Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient

To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rRNA gene fragments. Ammonia-oxidizing bacteria communities at sampling sites with strongest marine influence were dominated by Nitrosospira cluster 1-like sequences and those with strongest freshwater influence were dominated by Nitrosomonas oligotropha-like sequences. Nitrosomonas sp. Nm143 was the prevailing sequence type in communities at intermediate brackish sites. Diversity indices of AOB communities were similar at marine- and freshwater-influenced sites and did not indicate lower species diversity at intermediate brackish sites. The presence of sequences highly similar to the halophilic Nitrosomonas marina and the freshwater strain Nitrosomonas oligotropha at identical sampling sites indicates that AOB communities in the estuary are adapted to a range of salinities, while individual strains may be active at different salinities. Ammonia-oxidizing bacteria communities that were dominated by Nitrosospira cluster 1 sequence types, for which no cultured representative exists, were subjected to stable isotope probing (SIP) with 13C-HCO3-, to label the nucleic acids of active autotrophic nitrifiers. Analysis of 13C-associated 16S rRNA gene fragments, following CsCl density centrifugation, by cloning and DGGE indicated sequences highly similar to the AOB Nitrosomonas sp. Nm143 and Nitrosomonas cryotolerans and to the nitrite oxidizer Nitrospira marina. No sequence with similarity to the Nitrosospira cluster 1 clade was recovered during SIP analysis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain.     

Differences between betaproteobacterial ammonia-oxidizing communities in marine sediments and those in overlying water

To assess links between betaproteobacterial ammonia-oxidizing bacteria (AOB) in marine sediment and in overlying water, communities in Loch Duich, Scotland, were characterized by analysis of clone libraries and denaturant gradient gel electrophoresis of 16S rRNA gene fragments. Nitrosospira cluster 1-like sequences were isolated from both environments, but different sequence types dominated water and sediment samples. Detailed phylogenetic analysis of marine Nitrosospira cluster 1-like sequences in Loch Duich and surrounding regions suggests the existence of at least two different phylogenetic subgroups, potentially indicative of new lineages within the betaproteobacterial AOB, representing different marine ecotypes.     

封闭循环养殖系统中β变形菌亚纲氨氧化细菌的引物特异性

摘要:【目的】为探讨4 对不同的引物对封闭循环养殖系统生物膜中β 变形菌亚纲氨氧化细菌(β-AOB) 的特异性差异。【方法】采用16S rDNA 文库克隆技术对β-AOB 的多样性进行了分析。【结果】以引物CTO189f/CTO654r 扩增构建的文库中所含β-AOB 比例最高,可达67. 3%。不同封闭循环养殖系统的生物膜对引物的扩增效率有明显的影响,其中以养殖尼罗罗非鱼的封闭循环养殖系统生物膜为DNA 来源的,引物均有较高的扩增效率。【结论】针对封闭循环养殖系统生物膜中的β-AOB,特异性最高的是CTO189f /CTO654r 引物。     

Comparison of ammonia-oxidizing bacterial community structure in membrane-assisted bioreactors using PCR-DGGE and FISH

The ammonia-oxidizing bacterial (AOB) communities in three membrane bioreactors (MBRs) were monitored for 2 months after an acclimation period in order to investigate the influence of sludge age and medium type on AOB changeability and its connection with nitrification effectiveness. One MBR with a sludge age of 4 days was fed with a synthetic medium, whereas the other two with sludge ages of 8 and 32 days were fed with landfill leachate. The research revealed that landfill leachate can be effectively treated in an MBR with a higher sludge age for longer periods of time and that this improvement in performance was correlated with an increase in AOB biodiversity. Interestingly, the medium type has a stronger influence on AOB biocenosis formation than the sludge age.     

Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds

An annual investigation into the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in fresh water aquaculture ponds was performed by quantitative PCR of the amoA gene. The results showed that AOB were the main ammonia-oxidizing microorganisms in water, and significantly higher copy numbers of the AOB amoA gene were observed in the summer (Aug 2012), while no significant differences were detected among the other three seasons. AOA showed low abundances throughout the year. The predominance of AOB in aquaculture water was suggested to be related to photoinhibition. Both the AOB and AOA amoA genes in aquaculture pond sediments showed typical seasonal patterns. The maximum density of AOB was observed in the autumn (Nov 2012) and winter (Jan 2013), while the maximum density of AOA was observed in winter. The minimum densities of both AOA and AOB occurred in the summer. The concentration of the AOA amoA gene was higher than that of the AOB amoA gene in sediments by almost one order of magnitude, which indicates that AOA are the dominant ammonia-oxidizing microorganisms in the aquaculture pond sediments. Dissolved oxygen is suggested to be the key factor determining the predominance of AOA in pond sediments.     

Seasonal and annual genotypic variation and the effect of climate on population genetic structure of the cereal aphid Sitobion avenae in northern France

Changes in the genetic structure and genotypic variation of the aphid Sitobion avenae collected from cereal crops in northern France were examined by analysing variation at five microsatellite loci across several years and seasons. Little regional and temporal differentiation was detected, as shown by very low FST among populations. Repeated genotypes, significant heterozygote deficits, positive FIS values and frequent linkage disequilibria were found in nearly all samples, suggesting an overall pattern of reproductive mode variation in S. avenae populations. In addition, samples from Brittany (Bretagne) showed greater signs of asexual reproduction than those from the north of France, indicating a trend toward increasing sexuality northward. These patterns of reproductive variation in S. avenae are consistent with theoretical models of selection of aphid reproductive modes by climate. Contrasting with little changes in allelic frequencies, genotypic composition varied substantially in time and, to a lesser extent, in space. An important part of changes in genotypic arrays was due to the variation in frequency distribution of common genotypes, i.e. those that were found at several instances in the samples. Genotypic composition was also shown to vary according to climate, as genotypic diversity in spring was significantly correlated with the severity of the previous winter and autumn. We propose that the genetic homogeneity among S. avenae populations shown here across large temporal and spatial scales is the result of two forces: (i) migration conferred by high dispersal capabilities, and (ii) selection over millions of hectares of cereals (mostly wheat) bred from a narrow genetic base.     

Seasonal and annual variations in the prevalence of helminths in a cyclic population of Clethrionomys glareolus

Six cestode and two nematode species were recovered from a cyclic population of Clethrionomys glareolus in southern Norway. The cestode Aprostatandrya macrocephala and the nematode Heligmosomum glareoli were euconstant species which displayed late spring/early summer peaks in numbers after which they declined. This decrease in prevalence was correlated with decreasing mean age of the host population. Increases in the prevalence of infections with the nematode Syphacia nigeriana in bank voles were correlated to increasing numbers of Microius agrestis in the mixed woods. Cestode larvae were at maximum prevalence during peak years of bank vole abundance. Pathological conditions such as ascites and peritoneal adhesions, as well as splenic and adrenal hypertrophy, were associated with cestode larvae. There was no general trend of an increase in the prevalence of helminth infection with increasing population density of the bank voles.     

Seasonal and management influences on bacterial community structure in an upland grassland soil

Floristically diverse Nardo-Galion upland grasslands are common in Ireland and the UK and are valuable in agricultural, environmental and ecological terms. Under improvement (inputs of lime, fertiliser and re-seeding), they convert to mesotrophic grassland containing very few plant species. The effects of upland grassland improvement and seasonality on soil microbial communities were investigated at an upland site. Samples were taken at five times in one year in order to observe seasonal trends, and bacterial community structure was monitored using automated ribosomal intergenic spacer analysis (ARISA), a DNA-fingerprinting approach. Differences in soil chemistry and bacterial community structure between unimproved and improved grassland soils were noted. Season was also found to cause mild fluctuations in bacterial community structure, with soil samples from colder months (October and December) more correlated with change in ribotype profiles than samples from warmer months. However, for the majority of seasons clear differences in bacterial community structures from unimproved and improved soils could be seen, indicating seasonal influences did not obscure effects associated with improvement.     

Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes

The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ± 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.     

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

Aims:  To investigate whether the ammonia-oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co-evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification.
Methods and Results:  Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium-enriched tap water and operated in parallel for 134 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated co-evolvement of the AOB communities over time. During start-up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Δ _{t (week)}) were medium to high (12–22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Δ _{t (week)} < 5%). Further pragmatic processing of the DGGE profiles revealed a high range-weighted richness and a medium functional organization of the AOB communities.
Conclusions:  After a start-up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co-evolvement in the replicate SBR.
Significance and Impact of the Study:  Replicates in identical set-ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.     

Seasonal roosts of Red-lored Amazons in Ecuador provide information about population size and structure

ABSTRACT.   Data from roosts of Amazona parrots may be useful in creating demographic models, because these birds exhibit high roost fidelity and pairs are conspicuous in flight. However, few investigators have attempted to track changes in the number of pairs using such roosts. We studied Red-lored Amazons ( Amazona autumnalis ) at a communal roost in southwest Ecuador over a 1-yr period to understand better their population structure. Population size was estimated at 214 individuals. Counts revealed seasonal variation in numbers, but the occurrence of pairs and singles was seldom correlated. The number of paired individuals using the roost was lower during the breeding period. In contrast, the number of single birds at the roost nearly doubled during the breeding period. Overall, our data suggest that parental responsibilities during the nesting period explain fluctuations in the number of birds at the roost, and such fluctuations can be used to estimate the reproductive portion of the population. Protection of the small mangrove islands where the parrots roost would likely benefit a population that occupies a much larger area and would, at the same time, provide a useful tool for demographic studies of this poorly known neotropical parrot.     

Sexual systems and population genetic structure in an annual plant: testing the metapopulation model

The need for reproductive assurance during dispersal, along with the pressure of local mate competition, means that the importance of frequent or repeated colonization is implicit in the literature on sexual system evolution. However, there have been few empirical tests of the association between colonization history and sexual system in plants, and none within a single species. Here we use patterns of genetic diversity to provide such a test in the Mercurialis annua species complex, which spans the range of systems from self-compatible monoecy through androdioecy to dioecy. This variation has been hypothesized to result from differing patterns of metapopulation turnover and recolonization. Because monoecy should be favored during colonization, androdioecy and dioecy will be maintained only in regions with low rates of local extinction and recolonization, and these differences should also be reflected in patterns of neutral genetic diversity. We show that monoecious populations of M. annua display lower within-population genetic diversity than androdioecious populations and higher genetic differentiation than dioecious and androdioecious populations, as predicted by metapopulation models. In contrast, regional diversity in M. annua appears to be primarily a product of postglacial range expansion from two refugia in the eastern and western Mediterranean Basin.     

不同土壤细菌种群结构对氯嘧磺隆胁迫的响应及降解菌系的获得

应用PCR-DGGE、DNA测序等方法,在室内驯化条件下研究了8种来源于中国不同地区土壤样品细菌种群结构对氯嘧磺隆胁迫的响应。结果表明:在氯嘧磺隆100～500mg·L-1浓度梯度下,土壤细菌群落组成有明显的更迭现象,多样性发生明显变化,驯化至10周,绝大部分细菌种群消失,样品的细菌种群结构趋于简单并呈现趋同效应;DNA测序结果表明,在驯化第10周可培养Methylophilus sp.、Beta proteobacterium、uncultured bacterium成为优势菌属,所获细菌种群出现的16个优势种群中有10个与已知的具有有机污染物降解功能和有机污染环境修复功能细菌的相似性大于97%;其中5个与嗜甲基菌16S rDNA部分序列相似性达98%以上。获得了一组对氯嘧磺隆具有降解作用的细菌菌系,可在5d内将100mg·L-1氯嘧磺隆降解67%;其主要组成为嗜甲基菌属(Methylophilus sp.)、丛毛单胞菌属(Comamonas sp.)、鞘酯杆菌属(Sphingobacterium sp.)和嗜氢菌属(Hydrogenophi-lus sp.)。     

Abundance and population structure of ammonia-oxidizing bacteria that inhabit canal sediments receiving effluents from municipal wastewater treatment plants

A polyphasic, culture-independent study was conducted to investigate the abundance and population structure of ammonia-oxidizing bacteria (AOB) in canal sediments receiving wastewater discharge. The abundance of AOB ranged from 0.2 to 1.9% and 1.6 to 5.7% of the total bacterial fraction by real-time PCR and immunofluorescence staining, respectively. Clone analysis and restriction endonuclease analysis revealed that the AOB communities influenced by the wastewater discharge were dominated by Nitrosomonas, were similar to each other, and were less diverse than the communities outside of the immediate discharge zone.     

Seasonal variation and annual fluctuation in granite outcrop plant communities

Permanent quadrats in granite outcrop plant communities allowed us to monitor seasonal variation and annual fluctuation in community structure. Seasonal species turn-over was significant in communities on shallow soil, but not in communities on deeper soil where seasonal dominance shifts were common. Exceptional meteorological events appeared to mediate phenomena of competitive release in some island communities. A decrease in the abundance of Arenaria uniflora in Lichen-annual island communities, following a spring drought, was correlated with an increase in the abundance of Sedum smallii, a shallower-soil species. Richness in Annual-perennial island communities was higher in spring 1985 than in 1984 or 1986, and this occurred as the dominant species, Senecio tomentosus, temporarily declined in importance following a severe drought in late summer 1984. Significant annual fluctuation in the cover of Viguiera porteri could also be related to variations in the summer precipitation regime. Overall, plant responses to drought were individualistic and depended largely on the timing of these meteorological events in relation to the life-stages and/or the physiological status of the plants.Abbreviations AP = Annual-perennial island communities - HST = Herb-shrub-tree island communities - LA = Lichen-annual island communities - SS = Sedum smallii island communities     

Seasonal and annual respiration of a ponderosa pine ecosystem

The net ecosystem exchange of CO₂ between forests and the atmosphere, measured by eddy covariance, is the small difference between two large fluxes of photosynthesis and respiration. Chamber measurements of soil surface CO₂ efflux (F_s), wood respiration (F_w) and foliage respiration (F_f) help identify the contributions of these individual components to net ecosystem exchange. Models developed from the chamber data also provide independent estimates of respiration costs. We measured CO₂ efflux with chambers periodically in 1996–97 in a ponderosa pine forest in Oregon, scaled these measurements to the ecosystem, and computed annual totals for respiration by component. We also compared estimated half-hourly ecosystem respiration at night (F_nc) with eddy covariance measurements. Mean foliage respiration normalized to 10 °C was 0.20 μmol m^–2 (hemi-leaf surface area) s^–1, and reached a maximum of 0.24 μmol m^–2 HSA s^–1 between days 162 and 208. Mean wood respiration normalized to 10 °C was 5.9 μmol m^–3 sapwood s^–1, with slightly higher rates in mid-summer, when growth occurs. There was no significant difference (P > 0.10) between wood respiration of young (45 years) and old trees (250 years). Soil surface respiration normalized to 10 °C ranged from 0.7 to 3.0 μmol m^–2 (ground) s^–1 from days 23 to 329, with the lowest rates in winter and highest rates in late spring. Annual CO₂ flux from soil surface, foliage and wood was 683, 157, and 54 g C m^–2 y^–1, with soil fluxes responsible for 76% of ecosystem respiration. The ratio of net primary production to gross primary production was 0.45, consistent with values for conifer sites in Oregon and Australia, but higher than values reported for boreal coniferous forests. Below-ground carbon allocation (root turnover and respiration, estimated as F_s– litterfall carbon) consumed 61% of GPP; high ratios such as this are typical of sites with more water and nutrient constraints. The chamber estimates were moderately correlated with change in CO₂ storage in the canopy (F_stor) on calm nights (friction velocity u* < 0.25 m s^–1; R² = 0.60); F_stor was not significantly different from summed chamber estimates. On windy nights (u* > 0.25 m s^–1), the sum of turbulent flux measured above the canopy by eddy covariance and F_stor was only weakly correlated with summed chamber estimates (R² = 0.14); the eddy covariance estimates were lower than chamber estimates by 50%.     

Genetic structure of the annual weed Senecio vulgaris in relation to habitat type and population size

Throughout the world, the highly selfing annual common groundsel, Senecio vulgaris (Asteraceae) is a common weed. Recently, it has also colonized ecological compensation areas in agro-ecosystems. We investigated the genetic structure of S. vulgaris using random amplified polymorphic DNA (RAPD) profiles of 80 plants from nine populations representing three habitat types in two regions in Switzerland. RAPD variation among regions (19.8%), among populations within regions (19.2%) and within populations (61.1%) was highly significant (ANOVA; P < 0.001). Gene flow estimated from the observed differentiation among populations (PhiST = 0.382) was low (assuming Wright's island model, Nem = 0.404). Genetic distances between pairs of populations were significantly correlated with geographical distances (Mantel test; r = 0.37, P < 0.03). Molecular variance obtained with AMOVA was lowest in the small populations in compensation areas (1.13), intermediate in vineyard populations (2.49), all located in northern Switzerland and highest in the larger vegetable field populations from western Switzerland (3.41; P < 0.05). Overall, there was a positive correlation of molecular variance and population size (P < 0.05), as expected under genetic drift. However, molecular variance was negatively correlated with population size among populations in ecological compensation areas, suggesting that selection was also important. We also applied triazine herbicide to leaves of three offspring of each of the 80 plants. Plants from populations of compensation areas showed higher mean levels and reduced variation in the resistance to triazine herbicide than plants from vineyards and vegetable fields. This suggests that compensation areas were colonized from adjacent corn fields, in which there has been selection for herbicide resistance. We discuss the implications of our results for the biological control of S. vulgaris.     

Seasonal dynamics in community structure,abundance, body size and sex ratio in two species of Neotropical annual fishes

Seven ephemeral pools on the coastal plain of southern Brazil were found to be inhabited by three annual and 22 non‐annual fish species. Two common annual species (Austrolebias minuano and Cynopoecilus fulgens) exhibited clear seasonal dynamics, with the appearance of young fishes in the austral autumn (May to June) and a decline in abundance over the seasonal cycle. The third annual species, Austrolebias wolterstorffii, was rare. No seasonal dynamics were observed in non‐annual fishes. The relative abundance of non‐annual fishes compared with annual fishes increased over the seasonal cycle, but they coexisted widely. The size structure of annual fishes suggested the presence of a single age cohort in most pools though a second age cohort was registered in one pool in August, coinciding with a large flooding. Strong sexual dimorphism in body size was found in C. fulgens throughout the seasonal cycle, while no sexual dimorphism in body size was found in A. minuano. Female‐biased sex ratios were recorded in both common annual fish species in the last three sampling dates (in spring), but not during the first two sampling dates (in winter). The natural lifespan of annual fishes was <8 months. Annual fishes disappeared before habitat desiccation in half of the pools, while non‐annual fishes were still present.     

Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents

The Seine River is strongly affected by the effluents from the Acheres wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was to investigate the diversity of the ammonia-oxidizing bacterial population by identifying autochthonous bacteria from upstream and/or allochthonous ammonia-oxidizing bacteria from the WWTP effluents. Measurements of potential nitrifying activity, competitive PCR, and denaturing gradient gel electrophoresis (DGGE) of 16S ribosomal DNA fragments specific to ammonia-oxidizing bacteria (AOB) were used to explore the succession and shifts of the ammonia-oxidizing community in the lower Seine River and to analyze the temporal and spatial functioning of the system at several different sampling dates. A major revelation was the stability of the patterns. The CTO primers used in this study (G. A. Kowalchuk, J. R. Stephen, W. D. Boer, J. I. Prosser, T. M. Embley, and J. W. Woldendorp, Appl. Environ. Microbiol. 63:1489-1497, 1997) were shown not to be completely specific to AOB of the beta subclass of Proteobacteria. We further demonstrated that when DGGE patterns are interpreted, all the different bands must be sequenced, as one major DGGE band proved to be affiliated with a group of non-AOB in the beta subclass of Proteobacteria. The majority of AOB (75 to 90%) present in the lower Seine river downstream of the effluent output belong to lineage 6a, represented by Nitrosomonas oligotropha- and Nitrosomonas ureae-like bacteria. This dominant lineage was represented by three bands on the DGGE gel. The major lineage-6a AOB species, introduced by the WWTP effluents, survived and might have grown in the receiving medium far downstream, in the estuary; it represented about 40% of the whole AOB population. The other two species belonging to lineage 6a seem to be autochthonous bacteria. One of them developed a few kilometers downstream of the WWTP effluent input in an ammonia-enriched environment, and the other appeared in the freshwater part of the estuary and was apparently more adapted to estuarine conditions, i.e., an increase in the amount of suspended matter, a low ammonia concentration, and high turnover of organic matter. The rest of the AOB population was represented in equal proportions by Nitrosospira- and Nitrosococcus mobilis-like species.