amoA Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary,United Kingdom

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]⁻¹ day⁻¹ in June, increasing to 37.4 μmol N gdw⁻¹ day⁻¹ in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw⁻¹ day⁻¹ in June, increasing to 11.7 μmol N gdw⁻¹ day⁻¹ in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.     

Variation in Nitrate Accumulation, Nitrate Reductase Activity and Nitrite Reductase Activity along Primary and Nodal Roots of Corn (Zea mays L.) Seedlings

Significant differences in NO₃ accumulation and nitrate reductaseactivity (NRA) were noted in the successive segments of developingyoung primary and nodal roots. This variation was also foundto be a function of root age. Nitrite reductase activity (NiRA)on the other hand had little variation among various segmentsof primary and nodal roots and also as a function of root age.These data suggest root NO₃ accumulation and root NRA are twoprocesses which are not directly linked. ¹ Present address: Division of Plant Physiology, Indian AgriculturalResearch Institute, New Delhi-110012, India. (Received December 3, 1983; Accepted June 18, 1983)     

Decreasing Abundance,Increasing Diversity and Changing Structure of the Wild Bee Community (Hymenoptera: Anthophila) along an Urbanization Gradient

Background

Wild bees are important pollinators that have declined in diversity and abundance during the last decades. Habitat destruction and fragmentation associated with urbanization are reported as part of the main causes of this decline. Urbanization involves dramatic changes of the landscape, increasing the proportion of impervious surface while decreasing that of green areas. Few studies have investigated the effects of urbanization on bee communities. We assessed changes in the abundance, species richness, and composition of wild bee community along an urbanization gradient.

Methodology/Principal Findings

Over two years and on a monthly basis, bees were sampled with colored pan traps and insect nets at 24 sites located along an urbanization gradient. Landscape structure within three different radii was measured at each study site. We captured 291 wild bee species. The abundance of wild bees was negatively correlated with the proportion of impervious surface, while species richness reached a maximum at an intermediate (50%) proportion of impervious surface. The structure of the community changed along the urbanization gradient with more parasitic species in sites with an intermediate proportion of impervious surface. There were also greater numbers of cavity-nesting species and long-tongued species in sites with intermediate or higher proportion of impervious surface. However, urbanization had no effect on the occurrence of species depending on their social behavior or body size.

Conclusions/Significance

We found nearly a third of the wild bee fauna known from France in our study sites. Indeed, urban areas supported a diverse bee community, but sites with an intermediate level of urbanization were the most speciose ones, including greater proportion of parasitic species. The presence of a diverse array of bee species even in the most urbanized area makes these pollinators worthy of being a flagship group to raise the awareness of urban citizens about biodiversity.     

Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

Steep vertical gradients of oxidants (O₂ and NO₃⁻) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities.     

Reproductive Biology of an Amphicarpic Annual, Polygonum thunbergii (Polygonaceae): Spatio-temporal Changes in Growth, Structure and Reproductive Components of a Population over an Environmental Gradient

Abstract The process and mechanisms of spatio-temporal changes in growth, population structure, as well as various yield and reproductive components of a population of an amphicarpic annual, Polygonum thunbergii (Polygonaceae), with two reproductive systems (aerial chasmogamous flowers and subterranean cleistogamous flowers) along an environmental gradient (light, moisture and soil nitrogen levels) were investigated in the field.
The results clearly demonstrate that growth and allocation patterns, population structure, and reproductive output of individuals changed sharply along the environmental gradient in response to seasonal and spatial changes in resource availability. Models predicted that light conditions bring about one-sided competition, whereas nutrient conditions in the soil engender two-sided competition. As expected, the degree of one-sided competition was prominent in the case of a planophile, Polygonum thunbergii. Allocation patterns, seed outputs, individual seed size as well as relative energy costs of chasmogamous and cleistogamous seed as affected by light and nutrient levels were also critically analyzed. The most noteworthy finding was that the size of chasmogamous seeds sharply decreased in response to a decrease in the light regime, while cleistogamous seed size remained constant along the gradient. However, relative cost of both chasmogamous and cleistogamous seeds sharply increased with decrease in the light level, reflecting different degrees of environmental stress, biotic interference, or both.     

Decline of Photosynthetic Pigments,Ribulose-1,5-Bisphosphate Carboxylase and Soluble Protein Contents,Nitrate Reductase and Photosynthetic Activities,and Changes in Thylakoid Membrane Protein Pattern in Canopy Shade Grapevine (Vitis Vinifera L. cv. Moscato Giallo) Leaves

In canopy shade leaves of grapevine (Vitis vinifera L. cv. Moscato giallo) grown in the field the contents of chlorophyll (Chl), carotenoids (Car), and soluble protein per fresh mass were lower than in sun leaves. RuBPC activity, in vivo nitrate reductase activity (indicator of nitrate utilisation), apparent electron transport rate, and photochemical fluorescence quenching were also significantly reduced in canopy shade leaves. When various photosynthetic activities were followed in isolated thylakoids, canopy shade leaves exerted a marked inhibition of whole chain and photosystem (PS) 2 activity. Smaller inhibition of PS1 activity was observed even in high-level canopy shade (HS) leaves. The artificial exogenous electron donors, DPC and NH₂OH, significantly restored the loss of PS2 activity in HS leaves. Similar results were obtained when F_v/F_m was evaluated by Chl fluorescence measurements. The marked loss of PS2 activity in canopy shade leaves was due to the loss of 47, 43, 33, 28–25, 23, 17, and 10 kDa polypeptides.     

Gene Expression Profiles of Spleen, Liver, and Head Kidney in Turbot (Scophthalmus maximus) Along the Infection Process with Philasterides dicentrarchi Using an Immune-Enriched Oligo-Microarray

We evaluated the expression profiles of turbot in spleen, liver, and head kidney across five temporal points of the Philasterides dicentrarchi infection process using an 8x15K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify 221 differentially expressed (DE) genes (8.1% of the whole microarray), 113 in spleen, 83 in liver, and 90 in head kidney, in at least 1 of the 5 temporal points sampled for each organ. Most of these genes could be annotated (83.0%) and functionally categorized using GO terms (69.1%) after the additional sequencing of DE genes from the 5' end. Many DE genes were related to innate and acquired immune functions. A high proportion of DE genes were organ-specific (70.6%), although their associated GO functions showed notable similarities in the three organs. The most striking difference in functional distribution was observed between the up- and downregulated gene groups. Upregulated genes were mostly associated to immune functions, while downregulated ones mainly involved metabolism-related genes. Genetic response appeared clustered in a few groups of genes with similar expression profiles along the temporal series. The information obtained will aid to understand the turbot immune response and will specifically be valuable to develop strategies of defense to P. dicentrarchi to achieve more resistant broodstocks for turbot industry.     

Gene Expression Profiles of the Spleen, Liver, and Head Kidney in Turbot (Scophthalmus maximus) Along the Infection Process with Aeromonas salmonicida Using an Immune-Enriched Oligo-microarray

We evaluated the expression profiles of turbot in the spleen, liver, and head kidney across five temporal points of the Aeromonas salmonicida infection process using an 8?×?15?K Agilent oligo-microarray. The microarray included 2,176 different fivefold replicated gene probes designed from a turbot 3' sequenced EST database. We were able to identify 471 differentially expressed (DE) genes (17.3% of the whole microarray), 223 in the spleen, 246 in the liver, and 125 in the head kidney, in at least one of the five temporal points sampled for each organ. Most of these genes could be annotated (83.0%) and functionally categorized using Gene Ontology terms (69.1%) after the additional sequencing of DE genes from the 5' end. Many DE genes were related to innate and acquired immune functions in accordance to previous studies with this pathogen in other fish species. A high proportion of DE genes were organ specific (77.1%), but their associated GO functions were rather similar in the three organs. The most striking difference in functional distribution was observed between the up- and down-regulated gene groups. Up-regulated genes were mostly associated to key immune functions while down-regulated ones mainly involved metabolism- and transport-related genes. Genetic response appeared clustered in groups of genes with similar expression profiles along the temporal series. The spleen showed the most clustering while the liver and head kidney displayed a higher diversification. The information obtained will aid to understand the turbot immune response and will specifically be valuable to develop strategies of defense to A. salmonicida to achieve more resistant broodstocks for turbot industry.