe agar, of which 11 of 177 (6% of the total) of the isolates were antagonistic to Aeromonas salmonicida. Four of these cultures, which were identified tentatively as A. hydrophila, Vibrio fluvialis, Carnobacterium sp. and an unidentified Gram-positive coccus, were beneficial to fish when fed singly or as an equi-mixture. Feed supplemented with the putative probiotics indicated survival of the organisms in the gastrointestinal tract for 7 days. Feeding with the probiotics for 7 and 14 days led to better survival following challenge with A. salmonicida. There was no indication of serum or mucus antibodies to A. salmonicida, but there was an increased number of erythrocytes, macrophages, lymphocytes and leucocytes, and enhanced lysozyme activity in the fish. [source] JET-SUSPENDED, CALCITE-BALLASTED CYANOBACTERIAL WATERWARTS IN A DESERT SPRING1JOURNAL OF PHYCOLOGY, Issue 3 2002Ferran Garcia-Pichel We describe a population of colonial cyanobacteria (waterwarts) that develops as the dominant primary producer in a bottom-fed, O2 -poor, warm spring in the Cuatro Ciénegas karstic region of the Mexican Chihuahuan Desert. The centimeter-sized waterwarts were suspended within a central, conically shaped, 6-m deep well by upwelling waters. Waterwarts were built by an Aphanothece -like unicellular cyanobacterium and supported a community of epiphytic filamentous cyanobacteria and diatoms but were free of heterotrophic bacteria inside. Sequence analysis of 16S rRNA genes revealed that this cyanobacterium is only distantly related to several strains of other unicellular cyanobacteria (Merismopedia, Cyanothece, Microcystis). Waterwarts contained orderly arrangements of mineral crystallites, made up of microcrystalline low-magnesium calcite with high levels of strontium and sulfur. Waterwarts were 95.9% (v/v) glycan, 2.8% cells, and 1.3% mineral grains and had a buoyant density of 1.034 kg·L,1. An analysis of the hydrological properties of the spring well and the waterwarts demonstrated that both large colony size and the presence of controlled amounts of mineral ballast are required to prevent the population from being washed out of the well. The unique hydrological characteristics of the spring have likely selected for both traits. The mechanisms by which controlled nucleation of extracellular calcite is achieved remain to be explored. [source] Backpacking in Yosemite and Kings Canyon National Parks and Neighboring Wilderness Areas: How Safe Is the Water to Drink?JOURNAL OF TRAVEL MEDICINE, Issue 4 2008Robert W. Derlet MD Objective The objective of this study was to determine the risk of acquiring disease from popular Sierra Nevada wilderness area lakes and streams. This study examines the relative risk factors for harmful waterborne microorganisms using coliforms as an indicator. Methods Water was collected in the backcountry Yosemite and Kings Canyon National Parks and neighboring wilderness areas. A total of 72 sites from lakes or streams were selected to statistically differentiate the risk categories: (1) natural areas rarely visited by humans or domestic animals; (2) human day use,only areas; (3) high use by backpackers; (4) high use by pack animals; and (5) cattle- and sheep-grazing tracts. Water was collected in sterile test tubes and Millipore coliform samplers during the summer of 2006. Water was analyzed at the university microbiology lab, where bacteria were harvested and then subjected to analysis using standardized techniques. Statistical analysis to compare site categories was performed using Fisher's exact test. Results Coliforms were found in none of the 13 wild sites, none of the 12 day hike sites, and only 3 of 18 backpacker sites (17%). In contrast, 14 of 20 sites (70%) with pack animal traffic yielded coliforms, and all 9 sites (100%) below the cattle-grazing areas grew coliforms. Differences between backpacker versus cattle or pack areas were significant, p , 0.05. All samples grew normal aquatic bacteria. Sites below cattle grazing and pack animal use tended to have more total heterotrophic bacteria. Conclusions Alpine wilderness water below cattle areas used by pack animals is at risk for containing coliform organisms. Water from wild, day hike, or backpack areas showed far less risk for coliforms. [source] The Glycine Decarboxylase Complex is not Essential for the Cyanobacterium Synechocystis sp.PLANT BIOLOGY, Issue 1 2005Strain PCC 680 Abstract: In order to investigate the metabolic importance of glycine decarboxylase (GDC) in cyanobacteria, mutants were generated defective in the genes encoding GDC subunits and the serine hydroxymethyl-transferase (SHMT). It was possible to mutate the genes for GDC subunits P, T, or H protein in the cyanobacterial model strain Synechocystis sp. PCC 6803, indicating that GDC is not necessary for cell viability under standard conditions. In contrast, the SHMT coding gene was found to be essential. Almost no changes in growth, pigmentation, or photosynthesis were detected in the GDC subunit mutants, regardless of whether or not they were cultivated at ambient or high CO2 concentrations. The mutation of GDC led to an increased glycine/serine ratio in the mutant cells. Furthermore, supplementation of the medium with low glycine concentrations was toxic for the mutants but not for wild type cells. Conditions stimulating photorespiration in plants, such as low CO2 concentrations, did not induce but decrease the expression of the GDC and SHMT genes in Synechocystis. It appears that, in contrast to heterotrophic bacteria and plants, GDC is dispensable for Synechocystis and possibly other cyanobacteria. [source] Effect of practical diets with different protein levels on the performance of Farfantepenaeus paulensis juveniles nursed in a zero exchange suspended microbial flocs intensive systemAQUACULTURE NUTRITION, Issue 2 2010E.L.C. BALLESTER Abstract Farfantepenaeus paulensis juveniles (72 ± 24 mg), were reared in a suspended microbial flocs system and fed practical diets containing increasing amounts of crude protein (250, 300, 350, 400 and 450 g kg,1 CP). Development of microbial flocs was promoted by high aeration rates and fertilization with wheat bran and molasses. Flocs were composed of detritus in the form of flocculated matter colonized by heterotrophic bacteria, cocoid and filamentous cyanobacteria, flagellate and ciliate protozoa and rotifers. Proximate composition analysis of the suspended microbial floc showed CP levels of 304 g kg,1. After 45 days, mean shrimp survival were above 89%, with no significant differences between treatments. Shrimp fed diets with 350 g kg,1 or higher CP content achieved significant higher (P < 0.05) final weight (0.66,0.68 g), weight gain (0.58,0.61 g) and instantaneous growth rate (0.049,0.050), with feed conversion rates (2.17,2.30) significantly lower (P < 0.05). Results show that, when rearing is carried out in a suspended microbial flocs system, dietary CP levels can be kept at 350 g kg,1. Furthermore, results confirm that microbial-based systems allow shrimp culture without compromising the surrounding environment and shows the possible reduction of production costs and fish meal dependence. [source] Nitrogen budget for a low-salinity, zero-water exchange culture system: II.AQUACULTURE RESEARCH, Issue 9 2008Evaluation of isonitrogenous feeding of various dietary protein levels to Litopenaeus vannamei (Boone) Abstract This study evaluated the effects of isonitrogenous feeding (60 g dietary protein per kilogram of body weight per day) using experimental feeds with 25%, 30%, 35% and 40% protein on the nitrogen budget, ammonia efflux rate, growth and survival of juvenile Litopenaeus vannamei raised in a low-salinity (4 g L,1) zero-water exchange culture system for 4 weeks. No significant differences in weight gain or instantaneous growth rate were observed between the dietary treatments with 35% and 40% protein after 3 weeks of study, or between treatments with 25% and 30% protein after 4 weeks of study. High mortality rates were observed for the 35% and 40% protein treatments, probably associated with high nitrite levels (4.80 and 7.36 mg NO2 -NL,1 respectively) in water. Among the various dietary treatments, 39,46.3% of feed nitrogen was converted to shrimp biomass, 32.8,38.0% and 14.4,39.9% remained within the system as organic and inorganic nitrogen, respectively, and 32.5,39.3% was unaccounted for. The results of the present study showed high nitrogen utilization efficiencies. However, as the nitrogen loading of the zero-water exchange system increased, so did the nitrogen excretion of shrimp, causing a deteriorated general condition of the shrimp, demonstrated by the low ammonia efflux rates recorded at the end of the trial. This study confirms that low-salinity closed systems are particularly susceptible to nitrogen loading. Thus, in these culture systems, low-protein feeds may perform better as they provide more carbon for heterotrophic bacteria and less nitrogen to be degraded and transformed into nitrogenous wastes. [source] Nitrogen budget for a low salinity, zero-water exchange culture system: I. Effect of dietary protein level on the performance of Litopenaeus vannamei (Boone)AQUACULTURE RESEARCH, Issue 8 2007Mayra L. González-Félix Abstract A 4-week study was conducted to evaluate the effects of different dietary protein levels (25%, 30%, 35% and 40%) on the growth and survival of juvenile Litopenaeus vannamei raised in a low salinity (4.6 g L,1), zero-water exchange culture system, as well as on the nitrogen budget and ammonia efflux rate. No significant differences were observed among the dietary treatments for final weight, weight gain or survival of shrimp, although the best performance was observed in the 25% protein treatment group. Both weight and survival decreased as the dietary protein increased. Significant differences (P<0.05) were observed in the ammonia concentration among dietary treatments during the first 2 weeks of the experiment. The highest concentration was measured in the 40% dietary protein treatment (5.88 mg NH4-N L,1). The nitrogen budget showed that the nitrogen loss increased as the dietary protein increased under the experimental conditions; the largest amount of nitrogen recovered as shrimp biomass (42.9%) was in the 25% protein treatment group, and the largest amount of unaccounted nitrogen (39.5%) was in the 40% protein treatment. Under these conditions, utilization of low-protein diets resulted in better performance, presumably because they provided more carbon for heterotrophic bacteria and reduced the nitrogen loading of the system. [source] | ||||||||||||||||||||||||||||||||||