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Sample records for abundance distribution diversity

  1. Liana Abundance, Diversity, and Distribution on Barro Colorado Island, Panama

    PubMed Central

    Schnitzer, Stefan A.; Mangan, Scott A.; Dalling, James W.; Baldeck, Claire A.; Hubbell, Stephen P.; Ledo, Alicia; Muller-Landau, Helene; Tobin, Michael F.; Aguilar, Salomon; Brassfield, David; Hernandez, Andres; Lao, Suzanne; Perez, Rolando; Valdes, Oldemar; Yorke, Suzanne Rutishauser

    2012-01-01

    Lianas are a key component of tropical forests; however, most surveys are too small to accurately quantify liana community composition, diversity, abundance, and spatial distribution – critical components for measuring the contribution of lianas to forest processes. In 2007, we tagged, mapped, measured the diameter, and identified all lianas ≥1 cm rooted in a 50-ha plot on Barro Colorado Island, Panama (BCI). We calculated liana density, basal area, and species richness for both independently rooted lianas and all rooted liana stems (genets plus clones). We compared spatial aggregation patterns of liana and tree species, and among liana species that varied in the amount of clonal reproduction. We also tested whether liana and tree densities have increased on BCI compared to surveys conducted 30-years earlier. This study represents the most comprehensive spatially contiguous sampling of lianas ever conducted and, over the 50 ha area, we found 67,447 rooted liana stems comprising 162 species. Rooted lianas composed nearly 25% of the woody stems (trees and lianas), 35% of woody species richness, and 3% of woody basal area. Lianas were spatially aggregated within the 50-ha plot and the liana species with the highest proportion of clonal stems more spatially aggregated than the least clonal species, possibly indicating clonal stem recruitment following canopy disturbance. Over the past 30 years, liana density increased by 75% for stems ≥1 cm diameter and nearly 140% for stems ≥5 cm diameter, while tree density on BCI decreased 11.5%; a finding consistent with other neotropical forests. Our data confirm that lianas contribute substantially to tropical forest stem density and diversity, they have highly clumped distributions that appear to be driven by clonal stem recruitment into treefall gaps, and they are increasing relative to trees, thus indicating that lianas will play a greater role in the future dynamics of BCI and other neotropical forests. PMID:23284889

  2. Distribution, abundance and diversity of the extremely halophilic bacterium Salinibacter ruber

    PubMed Central

    Antón, Josefa; Peña, Arantxa; Santos, Fernando; Martínez-García, Manuel; Schmitt-Kopplin, Philippe; Rosselló-Mora, Ramon

    2008-01-01

    Since its discovery in 1998, representatives of the extremely halophilic bacterium Salinibacter ruber have been found in many hypersaline environments across the world, including coastal and solar salterns and solar lakes. Here, we review the available information about the distribution, abundance and diversity of this member of the Bacteroidetes. PMID:18957079

  3. Distribution, abundance and diversity of crustose coralline algae on the Great Barrier Reef

    NASA Astrophysics Data System (ADS)

    Dean, Angela J.; Steneck, Robert S.; Tager, Danika; Pandolfi, John M.

    2015-06-01

    The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem. Crustose coralline algae (CCA) are important contributors to reef calcium carbonate and can facilitate coral recruitment. Despite the importance of CCA, little is known about species-level distribution, abundance, and diversity, and how these vary across the continental shelf and key habitat zones within the GBR. We quantified CCA species distributions using line transects ( n = 127) at 17 sites in the northern and central regions of the GBR, distributed among inner-, mid-, and outer-shelf regions. At each site, we identified CCA along replicate transects in three habitat zones: reef flat, reef crest, and reef slope. Taxonomically, CCA species are challenging to identify (especially in the field), and there is considerable disagreement in approach. We used published, anatomically based taxonomic schemes for consistent identification. We identified 30 CCA species among 12 genera; the most abundant species were Porolithon onkodes, Paragoniolithon conicum (sensu Adey), Neogoniolithon fosliei, and Hydrolithon reinboldii. Significant cross-shelf differences were observed in CCA community structure and CCA abundance, with inner-shelf reefs exhibiting lower CCA abundance than outer-shelf reefs. Shelf position, habitat zone, latitude, depth, and the interaction of shelf position and habitat were all significantly associated with variation in composition of CCA communities. Collectively, shelf position, habitat, and their interaction contributed to 22.6 % of the variation in coralline communities. Compared to mid- and outer-shelf sites, inner-shelf sites exhibited lower relative abundances of N. fosliei and Lithophyllum species. Reef crest habitats exhibited greater abundance of N. fosliei than reef flat and reef slope habitats. Reef slope habitats exhibited lower abundance of P. onkodes, but greater abundance of Neogoniolithon clavycymosum than reef crest and reef slope habitats. These findings

  4. [Diversity, abundance and distribution of benthic macrofauna on rocky shores from North Sucre State, Venezuela].

    PubMed

    Fernandez, Johanna; Jiménez, Mayré; Allen, Thays

    2014-09-01

    The rocky intertidal zone is among the most extreme physical environments on Earth. Organisms living in this area are constantly stricken by physico-chemical and biological factors. Due to the ecological importance of these areas, we studied the diversity, abundance and distribution of the rocky coastline benthic macrofauna, from the North coast of Sucre State, Venezuela. We performed bimonthly samplings from November 2008 to September 2009. The collection of biological material in the littoral zone (supra, mid and infralittoral) was done manually with a grid of 0.25m2. Organisms were preserved in 10% formalin for later identification and analysis (ecological parameters and Kruskal-Wallis test to the abundance and diversity). We found a total 19,020 organisms (86 spp.), in 8 phyla, 45 families and 47 genera. Mollusks were the most abundant and diverse (58 spp.), followed by arthropods (12 spp.), annelids (7 spp.), echinoderms (5 spp.), and the less represented cnidarians, sipunculids, nemertinids and urochordates (1 sp.). The zonation found coincided with the universal scheme of zonation. The towns of Rio Boca and Rio Caribe presented the highest values of ecological parameters, and the lowest were found in Playa Grande. Statistical significant differences were found in the abundance and diversity of macrofauna among the three zones. The little information on the composition and distribution of macrobenthic rocky coastline, prevents a better comparison, however the results contribute to the knowledge of the marine biodiversity in this region.

  5. Abundance, distribution, and diversity of viruses in alkaline, hypersaline Mono Lake, California.

    PubMed

    Jiang, S; Steward, G; Jellison, R; Chu, W; Choi, S

    2004-01-01

    Mono Lake is a large (180 km2), alkaline (pH approximately 10), moderately hypersaline (70-85 g kg(-1)) lake lying at the western edge of the Great Basin. An episode of persistent chemical stratification (meromixis) was initiated in 1995 and has resulted in depletion of oxygen and accumulation of ammonia and sulfide beneath the chemocline. Although previous studies have documented high bacterial abundances and marked seasonal changes in phytoplankton abundance and community composition, there have been no previous reports on the occurrence of viruses in this unique lake. Based on the high concentrations and diversity of microbial life in this lake, we hypothesized that planktonic viruses are also abundant and diverse. To examine the abundance and distribution of viruses and bacteria, water samples were collected from four stations along 5 to 15 vertical depths at each station. Viral abundance ranged from 1 x 10(8) to 1 x 10(9) mL(-1), among the highest observed in any natural aquatic system examined so far. Increases (p < 0.1) in viral densities were observed in the anoxic bottom water at multiple stations. However, regression analysis indicated that viral abundance could not be predicted by any single environmental parameter. Pulsed field gel electrophoresis revealed a diverse viral community in Mono Lake with genome sizes ranging from approximately 14 to >400 kb with most of the DNA in the 30 to 60 kb size range. Cluster analysis grouped the anoxic bottom-water viral community into a unique cluster differentiating it from surface and mid-water viral communities. A hybridization study using an indigenous viral isolate as a probe revealed an episodic pattern of temporal phage distribution with strong niche stratification between oxic and anoxic waters.

  6. Using species abundance distribution models and diversity indices for biogeographical analyses

    NASA Astrophysics Data System (ADS)

    Fattorini, Simone; Rigal, François; Cardoso, Pedro; Borges, Paulo A. V.

    2016-01-01

    We examine whether Species Abundance Distribution models (SADs) and diversity indices can describe how species colonization status influences species community assembly on oceanic islands. Our hypothesis is that, because of the lack of source-sink dynamics at the archipelago scale, Single Island Endemics (SIEs), i.e. endemic species restricted to only one island, should be represented by few rare species and consequently have abundance patterns that differ from those of more widespread species. To test our hypothesis, we used arthropod data from the Azorean archipelago (North Atlantic). We divided the species into three colonization categories: SIEs, archipelagic endemics (AZEs, present in at least two islands) and native non-endemics (NATs). For each category, we modelled rank-abundance plots using both the geometric series and the Gambin model, a measure of distributional amplitude. We also calculated Shannon entropy and Buzas and Gibson's evenness. We show that the slopes of the regression lines modelling SADs were significantly higher for SIEs, which indicates a relative predominance of a few highly abundant species and a lack of rare species, which also depresses diversity indices. This may be a consequence of two factors: (i) some forest specialist SIEs may be at advantage over other, less adapted species; (ii) the entire populations of SIEs are by definition concentrated on a single island, without possibility for inter-island source-sink dynamics; hence all populations must have a minimum number of individuals to survive natural, often unpredictable, fluctuations. These findings are supported by higher values of the α parameter of the Gambin mode for SIEs. In contrast, AZEs and NATs had lower regression slopes, lower α but higher diversity indices, resulting from their widespread distribution over several islands. We conclude that these differences in the SAD models and diversity indices demonstrate that the study of these metrics is useful for

  7. Distribution, abundance, diversity and habitat associations of fishes across a bioregion experiencing rapid coastal development

    NASA Astrophysics Data System (ADS)

    McLean, Dianne L.; Langlois, Tim J.; Newman, Stephen J.; Holmes, Thomas H.; Birt, Matthew J.; Bornt, Katrina R.; Bond, Todd; Collins, Danielle L.; Evans, Scott N.; Travers, Michael J.; Wakefield, Corey B.; Babcock, Russ C.; Fisher, Rebecca

    2016-09-01

    Knowledge of the factors that influence spatial patterns in fish abundance, distribution and diversity are essential for informing fisheries and conservation management. The present study was conducted in the nearshore Pilbara bioregion of north-western Australia where the dynamic marine environment is characterised by large embayments, numerous islands and islets, coexisting with globally significant petrochemical and mineral industries. Within Western Australia, this nearshore bioregion has high biodiversity and is considered to play an essential role in the recruitment of species of commercial importance. To better inform future investigations into both ecological processes and planning scenarios for management, a rapid assessment of the distribution, abundance and associations with nearshore habitats of fishes across the region was conducted. Baited remote underwater stereo-video systems (stereo-BRUVs) were used to simultaneously sample the fish assemblage and habitat composition. Generalised additive mixed models (GAMMs) were used to determine whether the abundance of fishes were related to habitat and a range of environmental variables (visibility, depth, distance to 30 m and 200 m depth isobars, boat ramps and the nearest large embayment (Exmouth Gulf). A diverse fish assemblage comprising 343 species from 58 families was recorded. The abundance and distribution patterns of fishery-target species and of the five most common and abundant species and families were linked positively with areas of high relief, hard coral cover, reef and macroalgae and negatively with the distance to the nearest oceanic waters (200 m depth isobar). This study provides information that can contribute to future marine spatial planning scenarios for management of the Pilbara using a unique, analytical approach that has broad application in biogeography.

  8. Distribution, abundance, and diversity patterns of the thermoacidophilic "deep-sea hydrothermal vent euryarchaeota 2".

    PubMed

    Flores, Gilberto E; Wagner, Isaac D; Liu, Yitai; Reysenbach, Anna-Louise

    2012-01-01

    Cultivation-independent studies have shown that taxa belonging to the "deep-sea hydrothermal vent euryarchaeota 2" (DHVE2) lineage are widespread at deep-sea hydrothermal vents. While this lineage appears to be a common and important member of the microbial community at vent environments, relatively little is known about their overall distribution and phylogenetic diversity. In this study, we examined the distribution, relative abundance, co-occurrence patterns, and phylogenetic diversity of cultivable thermoacidophilic DHVE2 in deposits from globally distributed vent fields. Results of quantitative polymerase chain reaction assays with primers specific for the DHVE2 and Archaea demonstrate the ubiquity of the DHVE2 at deep-sea vents and suggest that they are significant members of the archaeal communities of established vent deposit communities. Local similarity analysis of pyrosequencing data revealed that the distribution of the DHVE2 was positively correlated with 10 other Euryarchaeota phylotypes and negatively correlated with mostly Crenarchaeota phylotypes. Targeted cultivation efforts resulted in the isolation of 12 axenic strains from six different vent fields, expanding the cultivable diversity of this lineage to vents along the East Pacific Rise and Mid-Atlantic Ridge. Eleven of these isolates shared greater than 97% 16S rRNA gene sequence similarity with one another and the only described isolate of the DHVE2, Aciduliprofundum boonei T469(T). Sequencing and phylogenetic analysis of five protein-coding loci, atpA, EF-2, radA, rpoB, and secY, revealed clustering of isolates according to geographic region of isolation. Overall, this study increases our understanding of the distribution, abundance, and phylogenetic diversity of the DHVE2.

  9. Seeding Method Influences Warm-Season Grass Abundance and Distribution but not Local Diversity in Grassland Restoration

    USGS Publications Warehouse

    Yurkonis, K.A.; Wilsey, B.J.; Moloney, K.A.; Drobney, P.; Larson, D.L.

    2010-01-01

    Ecological theory predicts that the arrangement of seedlings in newly restored communities may influence future species diversity and composition. We test the prediction that smaller distances between neighboring seeds in drill seeded grassland plantings would result in lower species diversity, greater weed abundance, and larger conspecific patch sizes than otherwise similar broadcast seeded plantings. A diverse grassland seed mix was either drill seeded, which places seeds in equally spaced rows, or broadcast seeded, which spreads seeds across the ground surface, into 24 plots in each of three sites in 2005. In summer 2007, we measured species abundance in a 1 m2 quadrat in each plot and mapped common species within the quadrat by recording the most abundant species in each of 64 cells. Quadrat-scale diversity and weed abundance were similar between drilled and broadcast plots, suggesting that processes that limited establishment and controlled invasion were not affected by such fine-scale seed distribution. However, native warm-season (C4) grasses were more abundant and occurred in less compact patches in drilled plots. This difference in C4 grass abundance and distribution may result from increased germination or vegetative propagation of C4 grasses in drilled plots. Our findings suggest that local plant density may control fine-scale heterogeneity and species composition in restored grasslands, processes that need to be further investigated to determine whether seed distributions can be manipulated to increase diversity in restored grasslands. ?? 2010 Society for Ecological Restoration International.

  10. Seeding method influences warm-season grass abundance and distribution but not local diversity in grassland restoration

    USGS Publications Warehouse

    Yurkonis, Kathryn A.; Wilsey, Brian J.; Moloney, Kirk A.; Drobney, Pauline; Larson, Diane L.

    2010-01-01

    Ecological theory predicts that the arrangement of seedlings in newly restored communities may influence future species diversity and composition. We test the prediction that smaller distances between neighboring seeds in drill seeded grassland plantings would result in lower species diversity, greater weed abundance, and larger conspecific patch sizes than otherwise similar broadcast seeded plantings. A diverse grassland seed mix was either drill seeded, which places seeds in equally spaced rows, or broadcast seeded, which spreads seeds across the ground surface, into 24 plots in each of three sites in 2005. In summer 2007, we measured species abundance in a 1 m2 quadrat in each plot and mapped common species within the quadrat by recording the most abundant species in each of 64 cells. Quadrat-scale diversity and weed abundance were similar between drilled and broadcast plots, suggesting that processes that limited establishment and controlled invasion were not affected by such fine-scale seed distribution. However, native warm-season (C4) grasses were more abundant and occurred in less compact patches in drilled plots. This difference in C4 grass abundance and distribution may result from increased germination or vegetative propagation of C4 grasses in drilled plots. Our findings suggest that local plant density may control fine-scale heterogeneity and species composition in restored grasslands, processes that need to be further investigated to determine whether seed distributions can be manipulated to increase diversity in restored grasslands.

  11. Distribution, Abundance, and Diversity Patterns of the Thermoacidophilic “Deep-Sea Hydrothermal Vent Euryarchaeota 2”

    PubMed Central

    Flores, Gilberto E.; Wagner, Isaac D.; Liu, Yitai; Reysenbach, Anna-Louise

    2011-01-01

    Cultivation-independent studies have shown that taxa belonging to the “deep-sea hydrothermal vent euryarchaeota 2” (DHVE2) lineage are widespread at deep-sea hydrothermal vents. While this lineage appears to be a common and important member of the microbial community at vent environments, relatively little is known about their overall distribution and phylogenetic diversity. In this study, we examined the distribution, relative abundance, co-occurrence patterns, and phylogenetic diversity of cultivable thermoacidophilic DHVE2 in deposits from globally distributed vent fields. Results of quantitative polymerase chain reaction assays with primers specific for the DHVE2 and Archaea demonstrate the ubiquity of the DHVE2 at deep-sea vents and suggest that they are significant members of the archaeal communities of established vent deposit communities. Local similarity analysis of pyrosequencing data revealed that the distribution of the DHVE2 was positively correlated with 10 other Euryarchaeota phylotypes and negatively correlated with mostly Crenarchaeota phylotypes. Targeted cultivation efforts resulted in the isolation of 12 axenic strains from six different vent fields, expanding the cultivable diversity of this lineage to vents along the East Pacific Rise and Mid-Atlantic Ridge. Eleven of these isolates shared greater than 97% 16S rRNA gene sequence similarity with one another and the only described isolate of the DHVE2, Aciduliprofundum boonei T469T. Sequencing and phylogenetic analysis of five protein-coding loci, atpA, EF-2, radA, rpoB, and secY, revealed clustering of isolates according to geographic region of isolation. Overall, this study increases our understanding of the distribution, abundance, and phylogenetic diversity of the DHVE2. PMID:22363325

  12. Diversity, Abundance, and Distribution of nirS-Harboring Denitrifiers in Intertidal Sediments of the Yangtze Estuary.

    PubMed

    Zheng, Yanling; Hou, Lijun; Liu, Min; Gao, Juan; Yin, Guoyu; Li, Xiaofei; Deng, Fengyu; Lin, Xianbiao; Jiang, Xiaofen; Chen, Fei; Zong, Haibo; Zhou, Junliang

    2015-07-01

    Denitrification plays a critical role in nitrogen removal in estuarine and coastal ecosystems. In this study, the community composition, diversity, abundance, and distribution of cytochrome cd1-type nitrite reductase gene (nirS)-harboring denitrifiers in intertidal sediments of the Yangtze Estuary were analyzed using polymerase chain reaction (PCR)-based clone libraries and quantitative PCR techniques. Clone library analysis showed that the nirS-encoding bacterial biodiversity was significantly higher at the lower salinity sites than at the higher salinity sites. However, there was no significant seasonal difference in the nirS gene diversity between summer and winter. Phylogenetic analysis revealed that the nirS-harboring denitrifier communities at the study area had distinctive spatial heterogeneity along the estuary. At the lower salinity sites, the nirS-harboring bacterial community was co-dominated by clusters III and VII; while at the higher salinity sites, it was dominated by cluster I. Canonical correspondence analysis indicated that the community compositions of nirS-type denitrifiers were significantly correlated with salinity, ammonium, and nitrate. Quantitative PCR results showed that the nirS gene abundance was in the range of 1.01 × 10(6) to 9.00 × 10(7) copies per gram dry sediment, without significant seasonal variation. Among all the environmental factors, the nirS gene abundance was only significantly related to the change of salinity. These results can extend our current knowledge about the composition and dynamics of denitrification microbial community in the estuarine ecosystem.

  13. Perceptions of species abundance, distribution, and diversity: Lessons from four decades of sampling on a government-managed reserve

    USGS Publications Warehouse

    Gibbons, J. Whitfield; Burke, Vincent J.; Lovich, Jefferey E.; Semlitsch, Raymond D.; Tuberville, Tracey D.; Bodie, J. Russell; Greene, Judith L.; Niewiarowski, Peter H.; Whiteman, Howard H.; Scott, David E.; Pechmann, Joseph H. K.; Harrison, Christopher R.; Bennett, Stephen H.; Krenz, John D.; Mills, Mark S.; Buhlmann, Kurt A.; Lee, John R.; Seigel, Richard A.; Tucker, Anton D.; Mills, Tony M.; Lamb, Trip; Dorcas, Michael E.; Congdon, Justin D.; Smith, Michael H.; Nelson, David H.; Dietsch, M. Barbara; Hanlin, Hugh G.; Ott, Jeannine A.; Karapatakis, Deno J.

    1997-01-01

    We examined data relative to species abundance, distribution, and diversity patterns of reptiles and amphibians to determine how perceptions change over time and with level of sampling effort. Location data were compiled on more than one million individual captures or observations of 98 species during a 44-year study period on the US Department of Energy’s (DOE) Savannah River Site National Environmental Research Park (SRS-NERP) in South Carolina. We suggest that perceptions of herpetofaunal species diversity are strongly dependent on level of effort and that land management decisions based on short-term data bases for some faunal groups could result in serious errors in environmental management. We provide evidence that acquiring information on biodiversity distribution patterns is compatible with multiyear spatially extensive research programs and also provide a perspective of what might be achieved if long-term, coordinated research efforts were instituted nationwide. To conduct biotic surveys on government-managed lands, we recommend revisions in the methods used by government agencies to acquire and report biodiversity data. We suggest that government and industry employees engaged in biodiversity survey efforts develop proficiency in field identification for one or more major taxonomic groups and be encouraged to measure the status of populations quantitatively with consistent and reliable methodologies. We also suggest that widespread academic cooperation in the dissemination of information on regional patterns of biodiversity could result by establishment of a peer-reviewed, scientifically rigorous journal concerned with status and trends of the biota of the United States.

  14. Spatial Patterns in the Distribution, Diversity and Abundance of Benthic Foraminifera around Moorea (Society Archipelago, French Polynesia)

    PubMed Central

    2015-01-01

    Coral reefs are now subject to global threats and influences from numerous anthropogenic sources. Foraminifera, a group of unicellular shelled organisms, are excellent indicators of water quality and reef health. Thus we studied a set of samples taken in 1992 to provide a foraminiferal baseline for future studies of environmental change. Our study provides the first island-wide analysis of shallow benthic foraminifera from around Moorea (Society Archipelago). We analyzed the composition, species richness, patterns of distribution and abundance of unstained foraminiferal assemblages from bays, fringing reefs, nearshore and back- and fore-reef environments. A total of 380 taxa of foraminifera were recorded, a number that almost doubles previous species counts. Spatial patterns of foraminiferal assemblages are characterized by numerical abundances of individual taxa, cluster groups and gradients of species richness, as documented by cluster, Fisher α, ternary plot and Principal Component Analyses (PCA). The inner bay inlets are dominated by stress-tolerant, mostly thin-shelled taxa of Bolivina, Bolivinella, Nonionoides, Elongobula, and Ammonia preferring low-oxygen and/or nutrient-rich habitats influenced by coastal factors such as fresh-water runoff and overhanging mangroves. The larger symbiont-bearing foraminifera (Borelis, Amphistegina, Heterostegina, Peneroplis) generally live in the oligotrophic, well-lit back- and fore-reef environments. Amphisteginids and peneroplids were among the few taxa found in the bay environments, probably due to their preferences for phytal substrates and tolerance to moderate levels of eutrophication. The fringing reef environments along the outer bay are characterized by Borelis schlumbergeri, Heterostegina depressa, Textularia spp. and various miliolids which represent a hotspot of diversity within the complex reef-lagoon system of Moorea. The high foraminiferal Fisher α and species richness diversity in outer bay fringing reefs

  15. Diversity, abundance, and spatial distribution of riverine microbial communities response to effluents from swine farm versus farmhouse restaurant.

    PubMed

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-09-01

    The 454 pyrosequencing technique was applied to evaluate microbial community composition in sediment and water samples collected from the river receiving effluents from a swine farm and a farmhouse restaurant, respectively. For each sample, 4,600 effective sequences were selected and used to do the bacterial diversity and abundance analysis, respectively. Bacterial phylotype richness in the river sediment sample without effluent input was higher than the other samples, and the river water sample with addition of effluent from the swine farm had the least richness. Effluents from both the swine farm and the farmhouse restaurant have the potential to decrease the bacterial diversity and abundance in the river sediment and water, especially it is more significant in the river sediment. Effect of effluent from the swine farm on riverine bacterial communities was more significant than that from the farmhouse restaurant. Characterization of bacterial community composition in sediments from two tributaries of the downstream river showed that various effluents from the swine farm and the farmhouse restaurant have the similar potential to reduce the natural variability in riverine ecosystems, and contribute to the biotic homogenization in the river sediment.

  16. Diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface sediments of the South China Sea.

    PubMed

    Li, M; Hong, Y; Cao, H; Klotz, M G; Gu, J-D

    2013-03-01

    In marine ecosystems, both nitrite-reducing bacteria and anaerobic ammonium-oxidizing (anammox) bacteria, containing different types of NO-forming nitrite reductase-encoding genes, contribute to the nitrogen cycle. The objectives of study were to reveal the diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface environments. Results showed that higher diversity and abundance of nirS gene than nirK and Scalindua-nirS genes were evident in the sediments of the South China Sea (SCS), indicating bacteria containing nirS gene dominated the NO-forming nitrite-reducing microbial community in this ecosystem. Similar diversity and abundance distribution patterns of both nirS and Scalindua-nirS genes were detected in this study sites, but different from nirK gene. Further statistical analyses also showed both nirS and Scalindua-nirS genes respond similarly to environmental factors, but differed from nirK gene. These results suggest that bacteria containing nirS and Scalindua-nirS genes share similar niche in deep-sea subsurface sediments of the SCS, but differed from those containing nirK gene, indicating that community structures of nitrite-reducing bacteria are segregated by the functional modules (NirS vs. NirK) rather than the competing processes (anammox vs. classical denitrification).

  17. Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea.

    PubMed

    Dang, Hongyue; Luan, Xi-Wu; Chen, Ruipeng; Zhang, Xiaoxia; Guo, Lizhong; Klotz, Martin G

    2010-06-01

    The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.

  18. Effects of private-land use, livestock management, and human tolerance on diversity, distribution, and abundance of large african mammals.

    PubMed

    Kinnaird, Margaret F; O'brien, Timothy G

    2012-12-01

    Successful conservation of large terrestrial mammals (wildlife) on private lands requires that landowners be empowered to manage wildlife so that benefits outweigh the costs. Laikipia County, Kenya, is predominantly unfenced, and the land uses in the area allow wide-ranging wildlife to move freely between different management systems on private land. We used camera traps to sample large mammals associated with 4 different management systems (rhinoceros sanctuaries, no livestock; conservancies, intermediate stocking level; fenced ranches, high stocking level; and group ranches, high stocking level, no fencing, pastoralist clan ownership) to examine whether management and stocking levels affect wildlife. We deployed cameras at 522 locations across 8 properties from January 2008 through October 2010 and used the photographs taken during this period to estimate richness, occupancy, and relative abundance of species. Species richness was highest in conservancies and sanctuaries and lowest on fenced and group ranches. Occupancy estimates were, on average, 2 and 5 times higher in sanctuaries and conservancies as on fenced and group ranches, respectively. Nineteen species on fenced ranches and 25 species on group ranches were considered uncommon (occupancy < 0.1). The relative abundance of most species was highest or second highest in sanctuaries and conservancies. Lack of rights to manage and utilize wildlife and uncertain land tenure dampen many owners' incentives to tolerate wildlife. We suggest national conservation strategies consider landscape-level approaches to land-use planning that aim to increase conserved areas by providing landowners with incentives to tolerate wildlife. Possible incentives include improving access to ecotourism benefits, forging agreements to maintain wildlife habitat and corridors, resolving land-ownership conflicts, restoring degraded rangelands, expanding opportunities for grazing leases, and allowing direct benefits to landowners through

  19. Distribution, abundance, biomass and diversity of benthic infauna in the Northeast Chukchi Sea, Alaska: Relation to environmental variables and marine mammals

    NASA Astrophysics Data System (ADS)

    Schonberg, Susan V.; Clarke, Janet T.; Dunton, Kenneth H.

    2014-04-01

    In summer 2009 and 2010, as part of Chukchi Sea Offshore Monitoring in Drilling Area - Chemical and Benthos (COMIDA CAB) program, we performed a quantitative assessment of the biomass, abundance, and community structure of benthic infaunal populations of the Northeastern Chukchi Sea. This analysis documented a benthic species inventory of 361 taxa collected from 142 individual van Veen grab samples (0.1 m-2) at 52 stations. Infaunal abundance was dominated by Polychaeta, Mollusca, and Crustacea. Large concentrations of bivalves (up to 1235 m-2; 920.2 gww m-2) were collected south of Hanna Shoal where flow from two water masses converge and deposit labile carbon to the seafloor, as indicated by low surface sediment C:N ratios. Amphipods (up to 1640 m-2; 26.0 gww m-2), and polychaetes (up to 4665 m-2; 114.7 gww m-2) were documented from multiple stations west of and within Barrow Canyon. This high productivity was most likely due to the "canyon effect", where marine and coastal detrital carbon supplies are channeled by the canyon structure, enhancing carbon deposition and flux, which supports rich benthic communities within the canyon and surrounding areas. To examine the relationships between infaunal distributions of all collected taxa with the physical environment, we used a Biota and Environment matching (BIO-ENV) routine. A combination of water depth, bottom-water temperature and salinity, surface sediment total organic nitrogen (TON) and sediment C:N molar ratios correlated closest with infaunal abundance distribution (ρ=0.54), indicating that multiple factors influence the success of benthic communities. BIO-ENV routines produced similar correlation results when performed on targeted walrus prey items (bivalves (ρ=0.50), polychaetes (ρ=0.53), but gray whale prey items (amphipods) were not strongly correlated to any combination of physical environmental factors (ρ=0.24). Distributions of primary prey items for gray whales (amphipods) and walruses (bivalves

  20. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    PubMed

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p < 0.05), and decreased in the order of sand > clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p < 0.05), while the total organic carbon contents were positively related to the abundance of bacterial laccase-like genes in particle size fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients.

  1. Foraminifera Species Richness, Abundance, and Diversity Research in Bolinas, California

    NASA Astrophysics Data System (ADS)

    Brunwin, N.; Ingram, Z.; Mendez, M.; Sandoval, K.

    2015-12-01

    Foraminifera are abundant, diverse, respond rapidly to environmental change, and are present in all marine and estuarine environments, making them important indicator species. A survey of occurrence and distribution of foraminifera in the Bolinas Lagoon, Marin County, California was carried out by Hedman in 1975, but no study since has focused on foraminiferal composition within this important ecosystem. In July 2015, the Careers in Science (CiS) Intern Program collected samples at 12 sites previously examined in the 1975 study. Thirty-six samples were collected from the upper few centimeters of sediment from a variety of intertidal and subtidal environments within the lagoon. Foraminifera from each sample were isolated, identified and species richness, abundance and diversity quantified. Furthermore, comparisons of faunal composition represented in our recent collection and that of Hedman's 1975 report are made.

  2. Measuring β-diversity with species abundance data.

    PubMed

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  3. Peudomonas fluorescens diversity and abundance in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Amina, Melinai; Ahmed, Bensoltane; Khaladi, Mederbel

    2010-05-01

    It is now over 30 years since that a several plant associated strains of fluorescent Pseudomonas spp. are known to produce antimicrobial metabolites, playing a significant role in the biological control of a lot of plant diseases. For that, the interest in the use of these bacteria for biocontrol of plant pathogenic agents has increased. However, few comprehensive studies have described the abundance of this soil borne bacteria in the region of Mascara (Northern-Algerian West). In the connection of this problem, this work was done by monitoring the number of indigenous Pseudomonas fluorescens organisms in three stations characterizing different ecosystems, to document their abundance, diversity and investigate the relationship between P. fluorescens abundance and soil properties. Our quantitative plate counting results hence the conception of their ecology in the rhizosphere. Thus, quantitative results has confirmed that P. fluorescens are successful root colonizers with strong predominance and competed for many ecological niche, where their distribution were correlated significantly (P<0.05) with the majority of soil properties. Keywords: P. Fluorescens, Ecosystems, Abundance, Diversity, Correlated, Soil Properties.

  4. Diversity, Abundance, and Spatial Distribution of Sediment Ammonia-Oxidizing Betaproteobacteria in Response to Environmental Gradients and Coastal Eutrophication in Jiaozhou Bay, China▿ †

    PubMed Central

    Dang, Hongyue; Li, Jing; Chen, Ruipeng; Wang, Lin; Guo, Lizhong; Zhang, Zhinan; Klotz, Martin G.

    2010-01-01

    Ongoing anthropogenic eutrophication of Jiaozhou Bay offers an opportunity to study the influence of human activity on bacterial communities that drive biogeochemical cycling. Nitrification in coastal waters appears to be a sensitive indicator of environmental change, suggesting that function and structure of the microbial nitrifying community may be associated closely with environmental conditions. In the current study, the amoA gene was used to unravel the relationship between sediment aerobic obligate ammonia-oxidizing Betaproteobacteria (Beta-AOB) and their environment in Jiaozhou Bay. Protein sequences deduced from amoA gene sequences grouped within four distinct clusters in the Nitrosomonas lineage, including a putative new cluster. In addition, AmoA sequences belonging to three newly defined clusters in the Nitrosospira lineage were also identified. Multivariate statistical analyses indicated that the studied Beta-AOB community structures correlated with environmental parameters, of which nitrite-N and sediment sand content had significant impact on the composition, structure, and distribution of the Beta-AOB community. Both amoA clone library and quantitative PCR (qPCR) analyses indicated that continental input from the nearby wastewater treatment plants and polluted rivers may have significant impact on the composition and abundance of the sediment Beta-AOB assemblages in Jiaozhou Bay. Our work is the first report of a direct link between a sedimentological parameter and the composition and distribution of the sediment Beta-AOB and indicates the potential for using the Beta-AOB community composition in general and individual isolates or environmental clones in the Nitrosomonas oligotropha lineage in particular as bioindicators and biotracers of pollution or freshwater or wastewater input in coastal environments. PMID:20511433

  5. The shape of terrestrial abundance distributions.

    PubMed

    Alroy, John

    2015-09-01

    Ecologists widely accept that the distribution of abundances in most communities is fairly flat but heavily dominated by a few species. The reason for this is that species abundances are thought to follow certain theoretical distributions that predict such a pattern. However, previous studies have focused on either a few theoretical distributions or a few empirical distributions. I illustrate abundance patterns in 1055 samples of trees, bats, small terrestrial mammals, birds, lizards, frogs, ants, dung beetles, butterflies, and odonates. Five existing theoretical distributions make inaccurate predictions about the frequencies of the most common species and of the average species, and most of them fit the overall patterns poorly, according to the maximum likelihood-related Kullback-Leibler divergence statistic. Instead, the data support a low-dominance distribution here called the "double geometric." Depending on the value of its two governing parameters, it may resemble either the geometric series distribution or the lognormal series distribution. However, unlike any other model, it assumes both that richness is finite and that species compete unequally for resources in a two-dimensional niche landscape, which implies that niche breadths are variable and that trait distributions are neither arrayed along a single dimension nor randomly associated. The hypothesis that niche space is multidimensional helps to explain how numerous species can coexist despite interacting strongly.

  6. The shape of terrestrial abundance distributions

    PubMed Central

    Alroy, John

    2015-01-01

    Ecologists widely accept that the distribution of abundances in most communities is fairly flat but heavily dominated by a few species. The reason for this is that species abundances are thought to follow certain theoretical distributions that predict such a pattern. However, previous studies have focused on either a few theoretical distributions or a few empirical distributions. I illustrate abundance patterns in 1055 samples of trees, bats, small terrestrial mammals, birds, lizards, frogs, ants, dung beetles, butterflies, and odonates. Five existing theoretical distributions make inaccurate predictions about the frequencies of the most common species and of the average species, and most of them fit the overall patterns poorly, according to the maximum likelihood–related Kullback-Leibler divergence statistic. Instead, the data support a low-dominance distribution here called the “double geometric.” Depending on the value of its two governing parameters, it may resemble either the geometric series distribution or the lognormal series distribution. However, unlike any other model, it assumes both that richness is finite and that species compete unequally for resources in a two-dimensional niche landscape, which implies that niche breadths are variable and that trait distributions are neither arrayed along a single dimension nor randomly associated. The hypothesis that niche space is multidimensional helps to explain how numerous species can coexist despite interacting strongly. PMID:26601249

  7. Genetic diversity in aspen and its relation to arthropod abundance.

    PubMed

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2014-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen.

  8. Fish abundance, distribution, and habitat use

    NASA Astrophysics Data System (ADS)

    Hoffnagle, Timothy L.; Valdez, Richard A.; Speas, David W.

    The 1996 controlled flood in the Colorado River, Grand Canyon, was designed, in part, to improve conditions for juvenile native fishes by reshaping habitat and displacing non-native fishes. We examined changes in abundance and distributions of native and non-native fishes immediately before and after the controlled flood and recovery of affected species 2.5 and 6 months after. Catch-per-unit-effort (CPUE) of humpback chub and flannelmouth sucker did not differ in pre- versus post-flood periods. CPUE of plains killifish, bluehead sucker and fathead minnow decreased following the flood, and CPUE of speckled dace and rainbow trout increased. Juvenile humpback chub remained primarily along talus shorelines at all discharges, while at higher discharges, speckled dace shifted from mid-channel riffles to debris fans and talus and fathead minnows used primarily vegetated shorelines. There was evidence of some downstream displacement of plains killifish, fathead minnows and rainbow trout. Catch rates of all species showed seasonal variation following the flood, with summer recruitment of young-of-the-year, particularly fathead minnows and plains killifish. Although short-term reductions in catch rates of fathead minnows and plains killifish occurred, these populations returned to pre-flood densities by 6 months after the flood. Catch rates of all species before and after the flood were similar to those recorded in previous years. We determined that the controlled flood did not significantly alter native fish distributions or abundances through Grand Canyon.

  9. Abundance and Distribution of Geographically Isolated ...

    EPA Pesticide Factsheets

    Geographically isolated wetlands (GIWS) are important landscape elements involved in hydrologic, biogeochemical, and biological functioning. Their influence, under certain circumstances, can significantly affect other waters of the Unites States. However, there have been no data-based estimates of the abundance of GIWs at national scales in the US, frustrating efforts to properly manage the resource. We applied a distance-based floodplain and riparian zone proxy to existing data layers from the National Hydrography Dataset (1:24,000k) and applied a geospatial buffering process to National Wetlands Inventory data to quantify the abundance of connected wetlands at significant and relevant scales. Our analyses suggest GIWs are prevalent throughout the conterminous United States, with exceptional densities in portions of the Gulf and Atlantic Coastal Plains, the Prairie Pothole Region of the Upper Midwest, and significant densities elsewhere. Indeed, over 65,000 km2 of GIWs may exist. We provide further analyses of the types, distributions, and regional extent of these systems. Lastly, we also explore additional connectivity measures associated with adjacency and relative geographic isolation to floodplains and other elements of the hydrologic landscape. Presentation at INTECOL International Wetlands Conference (Changshu, China; Sept. 2016)

  10. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

    PubMed Central

    Mahmoud, Huda M.; Kalendar, Aisha A.

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

  11. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials.

    PubMed

    Mahmoud, Huda M; Kalendar, Aisha A

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications.

  12. An extensive comparison of species-abundance distribution models

    PubMed Central

    Baldridge, Elita; Harris, David J.; Xiao, Xiao

    2016-01-01

    A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD. PMID:28028483

  13. Floral abundance, richness, and spatial distribution drive urban garden bee communities.

    PubMed

    Plascencia, M; Philpott, S M

    2017-03-01

    In urban landscapes, gardens provide refuges for bee diversity, but conservation potential may depend on local and landscape features. Foraging and population persistence of bee species, as well as overall pollinator community structure, may be supported by the abundance, richness, and spatial distribution of floral resources. Floral resources strongly differ in urban gardens. Using hand netting and pan traps to survey bees, we examined whether abundance, richness, and spatial distribution of floral resources, as well as ground cover and garden landscape surroundings influence bee abundance, species richness, and diversity on the central coast of California. Differences in floral abundance and spatial distribution, as well as urban cover in the landscape, predicted different bee community variables. Abundance of all bees and of honeybees (Apis mellifera) was lower in sites with more urban land cover surrounding the gardens. Honeybee abundance was higher in sites with patchy floral resources, whereas bee species richness and bee diversity was higher in sites with more clustered floral resources. Surprisingly, bee species richness and bee diversity was lower in sites with very high floral abundance, possibly due to interactions with honeybees. Other studies have documented the importance of floral abundance and landscape surroundings for bees in urban gardens, but this study is the first to document that the spatial arrangement of flowers strongly predicts bee abundance and richness. Based on these findings, it is likely that garden managers may promote bee conservation by managing for floral connectivity and abundance within these ubiquitous urban habitats.

  14. Severe plant invasions can increase mycorrhizal fungal abundance and diversity.

    PubMed

    Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

    2013-07-01

    Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)--but not cheatgrass (Bromus tectorum)--support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance.

  15. Severe plant invasions can increase mycorrhizal fungal abundance and diversity

    PubMed Central

    Lekberg, Ylva; Gibbons, Sean M; Rosendahl, Søren; Ramsey, Philip W

    2013-01-01

    Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)—but not cheatgrass (Bromus tectorum)—support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance. PMID:23486251

  16. Lifting a veil on diversity: a Bayesian approach to fitting relative-abundance models.

    PubMed

    Golicher, Duncan J; O'Hara, Robert B; Ruíz-Montoya, Lorena; Cayuela, Luis

    2006-02-01

    Bayesian methods incorporate prior knowledge into a statistical analysis. This prior knowledge is usually restricted to assumptions regarding the form of probability distributions of the parameters of interest, leaving their values to be determined mainly through the data. Here we show how a Bayesian approach can be applied to the problem of drawing inference regarding species abundance distributions and comparing diversity indices between sites. The classic log series and the lognormal models of relative- abundance distribution are apparently quite different in form. The first is a sampling distribution while the other is a model of abundance of the underlying population. Bayesian methods help unite these two models in a common framework. Markov chain Monte Carlo simulation can be used to fit both distributions as small hierarchical models with shared common assumptions. Sampling error can be assumed to follow a Poisson distribution. Species not found in a sample, but suspected to be present in the region or community of interest, can be given zero abundance. This not only simplifies the process of model fitting, but also provides a convenient way of calculating confidence intervals for diversity indices. The method is especially useful when a comparison of species diversity between sites with different sample sizes is the key motivation behind the research. We illustrate the potential of the approach using data on fruit-feeding butterflies in southern Mexico. We conclude that, once all assumptions have been made transparent, a single data set may provide support for the belief that diversity is negatively affected by anthropogenic forest disturbance. Bayesian methods help to apply theory regarding the distribution of abundance in ecological communities to applied conservation.

  17. Relationships between plant diversity and grasshopper diversity and abundance in the Little Missouri National Grassland

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A continuing challenge in Orthoptera ecology is to understand what determines grasshopper species diversity at a given site. In this study, the objective was to determine if variation in grasshopper abundance and diversity between 23 sites in western North Dakota (USA) could be explained by variatio...

  18. Chloroflexi bacteria are more diverse, abundant, and similar in high than in low microbial abundance sponges.

    PubMed

    Schmitt, Susanne; Deines, Peter; Behnam, Faris; Wagner, Michael; Taylor, Michael W

    2011-12-01

    Some marine sponges harbor dense and phylogenetically complex microbial communities [high microbial abundance (HMA) sponges] whereas others contain only few and less diverse microorganisms [low microbial abundance (LMA) sponges]. We focused on the phylum Chloroflexi that frequently occurs in sponges to investigate the different associations with three HMA and three LMA sponges from New Zealand. By applying a range of microscopical and molecular techniques a clear dichotomy between HMA and LMA sponges was observed: Chloroflexi bacteria were more abundant and diverse in HMA than in LMA sponges. Moreover, different HMA sponges contain similar Chloroflexi communities whereas LMA sponges harbor different and more variable communities which partly resemble Chloroflexi seawater communities. A comprehensive phylogenetic analysis of our own and publicly available sponge-derived Chloroflexi 16S rRNA gene sequences (> 780 sequences) revealed the enormous diversity of this phylum within sponges including 29 sponge-specific and sponge-coral clusters (SSC/SCC) as well as a 'supercluster' consisting of > 250 sponge-derived and a single nonsponge-derived 16S rRNA gene sequence. Interestingly, the majority of sequences obtained from HMA sponges, but only a few from LMA sponges, fell into SSC/SCC clusters. This indicates a much more specific association of Chloroflexi bacteria with HMA sponges and suggests an ecologically important role for these prominent bacteria.

  19. Host trait combinations drive abundance and canopy distribution of atmospheric bromeliad assemblages

    PubMed Central

    Chaves, Cleber Juliano Neves; Dyonisio, Júlio César; Rossatto, Davi Rodrigo

    2016-01-01

    Epiphytes are strongly dependent on the conditions created by their host's traits and a certain degree of specificity is expected between them, even if these species are largely abundant in a series of tree hosts of a given environment, as in the case of atmospheric bromeliads. Despite their considerable abundance in these environments, we hypothesize that stochasticity alone cannot explain the presence and abundance of atmospheric bromeliads on host trees, since host traits could have a greater influence on the establishment of these bromeliads. We used secondary and reforested seasonal forests and three distinct silvicultures to test whether species richness, phylogenetic diversity and functional diversity of trees can predict the differential presence, abundance and distribution of atmospheric bromeliads on hosts. We compared the observed parameters of their assemblage with null models and performed successive variance hierarchic partitions of abundance and distribution of the assemblage to detect the influence of multiple traits of the tree hosts. Our results do not indicate direct relationships between the abundance of atmospheric bromeliads and phylogenetic or functional diversity of trees, but instead indicate that bromeliads occurred on fewer tree species than expected by chance. We distinguished functional tree patterns that can improve or reduce the abundance of atmospheric bromeliads, and change their distribution on branches and trunk. While individual tree traits are related to increased abundance, species traits are related to the canopy distribution of atmospheric bromeliad assemblages. A balance among these tree functional patterns drives the atmospheric bromeliad assemblage of the forest patches. PMID:26888951

  20. Landscape Effects on the Presence, Abundance and Diversity of Mosquitoes in Mediterranean Wetlands

    PubMed Central

    Roiz, David; Ruiz, Santiago; Soriguer, Ramon; Figuerola, Jordi

    2015-01-01

    Environment determines the distribution of mosquito-borne diseases in that it influences the vector-host-pathogen transmission cycle, including vector distribution, abundance and diversity. In this study, we analyse the relationship between environmental variables estimated by remote sensing and the spatial distribution (presence, abundance and diversity) of seven mosquito species vectors of West Nile and other pathogens (Usutu, avian malaria and dirofilariasis) in the Doñana Natural Park, Spain. Traps were distributed over an area of 54,984 ha divided into six ecological units: marshland, sand dunes, scrubland, ricefields, crops and fishponds. We collected mosquitoes once a month from up to 112 locations using BG-Sentinel traps baited with BG-lure and CO2 during March-November 2010. Hydroperiod, NDVI and Inundation surface were estimated at several resolution scales (100, 250, 500, 1000 and 2000 metres) from corrected and normalized Landsat Images. We sampled 972,346 female mosquitoes, the most abundant species being Culex theileri, Ochlerotatus caspius, Culex modestus, Culex perexiguus, Culex pipiens, Anopheles atroparvus and Ochlerotatus detritus. Our results suggest that: (1) hydroperiod, inundation surface and NDVI are strongly related to the spatial distribution of mosquitoes; (2) the spatial scales used to measure these variables affected quantification of these relationships, the larger scale being more informative; (3) these relationships are species-specific; (4) hydroperiod is negatively related to mosquito presence and richness; (5) Culex abundance is positively related to hydroperiod; (6) NDVI is positively related to mosquito diversity, presence and abundance, except in the case of the two salt marsh species (Oc. caspius and Oc. detritus); and (7) inundation surfaces positively condition the abundance and richness of most species except the salt marsh mosquitoes. Remote sensing data provided reliable information for monitoring mosquito populations

  1. Diversity and abundance of phosphonate biosynthetic genes in nature

    PubMed Central

    Yu, Xiaomin; Doroghazi, James R.; Janga, Sarath C.; Zhang, Jun Kai; Circello, Benjamin; Griffin, Benjamin M.; Labeda, David P.; Metcalf, William W.

    2013-01-01

    Phosphonates, molecules containing direct carbon–phosphorus bonds, compose a structurally diverse class of natural products with interesting and useful biological properties. Although their synthesis in protozoa was discovered more than 50 y ago, the extent and diversity of phosphonate production in nature remains poorly characterized. The rearrangement of phosphoenolpyruvate (PEP) to phosphonopyruvate, catalyzed by the enzyme PEP mutase (PepM), is shared by the vast majority of known phosphonate biosynthetic pathways. Thus, the pepM gene can be used as a molecular marker to examine the occurrence and abundance of phosphonate-producing organisms. Based on the presence of this gene, phosphonate biosynthesis is common in microbes, with ∼5% of sequenced bacterial genomes and 7% of genome equivalents in metagenomic datasets carrying pepM homologs. Similarly, we detected the pepM gene in ∼5% of random actinomycete isolates. The pepM-containing gene neighborhoods from 25 of these isolates were cloned, sequenced, and compared with those found in sequenced genomes. PEP mutase sequence conservation is strongly correlated with conservation of other nearby genes, suggesting that the diversity of phosphonate biosynthetic pathways can be predicted by examining PEP mutase diversity. We used this approach to estimate the range of phosphonate biosynthetic pathways in nature, revealing dozens of discrete groups in pepM amplicons from local soils, whereas hundreds were observed in metagenomic datasets. Collectively, our analyses show that phosphonate biosynthesis is both diverse and relatively common in nature, suggesting that the role of phosphonate molecules in the biosphere may be more important than is often recognized. PMID:24297932

  2. Distribution and Abundance of Mars' Atmospheric Argon

    NASA Technical Reports Server (NTRS)

    Sprague, A. L.; Boynton, W. V.; Kerry, K. E.; Nelli, Steven; Murphy, Jim; Reedy, R. C.; Metzger, A. E.; Hunten, D. M.; Janes, K. D.; Crombie, M. K.

    2005-01-01

    One and one half Mars years (MY 26 and 27) of atmospheric Argon measurements are described and studied in the context of understanding how Argon, a minor constituent of Mars atmosphere that does not condense at Mars temperatures, can be used to study martian circulation and dynamics. Argon data are from the 2001 Mars Odyssey Gamma Subsystem (GS) of the suite of three instruments comprising the Gamma Ray Spectrometer (GRS). A comprehensive data analysis including gamma-ray production and attenuation by the atmosphere is included. Of particular interest is the enhanced abundance of Ar over the observed Ar abundance at lower latitudes at south (up to a factor of 10) and north (up to a factor of 4) polar regions during winter. Calibration of the measurements to actual Ar abundance is possible because GS measurements cover the same latitude and season as measurements made by the gas chromatograph mass spectrometer (GCMS) on Viking Landers 1 and 2 (VL1 and VL2). [2].

  3. Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

    PubMed Central

    Kubo, Kyoko; Lloyd, Karen G; F Biddle, Jennifer; Amann, Rudolf; Teske, Andreas; Knittel, Katrin

    2012-01-01

    Members of the highly diverse Miscellaneous Crenarchaeotal Group (MCG) are globally distributed in various marine and continental habitats. In this study, we applied a polyphasic approach (rRNA slot blot hybridization, quantitative PCR (qPCR) and catalyzed reporter deposition FISH) using newly developed probes and primers for the in situ detection and quantification of MCG crenarchaeota in diverse types of marine sediments and microbial mats. In general, abundance of MCG (cocci, 0.4 μm) relative to other archaea was highest (12–100%) in anoxic, low-energy environments characterized by deeper sulfate depletion and lower microbial respiration rates (P=0.06 for slot blot and P=0.05 for qPCR). When studied in high depth resolution in the White Oak River estuary and Hydrate Ridge methane seeps, changes in MCG abundance relative to total archaea and MCG phylogenetic composition did not correlate with changes in sulfate reduction or methane oxidation with depth. In addition, MCG abundance did not vary significantly (P>0.1) between seep sites (with high rates of methanotrophy) and non-seep sites (with low rates of methanotrophy). This suggests that MCG are likely not methanotrophs. MCG crenarchaeota are highly diverse and contain 17 subgroups, with a range of intragroup similarity of 82 to 94%. This high diversity and widespread distribution in subsurface sediments indicates that this group is globally important in sedimentary processes. PMID:22551871

  4. Neutral theory predicts the relative abundance and diversity of genetic elements in a broad array of eukaryotic genomes.

    PubMed

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

    It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or "species" of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or "species" populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes.

  5. Diverse and abundant antibiotic resistance genes in Chinese swine farms.

    PubMed

    Zhu, Yong-Guan; Johnson, Timothy A; Su, Jian-Qiang; Qiao, Min; Guo, Guang-Xia; Stedtfeld, Robert D; Hashsham, Syed A; Tiedje, James M

    2013-02-26

    Antibiotic resistance genes (ARGs) are emerging contaminants posing a potential worldwide human health risk. Intensive animal husbandry is believed to be a major contributor to the increased environmental burden of ARGs. Despite the volume of antibiotics used in China, little information is available regarding the corresponding ARGs associated with animal farms. We assessed type and concentrations of ARGs at three stages of manure processing to land disposal at three large-scale (10,000 animals per year) commercial swine farms in China. In-feed or therapeutic antibiotics used on these farms include all major classes of antibiotics except vancomycins. High-capacity quantitative PCR arrays detected 149 unique resistance genes among all of the farm samples, the top 63 ARGs being enriched 192-fold (median) up to 28,000-fold (maximum) compared with their respective antibiotic-free manure or soil controls. Antibiotics and heavy metals used as feed supplements were elevated in the manures, suggesting the potential for coselection of resistance traits. The potential for horizontal transfer of ARGs because of transposon-specific ARGs is implicated by the enrichment of transposases--the top six alleles being enriched 189-fold (median) up to 90,000-fold in manure--as well as the high correlation (r(2) = 0.96) between ARG and transposase abundance. In addition, abundance of ARGs correlated directly with antibiotic and metal concentrations, indicating their importance in selection of resistance genes. Diverse, abundant, and potentially mobile ARGs in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of ARGs to the environment.

  6. Arthropod abundance and diversity in transgenic Bt soybean.

    PubMed

    Yu, Huilin; Li, Yunhe; Li, Xiangju; Wu, Kongming

    2014-08-01

    Before the commercialization of any insect-resistant genetically modified crop, it must be subjected to a rigorous premarket risk assessment. Here, possible effects of growing of transgenic Cry1Ac soybean on arthropod communities under field conditions were assessed for 2 yr and quantified in terms of arthropod community indices including the Shannon-Weaver diversity index, richness index, and dominance index. Our results showed no significant differences of diversity, richness, or dominant indices for Bt soybean compared with the recipient cultivar, conventional soybean, or sprayed conventional soybean. Conventional soybean treatment with insecticide had an adverse effect on the arthropod community after spraying, but arthropod community diversity recovered quickly. Bt soybean had no negative effect on the dominant distribution of subcommunities, including sucking pests, other pests, predators, parasitoids, and others except for lepidopteran pests. The dominance distribution of lepidopteran pests decreased significantly in Bt soybean because of the significant decrease in the numbers of Spodoptera litura (F.) and Ascotis selenaria Schiffermüller et Denis compared with the recipient cultivar. Our results showed that there were no negative effects of Cry1Ac soybean on the arthropod community in soybean field plots in the short term.

  7. Species abundance in a forest community in South China: A case of poisson lognormal distribution

    USGS Publications Warehouse

    Yin, Z.-Y.; Ren, H.; Zhang, Q.-M.; Peng, S.-L.; Guo, Q.-F.; Zhou, G.-Y.

    2005-01-01

    Case studies on Poisson lognormal distribution of species abundance have been rare, especially in forest communities. We propose a numerical method to fit the Poisson lognormal to the species abundance data at an evergreen mixed forest in the Dinghushan Biosphere Reserve, South China. Plants in the tree, shrub and herb layers in 25 quadrats of 20 m??20 m, 5 m??5 m, and 1 m??1 m were surveyed. Results indicated that: (i) for each layer, the observed species abundance with a similarly small median, mode, and a variance larger than the mean was reverse J-shaped and followed well the zero-truncated Poisson lognormal; (ii) the coefficient of variation, skewness and kurtosis of abundance, and two Poisson lognormal parameters (?? and ??) for shrub layer were closer to those for the herb layer than those for the tree layer; and (iii) from the tree to the shrub to the herb layer, the ?? and the coefficient of variation decreased, whereas diversity increased. We suggest that: (i) the species abundance distributions in the three layers reflects the overall community characteristics; (ii) the Poisson lognormal can describe the species abundance distribution in diverse communities with a few abundant species but many rare species; and (iii) 1/?? should be an alternative measure of diversity.

  8. Vascular plant abundance and diversity in an alpine heath under observed and simulated global change.

    PubMed

    Alatalo, Juha M; Little, Chelsea J; Jägerbrand, Annika K; Molau, Ulf

    2015-05-07

    Global change is predicted to cause shifts in species distributions and biodiversity in arctic tundra. We applied factorial warming and nutrient manipulation to a nutrient and species poor alpine/arctic heath community for seven years. Vascular plant abundance in control plots increased by 31%. There were also notable changes in cover in the nutrient and combined nutrient and warming treatments, with deciduous and evergreen shrubs declining, grasses overgrowing these plots. Sedge abundance initially increased significantly with nutrient amendment and then declined, going below initial values in the combined nutrient and warming treatment. Nutrient addition resulted in a change in dominance hierarchy from deciduous shrubs to grasses. We found significant declines in vascular plant diversity and evenness in the warming treatment and a decline in diversity in the combined warming and nutrient addition treatment, while nutrient addition caused a decline in species richness. The results give some experimental support that species poor plant communities with low diversity may be more vulnerable to loss of species diversity than communities with higher initial diversity. The projected increase in nutrient deposition and warming may therefore have negative impacts on ecosystem processes, functioning and services due to loss of species diversity in an already impoverished environment.

  9. Abundant Microsatellite Diversity and Oil Content in Wild Arachis Species

    PubMed Central

    Ren, Xiaoping; Chen, Yuning; Xiao, Yingjie; Zhao, Xinyan; Tang, Mei; Huang, Jiaquan; Upadhyaya, Hari D.; Liao, Boshou

    2012-01-01

    The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great

  10. Human impacts on regional avian diversity and abundance.

    PubMed

    Lepczyk, Christopher A; Flather, Curtis H; Radeloff, Volker C; Pidgeon, Anna M; Hammer, Roger B; Liu, Jianguo

    2008-04-01

    ecosystem-stress hypothesis for the majority of individual species and for overall species diversity when focusing on anthropogenic land cover. Nevertheless, the great variability in housing units across the land-cover gradient indicates that an intermediate-disturbance relationship is also supported. Our findings suggest preemptive conservation action should be taken, whereby areas with little anthropogenic land cover are given conservation priority. Nevertheless, conservation action should not be limited to pristine landscapes because our results showed that native avian richness and the relative abundance of many species peaked at intermediate housing densities and levels of anthropogenic land cover.

  11. Anaerobic ammonium oxidation (anammox) bacterial diversity, abundance, and activity in marsh sediments of the Yangtze Estuary

    NASA Astrophysics Data System (ADS)

    Hou, Lijun; Zheng, Yanling; Liu, Min; Gong, Jun; Zhang, Xiaoli; Yin, Guoyu; You, Li

    2013-07-01

    ammonium oxidation (anammox) as an important process of nitrogen cycle has been studied in estuarine environments. However, knowledge about the dynamics of anammox bacteria and their interactions with associated activity remains scarce in these environments. Here we report the anammox bacterial diversity, abundance, and activity in the Yangtze Estuary, using molecular and isotope-tracing techniques. The phylogenetic analysis of 16S rRNA indicated that high anammox bacterial diversity occurred in this estuary, including Scalindua, Brocadia, Kuenenia, and two novel clusters. The patterns of community composition and diversity of anammox bacteria differed across the estuary. Salinity was a key environmental factor defining the geographical distribution and diversity of the anammox bacterial community at the estuarine ecosystem. Temperature and organic carbon also had significant influences on anammox bacterial biodiversity. The abundance of anammox bacteria ranged from 2.63 × 106 and 1.56 × 107 gene copies g-1, and its spatiotemporal variations were related significantly to salinity, temperature, and nitrite content. The anammox activity was related to temperature, nitrite, and anammox bacterial abundance, with values of 0.94-6.61 nmol N g-1 h-1. The tight link between the anammox and denitrification processes implied that denitrifying bacteria may be a primary source of nitrite for the anammox bacteria in the estuarine marshes. On the basis of the 15N tracing experiments, the anammox process was estimated to contribute 6.6%-12.9% to the total nitrogen loss whereas the remainder was attributed to denitrification.

  12. Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales.

    PubMed

    Hendershot, J Nicholas; Read, Quentin D; Henning, Jeremiah A; Sanders, Nathan J; Classen, Aimée T

    2017-04-05

    Macroecology seeks to understand broad-scale patterns in the diversity and abundance of organisms, but macroecologists typically study aboveground macroorganisms. Belowground organisms regulate numerous ecosystem functions, yet we lack understanding of what drives their diversity. Here, we examine the controls on belowground diversity along latitudinal and elevational gradients. We performed a global meta-analysis of 325 soil communities across 20 studies conducted along temperature and soil pH gradients. Belowground taxa, whether bacterial or fungal, observed along a given gradient of temperature or soil pH were equally likely to show a linear increase, linear decrease, humped pattern, trough-shaped pattern, or no pattern in diversity along the gradient. Land-use intensity weakly affected the diversity-temperature relationship, but no other factor did so. Our study highlights disparities among diversity patterns of soil microbial communities. Belowground diversity may be controlled by the associated climatic and historical contexts of particular gradients, by factors not typically measured in community-level studies, or by processes operating at scales that do not match the temporal and spatial scales under study. Because these organisms are responsible for a suite of key processes, understanding the drivers of their distribution and diversity is fundamental to understanding the functioning of ecosystems. This article is protected by copyright. All rights reserved.

  13. The effects of coastal development on sponge abundance, diversity, and community composition on Jamaican coral reefs.

    PubMed

    Stubler, Amber D; Duckworth, Alan R; Peterson, Bradley J

    2015-07-15

    Over the past decade, development along the northern coast of Jamaica has accelerated, resulting in elevated levels of sedimentation on adjacent reefs. To understand the effects of this development on sponge community dynamics, we conducted surveys at three locations with varying degrees of adjacent coastal development to quantify species richness, abundance and diversity at two depths (8-10 m and 15-18 m). Sediment accumulation rate, total suspended solids and other water quality parameters were also quantified. The sponge community at the location with the least coastal development and anthropogenic influence was often significantly different from the other two locations, and exhibited higher sponge abundance, richness, and diversity. Sponge community composition and size distribution were statistically different among locations. This study provides correlative evidence that coastal development affects aspects of sponge community ecology, although the precise mechanisms are still unclear.

  14. Trends in aerosol abundances and distributions

    NASA Technical Reports Server (NTRS)

    Turco, R. P.; Mccormick, M. P.; Clancy, R. T.; Curran, R.; Deluisi, J.; Hamill, P.; Kent, G.; Rosen, J. M.; Toon, O. B.; Yue, G.

    1989-01-01

    The properties of aerosols that reside in the upper atmosphere are described. Special emphasis is given to the influence these aerosols have on ozone observation systems, mainly through radiative effects, and on ambient ozone concentrations, mainly through chemical effects. It has long been appreciated that stratospheric particles can interfere with the remote sensing of ozone distribution. The mechanism and magnitude of this interference are evaluated. Separate sections deal with the optical properties of upper atmospheric aerosols, long-term trends in stratospheric aerosols, perturbations of the stratospheric aerosol layer by volcanic eruptions, and estimates of the impacts that such particles have on remotely measured ozone concentrations. Another section is devoted to a discussion of the polar stratospheric clouds (PSC's). These unique clouds, recently discovered by satellite observation, are now thought to be intimately connected with the Antarctic ozone hole. Accordingly, interest in PSC's has grown considerably in recent years. This chapter describes what we know about the morphology, physical chemistry, and microphysics of PSC's.

  15. Deep-sea methane seep sediments in the Okhotsk Sea sustain diverse and abundant anammox bacteria.

    PubMed

    Shao, Sudong; Luan, Xiwu; Dang, Hongyue; Zhou, Haixia; Zhao, Yakun; Liu, Haitao; Zhang, Yunbo; Dai, Lingqing; Ye, Ying; Klotz, Martin G

    2014-02-01

    Marginal sea methane seep sediments sustain highly productive chemosynthetic ecosystems and are hotspots of intense biogeochemical cycling. Rich methane supply stimulates rapid microbial consumption of oxygen; these systems are thus usually hypoxic to anoxic. This and reported evidence for resident nitrogen fixation suggest the presence of an anaerobic ammonium-oxidizing (anammox) bacterial community in methane seep sediments. To test this hypothesis, we employed detection of genes encoding 16S rRNA gene and hydrazine dehydrogenase (hzo) to investigate the structure, abundance and distribution of the anammox bacterial community in the methane seep sediments of the Okhotsk Sea. Diverse complements of Candidatus Scalindua-related 16S rRNA and hzo gene sequences were obtained. Most of the deep-sea sites harbored abundant hzo genes with copy numbers as high as 10(7)  g(-1) sediment. In general, anammox bacterial signatures were significantly more abundant in the deep-water sediments. Sediment porewater NO3-, NOx- (i.e. NO3- + NO2-), NOx-/NH4+ and sediment silt content correlated with in situ distribution patterns of anammox bacterial marker genes, likely because they determine anammox substrate availability and sediment geochemistry, respectively. The abundance and distribution of anammox bacterial gene markers indicate a potentially significant contribution of anammox bacteria to the marine N cycle in the deep-sea methane seep sediments.

  16. Organizing Diverse, Distributed Project Information

    NASA Technical Reports Server (NTRS)

    Keller, Richard M.

    2003-01-01

    SemanticOrganizer is a software application designed to organize and integrate information generated within a distributed organization or as part of a project that involves multiple, geographically dispersed collaborators. SemanticOrganizer incorporates the capabilities of database storage, document sharing, hypermedia navigation, and semantic-interlinking into a system that can be customized to satisfy the specific information-management needs of different user communities. The program provides a centralized repository of information that is both secure and accessible to project collaborators via the World Wide Web. SemanticOrganizer's repository can be used to collect diverse information (including forms, documents, notes, data, spreadsheets, images, and sounds) from computers at collaborators work sites. The program organizes the information using a unique network-structured conceptual framework, wherein each node represents a data record that contains not only the original information but also metadata (in effect, standardized data that characterize the information). Links among nodes express semantic relationships among the data records. The program features a Web interface through which users enter, interlink, and/or search for information in the repository. By use of this repository, the collaborators have immediate access to the most recent project information, as well as to archived information. A key advantage to SemanticOrganizer is its ability to interlink information together in a natural fashion using customized terminology and concepts that are familiar to a user community.

  17. [Diversity and ichthyofaunistic abundance of the Rio Grande de Térraba, south of Costa Rica].

    PubMed

    Rodrigo Rojas, José; Rodríguez, Omar

    2008-09-01

    The diversity, abundance and distributional pattern of freshwater fish communities in the Térraba River, south Costa Rica, were investigated from the early dry season of 2004 to early rain season of 2005. There have been no preview studies on the freshwater fish distribution in Térraba. Therefore, the aims of this study were to determine fish species richness, abundance and distribution there. Fish sampling was done using a combination of gears such as gill net, fine mesh net and visual observation. Thirty three species, 26 genera and 14 families were collected in four sampling sites along the river. The number and biomass captured during the entire study was 984 individuals and 147 410.9 g respectively. Most of them are carnivorous species (48%), 33.3% are omnivorous and 12% detritivorous, and only two species are herbivorous. The most important species in relative abundance (56.5%) and biomass (53.7%) in the study area was the machaca (Brycon behreae). It should be clear that although the list of fish species that occur in Térraba River is reasonably complete, knowledge of their ichthyogeographic history patterns is superficial. The main community component was secondary freshwater species; with 17 invading brackish water species and one introduced species (tilapia O. niloticus). Nine species are reported for the first time in this river. The diversity index H' varied from 2.32 (El Brujo) to 1.67 (Coto), a similar pattern was also showed for the other indexes. Most of our results were similar to those of previous studies on freshwater fish distribution elsewhere, however no significant correlation between species distribution and environmental variables was found, and we hypothesized that the depth and water velocity and geomorphological are major environmental variables that influence the fish distribution. Our findings are opposed to the tendency, for species composition, to increase from upstream to the mouth of the river, which is probably due to two major

  18. Contrasting changes in the abundance and diversity of North American bird assemblages from 1971 to 2010.

    PubMed

    Schipper, Aafke M; Belmaker, Jonathan; de Miranda, Murilo Dantas; Navarro, Laetitia M; Böhning-Gaese, Katrin; Costello, Mark J; Dornelas, Maria; Foppen, Ruud; Hortal, Joaquín; Huijbregts, Mark A J; Martín-López, Berta; Pettorelli, Nathalie; Queiroz, Cibele; Rossberg, Axel G; Santini, Luca; Schiffers, Katja; Steinmann, Zoran J N; Visconti, Piero; Rondinini, Carlo; Pereira, Henrique M

    2016-12-01

    Although it is generally recognized that global biodiversity is declining, few studies have examined long-term changes in multiple biodiversity dimensions simultaneously. In this study, we quantified and compared temporal changes in the abundance, taxonomic diversity, functional diversity, and phylogenetic diversity of bird assemblages, using roadside monitoring data of the North American Breeding Bird Survey from 1971 to 2010. We calculated 12 abundance and diversity metrics based on 5-year average abundances of 519 species for each of 768 monitoring routes. We did this for all bird species together as well as for four subgroups based on breeding habitat affinity (grassland, woodland, wetland, and shrubland breeders). The majority of the biodiversity metrics increased or remained constant over the study period, whereas the overall abundance of birds showed a pronounced decrease, primarily driven by declines of the most abundant species. These results highlight how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occur in parallel with substantial losses of individuals. We further found that patterns of change differed among the species subgroups, with both abundance and diversity increasing for woodland birds and decreasing for grassland breeders. The contrasting changes between abundance and diversity and among the breeding habitat groups underscore the relevance of a multifaceted approach to measuring biodiversity change. Our findings further stress the importance of monitoring the overall abundance of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus confirming the importance of population abundance as an essential biodiversity variable.

  19. Multiple peaks of species abundance distributions induced by sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u , we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions.

  20. Environmental distribution, abundance and activity of the Miscellaneous Crenarchaeotal Group

    NASA Astrophysics Data System (ADS)

    Lloyd, K. G.; Biddle, J.; Teske, A.

    2011-12-01

    Many marine sedimentary microbes have only been identified by 16S rRNA sequences. Consequently, little is known about the types of metabolism, activity levels, or relative abundance of these groups in marine sediments. We found that one of these uncultured groups, called the Miscellaneous Crenarchaeotal Group (MCG), dominated clone libraries made from reverse transcribed 16S rRNA, and 454 pyrosequenced 16S rRNA genes, in the White Oak River estuary. Primers suitable for quantitative PCR were developed for MCG and used to show that 16S rRNA DNA copy numbers from MCG account for nearly all the archaeal 16S rRNA genes present. RT-qPCR shows much less MCG rRNA than total archaeal rRNA, but comparisons of different primers for each group suggest bias in the RNA-based work relative to the DNA-based work. There is no evidence of a population shift with depth below the sulfate-methane transition zone, suggesting that the metabolism of MCG may not be tied to sulfur or methane cycles. We classified 2,771 new sequences within the SSU Silva 106 database that, along with the classified sequences in the Silva database was used to make an MCG database of 4,646 sequences that allowed us to increase the named subgroups of MCG from 7 to 19. Percent terrestrial sequences in each subgroup is positively correlated with percent of the marine sequences that are nearshore, suggesting that membership in the different subgroups is not random, but dictated by environmental selective pressures. Given their high phylogenetic diversity, ubiquitous distribution in anoxic environments, and high DNA copy number relative to total archaea, members of MCG are most likely anaerobic heterotrophs who are integral to the post-depositional marine carbon cycle.

  1. Environmental correlates of species rank - abundance distributions in global drylands.

    PubMed

    Ulrich, Werner; Soliveres, Santiago; Thomas, Andrew D; Dougill, Andrew J; Maestre, Fernando T

    2016-06-01

    Theoretical models predict lognormal species abundance distributions (SADs) in stable and productive environments, with log-series SADs in less stable, dispersal driven communities. We studied patterns of relative species abundances of perennial vascular plants in global dryland communities to: i) assess the influence of climatic and soil characteristics on the observed SADs, ii) infer how environmental variability influences relative abundances, and iii) evaluate how colonisation dynamics and environmental filters shape abundance distributions. We fitted lognormal and log-series SADs to 91 sites containing at least 15 species of perennial vascular plants. The dependence of species relative abundances on soil and climate variables was assessed using general linear models. Irrespective of habitat type and latitude, the majority of the SADs (70.3%) were best described by a lognormal distribution. Lognormal SADs were associated with low annual precipitation, higher aridity, high soil carbon content, and higher variability of climate variables and soil nitrate. Our results do not corroborate models predicting the prevalence of log-series SADs in dryland communities. As lognormal SADs were particularly associated with sites with drier conditions and a higher environmental variability, we reject models linking lognormality to environmental stability and high productivity conditions. Instead our results point to the prevalence of lognormal SADs in heterogeneous environments, allowing for more evenly distributed plant communities, or in stressful ecosystems, which are generally shaped by strong habitat filters and limited colonisation. This suggests that drylands may be resilient to environmental changes because the many species with intermediate relative abundances could take over ecosystem functioning if the environment becomes suboptimal for dominant species.

  2. Diversity and abundance of phosphonate biosynthetic genes in nature

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phosphonates, molecules containing direct C-P bonds, comprise a structurally diverse class of natural products with interesting and useful biological properties. Although their synthesis in protozoa was discovered more than fifty years ago, the extent and diversity of phosphonate production in natur...

  3. Influence of edge on predator prey distribution and abundance

    NASA Astrophysics Data System (ADS)

    Ferguson, Steven H.

    2004-03-01

    I investigated the effect of spatial configuration on distribution and abundance of invertebrate trophic groups by counting soil arthropods under boxes (21 × 9.5 cm) arranged in six different patterns that varied in the amount of edge (137-305 cm). I predicted fewer individuals from the consumer trophic group (Collembola) in box groups with greater amount of edge. This prediction was based on the assumption that predators (mites, ants, spiders, centipedes) select edge during foraging and thereby reduce abundance of the less mobile consumer group under box patterns with greater edge. Consumer abundance (Collembola) was not correlated with amount of edge. Among the predator groups, mite, ant and centipede abundance related to the amount of edge of box groups. However, in contrast to predictions, abundance of these predators was negatively correlated with amount of edge in box patterns. All Collembola predators, with the exception of ants, were less clumped in distribution than Collembola. The results are inconsistent with the view that predators used box edges to predate the less mobile consumer trophic group. Alternative explanations for the spatial patterns other than predator-prey relations include (1) a negative relationship between edge and moisture, (2) a positive relationship between edge and detritus decomposition (i.e. mycelium as food for the consumer group), and (3) a negative relationship between edge and the interstices between adjacent boxes. Landscape patterns likely affect microclimate, food, and predator-prey relations and, therefore, future experimental designs need to control these factors individually to distinguish among alternative hypotheses.

  4. Assessing introduction risk using species' rank-abundance distributions.

    PubMed

    Chan, Farrah T; Bradie, Johanna; Briski, Elizabeta; Bailey, Sarah A; Simard, Nathalie; MacIsaac, Hugh J

    2015-01-22

    Mixed-species assemblages are often unintentionally introduced into new ecosystems. Analysing how assemblage structure varies during transport may provide insights into how introduction risk changes before propagules are released. Characterization of introduction risk is typically based on assessments of colonization pressure (CP, the number of species transported) and total propagule pressure (total PP, the total abundance of propagules released) associated with an invasion vector. Generally, invasion potential following introduction increases with greater CP or total PP. Here, we extend these assessments using rank-abundance distributions to examine how CP : total PP relationships change temporally in ballast water of ocean-going ships. Rank-abundance distributions and CP : total PP patterns varied widely between trans-Atlantic and trans-Pacific voyages, with the latter appearing to pose a much lower risk than the former. Responses also differed by taxonomic group, with invertebrates experiencing losses mainly in total PP, while diatoms and dinoflagellates sustained losses mainly in CP. In certain cases, open-ocean ballast water exchange appeared to increase introduction risk by uptake of new species or supplementation of existing ones. Our study demonstrates that rank-abundance distributions provide new insights into the utility of CP and PP in characterizing introduction risk.

  5. Rényi entropy, abundance distribution, and the equivalence of ensembles

    NASA Astrophysics Data System (ADS)

    Mora, Thierry; Walczak, Aleksandra M.

    2016-05-01

    Distributions of abundances or frequencies play an important role in many fields of science, from biology to sociology, as does the Rényi entropy, which measures the diversity of a statistical ensemble. We derive a mathematical relation between the abundance distribution and the Rényi entropy, by analogy with the equivalence of ensembles in thermodynamics. The abundance distribution is mapped onto the density of states, and the Rényi entropy to the free energy. The two quantities are related in the thermodynamic limit by a Legendre transform, by virtue of the equivalence between the micro-canonical and canonical ensembles. In this limit, we show how the Rényi entropy can be constructed geometrically from rank-frequency plots. This mapping predicts that non-concave regions of the rank-frequency curve should result in kinks in the Rényi entropy as a function of its order. We illustrate our results on simple examples, and emphasize the limitations of the equivalence of ensembles when a thermodynamic limit is not well defined. Our results help choose reliable diversity measures based on the experimental accuracy of the abundance distributions in particular frequency ranges.

  6. Rényi entropy, abundance distribution, and the equivalence of ensembles.

    PubMed

    Mora, Thierry; Walczak, Aleksandra M

    2016-05-01

    Distributions of abundances or frequencies play an important role in many fields of science, from biology to sociology, as does the Rényi entropy, which measures the diversity of a statistical ensemble. We derive a mathematical relation between the abundance distribution and the Rényi entropy, by analogy with the equivalence of ensembles in thermodynamics. The abundance distribution is mapped onto the density of states, and the Rényi entropy to the free energy. The two quantities are related in the thermodynamic limit by a Legendre transform, by virtue of the equivalence between the micro-canonical and canonical ensembles. In this limit, we show how the Rényi entropy can be constructed geometrically from rank-frequency plots. This mapping predicts that non-concave regions of the rank-frequency curve should result in kinks in the Rényi entropy as a function of its order. We illustrate our results on simple examples, and emphasize the limitations of the equivalence of ensembles when a thermodynamic limit is not well defined. Our results help choose reliable diversity measures based on the experimental accuracy of the abundance distributions in particular frequency ranges.

  7. Multiple factors affect diversity and abundance of ammonia-oxidizing microorganisms in iron mine soil.

    PubMed

    Xing, Yi; Si, Yan-Xiao; Hong, Chen; Li, Yang

    2015-07-01

    Ammonia oxidation by microorganisms is a critical process in the nitrogen cycle. In this study, four soil samples collected from a desert zone in an iron-exploration area and others from farmland and planted forest soil in an iron mine surrounding area. We analyzed the abundance and diversity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in iron-mining area near the Miyun reservoir using ammonia monooxygenase. A subunit gene (amoA) as molecular biomarker. Quantitative polymerase chain reaction was applied to explore the relationships between the abundance of AOA and AOB and soil physicochemical parameters. The results showed that AOA were more abundant than AOB and may play a more dominant role in the ammonia-oxidizing process in the whole region. PCR-denaturing gradient gel electrophoresis was used to analyze the structural changes of AOA and AOB. The results showed that AOB were much more diverse than AOA. Nitrosospira cluster three constitute the majority of AOB, and AOA were dominated by group 1.1b in the soil. Redundancy analysis was performed to explore the physicochemical parameters potentially important to AOA and AOB. Soil characteristics (i.e. water, ammonia, organic carbon, total nitrogen, available phosphorus, and soil type) were proposed to potentially contribute to the distributions of AOB, whereas Cd was also closely correlated to the distributions of AOB. The community of AOA correlated with ammonium and water contents. These results highlight the importance of multiple drivers in microbial niche formation as well as their affect on ammonia oxidizer composition, both which have significant consequences for ecosystem nitrogen functioning.

  8. Comparing Amino Acid Abundances and Distributions Across Carbonaceous Chondrite Groups

    NASA Technical Reports Server (NTRS)

    Burton, Aaron S.; Callahan, Michael P.; Glavin, Daniel P.; Elsila, Jamie E.; Dworkin, Jason P.

    2012-01-01

    Meteorites are grouped according to bulk properties such as chemical composition and mineralogy. These parameters can vary significantly among the different carbonaceous chondrite groups (CI, CM, CO, CR, CH, CB, CV and CK). We have determined the amino acid abundances of more than 30 primary amino acids in meteorites from each of the eight groups, revealing several interesting trends. There are noticeable differences in the structural diversity and overall abundances of amino acids between meteorites from the different chondrite groups. Because meteorites may have been an important source of amino acids to the prebiotic Earth and these organic compounds are essential for life as we know it, the observed variations of these molecules may have been important for the origins of life.

  9. Distribution and abundance of macrobenthic polychaetes along the South Indian coast.

    PubMed

    Musale, Amar S; Desai, Dattesh V

    2011-07-01

    Macrobenthic polychaetes play a significant role in marine benthic food chain. A study was carried out to observe the abundance and diversity of soft bottom macrobenthic polychaetes along the South Indian coast, along with observations on sediment characteristics. The present study indicated an increase in the polychaete diversity as compared to earlier reports. Sixty-three different forms of polychaetes were identified along the coast, which constitute the bulk of the macrobenthic fauna. Thirty-eight species of polychaetes showed higher abundance along the west coast, whereas 25 species showed higher abundance along the east coast. Seabed composition showed a spatial variation in its composition along the coast. Occurrence of Prionospio pinnata and Capitella capitata the deposit feeders and indicators of organic pollution suggesting the sampled area is organically rich. Polychaete abundance was found to be higher along the west coast and was attributed to loose texture of sediment due to high sand and sandy-silt resulting in higher interstitial space for organisms to harbor. Canonical correspondence analysis indicated that majority of polychaete species preferred low organic carbon, sandy silt, or sandy-clay substratum. The lower polychaete abundance at high organic carbon and high silt and clay areas can be attributed to avoidance of organisms to rich organic matter and suboxic levels, being a possible indication that these characteristics adversely affects the polychaete abundance and distribution.

  10. Global Distribution of Microbial Abundance and Biomass in Subseafloor Sediment

    NASA Astrophysics Data System (ADS)

    Kallmeyer, J.; Pockalny, R. A.; Adhikari, R. R.; Smith, D. C.; D'Hondt, S. L.

    2012-12-01

    Previously published cell counts were mostly from ocean margins and the eastern equatorial Pacific. Cell counts from these environments are generally similar from site to site and decrease logarithmically with sediment depth, although there can be sharp peaks of high cell densities in zones of anaerobic methane-oxidation. Recent counts from the South Pacific Gyre and the North Pacific Gyre are several orders of magnitude lower and show a more rapid decrease with depth than all previously published datasets. With these new data available, total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. The differences between cell counts from ocean margins and upwelling areas and cell counts from oceanic gyres raise three questions. First, how does the abundance of microbes in subseafloor sediment vary throughout the world ocean? Second, what property or properties are likely to control that variation? Third, how does this variation affect estimates of total subseafloor sedimentary biomass and Earth's total biomass? To address these questions, we compiled our cell counts from the South Pacific Gyre, the North Pacific Gyre and the eastern equatorial Pacific Ocean with previously published counts and parameterized the cell distribution at each site and determined two parameters, (i) cell concentration at 1 mbsf and (ii) rate of decrease in cell counts with depth. Both parameters are strongly correlated with mean sedimentation rate and distance to shore. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9*1029 cells (corresponding to 4.1 Pg C and ~0.6% of Earth's total living biomass). This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate

  11. Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth.

    PubMed

    McCoy, Connor O; Matsen, Frederick A

    2013-01-01

    In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply non-phylogenetic measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical phylogenetic diversity (PD), which is not abundance-weighted. Although alpha diversity measures that use abundance information in a phylogenetic framework do exist, they are not widely used within the microbial ecology community. The performance of abundance-weighted phylogenetic diversity measures compared to classical discrete measures has not been explored, and the behavior of these measures under rarefaction (sub-sampling) is not yet clear. In this paper we compare the ability of various alpha diversity measures to distinguish between different community states in the human microbiome for three different datasets. We also present and compare a novel one-parameter family of alpha diversity measures, BWPDθ, that interpolates between classical phylogenetic diversity (PD) and an abundance-weighted extension of PD. Additionally, we examine the sensitivity of these phylogenetic diversity measures to sampling, via computational experiments and by deriving a closed form solution for the expectation of phylogenetic quadratic entropy under re-sampling. On the three datasets, a phylogenetic measure always performed best, and two abundance-weighted phylogenetic diversity measures were the only measures ranking in the top four across all datasets. OTU-based measures, on the other hand, are less effective in distinguishing community types. In addition, abundance-weighted phylogenetic diversity measures are less sensitive to differing sampling intensity than their unweighted counterparts. Based on these results we encourage the use of abundance-weighted phylogenetic diversity measures, especially for cases such as microbial ecology where species delimitation is difficult.

  12. Aphid and ladybird beetle abundance depend on the interaction of spatial effects and genotypic diversity.

    PubMed

    Genung, Mark A; Crutsinger, Gregory M; Bailey, Joseph K; Schweitzer, Jennifer A; Sanders, Nathan J

    2012-01-01

    Intraspecific variation and genotypic diversity of host-plants can affect the structure of associated arthropod communities and the dynamics of populations. Similarly, neighboring plants can also affect interactions between host-plants and their associated arthropods. However, most studies on the effects of host-plant genotypes have largely ignored the potential effects of neighboring host-plants on arthropod communities. In this study, we used a common garden experiment to ask how spatial effects of neighboring patches, along with genotype identity and genotypic diversity in tall goldenrod (Solidago altissima), affect the abundances of a common goldenrod herbivore (Uroleucon nigrotuberculatum) and their dominant predator (Harmonia axyridis, a ladybird beetle). Aphid abundance varied 80-fold among genotypes, while ladybird beetle abundance was not affected by genotype identity. Additionally, there were strong effects of neighboring plots: aphid abundance in a focal plot was positively correlated to aphid abundance in nearby plots, suggesting strong spatial patterning in the abundance of aphids. Neither aphid nor ladybird beetle abundance was affected by genotypic diversity. However, focal plot genotypic diversity mediated the strength of the neighborhood effect (i.e., strong effects for genotype polyculture focal plots and weak effects for genotype monoculture focal plots). Our results show that aphids were directly influenced by host-plant genotype identity while ladybird beetles responded mainly to prey abundance, and suggest that genotypic diversity can influence the effects of spatial processes on the plant-herbivore interactions.

  13. Do phytoplankton communities evolve through a self-regulatory abundance-diversity relationship?

    PubMed

    Roy, Shovonlal

    2009-02-01

    A small group of phytoplankton species that produce toxic or allelopathic chemicals has a significant effect on plankton dynamics in marine ecosystems. The species of non-toxic phytoplankton, which are large in number, are affected by the toxin-allelopathy of those species. By analysis of the abundance data of marine phytoplankton collected from the North-West coast of the Bay of Bengal, an empirical relationship between the abundance of the potential toxin-producing species and the species diversity of the non-toxic phytoplankton is formulated. A change-point analysis demonstrates that the diversity of non-toxic phytoplankton increases with the increase of toxic species up to a certain level. However, for a massive increase of the toxin-producing species the diversity of phytoplankton at species level reduces gradually. Following the results, a deterministic relationship between the abundance of toxic phytoplankton and the diversity of non-toxic phytoplankton is developed. The abundance-diversity relationship develops a unimodal pathway through which the abundance of toxic species regulates the diversity of phytoplankton. These results contribute to the current understanding of the coexistence and biodiversity of phytoplankton, the top-down vs. bottom-up debate, and to that of abundance-diversity relationship in marine ecosystems.

  14. Integrating abundance and functional traits reveals new global hotspots of fish diversity.

    PubMed

    Stuart-Smith, Rick D; Bates, Amanda E; Lefcheck, Jonathan S; Duffy, J Emmett; Baker, Susan C; Thomson, Russell J; Stuart-Smith, Jemina F; Hill, Nicole A; Kininmonth, Stuart J; Airoldi, Laura; Becerro, Mikel A; Campbell, Stuart J; Dawson, Terence P; Navarrete, Sergio A; Soler, German A; Strain, Elisabeth M A; Willis, Trevor J; Edgar, Graham J

    2013-09-26

    Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of

  15. Herbivory: effects on plant abundance, distribution and population growth

    PubMed Central

    Maron, John L; Crone, Elizabeth

    2006-01-01

    Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant–consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics. PMID:17002942

  16. DIVERSITY OF TYPE Ia SUPERNOVAE IMPRINTED IN CHEMICAL ABUNDANCES

    SciTech Connect

    Tsujimoto, Takuji; Shigeyama, Toshikazu

    2012-12-01

    A time delay of Type Ia supernova (SN Ia) explosions hinders the imprint of their nucleosynthesis on stellar abundances. However, some occasional cases give birth to stars that avoid enrichment of their chemical compositions by massive stars and thereby exhibit an SN-Ia-like elemental feature including a very low [Mg/Fe] ( Almost-Equal-To - 1). We highlight the elemental feature of Fe-group elements for two low-Mg/Fe objects detected in nearby galaxies, and propose the presence of a class of SNe Ia that yield the low abundance ratios of [Cr, Mn, Ni/Fe]. Our novel models of chemical evolution reveal that our proposed class of SNe Ia (slow SNe Ia) is associated with ones exploding on a long timescale after their stellar birth and give a significant impact on the chemical enrichment in the Large Magellanic Cloud (LMC). In the Galaxy, on the other hand, this effect is unseen due to the overwhelming enrichment by the major class of SNe Ia that explode promptly (prompt SNe Ia) and eject a large amount of Fe-group elements. This nicely explains the different [Cr, Mn, Ni/Fe] features between the two galaxies as well as the puzzling feature seen in the LMC stars exhibiting very low Ca but normal Mg abundances. Furthermore, the corresponding channel of slow SN Ia is exemplified by performing detailed nucleosynthesis calculations in the scheme of SNe Ia resulting from a 0.8 + 0.6 M{sub Sun} white dwarf merger.

  17. Addressing the Needs of Diverse Distributed Students

    ERIC Educational Resources Information Center

    Shimoni, Rena; Barrington, Gail; Wilde, Russ; Henwood, Scott

    2013-01-01

    Two interrelated studies were undertaken to assist Alberta post-secondary institutions with meeting challenges associated with providing services to diverse distributed students that are of similar quality to services provided to traditional classroom students. The first study identified and assessed best practices in distributed learning; the…

  18. Diversity and abundance of leafhoppers in Canadian vineyards.

    PubMed

    Saguez, Julien; Olivier, Chrystel; Hamilton, Andrew; Lowery, Thomas; Stobbs, Lorne; Lasnier, Jacques; Galka, Brian; Chen, Xiangsheng; Mauffette, Yves; Vincent, Charles

    2014-05-29

    Leafhoppers (Hemiptera: Cicadellidae) are pests of many temperate crops, including grapevines (Vitis species). Uncontrolled populations can induce direct and indirect damage to crops due to feeding that results in significant yield losses and increased mortality in infected vineyards due to virus, bacteria, or phytoplasmas vectored by leafhoppers. The main objective of this work was to determine the diversity of leafhoppers found in vineyards of the three main Canadian production provinces, i.e., in British Columbia, Ontario, and Quebec. Approximately 18,000 specimens were collected in 80 commercial vineyards from 2006 to 2008. We identified 54 genera and at least 110 different species associated with vineyards, among which 22 were predominant and represented more than 91% of all the leafhoppers. Species richness and diversity were estimated by both Shannon's and Pielou's indices. For each province, results indicated a temporal variation in species composition. Color photographs provide a tool to quickly identify 72 leafhoppers commonly associated with vineyards.

  19. Diversity and Abundance of Leafhoppers in Canadian Vineyards

    PubMed Central

    Saguez, Julien; Olivier, Chrystel; Hamilton, Andrew; Lowery, Thomas; Stobbs, Lorne; Lasnier, Jacques; Galka, Brian; Chen, Xiangsheng; Mauffette, Yves; Vincent, Charles

    2014-01-01

    Leafhoppers (Hemiptera: Cicadellidae) are pests of many temperate crops, including grapevines (Vitis species). Uncontrolled populations can induce direct and indirect damage to crops due to feeding that results in significant yield losses and increased mortality in infected vineyards due to virus, bacteria, or phytoplasmas vectored by leafhoppers. The main objective of this work was to determine the diversity of leafhoppers found in vineyards of the three main Canadian production provinces, i.e., in British Columbia, Ontario, and Quebec. Approximately 18,000 specimens were collected in 80 commercial vineyards from 2006 to 2008. We identified 54 genera and at least 110 different species associated with vineyards, among which 22 were predominant and represented more than 91% of all the leafhoppers. Species richness and diversity were estimated by both Shannon's and Pielou's indices. For each province, results indicated a temporal variation in species composition. Color photographs provide a tool to quickly identify 72 leafhoppers commonly associated with vineyards. PMID:25373220

  20. Predator Diversity and Abundance Provide Little Support for the Enemies Hypothesis in Forests of High Tree Diversity

    PubMed Central

    Schuldt, Andreas; Both, Sabine; Bruelheide, Helge; Härdtle, Werner; Schmid, Bernhard; Zhou, Hongzhang; Assmann, Thorsten

    2011-01-01

    Predatory arthropods can exert strong top-down control on ecosystem functions. However, despite extensive theory and experimental manipulations of predator diversity, our knowledge about relationships between plant and predator diversity—and thus information on the relevance of experimental findings—for species-rich, natural ecosystems is limited. We studied activity abundance and species richness of epigeic spiders in a highly diverse forest ecosystem in subtropical China across 27 forest stands which formed a gradient in tree diversity of 25–69 species per plot. The enemies hypothesis predicts higher predator abundance and diversity, and concomitantly more effective top-down control of food webs, with increasing plant diversity. However, in our study, activity abundance and observed species richness of spiders decreased with increasing tree species richness. There was only a weak, non-significant relationship with tree richness when spider richness was rarefied, i.e. corrected for different total abundances of spiders. Only foraging guild richness (i.e. the diversity of hunting modes) of spiders was positively related to tree species richness. Plant species richness in the herb layer had no significant effects on spiders. Our results thus provide little support for the enemies hypothesis—derived from studies in less diverse ecosystems—of a positive relationship between predator and plant diversity. Our findings for an important group of generalist predators question whether stronger top-down control of food webs can be expected in the more plant diverse stands of our forest ecosystem. Biotic interactions could play important roles in mediating the observed relationships between spider and plant diversity, but further testing is required for a more detailed mechanistic understanding. Our findings have implications for evaluating the way in which theoretical predictions and experimental findings of functional predator effects apply to species-rich forest

  1. Abundances, diversity and seasonality of (non-extremophilic) Archaea in Alpine freshwaters.

    PubMed

    Reitschuler, Christoph; Hofmann, Katrin; Illmer, Paul

    2016-06-01

    The objectives of this study were to assess abundances and community compositions of Archaea within a heterogeneous set of freshwater systems in the Austrian Alps. Seasonal changes and geographical differences within Archaea, considering abiotic and biotic factors (e.g. temperature, pH, total organic carbon (TOC), NH4 (+), bacteria, fungi), were analysed in this context. Water samples were collected from 8 lakes, 10 creeks and the river Inn in 2014. Qualitative-quantitative data were derived via a comprehensive set of (quantitative) PCR assays and PCR-DGGE (denaturing gradient gel electrophoresis) based methodology, which was evaluated concerning specificity and reliability either previously or in this study. QPCR-derived archaeal abundances reached values of 10(3) copies mL(-1) on average, with a peak in winter-spring ('Cold Peak'), and covered 0-15 % (average: 1 %) of the microbial populations. This peak correlated with significantly raised TOC and low NH4 (+) levels during the cold seasons. Stagnant waters showed significantly higher archaeal abundances and diversities than flowing ones. Among methanogens, Methanosarcinales were the most common order. PCR-DGGE data showed that the archaeal communities were site-specific and could function as an ecological marker, in contrast to the more heterogeneous and unsteady bacterial and fungal community. This is attributable to the highly heterogeneous community of methanogenic Archaea (MA, Euryarchaeota), while only two species, Nitrosopumilus maritimus and Ca. Nitrososphaera gargensis, were found to be the ubiquitous representatives of ammonia-oxidizing Archaea (AOA, Thaumarchaeota) in Alpine freshwaters. This work emphasises the diversity, distribution and seasonality of non-extremophilic Archaea in Alpine freshwaters, with a first insight into their ecophysiological potential.

  2. Oceanic heterotrophic dinoflagellates: distribution, abundance, and role as microzooplankton

    SciTech Connect

    Lessard, E.J.

    1984-01-01

    The primary objectives of this thesis were to determine the distribution and abundance of heterotrophic dinoflagellates across the Gulf Stream system off Cape Hatteras and to assess the potential grazing impact of these microheterotrophs in plankton communities. A list of species encountered in this study and their trophic status based on epifluorescence is presented, as well as observations on the presence of external or internal symbionts. The abundance of heterotrophic dinoflagellates across the Gulf Stream region off Cape Hatteras was determined from bimonthly net tow samples over a year and from whole water samples in March. Their average abundance was twice that of net ciliates in the net plankton and ten times that of ciliates in the nanoplankton. An isotope technique was developed to measure grazing rates of individual dinoflaggellates and other microzooplankton which cannot be separated in natural populations on the basis of size. /sup 3/H-thymidine and /sup 14/C-bicarbonate were used to label natural heterotrophic (bacteria and bacterivores) and autotrophic (phytoplankton and herbivores) food, respectively. Estimates of the grazing impact of heterotrophic kinoflagellates relative to other groups of heterotrophs on phytoplankton and bacteria were made by combining abundance data and clearance rates. Such calculations suggested that heterotrophic dinoflagellates may be an important group of grazers in oceanic waters.

  3. Genetic diversity is positively associated with fine-scale momentary abundance of an invasive ant

    PubMed Central

    Gruber, Monica A M; Hoffmann, Benjamin D; Ritchie, Peter A; Lester, Philip J

    2012-01-01

    Many introduced species become invasive despite genetic bottlenecks that should, in theory, decrease the chances of invasion success. By contrast, population genetic bottlenecks have been hypothesized to increase the invasion success of unicolonial ants by increasing the genetic similarity between descendent populations, thus promoting co-operation. We investigated these alternate hypotheses in the unicolonial yellow crazy ant, Anoplolepis gracilipes, which has invaded Arnhem Land in Australia's Northern Territory. We used momentary abundance as a surrogate measure of invasion success, and investigated the relationship between A. gracilipes genetic diversity and its abundance, and the effect of its abundance on species diversity and community structure. We also investigated whether selected habitat characteristics contributed to differences in A. gracilipes abundance, for which we found no evidence. Our results revealed a significant positive association between A. gracilipes genetic diversity and abundance. Invaded communities were less diverse and differed in structure from uninvaded communities, and these effects were stronger as A. gracilipes abundance increased. These results contradict the hypothesis that genetic bottlenecks may promote unicoloniality. However, our A. gracilipes study population has diverged since its introduction, which may have obscured evidence of the bottleneck that would likely have occurred on arrival. The relative importance of genetic diversity to invasion success may be context dependent, and the role of genetic diversity may be more obvious in the absence of highly favorable novel ecological conditions. PMID:23139870

  4. Exploring Leeuwenhoek's legacy: the abundance and diversity of protozoa.

    PubMed

    Finlay, B J; Esteban, G F

    2001-09-01

    Towards the end of the 17th century, Leeuwenhoek built "magnifying glasses" that enabled him to see and describe protozoa for the first time. Continued exploration of the natural history of protozoa during the past 300 years has progressed far beyond simply documenting morphospecies (global total probably <20,000). We now realize that protozoan 'biodiversity' is multi-faceted (e.g. sibling species, variant genotypes and syntrophic consortia). Realization of their extraordinary abundance has secured for protozoa the position of dominant phagotrophs and regenerators of nutrients within microbial food webs. And studies of protozoa in the natural environment have done much to effect a paradigm shift in our understanding of why specific microbes live where they do and how they got there in the first place. In particular, the hypothesis of ubiquitous dispersal of protozoan species does seem to be supported by the evidence provided by morphospecies, sibling species and even individual genotypes.

  5. Summer Abundance and Distribution of Proteorhodopsin Genes in the Western Arctic Ocean

    PubMed Central

    Boeuf, Dominique; Lami, Raphaël; Cunnington, Emelyne; Jeanthon, Christian

    2016-01-01

    Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer. PMID:27790192

  6. Diverse and abundant multi-drug resistant E. coli in Matang mangrove estuaries, Malaysia.

    PubMed

    Ghaderpour, Aziz; Ho, Wing Sze; Chew, Li-Lee; Bong, Chui Wei; Chong, Ving Ching; Thong, Kwai-Lin; Chai, Lay Ching

    2015-01-01

    E.coli, an important vector distributing antimicrobial resistance in the environment, was found to be multi-drug resistant, abundant, and genetically diverse in the Matang mangrove estuaries, Malaysia. One-third (34%) of the estuarine E. coli was multi-drug resistant. The highest antibiotic resistance prevalence was observed for aminoglycosides (83%) and beta-lactams (37%). Phylogenetic groups A and B1, being the most predominant E. coli, demonstrated the highest antibiotic resistant level and prevalence of integrons (integron I, 21%; integron II, 3%). Detection of phylogenetic group B23 downstream of fishing villages indicates human fecal contamination as a source of E. coli pollution. Enteroaggregative E. coli (1%) were also detected immediately downstream of the fishing village. The results indicated multi-drug resistance among E. coli circulating in Matang estuaries, which could be reflective of anthropogenic activities and aggravated by bacterial and antibiotic discharges from village lack of a sewerage system, aquaculture farms and upstream animal husbandry.

  7. Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes.

    PubMed

    Samad, Md Sainur; Bertilsson, Stefan

    2017-01-01

    new insights into diversity, abundance, community composition and spatial as well as temporal distribution of freshwater methanotrophs in low-methane dimictic lakes.

  8. Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

    PubMed Central

    Samad, Md Sainur; Bertilsson, Stefan

    2017-01-01

    insights into diversity, abundance, community composition and spatial as well as temporal distribution of freshwater methanotrophs in low-methane dimictic lakes. PMID:28217121

  9. Non-Gaussian error distribution of 7Li abundance measurements

    NASA Astrophysics Data System (ADS)

    Crandall, Sara; Houston, Stephen; Ratra, Bharat

    2015-07-01

    We construct the error distribution of 7Li abundance measurements for 66 observations (with error bars) used by Spite et al. (2012) that give A(Li) = 2.21 ± 0.065 (median and 1σ symmetrized error). This error distribution is somewhat non-Gaussian, with larger probability in the tails than is predicted by a Gaussian distribution. The 95.4% confidence limits are 3.0σ in terms of the quoted errors. We fit the data to four commonly used distributions: Gaussian, Cauchy, Student’s t and double exponential with the center of the distribution found with both weighted mean and median statistics. It is reasonably well described by a widened n = 8 Student’s t distribution. Assuming Gaussianity, the observed A(Li) is 6.5σ away from that expected from standard Big Bang Nucleosynthesis (BBN) given the Planck observations. Accounting for the non-Gaussianity of the observed A(Li) error distribution reduces the discrepancy to 4.9σ, which is still significant.

  10. Abundance and diversity of microbial life in ocean crust.

    PubMed

    Santelli, Cara M; Orcutt, Beth N; Banning, Erin; Bach, Wolfgang; Moyer, Craig L; Sogin, Mitchell L; Staudigel, Hubert; Edwards, Katrina J

    2008-05-29

    Oceanic lithosphere exposed at the sea floor undergoes seawater-rock alteration reactions involving the oxidation and hydration of glassy basalt. Basalt alteration reactions are theoretically capable of supplying sufficient energy for chemolithoautotrophic growth. Such reactions have been shown to generate microbial biomass in the laboratory, but field-based support for the existence of microbes that are supported by basalt alteration is lacking. Here, using quantitative polymerase chain reaction, in situ hybridization and microscopy, we demonstrate that prokaryotic cell abundances on seafloor-exposed basalts are 3-4 orders of magnitude greater than in overlying deep sea water. Phylogenetic analyses of basaltic lavas from the East Pacific Rise (9 degrees N) and around Hawaii reveal that the basalt-hosted biosphere harbours high bacterial community richness and that community membership is shared between these sites. We hypothesize that alteration reactions fuel chemolithoautotrophic microorganisms, which constitute a trophic base of the basalt habitat, with important implications for deep-sea carbon cycling and chemical exchange between basalt and sea water.

  11. [Microbial community abundance and diversity in typical karst ecosystem to indicate soil carbon cycle].

    PubMed

    Jin, Zhen-Jiang; Tang, Hua-Feng; Li, Min; Huang, Bing-Fu; Li, Qiang; Zhang, Jia-Yu; Li, Gui-Wen

    2014-11-01

    The soil microbial characteristics were detected to clarify their indications in organic carbon cycle in karst system. Soil samples from three karst types (saddle, depression and slop) at 0-10 cm, 10-20 cm and 20-30 cm layers were collected in the Yaji Karst Experimental Site, a typical karst ecosystem. The microbial diversity and abundance were assayed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and fluorescence quantitative PCR. The data showed that the highest abundance of 16S rRNA and 18S rRNA were in depression with 1.32 x 10(11) copies x g(-1) and in saddle with 1.12 x 10(10) copies x g(-1), respectively. The abundance of 16S rRNA in saddle and depression decreased from top to bottom, while that of 18S rRNA in three karst forms decreased, which showed that the abundance changed consistently with soil organic carbon (SOC). The 3 diversity indices of 16S rRNA and 6 diversity indices of 18S rRNA increased from top to bottom in soil profiles of three karst forms. These results showed that microbial diversity changed conversely with the abundance and SOC in soil profile. It can be concluded that the abundance was more important than the diversity index for soil carbon cycle in karst system.

  12. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

    PubMed

    Kembel, Steven W; Wu, Martin; Eisen, Jonathan A; Green, Jessica L

    2012-01-01

    The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms. Despite this fact, many studies assume that the abundance of 16S gene sequences is a surrogate measure of the relative abundance of the organisms containing those sequences. Here we present a method that uses data on sequences and genomic copy number of 16S genes along with phylogenetic placement and ancestral state estimation to estimate organismal abundances from environmental DNA sequence data. We use theory and simulations to demonstrate that 16S genomic copy number can be accurately estimated from the short reads typically obtained from high-throughput environmental sequencing of the 16S gene, and that organismal abundances in microbial communities are more strongly correlated with estimated abundances obtained from our method than with gene abundances. We re-analyze several published empirical data sets and demonstrate that the use of gene abundance versus estimated organismal abundance can lead to different inferences about community diversity and structure and the identity of the dominant taxa in microbial communities. Our approach will allow microbial ecologists to make more accurate inferences about microbial diversity and abundance based on 16S sequence data.

  13. [Abundance and diversity of methanotrophic Gammaproteobacteria in northern wetlands].

    PubMed

    Danilova, O V; Dedysh, S N

    2014-01-01

    Numeric abundance, identity and pH preferences of methanotrophic Gammaproteobacteria (type I methanotrophs) inhabiting the northern acidic wetlands were studied. The rates of methane oxidation by peat samples from six-wetlands of European Northern Russia (pH 3.9-4.7) varied from 0.04 to 0.60 μg CH4 g(-1) peat h(-1). The number of cells revealed by hybridization with fluorochrome-labeled probes M84 + M705 specific for type I methanotrophs was 0.05-2.16 x 10(5) cells g(-1) dry peat, i.e. 0.4-12.5% of the total number of methanotrophs and 0.004-0.39% of the total number of bacteria. Analysis of the fragments of the pmoA gene encoding particulate methane monooxygenase revealed predominance of the genus Methylocystis (92% of the clones) in the studied sample of acidic peat, while the proportion of the pmoA sequences of type I methanotrophs was insignificant (8%). PCR amplification of the 16S rRNA gene fragments of type I methanotrophs with TypeIF-Type IR primers had low specificity, since only three sequences out of 53 analyzed belonged to methanotrophs and exhibited 93-99% similarity to those of Methylovulum, Methylomonas, and Methylobacter species. Isolates of type I methanotrophs obtained from peat (strains SH10 and 83A5) were identified as members of the species Methylomonaspaludis and Methylovulum miyakonense, respectively. Only Methylomonaspaludum SH10 was capable of growth in acidic media (pH range for growth 3.8-7.2 with the optimum at pH 5.8-6.2), while Methylovulum miyakonense 83A5 exhibited the typical growth characteristics of neutrophilic methanotrophs (pH range for growth 5.5-8.0 with the optimum at pH 6.5-7.5).

  14. Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea.

    PubMed

    Quero, Grazia Marina; Luna, Gian Marco

    2014-10-01

    Bacteria are fundamental players in the functioning of the ocean, yet relatively little is known about the diversity of bacterioplankton assemblages and the factors shaping their spatial distribution. We investigated the diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations. Bacterioplankton diversity was investigated using a whole-assemblage genetic fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA) coupled with 16S rDNA amplicon pyrosequencing. The main physico-chemical variables showed clear differences between coastal and offshore stations, with the latter displaying generally higher temperature, salinity and oxygen content. Bacterioplankton richness was higher in coastal than offshore waters. Bacterial community composition (BCC) differed significantly between coastal and offshore waters, and appeared to be influenced by temperature (explaining up to 30% of variance) and by the trophic state. Pyrosequencing evidenced dominance of Alphaproteobacteria (SAR11 cluster), uncultured Gammaproteobacteria (Rhodobacteraceae) and Cyanobacteria (Synechococcus). Members of the Bacteroidetes phylum were also abundant, and accounted for 25% in the station characterized by the higher organic carbon availability. Bacterioplankton assemblages included a few dominant taxa and a very large proportion (85%) of rare (<0.1%) bacteria, the vast majority of which was unique to each sampling station. The first detailed census of bacterioplankton taxa in the SAd sub-basin, performed using next generation sequencing, indicates that assemblages are highly heterogeneous, spatially structured according to the environmental conditions, and comprise a large number of rare taxa. The high turnover diversity, particularly evident at the level of the rare taxa, suggests to direct future investigations toward larger

  15. Diversity and abundance of dung beetles (Coleoptera: Scaraebidae) at several different ecosystem functions in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Din, Abdullah Muhaimin Mohammad; Yaakop, Salmah; Hazmi, Izfa Riza

    2015-09-01

    Dung beetles has known for its bioindicator characteristic. Sensitive towards forest disturbance, dung beetles population and diversity will be less in disturbed and modified area. The objective of this study is to evaluate the diversity and distribution of dung beetles in different type of ecosystems in Peninsular Malaysia. Fifteen baited pitfall traps aligned in three transects were used in this study. Samples were collected after 24 h and repeated three time collections and identified afterwards. Two ecosystem types were selected, which are forested and agricultural ecosystem (livestock and plantation). A total of 4249 individuals, 47 species, in 11 genera was successfully collected from all localities. The H' index for Fraser Hill, Langkawi, Bangi Reserve Forest, Selangor (HSB), Sungkai Reserve Forest, Perak (SRF), Chini Lake, Bera Lake, chicken farm, goat farm, Longan plantation, and palm oil plantation were 1.58, 1.74, 2.17, 2.63, 1.80, 1.52, 1.63, 0.46, 0.00 and 1.98 respectively.Forest ecosystem, SRF shows the highest abundance (1486 individuals) and diversity, while for agricultural ecosystem,palm oil plantation shows the highest with 273 individuals and 16 species. Based onDetrended Correspondence Analysis (DCA) shows two groups that separate forest ecosystem with the agricultural ecosystem, with palm oil is the nearest to the forest. Palm oil ecosystem can sustain a dung beetles population due to the area can provide the requirements for the dung beetles to survive, such as food which comes from local domestic cows, shade from sunlight provide by the palm oil trees, and ground cover from small plants and shrubs.Even though modified ecosystem should have lower diversity of dung beetles, but some factors must be measured as well in order to have a better point of view.

  16. Anthropic effects on sand fly (Diptera: Psychodidae) abundance and diversity in an Amazonian rural settlement, Brazil.

    PubMed

    Ramos, Walkyria Rodrigues; Medeiros, Jansen Fernandes; Julião, Genimar Rebouças; Ríos-Velásquez, Claudia María; Marialva, Eric Fabrício; Desmouliére, Sylvain J M; Luz, Sérgio Luiz Bessa; Pessoa, Felipe Arley Costa

    2014-11-01

    Sand flies (Diptera: Psychodidae) are responsible for the transmission of protozoan parasites that cause leishmaniases. They are found predominantly in forests, but some species exploit environments that have been subject to deforestation and subsequent human colonization. Studies conducted in Brazil over the past 30 years show that some species are adapting to peri-urban and urban settings. We evaluated sand fly diversity and abundance in the rural settlement of Rio Pardo, Presidente Figueiredo Municipality, Amazonas State, Brazil. Settlement households were divided into four categories. These categories were determined by the human population density and the degree of deforestation in the immediate area. We used CDC light traps to sample the area surrounding 24 households (6 households in each category). Samples were taken on six occasions during September-November 2009 and June-August 2010. A total of 3074 sand fly specimens were collected, including 1163 females and 1911 males. These were classified into 13 genera and 52 species. The greatest abundance of sand flies and the greatest richness of species were observed in areas where human population density was highest. Our results show that changes in the human occupancy and vegetation management in rural settlements may affect the population dynamics and distribution of sand fly species, thereby affecting the local transmission of cutaneous leishmaniases.

  17. Diversity and abundance of mosquitoes (Diptera:Culicidae) in an urban park: larval habitats and temporal variation.

    PubMed

    Medeiros-Sousa, Antônio R; Ceretti-Júnior, Walter; de Carvalho, Gabriela C; Nardi, Marcello S; Araujo, Alessandra B; Vendrami, Daniel P; Marrelli, Mauro T

    2015-10-01

    Urban parks are areas designated for human recreation but also serve as shelter and refuge for populations of several species of native fauna, both migratory and introduced. In Brazil, the effect of annual climate variations on Aedes aegypti and dengue epidemics in large cities like São Paulo is well known, but little is known about how such variations can affect the diversity of mosquito vectors in urban parks and the risk of disease transmission by these vectors. This study investigates the influence of larval habitats and seasonal factors on the diversity and abundance of Culicidae fauna in Anhanguera Park, one of the largest remaining green areas in the city of São Paulo. Species composition and richness and larval habitats were identified. Seasonality (cold-dry and hot-rainy periods) and year were considered as explanatory variables and the models selection approach was developed to investigate the relationship of these variables with mosquito diversity and abundance. A total of 11,036 specimens from 57 taxa distributed in 13 genera were collected. Culex nigripalpus, Cx. quinquefasciatus and Aedes albopictus were the most abundant species. Bamboo internodes and artificial breeding sites showed higher abundance, while ponds and puddles showed greater richness. Significant relationships were observed between abundance and seasonality, with a notable increase in the mosquitos abundance in the warm-rainy periods. The Shannon and Berger-Parker indices were related with interaction between seasonality and year, however separately these predictors showed no relationship with ones. The increased abundance of mosquitoes in warm-rainy months and the fact that some of the species are epidemiologically important increase not only the risk of pathogen transmission to people who frequent urban parks but also the nuisance represented by insect bites. The findings of this study highlight the importance of knowledge of culicid ecology in green areas in urban environments.

  18. Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments.

    PubMed

    Webster, Gordon; O'Sullivan, Louise A; Meng, Yiyu; Williams, Angharad S; Sass, Andrea M; Watkins, Andrew J; Parkes, R John; Weightman, Andrew J

    2015-02-01

    Archaea are widespread in marine sediments, but their occurrence and relationship with natural salinity gradients in estuarine sediments is not well understood. This study investigated the abundance and diversity of Archaea in sediments at three sites [Brightlingsea (BR), Alresford (AR) and Hythe (HY)] along the Colne Estuary, using quantitative real-time PCR (qPCR) of 16S rRNA genes, DNA hybridization, Archaea 16S rRNA and mcrA gene phylogenetic analyses. Total archaeal 16S rRNA abundance in sediments were higher in the low-salinity brackish sediments from HY (2-8 × 10(7) 16S rRNA gene copies cm(-3)) than the high-salinity marine sites from BR and AR (2 × 10(4)-2 × 10(7) and 4 × 10(6)-2 × 10(7) 16S rRNA gene copies cm(-3), respectively), although as a proportion of the total prokaryotes Archaea were higher at BR than at AR or HY. Phylogenetic analysis showed that members of the 'Bathyarchaeota' (MCG), Thaumarchaeota and methanogenic Euryarchaeota were the dominant groups of Archaea. The composition of Thaumarchaeota varied with salinity, as only 'marine' group I.1a was present in marine sediments (BR). Methanogen 16S rRNA genes from low-salinity sediments at HY were dominated by acetotrophic Methanosaeta and putatively hydrogentrophic Methanomicrobiales, whereas the marine site (BR) was dominated by mcrA genes belonging to methylotrophic Methanococcoides, versatile Methanosarcina and methanotrophic ANME-2a. Overall, the results indicate that salinity and associated factors play a role in controlling diversity and distribution of Archaea in estuarine sediments.

  19. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

    PubMed Central

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-01-01

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses. PMID:27892507

  20. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons

    NASA Astrophysics Data System (ADS)

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-11-01

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

  1. Variations in abundance, diversity and community composition of airborne fungi in swine houses across seasons.

    PubMed

    Kumari, Priyanka; Woo, Cheolwoon; Yamamoto, Naomichi; Choi, Hong-Lim

    2016-11-28

    We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

  2. Macrobenthos composition, distribution and abundance within Sungai Pulai estuary, Johor, Malaysia

    NASA Astrophysics Data System (ADS)

    Shi, Guan Wan; Min, Lee Di; Ghaffar, Mazlan Abd; Ali, Masni Md; Cob, Zaidi Che

    2014-09-01

    Macrobenthos are very useful organisms for monitoring marine environmental and widely use in marine ecology research. They are able to monitor the difference phase in the recovery stage of disturbed sites by appear different species macrobenthos after the cessation of the impact. Univariate and multivariate methods were use to study the macrobenthos community within Sungai Pulai estuary, Johor, Malaysia. Five sub-samples were taken at each sampling sites by using 10 cm diameter corer. Crustaceans were the most abundant at Tanjung Adang (St. 1) and the station of non-seagrass area (St. 2) while polychaetes were the most abundant at Merambong Shoal (St. 3). Higher density of macrobenthos was found at St.3 followed by St. 1 and St. 2. The commonly used population indices such as diversity, richness, evenness and dominance were employed to determine the differences in diversity and abundance of macrobenthos. The diversity, richness and evenness index values showed slight increment from Station 1 to Station 3, while the dominance index decreasing trend from Station 1 to Station 3. A total 21 polychaete families were collected in Sungai Pulai estuary, which was dominated by the Spionidae, Capitellidae and Glyceridae. Cluster (Bray-Curtis similarities) analyses revealed that the Tanjung Adang and Merambong Shoal population were clearly separated from the station non-seagrass. For the time being factors that influence the pattern of distribution of the macrobenthos cannot be determined and subjected to further studies.

  3. Water Vapour Abundance and Distribution in the Lower Venusian Atmosphere

    NASA Astrophysics Data System (ADS)

    Chamberlain, S.; Bailey, J.

    2012-04-01

    We present ground-based observations and modelling studies of water vapour abundance and distribution in the Venusian lower atmosphere through analysis of absorption band depths within the 1.18 μm window. The lower atmosphere of Venus is difficult to study by both in situ and remote instruments. This is due to the planet wide cloud cover that obscures visual wavelengths and surface pressures approaching 100 times that of the Earth. In 1984 ground based observations resulted in the discovery of atmospheric windows on the Venusian nightside (Allen and Crawford, 1984). Here, near infrared radiation originating at the surface and lower atmosphere, pass relatively unimpeded through the Venus clouds. This discovery enabled remote studies of the Venusian subcloud region. Determining the abundance and distribution of water vapour is key to understanding the development, maintenance and links between major radiative and dynamical features of the Venus atmosphere. Water vapour in the lower atmosphere plays an important role in heat transfer and is pertinent to the runaway greenhouse effect and dynamical superrotation observed on Venus. Detailed studies of water vapour abundance and distribution throughout the lower atmosphere of Venus are therefore needed in order to develop accurate chemical, radiative and dynamical models. Ground-based spatially resolved near infrared spectroscopic observations of the Venusian nightside have been obtained from Siding Spring Observatory at each inferior conjunction since 2002. Observations have been made using the IRIS2 instrument on the Anglo-Australian Telescope and CASPIR on the 2.3m ANU telescope. The model VSTAR (Bailey and Kedziora-Chudczer 2012) is used to simulate the observed Venus spectra as seen through the Earth's atmosphere and best fit water vapour abundances are found for approximately 300 locations across the Venus nightside disk. Recent improvements in ground-based near-infrared instruments allow a substantial improvement

  4. Diversity and abundance of the abnormal chromosome 10 meiotic drive complex in Zea mays

    PubMed Central

    Kanizay, L B; Pyhäjärvi, T; Lowry, E G; Hufford, M B; Peterson, D G; Ross-Ibarra, J; Dawe, R K

    2013-01-01

    Maize Abnormal chromosome 10 (Ab10) contains a classic meiotic drive system that exploits the asymmetry of meiosis to preferentially transmit itself and other chromosomes containing specialized heterochromatic regions called knobs. The structure and diversity of the Ab10 meiotic drive haplotype is poorly understood. We developed a bacterial artificial chromosome (BAC) library from an Ab10 line and used the data to develop sequence-based markers, focusing on the proximal portion of the haplotype that shows partial homology to normal chromosome 10. These molecular and additional cytological data demonstrate that two previously identified Ab10 variants (Ab10-I and Ab10-II) share a common origin. Dominant PCR markers were used with fluorescence in situ hybridization to assay 160 diverse teosinte and maize landrace populations from across the Americas, resulting in the identification of a previously unknown but prevalent form of Ab10 (Ab10-III). We find that Ab10 occurs in at least 75% of teosinte populations at a mean frequency of 15%. Ab10 was also found in 13% of the maize landraces, but does not appear to be fixed in any wild or cultivated population. Quantitative analyses suggest that the abundance and distribution of Ab10 is governed by a complex combination of intrinsic fitness effects as well as extrinsic environmental variability. PMID:23443059

  5. Geographic variation in cowbird distribution, abundance, and parasitism

    USGS Publications Warehouse

    Morrison, M.L.; Hahn, D.C.; George, T. Luke; Dobkin, David S.

    2002-01-01

    We evaluated geographical patterns in the abundance and distribution of Brown-headed Cowbirds (Molothrus ater), and in the frequency of cowbird parasitism, across North America in relation to habitat fragmentation. We found no distinctive parasitism patterns at the national or even regional scales, but the species is most abundant in the Great Plains, the heart of their original range, and least common in the southeastern U.S. This situation is dynamic, because both the Brown-headed and two other cowbird species are actively expanding their ranges in the southern U.S. We focused almost entirely in this paper on the Brown-headed Cowbird, because it is the only endemic North American cowbird, its distribution is much wider, and it has been much more intensively studied. We determined that landscape is the most meaningful unit of scale for comparing cowbird parasitism patterns as, for example, in comparisons of northeastern and central hardwood forests within agricultural matrices, and suburbanized areas versus western coniferous forests. We concluded that cowbird parasitism patterns were broadly similar within all landscapes. Even comparisons between prominently dissimilar landscapes, such as hardwoods in agriculture and suburbia versus coniferous forest, display a striking similarity in the responses of cowbirds. Our review clearly indicated that proximity of feeding areas is the key factor influencing presence and parasitism patterns within the landscape. We considered intensity of landscape fragmentation from forest-dominated landscapes altered in a forest management context to fragmentation characterized by mixed suburbanization or agricultural development. Our review consistently identified an inverse relationship between extent of forest cover across the landscape and cowbird presence. Invariably, the variation seen in parasitism frequencies within a region was at least partially explained as a response to changes in forest cover. The most salient geographic

  6. Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

    PubMed

    Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

    2014-01-01

    Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions.

  7. Volatile Abundance and Distribution in the Tempel 1 Ejecta Cloud

    NASA Astrophysics Data System (ADS)

    Moretto, Mark J.; Feaga, Lori M.; A'Hearn, Michael F.; Protopapa, Silvia; Sunshine, Jessica M.; Farnham, Tony L.

    2015-11-01

    On 4 Jul 2005 the Deep Impact Impactor Spacecraft collided with comet Tempel 1, creating an ejecta cloud that was observed by the Deep Impact Flyby Spacecraft (DIF) as well as Earth and space based observatories. The High Resolution Instrument Infrared Spectrometer (HRI-IR) onboard DIF acquired several spectral scans of this ejecta cloud in the minutes immediately after impact. HRI-IR has a spectral range of 1.05 to 4.85 microns. This spectral range allows for water vapor, water ice, organics, CO2 and CO to be detected simultaneously, if each species is sufficiently abundant.We present an analysis of the quantity and spatial distribution of water, organics and CO2 in the Tempel 1 ejecta cloud. Variation in abundance, either absolute or relative, will be compared to morphological features in the ejecta cloud present in visible images acquired by the Medium and High Resolution Imagers onboard DIF. The composition of the ejecta cloud will also be compared with that of the 2 Jul 2005 natural outburst and quiescent activity levels at Tempel 1.

  8. Diversity of Abundance Patterns of Light Neutron-capture Elements in Very-metal-poor Stars

    NASA Astrophysics Data System (ADS)

    Aoki, Misa; Ishimaru, Yuhri; Aoki, Wako; Wanajo, Shinya

    2017-03-01

    We determine the abundances of neutron-capture elements from Sr to Eu for five very-metal-poor stars (-3 < [{Fe}/{{H}}] < -2) in the Milky Way halo to reveal the origin of light neutron-capture elements. Previous spectroscopic studies have shown evidence of at least two components in the r-process; one referred to as the “main r-process” and the other as the “weak r-process,” which is mainly responsible for producing heavy and light neutron-capture elements, respectively. Observational studies of metal-poor stars suggest that there is a universal pattern in the main r-process, similar to the abundance pattern of the r-process component of solar-system material. Still, it is uncertain whether the abundance pattern of the weak r-process shows universality or diversity, due to the sparseness of measured light neutron-capture elements. We have detected the key elements, Mo, Ru, and Pd, in five target stars to give an answer to this question. The abundance patterns of light neutron-capture elements from Sr to Pd suggest a diversity in the weak r-process. In particular, scatter in the abundance ratio between Ru and Pd is significant when the abundance patterns are normalized at Zr. Our results are compared with the elemental abundances predicted by nucleosynthesis models of supernovae with parameters such as electron fraction or proto-neutron-star mass, to investigate sources of such diversity in the abundance patterns of light neutron-capture elements. This paper presents that the variation in the abundances of observed stars can be explained with a small range of parameters, which can serve as constraints on future modeling of supernova models. Study based on data collected with the Subaru Telescope, operated by the National Astronomical Observatory of Japan.

  9. Abundance and diversity of soybean-nodulating rhizobia in black soil are impacted by land use and crop management.

    PubMed

    Yan, Jun; Han, Xiao Zeng; Ji, Zhao Jun; Li, Yan; Wang, En Tao; Xie, Zhi Hong; Chen, Wen Feng

    2014-09-01

    To investigate the effects of land use and crop management on soybean rhizobial communities, 280 nodule isolates were trapped from 7 fields with different land use and culture histories. Besides the known Bradyrhizobium japonicum, three novel genospecies were isolated from these fields. Grassland (GL) maintained a higher diversity of soybean bradyrhizobia than the other cultivation systems. Two genospecies (Bradyrhizobium spp. I and III) were distributed widely in all treatments, while Bradyrhizobium sp. II was found only in GL treatment. Cultivation with soybeans increased the rhizobial abundance and diversity, except for the soybean monoculture (S-S) treatment. In monoculture systems, soybeans favored Bradyrhizobium sp. I, while maize and wheat favored Bradyrhizobium sp. III. Fertilization decreased the rhizobial diversity indexes but did not change the species composition. The organic carbon (OC) and available phosphorus (AP) contents and pH were the main soil parameters positively correlated with the distribution of Bradyrhizobium spp. I and II and Bradyrhizobium japonicum and negatively correlated with Bradyrhizobium sp. III. These results revealed that different land uses and crop management could not only alter the diversity and abundance of soybean rhizobia, but also change interactions between rhizobia and legume or nonlegume plants, which offered novel information about the biogeography of rhizobia.

  10. Species diversity and seasonal abundance of Culicoides biting midges in northwestern Argentina.

    PubMed

    Aybar, C A Veggiani; Juri, M J Dantur; De Grosso, M S Lizarralde; Spinelli, G R

    2010-03-01

    The species diversity and seasonal abundance of biting midges of the genus Culicoides (Diptera: Ceratopogonidae) were studied in northwestern Argentina during the period 2003-2005. A total of 5437 Culicoides specimens were collected using CDC light traps in three areas of the mountainous rainforest area. The most common species were Culicoides paraensis (Goeldi) and C. insignis Lutz, Culicoides lahillei (Iches), C. venezuelensis Ortiz & Mirsa, C. debilipalpis Lutz and C. crescentis Wirth & Blanton were also collected. Culicoides paraensis was abundant during the summer, and C. insignis and C. lahillei during late summer and early fall. Accumulated rainfall was the climatic variable most related to fluctuation in abundance of C. paraensis.

  11. [Abundance and diversity of littoral invertebrates in the Socorro Island, Revillagigedo Archipelago, Mexico].

    PubMed

    Mille-Pagaza, Silvia; Carrillo-Laguna, J; Pérez-Chi, A; Sánchez-Salazar, M E

    2002-03-01

    Composition, abundance, diversity and distribution of the littoral benthic invertebrates of Socorro Island with transects (parallel to the coast and with 1 m2 quadrats) were analyzed. During the spring of 1991 and 1992 samples were taken from the upper and middle levels of the intertidal zone in Vargas Lozano, Braithwaite, Blanca SW, Blanca NE, Binners, Grayson, Academia and Norte bays. The 161 species found belong to Porifera, Cnidaria, Platyhelmintha, Nemertina, Sipunculida, Annelida, Mollusca, Anthropoda and Echinodermata. Crustaceans and mollusks were the richest groups in both years, as in other rocky shores. Highest total density was found in Blanca NE bay in both samplings, with 281 orgs./m2 in the first and 172 orgs./m2 in the second. Most frequently found species were Isognomon janus (Mollusca, Pelecypoda), Littorina pullata (Mollusca, Gastropoda), Hipponix panamensis (Mollusca, Gastropoda), Pachygrapsus transversus (Crustacea, Grapsoidea) and Turbo funiculosus (Mollusca, Gastropoda). Because of the complexity of the habitat structure, Vargas Lozano was the bay with the highest specific richness (83 species), greatest diversity (4.7 bits/individual) and lowest dominance (0.065). Most species were classified as accidentals with the Dajoz's frequency classification, while the dominant species were accessories and only I. janus, in the spring 1991, was a constant species. Two kinds of bays were distinguished: those with some dominant species (density) and those in which there was no evident dominance by a particular species. Consequently, the diversity and evenness values were set apart: homogeneous communities (Vargas Lozano and Binners) and heterogeneous communities (Grayson bay and others), characterized by intermediate evenness values. The Jaccard similarity index identified two regions: one formed by bays found mainly in the southwest part of the island (Binners, Vargas Lozano, Braithwaite, Grayson and Blanca SW) and the other found in the northern

  12. Relationship of Course Woody Debris to Red-Cockaded Woodpecker Prey Diversity and Abundance

    SciTech Connect

    Horn, G.S.

    1999-09-03

    The abundance of diversity of prey commonly used by the red-cockaded woodpecker were monitored in experimental plots in which course woody debris was manipulated. In one treatment, all the woody debris over four inches was removed. In the second treatment, the natural amount of mortality remained intact. The overall diversity of prey was unaffected; however, wood roaches were significantly reduced by removal of woody debris. The latter suggests that intensive utilizations or harvesting practices may reduce foraging.

  13. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

    PubMed Central

    Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package “traitor” to facilitate assessments of missing trait data. PMID:26881747

  14. Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation.

    PubMed

    Májeková, Maria; Paal, Taavi; Plowman, Nichola S; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R; Luke, Sarah H; Sam, Katerina; Le Bagousse-Pinguet, Yoann; Lepš, Jan; Götzenberger, Lars; de Bello, Francesco

    2016-01-01

    Functional diversity (FD) is an important component of biodiversity that quantifies the difference in functional traits between organisms. However, FD studies are often limited by the availability of trait data and FD indices are sensitive to data gaps. The distribution of species abundance and trait data, and its transformation, may further affect the accuracy of indices when data is incomplete. Using an existing approach, we simulated the effects of missing trait data by gradually removing data from a plant, an ant and a bird community dataset (12, 59, and 8 plots containing 62, 297 and 238 species respectively). We ranked plots by FD values calculated from full datasets and then from our increasingly incomplete datasets and compared the ranking between the original and virtually reduced datasets to assess the accuracy of FD indices when used on datasets with increasingly missing data. Finally, we tested the accuracy of FD indices with and without data transformation, and the effect of missing trait data per plot or per the whole pool of species. FD indices became less accurate as the amount of missing data increased, with the loss of accuracy depending on the index. But, where transformation improved the normality of the trait data, FD values from incomplete datasets were more accurate than before transformation. The distribution of data and its transformation are therefore as important as data completeness and can even mitigate the effect of missing data. Since the effect of missing trait values pool-wise or plot-wise depends on the data distribution, the method should be decided case by case. Data distribution and data transformation should be given more careful consideration when designing, analysing and interpreting FD studies, especially where trait data are missing. To this end, we provide the R package "traitor" to facilitate assessments of missing trait data.

  15. North American amphibians: distribution and diversity

    USGS Publications Warehouse

    : Green, David M.; Weir, Linda A.; Casper, Gary S.; Lannoo, Michael

    2014-01-01

    Some 300 species of amphibians inhabit North America. The past two decades have seen an enormous growth in interest about amphibians and an increased intensity of scientific research into their fascinating biology and continent-wide distribution. This atlas presents the spectacular diversity of North American amphibians in a geographic context. It covers all formally recognized amphibian species found in the United States and Canada, many of which are endangered or threatened with extinction. Illustrated with maps and photos, the species accounts provide current information about distribution, habitat, and conservation. Researchers, professional herpetologists, and anyone intrigued by amphibians will value North American Amphibians as a guide and reference.

  16. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    SciTech Connect

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  17. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    DOE PAGES

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; ...

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

  18. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.

    PubMed

    Aziz, Ramy K; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A

    2015-01-01

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  19. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    PubMed Central

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-01-01

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution. PMID:26005436

  20. Increasing aridity reduces soil microbial diversity and abundance in global drylands.

    PubMed

    Maestre, Fernando T; Delgado-Baquerizo, Manuel; Jeffries, Thomas C; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Quero, José Luis; García-Gómez, Miguel; Gallardo, Antonio; Ulrich, Werner; Bowker, Matthew A; Arredondo, Tulio; Barraza-Zepeda, Claudia; Bran, Donaldo; Florentino, Adriana; Gaitán, Juan; Gutiérrez, Julio R; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Mau, Rebecca L; Miriti, Maria; Naseri, Kamal; Ospina, Abelardo; Stavi, Ilan; Wang, Deli; Woods, Natasha N; Yuan, Xia; Zaady, Eli; Singh, Brajesh K

    2015-12-22

    Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

  1. Increasing aridity reduces soil microbial diversity and abundance in global drylands

    PubMed Central

    Delgado-Baquerizo, Manuel; Jeffries, Thomas C.; Eldridge, David J.; Ochoa, Victoria; Gozalo, Beatriz; Quero, José Luis; García-Gómez, Miguel; Gallardo, Antonio; Ulrich, Werner; Bowker, Matthew A.; Arredondo, Tulio; Barraza-Zepeda, Claudia; Bran, Donaldo; Florentino, Adriana; Gaitán, Juan; Gutiérrez, Julio R.; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Mau, Rebecca L.; Miriti, Maria; Naseri, Kamal; Ospina, Abelardo; Stavi, Ilan; Wang, Deli; Woods, Natasha N.; Yuan, Xia; Zaady, Eli; Singh, Brajesh K.

    2015-01-01

    Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands. PMID:26647180

  2. nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

    PubMed

    Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

    2016-10-01

    For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

  3. Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages.

    PubMed

    Hsieh, T C; Chao, Anne

    2016-08-26

    Measures of phylogenetic diversity are basic tools in many studies of systematic biology. Faith's PD (sum of branch lengths of a phylogenetic tree connecting all focal species) is the most widely used phylogenetic measure. Like species richness, Faith's PD based on sampling data is highly dependent on sample size and sample completeness. The sample-size- and sample-coverage-based integration of rarefaction and extrapolation of Faith's PD was recently developed to make fair comparison across multiple assemblages. However, species abundances are not considered in Faith's PD. Based on the framework of Hill numbers, Faith's PD was generalized to a class of phylogenetic diversity measures that incorporates species abundances. In this article, we develop both theoretical formulae and analytic estimators for seamless rarefaction and extrapolation for this class of abundance-sensitive phylogenetic measures, which includes simple transformations of phylogenetic entropy and of quadratic entropy. This work generalizes the previous rarefaction/extrapolation model of Faith's PD to incorporate species abundance, and also extends the previous rarefaction/extrapolation model of Hill numbers to include phylogenetic differences among species. Thus a unified approach to assessing and comparing species/taxonomic diversity and phylogenetic diversity can be established. A bootstrap method is suggested for constructing confidence intervals around the phylogenetic diversity, facilitating the comparison of multiple assemblages. Our formulation and estimators can be extended to incidence data collected from multiple sampling units. We also illustrate the formulae and estimators using bacterial sequence data from the human distal esophagus and phyllostomid bat data from three habitats. [Extrapolation; diversity; Hill numbers; interpolation; phylogenetic diversity; prediction; rarefaction; sample completeness; sample coverage.].

  4. Riparian Ficus Tree Communities: The Distribution and Abundance of Riparian Fig Trees in Northern Thailand

    PubMed Central

    Pothasin, Pornwiwan; Compton, Stephen G.; Wangpakapattanawong, Prasit

    2014-01-01

    Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010–2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance. PMID:25310189

  5. Riparian Ficus tree communities: the distribution and abundance of riparian fig trees in northern Thailand.

    PubMed

    Pothasin, Pornwiwan; Compton, Stephen G; Wangpakapattanawong, Prasit

    2014-01-01

    Fig trees (Ficus) are often ecologically significant keystone species because they sustain populations of the many seed-dispersing animals that feed on their fruits. They are prominent components of riparian zones where they may also contribute to bank stability as well as supporting associated animals. The diversity and distributions of riparian fig trees in deciduous and evergreen forests in Chiang Mai Province, Northern Thailand were investigated in 2010-2012. To record the diversity and abundance of riparian fig trees, we (1) calculated stem density, species richness, and diversity indices in 20×50 m randomly selected quadrats along four streams and (2) measured the distances of individual trees from four streams to determine if species exhibit distinct distribution patterns within riparian zones. A total of 1169 individuals (from c. 4 ha) were recorded in the quadrats, representing 33 Ficus species (13 monoecious and 20 dioecious) from six sub-genera and about 70% of all the species recorded from northern Thailand. All 33 species had at least some stems in close proximity to the streams, but they varied in their typical proximity, with F. squamosa Roxb. and F. ischnopoda Miq the most strictly stream-side species. The riparian forests in Northern Thailand support a rich diversity and high density of Ficus species and our results emphasise the importance of fig tree within the broader priorities of riparian area conservation. Plans to maintain or restore properly functioning riparian forests need to take into account their significance.

  6. Landscape context affects genetic diversity at a much larger spatial extent than population abundance.

    PubMed

    Jackson, Nathan D; Fahrig, Lenore

    2014-04-01

    Regional landscape context influences the fate of local populations, yet the spatial extent of this influence (called the "scale of effect") is difficult to predict. Thus, a major problem for conservation management is to understand the factors governing the scale of effect such that landscape structure surrounding a focal area is measured and managed at the biologically relevant spatial scale. One unresolved question is whether and how scale of effect may depend on the population response measured (e.g., abundance vs. presence/absence). If scales of effect differ across population outcomes of a given species, management based on one outcome may compromise another, further complicating conservation decision making. Here we used an individual-based simulation model to investigate how scales of effect of landscapes that vary in the amount and fragmentation of habitat differ among three population responses (local abundance, presence/absence, and genetic diversity). We also explored how the population response measured affects the relative importance of habitat amount and fragmentation in shaping local populations, and how dispersal distance mediates the magnitude and spatial scale of these effects. We found that the spatial scale most strongly influencing local populations depended on the outcome measured and was predicted to be small for abundance, medium-sized for presence/absence, and large for genetic diversity. Increasing spatial scales likely resulted from increasing temporal scales over which outcomes were regulated (with local genetic diversity being regulated over the largest number of generations). Thus, multiple generations of dispersal and gene flow linked local population patterns to regional population size. The effects of habitat amount dominated the effects of fragmentation for all three outcomes. Increased dispersal distance strongly reduced abundance, but not presence/absence or genetic diversity. Our results suggest that managing protected species

  7. The influence of pearl oyster farming on reef fish abundance and diversity in Ahe, French Polynesia.

    PubMed

    Cartier, Laurent E; Carpenter, Kent E

    2014-01-15

    Many cultured pearl farms are located in areas of the Pacific that have thriving, highly diverse fish communities but the impacts of farming on these communities are poorly understood. We studied the effects of pearl oyster farming on shore fish abundance and diversity in the lagoon of Ahe, French Polynesia by adapting roving diver census methods to the coral reef bommies of the lagoon and compared 16 sites with high pearl farming impact to others with no direct impact. Pearl farming has a slightly positive effect on reef fish abundance (N) and no significant impact on fish diversity (H) or community composition. This is important when considering the ecological sustainability of pearl farming in French Polynesia and suggests that a potential synergy between pearl farms and marine conservation should be further explored.

  8. Effect of habitat complexity on richness, abundance and distributional pattern of forest birds.

    PubMed

    Ghadiri Khanaposhtani, Maryam; Kaboli, Mohammad; Karami, Mahmoud; Etemad, Vahid

    2012-08-01

    Structurally complex forests provide more diverse conditions in comparison to homogenous forests because of greater variety of microhabitats and trees. This study assesses the association of bird species richness, abundance, and distributional pattern with habitat complexity (HC) in Kheyrud Forest in the north of Iran. Birds were surveyed during spring 2009 by 100 point counts. In each point count six habitat features related to the index of HC were computed and scored from 0 to 3. Then the scores were summed and divided into two groups of low and high complexity, HC ≤ 6 and HC > 6, respectively. To compare bird richness and abundance in different HCs, a two sample t-test was used. Presence and absence of bird species at each plot as a dependent variable were compared with the vegetation characteristics as an independent variable by means of the Canonical Correspondence Analysis. The results revealed bird species richness and abundance were significantly higher in more complex habitats. Bird species can be divided into two groups, the first group including species which associated with late successional stages and the second group, species belonging to early successional stages. Numbers of birds belonging to the first group declined in less complex forests, whereas the numbers of birds belonging to the second group increased. At the stand scale, our results reveal that bird abundance and richness are strongly associated with the complexity of vegetation structure in the study area.

  9. Effect of Habitat Complexity on Richness, Abundance and Distributional Pattern of Forest Birds

    NASA Astrophysics Data System (ADS)

    Ghadiri Khanaposhtani, Maryam; Kaboli, Mohammad; Karami, Mahmoud; Etemad, Vahid

    2012-08-01

    Structurally complex forests provide more diverse conditions in comparison to homogenous forests because of greater variety of microhabitats and trees. This study assesses the association of bird species richness, abundance, and distributional pattern with habitat complexity (HC) in Kheyrud Forest in the north of Iran. Birds were surveyed during spring 2009 by 100 point counts. In each point count six habitat features related to the index of HC were computed and scored from 0 to 3. Then the scores were summed and divided into two groups of low and high complexity, HC ≤ 6 and HC > 6, respectively. To compare bird richness and abundance in different HCs, a two sample t-test was used. Presence and absence of bird species at each plot as a dependent variable were compared with the vegetation characteristics as an independent variable by means of the Canonical Correspondence Analysis. The results revealed bird species richness and abundance were significantly higher in more complex habitats. Bird species can be divided into two groups, the first group including species which associated with late successional stages and the second group, species belonging to early successional stages. Numbers of birds belonging to the first group declined in less complex forests, whereas the numbers of birds belonging to the second group increased. At the stand scale, our results reveal that bird abundance and richness are strongly associated with the complexity of vegetation structure in the study area.

  10. The Abundance and Spatial Distribution of Soft Sediment Communities in Tanjung Bungah, Malaysia: A Preliminary Study

    PubMed Central

    Darif, Nur Aqilah Muhamad; Samad, Nur Shakila Abdul; Salleh, Sazlina; Mohammad, Mahadi; Nordin, Noor Alia Ahmad; Javeed, Aysha Mariam Mohamed; Jonik, Michelle Glory G; Zainudin, Muhamad Hilal Mohd

    2016-01-01

    Benthic faunal communities are important components in the intertidal zones. The diversity and abundance of the benthic communities are subjected to different natural and anthropogenic disturbances. The study was conducted as one off sampling on 6th November 2013 (1) to investigate the abundance and distribution of soft sediment communities in relation to environmental variables and (2) investigate the changes of population structure and diversity using spatial scales of 1 m, 10 m, and 100 m. Results indicated a total of 110 individuals of macrobenthos consisting of 7 different groups (Annelida, Bivalvia, Crustacea, Gastropoda, Nematoda, Nemertea, Polychaeta) and 4 different groups of meiobenthos (Copepoda, Nematoda, Ostracoda, Polychaeta) consisting 920 individuals were recorded. Dissolved oxygen played the most significant role in affecting the distribution of soft sediment communities while ammonia concentrations only affected marcobenthic organisms. However, sediment grain size did not show significant correlation (p>0.05) on soft sediment communities. Hence, understanding how different properties of benthos respond to changes in environmental variables is crucial in determining how the impacts on the sediment are tolerated by the benthic organisms. PMID:27965743

  11. Diverse and abundant multi-drug resistant E. coli in Matang mangrove estuaries, Malaysia

    PubMed Central

    Ghaderpour, Aziz; Ho, Wing Sze; Chew, Li-Lee; Bong, Chui Wei; Chong, Ving Ching; Thong, Kwai-Lin; Chai, Lay Ching

    2015-01-01

    E.coli, an important vector distributing antimicrobial resistance in the environment, was found to be multi-drug resistant, abundant, and genetically diverse in the Matang mangrove estuaries, Malaysia. One-third (34%) of the estuarine E. coli was multi-drug resistant. The highest antibiotic resistance prevalence was observed for aminoglycosides (83%) and beta-lactams (37%). Phylogenetic groups A and B1, being the most predominant E. coli, demonstrated the highest antibiotic resistant level and prevalence of integrons (integron I, 21%; integron II, 3%). Detection of phylogenetic group B23 downstream of fishing villages indicates human fecal contamination as a source of E. coli pollution. Enteroaggregative E. coli (1%) were also detected immediately downstream of the fishing village. The results indicated multi-drug resistance among E. coli circulating in Matang estuaries, which could be reflective of anthropogenic activities and aggravated by bacterial and antibiotic discharges from village lack of a sewerage system, aquaculture farms and upstream animal husbandry. PMID:26483759

  12. Microbial carbonate abundance compared with fluctuations in metazoan diversity over geological time

    NASA Astrophysics Data System (ADS)

    Riding, Robert

    2006-03-01

    Secular variation in microbial carbonate abundance may be reflected by stromatolite morphotype diversity and reefal microbial carbonate abundance. These datasets reveal long-term changes over the past 3000 Myr that include a peak of abundance 1250 Myr ago, Late Proterozoic decline, Cambrian resurgence, and fluctuating decline during the remainder of the Phanerozoic. It is conceivable that Proterozoic metazoan diversification coincided with inception of stromatolite decline ˜1250 Myr ago, but microbial carbonate increase during Cambrian metazoan radiation together with failure of microbial carbonates to increase in the aftermaths of the End-Ordovician, End-Triassic and End-Cretaceous Mass Extinctions suggest that factors in addition to metazoan competition significantly influenced long-term changes in microbial carbonate abundance.

  13. Rich and rare—First insights into species diversity and abundance of Antarctic abyssal Gastropoda (Mollusca)

    NASA Astrophysics Data System (ADS)

    Schwabe, Enrico; Michael Bohn, Jens; Engl, Winfried; Linse, Katrin; Schrödl, Michael

    2007-08-01

    The abyssal depths of the polar oceans are thought to be low in diversity compared with the shallower polar shelves and temperate and tropical deep-sea basins. Our recent study on the gastropod fauna of the deep Southern Ocean gives evidence of the existence of a rich gastropod assemblage at abyssal depths. During the ANDEEP I and II expeditions to the southern Drake Passage, Northwestern Weddell Sea, and South Sandwich Trench, gastropods were collected by bottom and Agassiz trawls, epibenthic sledge, and multicorer, at 40 stations in depths between 127 and 5194 m. On the whole, 473 specimens, corresponding to 93 species of 36 families, were obtained. Of those, 414 specimens were caught below 750 m depth and refer to 84 (90%) benthic species of 32 (89%) families. Most families were represented by a single species only. The numerically dominant families were Skeneidae and Buccinidae (with 10 and 11 species, respectively), Eulimidae and Trochidae (with 9 species each), and Turridae (6 species). Thirty-Seven benthic deep-sea species (44%) were represented by a single specimen, and another 20 species (24%) were found at a single station, suggesting that more than two thirds of Antarctic deep-sea gastropod species are very rare or have a very scattered distribution. Of the 27 species occurring at two or more deep-sea stations, 14 were collected with different gear. Approximately half of the deep-water species are new to science or have been recently described. The present investigation increases the total number of recorded benthic Antarctic deep-sea gastropods (below 750 m) from 115 to 177. The previously known depth ranges have been extended, often considerably, for 31 species. The collected deep-sea gastropods comprise both eurybathic shelf species (29%) and apparently true deep-sea species (58%); some of the latter may belong to a so far unknown Antarctic abyssal fauna. Geographical ranges of the collected Antarctic benthic deep-sea gastropod species appear limited

  14. Abundance and distribution of Legionellaceae in Puerto Rican waters.

    PubMed Central

    Ortiz-Roque, C M; Hazen, T C

    1987-01-01

    Waters in marine and freshwater areas of Puerto Rico were analyzed for the presence of Legionella spp. by direct fluorescent antibody assay with guinea pig confirmation. Several species, including L. bozemanii, L. dumoffii, L. gormanii, L. longbeachae, L. micdadei, and L. pneumophila, were widely distributed among all sites. Legionellaceae, including L. pneumophila, were found in high densities in water collected in the rain forest from epiphytes in trees 30 ft. (about 9.25 m) above the ground. Both interspecific and intersite variations were significant. L. pneumophila was the most abundant species at all sites, with average densities of 10(4) cells ml-1, very close to the range which is potentially pathogenic for humans. Densities of L. pneumophila were highest in sewage-contaminated coastal waters. These are the highest densities of Legionella spp. ever reported for marine habitats. Densities of L. pneumophila were positively correlated with concentrations of sulfates, phosphates, and pH. A survey of 88 fatal atypical pneumonia cases at a Puerto Rico hospital showed that 15% of the patients had L. pneumophila infections. This study establishes L. pneumophila as a relatively common cause of atypical pneumonia in Puerto Rico and suggests natural aquatic habitats as possible sources or reservoirs of pathogenic Legionella spp. in the tropics. Images PMID:3314710

  15. Size-related bacterial diversity and tetracycline resistance gene abundance in the air of concentrated poultry feeding operations.

    PubMed

    Gao, Min; Jia, Ruizhi; Qiu, Tianlei; Han, Meilin; Wang, Xuming

    2017-01-01

    Concentrated animal-feeding operations (CAFOs) are considered a source of airborne human pathogens and antibiotic resistance genes. Although bacterial abundance and diversity have been well studied, limited information on the size distribution of bioaerosols has prevented a clear understanding of the health effects of exposure to bioaerosols from CAFOs. Here, different sizes of particles were sampled from the inside and outside of atmospheric environments of layer and broiler feeding operations using 8-stage Andersen samplers. The quantitative real-time polymerase chain reaction (qPCR) and 16S rDNA-based sequencing were used to analyze the characteristics of biological abundance and diversity, respectively, according to size. The results indicated that size-related differences occurred in terms of airborne bacterial richness, diversity, and concentration at poultry-feeding operations. The richness of biological genera in the urban atmospheric environment was lower than in concentrated poultry-feeding operations. The biological diversity of airborne bacterial genera, including genera associated with potential pathogens, varied according to size. The bacterial lineages of bioaerosols present in the 7 size stages for layers clustered apart from those for broilers, suggesting that the type of poultry house is a more important factor than the particle size in shaping the microbial communities. In most cases, the concentrations of the 16S rDNA, Escherichia coli, tetW, and tetL genes increased as the particle size increased, with the geometric mean diameters varying from 4.7 to 5.8 μm. These results regarding the size-related differences in the diversity and abundance of bioaerosols will facilitate a better understanding of the potential health impact on both poultry and humans working in such environments.

  16. Diversity and abundance of Crenarchaeota in terrestrial habitats studied by 16S RNA surveys and real time PCR.

    PubMed

    Ochsenreiter, Torsten; Selezi, Drazenka; Quaiser, Achim; Bonch-Osmolovskaya, Liza; Schleper, Christa

    2003-09-01

    Novel phylogenetic lineages of as yet uncultivated crenarchaeota have been frequently detected in low to moderate-temperature, marine and terrestrial environments. In order to gain a more comprehensive view on the distribution and diversity of Crenarchaeota in moderate habitats, we have studied 18 different terrestrial and freshwater samples by 16S rDNA-based phylogenetic surveys. In seven different soil samples of diverse geographic areas in Europe (forest, grassland, ruderal) and Asia (permafrost, ruderal) as well as in two microbial mats, we have consistently found one particular lineage of crenarchaeota. The diversity of Crenarchaeota in freshwater sediments was considerably higher with respresentative 16S rDNA sequences distributed over four different groups within the moderate crenarchaeota. Systematic analysis of a 16S rDNA universal library from a sandy ecosystem containing 800 clones exclusively revealed the presence of the soil-specific crenarchaeotal cluster. With primers specific for non-thermophilic crenarchaeota we established a rapid method to quantify archaeal 16S rDNA in real time PCR. The relative abundance of crenarchaeotal rDNA was 0.5-3% in the bulk soil sample and only 0.16% in the rhizosphere of the sandy ecosystem. A nearby agricultural setting yielded a relative abundance of 0.17% crenarchaeotal rDNA. In total our data suggest that soil crenarchaeota represent a stable and specific component of the microbiota in terrestrial habitats.

  17. Predicting the offshore distribution and abundance of marine birds with a hierarchical community distance sampling model.

    PubMed

    Goyert, Holly F; Gardner, Beth; Sollmann, Rahel; Veit, Richard R; Gilbert, Andrew T; Connelly, Emily E; Williams, Kathryn A

    2016-09-01

    Proposed offshore wind energy development on the Atlantic Outer Continental Shelf has brought attention to the need for baseline studies of the distribution and abundance of marine birds. We compiled line transect data from 15 shipboard surveys (June 2012-April 2014), along with associated remotely sensed habitat data, in the lower Mid-Atlantic Bight off the coast of Delaware, Maryland, and Virginia, USA. We implemented a recently developed hierarchical community distance sampling model to estimate the seasonal abundance of 40 observed marine bird species. Treating each season separately, we included six oceanographic parameters to estimate seabird abundance: three static (distance to shore, slope, sediment grain size) and three dynamic covariates (sea surface temperature [SST], salinity, primary productivity). We expected that avian bottom-feeders would respond primarily to static covariates that characterize seafloor variability, and that surface-feeders would respond more to dynamic covariates that quantify surface productivity. We compared the variation in species-specific and community-level responses to these habitat features, including for rare species, and we predicted species abundance across the study area. While several protected species used the study area in summer during their breeding season, estimated abundance and observed diversity were highest for nonbreeding species in winter. Distance to shore was the most common significant predictor of abundance, and thus useful in estimating the potential exposure of marine birds to offshore development. In many cases, our expectations based on feeding ecology were confirmed, such as in the first winter season, when bottom-feeders associated significantly with the three static covariates (distance to shore, slope, and sediment grain size), and surface-feeders associated significantly with two dynamic covariates (SST, primary productivity). However, other cases revealed significant relationships between

  18. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas

    PubMed Central

    Yu, Shaolan; Yao, Peng; Liu, Jiwen; Zhao, Bin; Zhang, Guiling; Zhao, Meixun; Yu, Zhigang; Zhang, Xiao-Hua

    2016-01-01

    The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO32-), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO32-, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO32-. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits. PMID:26904010

  19. Species composition, diversity and relative abundance of amphibians in forests and non-forest habitats on Langkawi Island, Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Nur Johana, J.; Muzzneena, A. M.; Grismer, L. L.; Norhayati, A.

    2016-11-01

    Anurans on Langkawi Island, Peninsular Malaysia exhibit variation in their habits and forms, ranging from small (SVL < 25 mm) to large (SVL > 150 mm), and occupy a range of habitats, such as riverine forests, agricultural fields, peat swamps, and lowland and upland dipterocarp forests. These variations provide a platform to explore species diversity, distribution, abundance, microhabitat, and other ecological parameters to understand the distribution patterns and to facilitate conservation and management of sensitive or important species and areas. The objective of this study was to evaluate the diversity and distribution of anuran species in different types of habitat on Langkawi Island. Specimens were collected based on active sampling using the Visual Encounter Survey (VES) method. We surveyed anuran species inhabiting seven types of habitat, namely agriculture (AG), coastal (CL), forest (FT), pond (PD), mangrove (MG), riparian forest (RF) and river (RV). A total of 775 individuals were sampled from all localities, representing 23 species from 12 genera and included all six families of frogs in Malaysia. FT and RF showed high values of Shannon Index, H', 2.60 and 2.38, respectively, followed by the other types of habitat, CL (1.82), RV (1.71), MG (1.56), PD (1.54), and AG (1.53). AG had the highest abundance (156 individuals) compared to other habitat types. Based on Cluster Analysis by using Jaccard coefficient (UPGMA), two groups can be clearly seen and assigned as forested species group (FT and RF) and species associating with human activity (AG, CL, PD, MG and RV). Forest species group is more diverse compared to non-forest group. Nevertheless, non-forest species are found in abundance, highlighting the relevance of these disturbed habitats in supporting the amphibians.

  20. Weed management practices affect the diversity and relative abundance of physic nut mites.

    PubMed

    Saraiva, Althiéris de Sousa; Sarmento, Renato A; Erasmo, Eduardo A L; Pedro-Neto, Marçal; de Souza, Danival José; Teodoro, Adenir V; Silva, Daniella G

    2015-03-01

    Crop management practices determine weed community, which in turn may influence patterns of diversity and abundance of associated arthropods. This study aimed to evaluate whether local weed management practices influence the diversity and relative abundance of phytophagous and predatory mites, as well as mites with undefined feeding habits--of the families Oribatidae and Acaridae--in a physic nut (Jatropha curcas L.) plantation subjected to (1) within-row herbicide spraying and between-row mowing; (2) within-row herbicide spraying and no between-row mowing; (3) within-row weeding and between-row mowing; (4) within-row weeding and no between-row mowing; and (5) unmanaged (control). The herbicide used was glyphosate. Herbicide treatments resulted in higher diversity and relative abundance of predatory mites and mites with undefined feeding habit on physic nut shrubs. This was probably due to the toxic effects of the herbicide on mites or to removal of weeds. Within-row herbicide spraying combined with between-row mowing was the treatment that most contributed to this effect. Our results show that within-row weeds harbor important species of predatory mites and mites with undefined feeding habit. However, the dynamics of such mites in the system can be changed according to the weed management practice applied. Among the predatory mites of the family Phytoseiidae Amblydromalus sp. was the most abundant, whereas Brevipalpus phoenicis was the most frequent phytophagous mite and an unidentified oribatid species was the most frequent mite with undefined feeding habit.

  1. Arthropods associated with fungal galls: do large galls support more abundant and diverse inhabitants?

    NASA Astrophysics Data System (ADS)

    Funamoto, Daichi; Sugiura, Shinji

    2017-02-01

    Fungus-induced galls can attract spore-feeding arthropods as well as gall-feeding ones, resulting in diverse communities. Do large fungal galls support more abundant and diverse arthropod communities than small fungal galls? To address this question, we investigated the structure of the arthropod community associated with bud galls induced by the fungus Melanopsichium onumae on the tree species Cinnamomum yabunikkei (Lauraceae) in central Japan. Thirteen species of arthropods were associated with M. onumae galls. Dominant arthropod species were represented by the larvae of a salpingid beetle (a spore feeder), a nitidulid beetle (a spore feeder), a cosmopterigid moth (a spore feeder), an unidentified moth (a gall tissue feeder), and a drosophilid species (a gall tissue feeder). Arthropod abundance and species richness were positively correlated with gall diameter. The majority of the most abundant species were more frequently found in large galls than in small ones, indicating that large fungal galls, which have more food and/or space for arthropods, could support a more abundant and diverse arthropod community.

  2. Experimental simulation of pollinator decline causes community-wide reductions in seedling diversity and abundance.

    PubMed

    Lundgren, Rebekka; Totland, Ørjan; Lázaro, Amparo

    2016-06-01

    Pollinator decline can disrupt the mutualistic interactions between plants and pollinators and potentially affect the maintenance of plant populations. However, there is still little knowledge on how changes in pollinator abundance can affect seedling recruitment, which is essential for population persistence. We experimentally simulated a community-wide reduction in pollinator availability during four years to examine its effects on seedling recruitment in 10 perennial herbs in a Norwegian hay meadow. Our experimental reduction in pollinator availability significantly reduced community-wide seedling diversity. Overall seedling abundance was also consistently lower under reduced pollinator availability, although this effect was only significant when the most abundant plant species in the community was excluded from the analysis. Despite an overall negative effect on seedling abundance, the experimental reduction in pollinator availability had contrasting effects on individual plant species. This tended to cause a larger change in seedling species composition in the experimental than in the control plots after the four study years. Our study demonstrates for the first time a direct causal link between reduced pollinator availability and reduced plant diversity and abundance.

  3. Diversity and distribution of pigmented heterotrophic bacteria in marine environments.

    PubMed

    Du, Hailian; Jiao, Nianzhi; Hu, Yaohua; Zeng, Yonghui

    2006-07-01

    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 x 10(3) 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

  4. Abundance, diversity and community characterization of aquatic Coleoptera in a rice field of Northeastern Argentina.

    PubMed

    Gómez Lutz, María Constanza; Kehr, Arturo I; Fernández, Liliana A

    2015-09-01

    Rice fields occupy large areas in Northeastern Argentina, and in Corrientes this widespead activity has become a feature in the landscape, as it is one of the main producing provinces. The aquatic Coleoptera is part of the fauna inhabiting these artificial environments but little is known about this group in irrigated rice fields. The aims of this study were to determine the diversity and species richness of coleopterans in a typical rice field, and to characterize the community of water beetles through different abundance models. For this, samples were collected from an active rice field located in "El Sombrero" town, in Corrientes Province, between November 2011 and April 2012. An entomological net of 30 cm diameter was used, and species richness, diversity and equitability were calculated monthly; besides, the community composition was characterized by means of rank-abundance models. A total of 74 species of aquatic coleopterans were identified. January and February resulted the months with the highest diversity. The aquatic Coleoptera species found in most of the sampled months were adjusted to the logarithmic rank-abundance model. The data suggests that, if it is properly managed, rice cropping in Northeastern Argentina can support a diverse aquatic coleopteran fauna.

  5. Microbiome interplay: plants alter microbial abundance and diversity within the built environment.

    PubMed

    Mahnert, Alexander; Moissl-Eichinger, Christine; Berg, Gabriele

    2015-01-01

    The built indoor microbiome has importance for human health. Residents leave their microbial fingerprint but nothing is known about the transfer from plants. Our hypothesis that indoor plants contribute substantially to the microbial abundance and diversity in the built environment was experimentally confirmed as proof of principle by analyzing the microbiome of the spider plant Chlorophytum comosum in relation to their surroundings. The abundance of Archaea, Bacteria, and Eukaryota (fungi) increased on surrounding floor and wall surfaces within 6 months of plant isolation in a cleaned indoor environment, whereas the microbial abundance on plant leaves and indoor air remained stable. We observed a microbiome shift: the bacterial diversity on surfaces increased significantly but fungal diversity decreased. The majority of cells were intact at the time of samplings and thus most probably alive including diverse Archaea as yet unknown phyllosphere inhabitants. LEfSe and network analysis showed that most microbes were dispersed from plant leaves to the surrounding surfaces. This led to an increase of specific taxa including spore-forming fungi with potential allergic potential but also beneficial plant-associated bacteria, e.g., Paenibacillus. This study demonstrates for the first time that plants can alter the microbiome of a built environment, which supports the significance of plants and provides insights into the complex interplay of plants, microbiomes and human beings.

  6. The Abundance and Distribution of Presolar Materials in Cluster IDPS

    NASA Technical Reports Server (NTRS)

    Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko; Ito, Motoo

    2007-01-01

    Presolar grains and remnants of interstellar organic compounds occur in a wide range of primitive solar system materials, including meteorites, interplanetary dust particles (IDPs), and comet Wild-2 samples. Among the most abundant presolar phases are silicate stardust grains and molecular cloud material. However, these materials have also been susceptible to destruction and alteration during parent body and nebular processing. In addition to their importance as direct samples of remote and ancient astrophysical environments, presolar materials thus provide a measure of how well different primitive bodies have preserved the original solar system starting materials. The matrix normalized abundances of presolar silicate grains in meteorites range from 20 ppm in Semarkona and Bishunpur to 170 ppm for Acfer 094. The lower abundances of presolar silicates in Bishunpur and Semarkona has been ascribed to the destruction of presolar silicates during aqueous processes. Presolar silicates appear to be significantly more abundant in anhydrous IDPs, possibly because these materials did not experience parent body hydrothermal alteration. Among IDPs the estimated abundances of presolar silicates vary by more than an order of magnitude, from 480 to 5500 ppm. The wide disparity in the abundances of presolar silicates of IDPs may be a consequence of the relatively small total area analyzed in those studies and the fine grain sizes of the IDPs. Alternatively, there may be a wide range in presolar silicate abundances between different IDPs. This view is supported by the observation that 15N-rich IDPs have higher presolar silicate abundances than those with isotopically normal N.

  7. Distribution and abundance of fish populations in Harike wetland--a Ramsar site in India.

    PubMed

    Dua, Anish; Parkash, Chander

    2009-03-01

    Harike wetland was declared a Ramsar site in 1990. It is located at the confluence of two major rivers of Indus rivers system, the Beas and the Sutlej, but was never explored extensively for its existing fish biodiversity. Earlier only 27 fish species of commercial value were reported from the wetland. Acknowledging its importance for rich diversity fish assemblages in seven different reaches of Harike wetland were studied to determine their abundance and distribution. 61 fish species of 35 genera were recorded from Harike wetland during the present study. Cirrihinus mrigala and Cyprinus carpio belonging to family Cyprinidae were the dominant fish species. Lake and Riyasat having many microhabitats supported highest diversity of fishes (60 and 56 respectively) followed by Beas (20) Sutlej (14), Confluence (12), Reservoir (9) and Downstream (8). Among the IUCN designated threatened species, 1 Critically Endangered, 4 Endangered and 13 Vulnerable fish species of India are found in Harike wetland. Species diversity index, dominance, evenness and catch per unit effort were calculated to ascertain the fish distribution in Harike wetland.

  8. Temporal variations in the abundance and composition of biofilm communities colonizing drinking water distribution pipes.

    PubMed

    Kelly, John J; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

    2014-01-01

    Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter.

  9. Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes

    PubMed Central

    Kelly, John J.; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

    2014-01-01

    Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter. PMID:24858562

  10. Community-Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance.

    PubMed

    Sonnemann, Ilja; Pfestorf, Hans; Jeltsch, Florian; Wurst, Susanne

    2015-01-01

    Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root

  11. Community- Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance

    PubMed Central

    Jeltsch, Florian; Wurst, Susanne

    2015-01-01

    Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root

  12. The abundance and distribution of water vapor in Jupiter's atmosphere

    NASA Technical Reports Server (NTRS)

    Bjoraker, Gordon L.; Larson, Harold P.; Kunde, Virgil G.

    1986-01-01

    The atmospheric transmission window between 1800 and 2250 cm(-1) in Jupiter's atmosphere was observed from the Kuiper Airborne Observatory (KAO) and by the infrared spectrometer (IRIS) on Voyager. The vertical distribution of H2O was derived for the 1 to 6 bar portion of Jupiter's troposphere. The spatial variation of H2O was measured using IRIS spectra of the Hot Spots in the North and South Equatorial Belts, the Equatorial Zone, and for an average of the North and South Tropical Zones. The H2O column abundance above the 4 bar level is the same in the zones as in the SEB Hot Spots, about 20 cm-amagat. The NEB Hot Spots are desiccated by a factor of 3 with respect to the rest of Jupiter. For an average between -40 to 40 deg latitude, the H2O mole fraction, qH2O, is saturated for P less than 2 bars, qH2O = 4x10 to the -6 in the 2 to 4 bar range and it increases to 3x10 to the -5 at 6 bars. A similar vertical profile applies to the spatially resolved zone and belt spectra, except that H2O falls off more rapidly at P less than 4 bars in the NEB Hot Spots. The massive H2O cloud at 5 bars, T = 273 K, proposed in solar composition models, is inconsistent with the observations. Instead, a thin H2O ice cloud would form at 2 bars, T = 200 K. The O/H ratio in Jupiter, inferred from H2O measurements in both belts and zones at 6 bars, is depleted by a factor of 50 with respect to the Sun. The implications for the origin of Jupiter of globally depleted O/H, but enhanced C/H and N/H, are discussed.

  13. The abundance and distribution of water vapor in Jupiter's atmosphere

    NASA Technical Reports Server (NTRS)

    Bjoraker, Gordon L.; Larson, Harold P.; Kunde, Virgil G.

    1986-01-01

    The atmospheric transmission window between 1800 and 2250/cm in Jupiter's atmosphere was observed from the Kuiper Airborne Observatory and by the IR spectrometer (IRIS) on Voyager. The vertical distribution of H2O was derived for the 1-6 bar portion of Jupiter's troposphere. The spatial variation of H2O was measured using IRIS spectra of the Hot Spots in the North and South Equatorial Belts (NEB, SEB) and the Equatorial Zone and for an average of the North and South Tropical Zones. The H2O column abundance above the 4 bar level is the same in the zones as in the SEB Hot Spots, about 20 cm amagats. The NEB Hot Spots are desiccated by a factor of 3 with respect to the rest of Jupiter. For an average between -40 and +40 deg latitude, the H2O mole fraction, qH2O, is saturated for P less than 2 bars, qH2O = 4 millionths in the 2-4 bar range, and it increases to 3/100,000 at 6 bars. A similar vertical profile applies to the spatially resolved zone and belt spectra, except that H2O falls off more rapidly at P less than 4 bars in the NEB Hot Spots. A massive H2O cloud at 5 bars, T = 273 K is inconsistent with the observations. Instead, a thin H2O ice cloud would form at 2 bars, T = 200 K. The O/H ratio in Jupiter, inferred from H2O measurements in both belts and zones at 6 bars, is depleted by a factor of 50 with respect to the sun.

  14. Diversity, distribution and sources of bacteria in residential kitchens

    PubMed Central

    Flores, Gilberto E.; Bates, Scott T.; Caporaso, J. Gregory; Lauber, Christian L.; Leff, Jonathan W.; Knight, Rob; Fierer, Noah

    2016-01-01

    Summary Bacteria readily colonize kitchen surfaces, and the exchange of microbes between humans and the kitchen environment can impact human health. However, we have a limited understanding of the overall diversity of these communities, how they differ across surfaces, and sources of bacteria to kitchen surfaces. Here we used high-throughput sequencing of the 16S rRNA gene to explore biogeographical patterns of bacteria across >80 surfaces within the kitchens of each of four households. In total, 34 bacterial and two archaeal phyla were identified, with most sequences belonging to the Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. Genera known to contain common food-borne pathogens were low in abundance but broadly distributed throughout the kitchens, with different taxa exhibiting distinct distribution patterns. The most diverse communities were associated with infrequently cleaned surfaces such as fans above stoves, refrigerator/freezer door seals, and floors. In contrast, the least diverse communities were observed in and around sinks, which were dominated by biofilm-forming gram-negative lineages. Community composition was influenced by conditions on individual surfaces, usage patterns, and dispersal from source environments. Human skin was the primary source of bacteria across all kitchen surfaces, with contributions from food and faucet water dominating in a few specific locations. This study demonstrates that diverse bacterial communities are widely distributed in residential kitchens and that the composition of these communities is often predictable. These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces. PMID:23171378

  15. Spatial heterogeneity of zooplankton abundance and diversity in the Saudi coastal waters of the Southern Red Sea

    NASA Astrophysics Data System (ADS)

    Al-Aidaroos, Ali; El-Sherbiny, Mohsen; Mantha, Gopikrishna

    2013-04-01

    The horizontal distribution, abundance and diversity of zooplankton has been studied at 50 stations along the Saudi coastal waters of the southern Red Sea (27 stations around Farasan archipelago, 9 around Al-Qunfodah and 14 around Al-Lith) during March-April 2011 using a plankton net of 150 µm. The zooplankton standing crop fluctuated between 1058 and 25787 individuals/m3 with an average of 5231 individuals/m3. Zooplankton was dominated by holoplanktonic forms that representing 80.26 % of total zooplankton, while meroplanktonic constituting 19.74% and dominated by mollusc larvae. Copepods appeared to be the predominant component, formed an average of 69.69 % of the total zooplankton count followed by chaetognaths and urochordates (4.5 and 4.1% of total zooplankton respectively). A total of 100 copepods species in addition to several species of other planktonic groups (cladocerans, chaetognaths, urochordates) were recorded in the study area. The copepod diversity decreased northward (94, 69 and 62 species at Farasan, Al-Qunfodah and Al-Lith respectively). In general, adult cyclopoid copepods dominated the zooplankton community in term of abundance and species number (19.55 %, 65 species) with dominance of Oncaea media, Oithona similis and Farranula carinata followed by adult calanoid copepods (19.38%, 35 species) with dominance of Paracalanus aculeatus, Clausocalanus minor, Acartia (Acanthacartia) fossae and Centropages orsinii. Harapacticoids densities were low in abundance, represented only by 5 species and dominated mainly by Euterpina acutifronis. Some copepod species decreased northward: Acartia amboinensis, Canthocalanus pauper, Labidocera acuta, Corycaeus flaccus, C. typicus, C. agilis, C. catus, C. giesbrechti, C. latus, C. furcifer and Euterpina acutifronis, while others increased northward (Acartia fossae, Undinula vulgaris and Centropages orsinii). Among copepod orders, Monstrilloida and Siphonostomatoida were observed only in southern area (Farasan

  16. Effects of human trampling on abundance and diversity of vascular plants, bryophytes and lichens in alpine heath vegetation, Northern Sweden.

    PubMed

    Jägerbrand, Annika K; Alatalo, Juha M

    2015-01-01

    This study investigated the effects of human trampling on cover, diversity and species richness in an alpine heath ecosystem in northern Sweden. We tested the hypothesis that proximity to trails decreases plant cover, diversity and species richness of the canopy and the understory. We found a significant decrease in plant cover with proximity to the trail for the understory, but not for the canopy level, and significant decreases in the abundance of deciduous shrubs in the canopy layer and lichens in the understory. Proximity also had a significant negative impact on species richness of lichens. However, there were no significant changes in species richness, diversity or evenness of distribution in the canopy or understory with proximity to the trail. While not significant, liverworts, acrocarpous and pleurocarpous bryophytes tended to have contrasting abundance patterns with differing proximity to the trail, indicating that trampling may cause shifts in dominance hierarchies of different groups of bryophytes. Due to the decrease in understory cover, the abundance of litter, rock and soil increased with proximity to the trail. These results demonstrate that low-frequency human trampling in alpine heaths over long periods can have major negative impacts on lichen abundance and species richness. To our knowledge, this is the first study to demonstrate that trampling can decrease species richness of lichens. It emphasises the importance of including species-level data on non-vascular plants when conducting studies in alpine or tundra ecosystems, since they often make up the majority of species and play a significant role in ecosystem functioning and response in many of these extreme environments.

  17. Distribution and abundance of freshwater decapods in an Atlantic rainforest catchment with a dammed future.

    PubMed

    Silva-Junior, E F; Silva-Araújo, M; Moulton, T P

    2017-03-13

    Variations in physical characteristics along the course of a river influence habitat availability which reflects in species distribution. Knowledge of ecology and diversity of lotic species is important for evaluating how river ecosystems will respond to environmental impacts. Freshwater decapods are a group of high ecological and economic importance, but the knowledge about factors influencing their distribution is scarce in Brazil. We performed a survey of decapods to describe their abundance and distribution as well as to study their relationships with stream physical variables and especially their association with different substrates types. We studied 23 sites located in 15 tributaries of Guapiaçú River, RJ, where we collected decapods in different substrates types and measured a set of physical variables. We found five decapods species, including amphidromous and non-amphidromous shrimps and crabs. Decapods were strongly associated with leaf-litter substrates and their abundance was related to a multivariate axis describing longitudinal changes in stream characteristics. We concluded that decapods occurring in the Guapiaçú catchment inhabit mainly small streams with preserved riparian forests where they find shelter and potential prey of invertebrates. The ongoing project to build a dam on the Guapiaçú River will have negative consequences to migrating shrimps and we strongly recommend that mitigating actions, such the construction of structures to allow the passage of migrating fauna, should be taken.

  18. Diversity, abundance and characterization of ruminal cysteine phytases suggest their important role in phytate degradation.

    PubMed

    Huang, Huoqing; Zhang, Rui; Fu, Dawei; Luo, Jianjie; Li, Zhongyuan; Luo, Huiying; Shi, Pengjun; Yang, Peilong; Diao, Qiyu; Yao, Bin

    2011-03-01

    A novel class of cysteine phytase showing ability to degrade phytate has recently been isolated from rumen bacteria. To expand our knowledge of this enzyme class, a total of 101 distinct cysteine phytase gene fragments were identified from the ruminal genomic DNA of Bore goats and Holstein cows, and most of them shared low identities (< 50%) with known sequences. By phylogenetic analysis, these sequences were separated into three clusters that showed substantial diversity. The two most abundant cysteine phytase genes of goat rumens were cloned and their protein products were characterized. Four findings were revealed based on our results. (i) Compared with soil and water environment, where β-propeller phytase is the most important phytate-degrading enzyme, cysteine phytase is the major phytate-degrading enzyme in the anaerobic ruminal environment. (ii) Cysteine phytase fragments in the rumen contents of goat and cow have the same diversity profile, although most of the sequences and their abundance differ in the two species. (iii) Each species has their respective high-abundance genes, which may play major roles for phytate degradation. (iv) Compared with previously reported cysteine phytases that have pH optimum at 4.5, the pH optima of the two most abundant secreted goat cysteine phytases are 6.5 and 6.0, which are within the pH range found in the rumens. This study provides valuable information about the diversity, abundance and enzymatic properties of the ruminal cysteine phytases and emphasizes the important role(s) of these cysteine phytases probably in the terrestrial cycle of phosphorus.

  19. Diversity, abundance, and possible sources of fecal bacteria in the Yangtze River.

    PubMed

    Sun, Haohao; He, Xiwei; Ye, Lin; Zhang, Xu-Xiang; Wu, Bing; Ren, Hongqiang

    2017-03-01

    The fecal bacteria in natural waters may pose serious risks on human health. Although many source tracking methods have been developed and used to determine the possible sources of the fecal pollution, little is known about the overall diversity and abundance of fecal bacterial community in natural waters. In this study, a method based on fecal bacterial sequence library was introduced to evaluate the fecal bacterial profile in the Yangtze River (Nanjing section). Our results suggested that the Yangtze River water harbors diverse fecal bacteria. Fifty-eight fecal operational taxonomic units (97% identity level) were detected in the Yangtze River water samples and the relative abundance of fecal bacteria in these samples ranged from 0.1 to 8%. It was also found that the relative abundances of the fecal bacteria in locations near to the downstream of wastewater treatment plants were obviously higher than those in other locations. However, the high abundance of fecal bacteria could decrease to the normal level in 2~4 km in the river due to degradation or dilution, and the overall fecal bacteria level changed little when the Yangtze River flew through the Nanjing City. Moreover, the fecal bacteria in the Yangtze River water were found to be highly associated (Spearman rho = 0.804, P < 0.001) with the potential pathogenic bacteria. Collectively, the findings in this study reveal the diversity, abundance, and possible sources of fecal bacteria in the Yangtze River and advance our understandings of the fecal bacteria community in the natural waters.

  20. Linking Carbonic Anhydrase Abundance and Diversity in Soils to Ecological Function

    NASA Astrophysics Data System (ADS)

    Pang, E.; Meredith, L. K.; Welander, P. V.

    2015-12-01

    Carbonic anhydrase (CA) is an ancient enzyme widespread among bacteria, archaea, and eukarya that catalyzes the following reaction: CO2 + H2O ⇌ HCO3- + H+. Its functions are critical for key cellular processes such as concentrating CO2 for autotrophic growth, pH regulation, and pathogen survival in hosts. Currently, there are six known CA classes (α, β, γ, δ, η, ζ) arising from several distinct evolutionary lineages. CA are widespread in sequenced genomes, with many organisms containing multiple classes of CA or multiple CA of the same class. Soils host rich microbial communities with diverse and important ecological functions, but the diversity and abundance of CA in soils has not been explored. CA appears to play an important, but poorly understood, role in some biogeochemical cycles such as those of CO2 and its oxygen isotope composition and also carbonyl sulfide (COS), which are potential tracers in predictive carbon cycle models. Recognizing the prevalence and functional significance of CA in soils, we used a combined bioinformatics and molecular biology approach to address fundamental questions regarding the abundance, diversity, and function of CA in soils. To characterize the abundance and diversity of the different CA classes in soils, we analyzed existing soil metagenomic and metatranscriptomic data from the DOE Joint Genome Institute databases. Out of the six classes of CA, we only found the α, β, and γ classes to be present in soils, with the β class being the most abundant. We also looked at genomes of sequenced soil microorganisms to learn what combination of CA classes they contain, from which we can begin to predict the physiological role of CA. To characterize the functional roles of the different CA classes in soils, we collected soil samples from a variety of biomes with diverse chemical and physical properties and quantified the rate of two CA-mediated processes: soil uptake of COS and acceleration of the oxygen isotope exchange

  1. Abundance, diversity and community composition of free-living protozoa on vegetable sprouts.

    PubMed

    Chavatte, N; Lambrecht, E; Van Damme, I; Sabbe, K; Houf, K

    2016-05-01

    Interactions with free-living protozoa (FLP) have been implicated in the persistence of pathogenic bacteria on food products. In order to assess the potential involvement of FLP in this contamination, detailed knowledge on their occurrence, abundance and diversity on food products is required. In the present study, enrichment and cultivation methods were used to inventory and quantify FLP on eight types of commercial vegetable sprouts (alfalfa, beetroot, cress, green pea, leek, mung bean, red cabbage and rosabi). In parallel, total aerobic bacteria and Escherichia coli counts were performed. The vegetable sprouts harbored diverse communities of FLP, with Tetrahymena (ciliate), Bodo saltans and cercomonads (flagellates), and Acanthamoeba and Vannella (amoebae) as the dominant taxa. Protozoan community composition and abundance significantly differed between the sprout types. Beetroot harbored the most abundant and diverse FLP communities, with many unique species such as Korotnevella sp., Vannella sp., Chilodonella sp., Podophrya sp. and Sphaerophrya sp. In contrast, mung bean sprouts were species-poor and had low FLP numbers. Sampling month and company had no significant influence, suggesting that seasonal and local factors are of minor importance. Likewise, no significant relationship between protozoan community composition and bacterial load was observed.

  2. Bee communities along a prairie restoration chronosequence: similar abundance and diversity, distinct composition.

    PubMed

    Tonietto, Rebecca K; Ascher, John S; Larkin, Daniel J

    2017-04-01

    Recognition of the importance of bee conservation has grown in response to declines of managed honey bees and some wild bee species. Habitat loss has been implicated as a leading cause of declines, suggesting that ecological restoration is likely to play an increasing role in bee conservation efforts. In the midwestern United States, restoration of tallgrass prairie has traditionally targeted plant community objectives without explicit consideration for bees. However, restoration of prairie vegetation is likely to provide ancillary benefits to bees through increased foraging and nesting resources. We investigated community assembly of bees across a chronosequence of restored eastern tallgrass prairies and compared patterns to those in control and reference habitats (old fields and prairie remnants, respectively). We collected bees for 3 yr and measured diversity and abundance of in-bloom flowering plants, vegetation structure, ground cover, and surrounding land use as predictors of bee abundance and bee taxonomic and functional diversity. We found that site-level variables, but not site type or restoration age, were significant predictors of bee abundance (bloom diversity, P = 0.004; bare ground cover, P = 0.02) and bee diversity (bloom diversity, P = 0.01). There were significant correlations between overall composition of bee and blooming plant communities (Mantel test, P = 0.002), and both plant and bee assemblages in restorations were intermediate between those of old fields and remnant prairies. Restorations exhibited high bee beta diversity, i.e., restored sites' bee assemblages were taxonomically and functionally differentiated from each other. This pattern was strong in younger restorations (<20 yr old), but absent from older restorations (>20 yr), suggesting restored prairie bee communities become more similar to one another and more similar to remnant prairie bee communities over time with the arrival of more species and functional groups of

  3. Abundance and distribution of water vapor in Jupiter's atmosphere

    SciTech Connect

    Bjoraker, G.L.; Larson, H.P.; Kunde, V.G.

    1986-09-01

    The atmospheric transmission window between 1800 and 2250 cm(-1) in Jupiter's atmosphere was observed from the Kuiper Airborne Observatory (KAO) and by the infrared spectrometer (IRIS) on Voyager. The vertical distribution of H/sub 2/O was derived for the 1 to 6 bar portion of Jupiter's troposphere. The spatial variation of H/sub 2/O was measured using IRIS spectra of the Hot Spots in the North and South Equatorial Belts, the Equatorial Zone, and for an average of the North and South Tropical Zones. The H/sub 2/O column abundance above the 4 bar level is the same in the zones as in the SEB Hot Spots, about 20 cm-amagat. The NEB Hot Spots are desiccated by a factor of 3 with respect to the rest of Jupiter. For an average between -40 to 40 deg latitude, the H/sub 2/O mole fraction, qH/sub 2/O, is saturated for P less than 2 bars, qH/sub 2/O = 4x10 to the -6 in the 2 to 4 bar range and it increases to 3x10 to the -5 at 6 bars. A similar vertical profile applies to the spatially resolved zone and belt spectra, except that H/sub 2/O falls off more rapidly at P less than 4 bars in the NEB Hot Spots. The massive H/sub 2/O cloud at 5 bars, T = 273 K, proposed in solar composition models, is inconsistent with the observations. Instead, a thin H/sub 2/O ice cloud would form at 2 bars, T = 200 K. The O/H ratio in Jupiter, inferred from H/sub 2/O measurements in both belts and zones at 6 bars, is depleted by a factor of 50 with respect to the Sun. The implications for the origin of Jupiter of globally depleted O/H, but enhanced C/H and N/H, are discussed.

  4. Terrestrial activity, abundance, diversity of amphibians in differently managed forest types

    SciTech Connect

    Bennett, S.H.; Gibbons, J.W.; Glanville, J.

    1980-04-01

    Diversity indices and relative abundances were determined for amphibians inhabiting three differently managed forest types in South Carolina. Study sites were contiguous around a small lake, and included a slash pine (Pinus ellioti) forest, a loblolly pine (Pinus taeda) forest and a hardwood (predominately oak-hickory) forest. Amphibians were collected using a drift fence and pitfall trap method. Captured animals were marked so that recaptures could be removed from calculations of indices. The dates of study were 30 June-10 August 1977 and 20 June-15 August 1978. The three study sites were similar in species diversity and the evenness component for combined summer data and for the summer of 1978. The hardwood forest had a higher diversity in the summer of 1977. The hardwood forest yielded approximately 50% more individual amphibians than either pine forest during both years.

  5. Native wildflower plantings support wild bee abundance and diversity in agricultural landscapes across the United States.

    PubMed

    Williams, Neal M; Ward, Kimiora L; Pope, Nathaniel; Isaacs, Rufus; Wilson, Julianna; May, Emily A; Ellis, Jamie; Daniels, Jaret; Pence, Akers; Ullmann, Katharina; Peters, Jeff

    2015-12-01

    Global trends in pollinator-dependent crops have raised awareness of the need to support managed and wild bee populations to ensure sustainable crop production. Provision of sufficient forage resources is a key element for promoting bee populations within human impacted landscapes, particularly those in agricultural lands where demand for pollination service is high and land use and management practices have reduced available flowering resources. Recent government incentives in North America and Europe support the planting of wildflowers to benefit pollinators; surprisingly, in North America there has been almost no rigorous testing of the performance of wildflower mixes, or their ability to support wild bee abundance and diversity. We tested different wildflower mixes in a spatially replicated, multiyear study in three regions of North America where production of pollinator-dependent crops is high: Florida, Michigan, and California. In each region, we quantified flowering among wildflower mixes composed of annual and perennial species, and with high and low relative diversity. We measured the abundance and species richness of wild bees, honey bees, and syrphid flies at each mix over two seasons. In each region, some but not all wildflower mixes provided significantly greater floral display area than unmanaged weedy control plots. Mixes also attracted greater abundance and richness of wild bees, although the identity of best mixes varied among regions. By partitioning floral display size from mix identity we show the importance of display size for attracting abundant and diverse wild bees. Season-long monitoring also revealed that designing mixes to provide continuous bloom throughout the growing season is critical to supporting the greatest pollinator species richness. Contrary to expectation, perennials bloomed in their first season, and complementarity in attraction of pollinators among annuals and perennials suggests that inclusion of functionally diverse

  6. The effect of urbanization on ant abundance and diversity: a temporal examination of factors affecting biodiversity.

    PubMed

    Buczkowski, Grzegorz; Richmond, Douglas S

    2012-01-01

    Numerous studies have examined the effect of urbanization on species richness and most studies implicate urbanization as the major cause of biodiversity loss. However, no study has identified an explicit connection between urbanization and biodiversity loss as the impact of urbanization is typically inferred indirectly by comparing species diversity along urban-rural gradients at a single time point. A different approach is to focus on the temporal rather than the spatial aspect and perform "before and after" studies where species diversity is cataloged over time in the same sites. The current study examined changes in ant abundance and diversity associated with the conversion of natural habitats into urban habitats. Ant abundance and diversity were tracked in forested sites that became urbanized through construction and were examined at 3 time points - before, during, and after construction. On average, 4.3 ± 1.2 unique species were detected in undisturbed plots prior to construction. Ant diversity decreased to 0.7 ± 0.8 species in plots undergoing construction and 1.5 ± 1.1 species in plots 1 year after construction was completed. With regard to species richness, urbanization resulted in the permanent loss of 17 of the 20 species initially present in the study plots. Recovery was slow and only 3 species were present right after construction was completed and 4 species were present 1 year after construction was completed. The second objective examined ant fauna recovery in developed residential lots based on time since construction, neighboring habitat quality, pesticide inputs, and the presence of invasive ants. Ant diversity was positively correlated with factors that promoted ecological recovery and negatively correlated with factors that promoted ecological degradation. Taken together, these results address a critical gap in our knowledge by characterizing the short- and long-term the effects of urbanization on the loss of ant biodiversity.

  7. Diversity and distribution of methanotrophic archaea at cold seeps.

    PubMed

    Knittel, Katrin; Lösekann, Tina; Boetius, Antje; Kort, Renate; Amann, Rudolf

    2005-01-01

    In this study we investigated by using 16S rRNA-based methods the distribution and biomass of archaea in samples from (i) sediments above outcropping methane hydrate at Hydrate Ridge (Cascadia margin off Oregon) and (ii) massive microbial mats enclosing carbonate reefs (Crimea area, Black Sea). The archaeal diversity was low in both locations; there were only four (Hydrate Ridge) and five (Black Sea) different phylogenetic clusters of sequences, most of which belonged to the methanotrophic archaea (ANME). ANME group 2 (ANME-2) sequences were the most abundant and diverse sequences at Hydrate Ridge, whereas ANME-1 sequences dominated the Black Sea mats. Other seep-specific sequences belonged to the newly defined group ANME-3 (related to Methanococcoides spp.) and to the Crenarchaeota of marine benthic group B. Quantitative analysis of the samples by fluorescence in situ hybridization (FISH) showed that ANME-1 and ANME-2 co-occurred at the cold seep sites investigated. At Hydrate Ridge the surface sediments were dominated by aggregates consisting of ANME-2 and members of the Desulfosarcina-Desulfococcus branch (DSS) (ANME-2/DSS aggregates), which accounted for >90% of the total cell biomass. The numbers of ANME-1 cells increased strongly with depth; these cells accounted 1% of all single cells at the surface and more than 30% of all single cells (5% of the total cells) in 7- to 10-cm sediment horizons that were directly above layers of gas hydrate. In the Black Sea microbial mats ANME-1 accounted for about 50% of all cells. ANME-2/DSS aggregates occurred in microenvironments within the mat but accounted for only 1% of the total cells. FISH probes for the ANME-2a and ANME-2c subclusters were designed based on a comparative 16S rRNA analysis. In Hydrate Ridge sediments ANME-2a/DSS and ANME-2c/DSS aggregates differed significantly in morphology and abundance. The relative abundance values for these subgroups were remarkably different at Beggiatoa sites (80% ANME-2a, 20

  8. Large spatial scale variability in bathyal macrobenthos abundance, biomass, α- and β-diversity along the Mediterranean continental margin.

    PubMed

    Baldrighi, Elisa; Lavaleye, Marc; Aliani, Stefano; Conversi, Alessandra; Manini, Elena

    2014-01-01

    The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project ("Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna"), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas.

  9. Large Spatial Scale Variability in Bathyal Macrobenthos Abundance, Biomass, α- and β-Diversity along the Mediterranean Continental Margin

    PubMed Central

    Baldrighi, Elisa; Lavaleye, Marc; Aliani, Stefano; Conversi, Alessandra; Manini, Elena

    2014-01-01

    The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project (“Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna”), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas. PMID:25225909

  10. Inherited microbial symbionts increase herbivore abundances and alter arthropod diversity on a native grass.

    PubMed

    Faeth, Stanley H; Shochat, Eyal

    2010-05-01

    Some microbial symbionts of plants are maternally inherited and thus functionally increase genetic and phenotypic variation within plant populations. This variation, coupled with that of the host plant and environment, may alter abundances, diversity, and trophic structure of associated plant and animal communities. Fungal endophytes in the genus Neotyphodium are vertically transmitted, asexual microbial symbionts of grasses that remain asymptomatic and rely upon their hosts for resources and transmission via seeds, often providing benefits to their hosts, including protection against herbivores. Endophyte infections may influence associated arthropod communities in agronomic grasses, but the long-term effects of endophytes and variation in host genotype and resource availability on arthropod communities in native grass populations are unknown. We conducted a long-term field experiment with four maternal genotypes of an infected (E+) native grass (Festuca arizonica) from whence the endophyte was experimentally removed (E-) and water availability was controlled, to test the effects of infection, plant genotype, and resources on abundances, biomass, diversity (richness and evenness), and trophic structure of the arthropod community. Generally, E+ grasses harbored more arthropods, including more herbivores, predators, and detritivores, suggesting that the effects of endophytes cascaded upward through trophic levels in terms of abundances, at least in early ontogeny of the host. That E+ plants harbored more herbivorous insects than E- plants suggests that infection does not increase but instead decreases resistance to herbivores, contrary to prevailing concepts of endophytes as defensive mutualists. Infection did not alter overall species richness of the arthropod community or richness of herbivores but reduced natural enemy richness, especially that of parasites, and increased richness of detritivores. Reduced richness and shifts in evenness of natural enemies on E

  11. Relationships between plant diversity and the abundance and α-diversity of predatory ground beetles (Coleoptera: Carabidae) in a mature Asian temperate forest ecosystem.

    PubMed

    Zou, Yi; Sang, Weiguo; Bai, Fan; Axmacher, Jan Christoph

    2013-01-01

    A positive relationship between plant diversity and both abundance and diversity of predatory arthropods is postulated by the Enemies Hypothesis, a central ecological top-down control hypothesis. It has been supported by experimental studies and investigations of agricultural and grassland ecosystems, while evidence from more complex mature forest ecosystems is limited. Our study was conducted on Changbai Mountain in one of the last remaining large pristine temperate forest environments in China. We used predatory ground beetles (Coleoptera: Carabidae) as target taxon to establish the relationship between phytodiversity and their activity abundance and diversity. Results showed that elevation was the only variable included in both models predicting carabid activity abundance and α-diversity. Shrub diversity was negatively and herb diversity positively correlated with beetle abundance, while shrub diversity was positively correlated with beetle α-diversity. Within the different forest types, a negative relationship between plant diversity and carabid activity abundance was observed, which stands in direct contrast to the Enemies Hypothesis. Furthermore, plant species density did not predict carabid α-diversity. In addition, the density of herbs, which is commonly believed to influence carabid movement, had little impact on the beetle activity abundance recorded on Changbai Mountain. Our study indicates that in a relatively large and heterogeneous mature forest area, relationships between plant and carabid diversity are driven by variations in environmental factors linked with altitudinal change. In addition, traditional top-down control theories that are suitable in explaining diversity patterns in ecosystems of low diversity appear to play a much less pronounced role in highly complex forest ecosystems.

  12. Relationships between Plant Diversity and the Abundance and α-Diversity of Predatory Ground Beetles (Coleoptera: Carabidae) in a Mature Asian Temperate Forest Ecosystem

    PubMed Central

    Zou, Yi; Sang, Weiguo; Bai, Fan; Axmacher, Jan Christoph

    2013-01-01

    A positive relationship between plant diversity and both abundance and diversity of predatory arthropods is postulated by the Enemies Hypothesis, a central ecological top-down control hypothesis. It has been supported by experimental studies and investigations of agricultural and grassland ecosystems, while evidence from more complex mature forest ecosystems is limited. Our study was conducted on Changbai Mountain in one of the last remaining large pristine temperate forest environments in China. We used predatory ground beetles (Coleoptera: Carabidae) as target taxon to establish the relationship between phytodiversity and their activity abundance and diversity. Results showed that elevation was the only variable included in both models predicting carabid activity abundance and α-diversity. Shrub diversity was negatively and herb diversity positively correlated with beetle abundance, while shrub diversity was positively correlated with beetle α-diversity. Within the different forest types, a negative relationship between plant diversity and carabid activity abundance was observed, which stands in direct contrast to the Enemies Hypothesis. Furthermore, plant species density did not predict carabid α-diversity. In addition, the density of herbs, which is commonly believed to influence carabid movement, had little impact on the beetle activity abundance recorded on Changbai Mountain. Our study indicates that in a relatively large and heterogeneous mature forest area, relationships between plant and carabid diversity are driven by variations in environmental factors linked with altitudinal change. In addition, traditional top-down control theories that are suitable in explaining diversity patterns in ecosystems of low diversity appear to play a much less pronounced role in highly complex forest ecosystems. PMID:24376582

  13. Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota.

    PubMed

    Lehtovirta, Laura E; Prosser, James I; Nicol, Graeme W

    2009-12-01

    Archaeal communities in many acidic forest soil systems are dominated by a distinct crenarchaeal lineage Group 1.1c. In addition, they are found consistently in other acidic soils including grassland pasture, moorland and alpine soils. To determine whether soil pH is a major factor in determining their presence and abundance, Group 1.1c community size and composition were investigated across a pH gradient from 4.5 to 7.5 that has been maintained for > 40 years. The abundances of Group 1.1c Crenarchaeota, total Crenarchaeota and total bacteria were assessed by quantitative PCR (qPCR) targeting 16S rRNA genes and the diversity of Group 1.1c crenarchaeal community was investigated by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. The abundance of Group 1.1c Crenarchaeota declined as the pH increased, whereas total Crenarchaeota and Bacteria showed no clear trend. Community diversity of Group 1.1c Crenarchaeota was also influenced with different DGGE bands dominating at different pH. Group 1.1c Crenarchaeota were also quantified in 13 other soils representing a range of habitats, soil types and pH. These results exhibited the same trend as that shown across the pH gradient with Group 1.1c Crenarchaeota representing a greater proportion of total Crenarchaeota in the most acidic soils.

  14. Abundance and Genetic Diversity of Microbial Polygalacturonase and Pectate Lyase in the Sheep Rumen Ecosystem

    PubMed Central

    Wang, Yaru; Luo, Huiying; Huang, Huoqing; Shi, Pengjun; Bai, Yingguo; Yang, Peilong; Yao, Bin

    2012-01-01

    Background Efficient degradation of pectin in the rumen is necessary for plant-based feed utilization. The objective of this study was to characterize the diversity, abundance, and functions of pectinases from microorganisms in the sheep rumen. Methodology/Principal Findings A total of 103 unique fragments of polygalacturonase (PF00295) and pectate lyase (PF00544 and PF09492) genes were retrieved from microbial DNA in the rumen of a Small Tail Han sheep, and 66% of the sequences of these fragments had low identities (<65%) with known sequences. Phylogenetic tree building separated the PF00295, PF00544, and PF09492 sequences into five, three, and three clades, respectively. Cellulolytic and noncellulolytic Butyrivibrio, Prevotella, and Fibrobacter species were the major sources of the pectinases. The two most abundant pectate lyase genes were cloned, and their protein products, expressed in Escherichia coli, were characterized. Both enzymes probably act extracellularly as their nucleotide sequences contained signal sequences, and they had optimal activities at the ruminal physiological temperature and complementary pH-dependent activity profiles. Conclusion/Significance This study reveals the specificity, diversity, and abundance of pectinases in the rumen ecosystem and provides two additional ruminal pectinases for potential industrial use under physiological conditions. PMID:22815874

  15. Species diversity and abundance of ticks in three habitats in southern Italy.

    PubMed

    Dantas-Torres, Filipe; Otranto, Domenico

    2013-04-01

    A 2-year study was conducted from March 2010 to March 2012 in a forested area in southern Italy to evaluate the species diversity and abundance of free-living ticks in 3 different habitats: (i) a meadow habitat within an enclosure inhabited by roe deer (Capreolus capreolus); (ii) a man-made trail located in a high-altitude, forested area; and (iii) a grassland near a house inhabited by 3 people. In total, 10,795 ticks were collected. Ixodes ricinus was the most abundant species (69.0%), followed by Haemaphysalis inermis (19.1%), Rhipicephalus turanicus (6.7%), Dermacentor marginatus (3.2%), and Hyalomma marginatum (1.0%). The least frequently collected species were Rhipicephalus bursa, Haemaphysalis parva, Haemaphysalis sulcata, and Haemaphysalis concinna, representing together less than 1% of the collections. Immature ticks predominated over adult ticks. In particular, immature stages of Ix. ricinus (i.e., 3246 larvae and 3554 nymphs) represented 63% of the total number of ticks collected. High levels of species diversity and abundance of ticks were recorded in all habitats and the daily number of ticks collected was negatively correlated with daily mean temperature, evapotranspiration, and saturation deficit. This study indicates that the southern Italian climate is suitable for different tick species, which may find a preferred 'climate niche' during a specific season, when a combination of factors (e.g., suitable meteorological and environmental conditions) associated with the presence of suitable hosts will facilitate their development and reproduction.

  16. Evolutionary entropy predicts the outcome of selection: Competition for resources that vary in abundance and diversity.

    PubMed

    Demetrius, Lloyd; Legendre, Stéphane

    2013-02-01

    Competition between individuals for resources which are limited and diverse in composition is the ultimate driving force of evolution. Classical studies of this event contend that the outcome is a deterministic process predicted by the growth rate of the competing types-a tenet called the Malthusian selection principle. Recent studies of competition indicate that the dynamics of selection is a stochastic process, regulated by the population size, the abundance and diversity of the resource, and predicted by evolutionary entropy-a statistical parameter which characterizes the rate at which the population returns to the steady state condition after a random endogenous or exogenous perturbation. This tenet, which we will call the entropic selection principle entails the following relations: This article delineates the analytic, computational and empirical support for this tenet. We show moreover that the Malthusian selection principle, a cornerstone of classical evolutionary genetics, is the limit, as population size and resource abundance tends to infinity of the entropic selection principle. The Malthusian tenet is an approximation to the entropic selection principle-an approximation whose validity increases with increasing population size and increasing resource abundance. Evolutionary entropy is a generic concept that characterizes the interaction dynamics of metabolic entities at several levels of biological organization: cellular, organismic and ecological. Accordingly, the entropic selection principle represents a general rule for explaining the processes of adaptation and evolution at each of these levels.

  17. Organic amendments enhance microbial diversity and abundance of functional genes in Australian Soils

    NASA Astrophysics Data System (ADS)

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2016-04-01

    Food and cash crops play important roles in Australia's economy with black, grey and red clay soil, widely use for growing cotton, wheat, corn and other crops in rotation. While the majority of cotton growers use nitrogen and phosphate fertilizers only in the form of agrochemicals, a few experiment with the addition of manure or composted plant material before planting. We hypothesized that the use of such organic amendments would enhance the soil microbial function through increased microbial diversity and abundance, thus contribute to improved soil sustainability. To test the hypothesis we collected soil samples from two cotton-growing farms in close geographical proximity and with mostly similar production practices other than one grower has been using composted plants as organic amendment and the second farmer uses only agrochemicals. We applied the Biolog Ecoplate system to study the metabolic signature of microbial communities and used qPCR to estimate the abundance of functional genes in the soil. The soil treated with organic amendments clearly showed higher metabolic activity of a more diverse range of carbon sources as well as higher abundance of genes involved in the nitrogen and phosphorous cycles. Since microbes undertake a large number of soil functions, the use of organic amendments can contribute to the sustainability of agricultural soils.

  18. Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

    PubMed Central

    Farag, Ibrahim F.; Davis, James P.; Youssef, Noha H.; Elshahed, Mostafa S.

    2014-01-01

    We investigated the global patterns of abundance, diversity, and community structure of members of the Aminicenantes (candidate phylum OP8). Our aim was to identify the putative ecological role(s) played by members of this poorly characterized bacterial lineages in various ecosystems. Analysis of near full-length 16S rRNA genes identified four classes and eight orders within the Aminicenantes. Within 3,134 datasets comprising ∼1.8 billion high throughput-generated partial 16S rRNA genes, 47,351 Aminicenantes-affiliated sequences were identified in 913 datasets. The Aminicenantes exhibited the highest relative abundance in hydrocarbon-impacted environments, followed by marine habitats (especially hydrothermal vents and coral-associated microbiome samples), and aquatic, non-marine habitats (especially in terrestrial springs and groundwater samples). While the overall abundance of the Aminicenantes was higher in low oxygen tension as well as non-saline and low salinity habitats, it was encountered in a wide range of oxygen tension, salinities, and temperatures. Analysis of the community structure of the Aminicenantes showed distinct patterns across various datasets that appear to be, mostly, driven by habitat variations rather than prevalent environmental parameters. We argue that the detection of the Aminicenantes across environmental extremes and the observed distinct community structure patterns reflect a high level of intraphylum metabolic diversity and adaptive capabilities that enable its survival and growth in a wide range of habitats and environmental conditions. PMID:24637619

  19. Global distribution of a key trophic guild contrasts with common latitudinal diversity patterns.

    PubMed

    Boyero, Luz; Pearson, Richard G; Dudgeon, David; Graça, Manuel A S; Gessner, Mark O; Albariño, Ricardo J; Ferreira, Verónica; Yule, Catherine M; Boulton, Andrew J; Arunachalam, Muthukumarasamy; Callisto, Marcos; Chauvet, Eric; Ramírez, Alonso; Chará, Julián; Moretti, Marcelo S; Gonçalves, José F; Helson, Julie E; Chará-Serna, Ana M; Encalada, Andrea C; Davies, Judy N; Lamothe, Sylvain; Cornejo, Aydeè; Li, Aggie O Y; Buria, Leonardo M; Villanueva, Verónica D; Zúñiga, María C; Pringle, Catherine M

    2011-09-01

    Most hypotheses explaining the general gradient of higher diversity toward the equator are implicit or explicit about greater species packing in the tropics. However, global patterns of diversity within guilds, including trophic guilds (i.e., groups of organisms that use similar food resources), are poorly known. We explored global diversity patterns of a key trophic guild in stream ecosystems, the detritivore shredders. This was motivated by the fundamental ecological role of shredders as decomposers of leaf litter and by some records pointing to low shredder diversity and abundance in the tropics, which contrasts with diversity patterns of most major taxa for which broad-scale latitudinal patterns haven been examined. Given this evidence, we hypothesized that shredders are more abundant and diverse in temperate than in tropical streams, and that this pattern is related to the higher temperatures and lower availability of high-quality leaf litter in the tropics. Our comprehensive global survey (129 stream sites from 14 regions on six continents) corroborated the expected latitudinal pattern and showed that shredder distribution (abundance, diversity and assemblage composition) was explained by a combination of factors, including water temperature (some taxa were restricted to cool waters) and biogeography (some taxa were more diverse in particular biogeographic realms). In contrast to our hypothesis, shredder diversity was unrelated to leaf toughness, but it was inversely related to litter diversity. Our findings markedly contrast with global trends of diversity for most taxa, and with the general rule of higher consumer diversity at higher levels of resource diversity. Moreover, they highlight the emerging role of temperature in understanding global patterns of diversity, which is of great relevance in the face of projected global warming.

  20. Effect of land use on the composition, diversity and abundance of insects drifting in neotropical streams.

    PubMed

    Gimenez, B C G; Lansac-Tôha, F A; Higuti, J

    2015-11-01

    Streams may exhibit differences in community structure of invertebrate drift, which may be a reflex of variation in environmental factors, able to change in conditions of anthropogenic interventions. The aim of this study was to analyze the composition, diversity and abundance of insects drifting in two neotropical streams under different land use and to identify the environmental factors involved in determining such patterns. 54 taxa of aquatic insects were identified in urban and rural streams. The results indicated significant differences in species composition due to the replacement of specialist species by generalist species in the urban stream. Higher diversity of taxa was recorded in the rural stream, with high levels of dissolved oxygen and high water flow, which favored the occurrence of sensitive groups to environmental disturbances, such as Ephemeroptera, Plecoptera, Trichoptera and Coleoptera taxa, that living mainly in clean and well oxygenated waters. On the other hand, a higher density of insects drifting, especially Chironomidae, was observed in the urban stream, where high values of pH, electrical conductivity and nitrogen were observed. These larvae are able to explore a wide range of environmental conditions, owing to their great capacity for physiological adaptation. Despite observing the expected patterns, there were no significant differences between streams for the diversity and abundance of species. Thus, the species composition can be considered as the best predictor of impacts on the drifting insect community.

  1. Methods for determining the abundance, diversity and activity of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Pereg, Lily

    2014-05-01

    The diversity and abundance of soil microbial communities play important roles in determining soil structure, quality and productivity. The past decade has seen an increase in the number and efficiency of methods for determining microbial diversity, abundance and function. Recognising that only a very small proportion of the soil microbial community can be cultured, most current studies use molecular techniques based on the 16S and 18S rRNA encoding sequences (DGGE, TRFLP, OFRG, ARISA, SSCP) as well as techniques based on the cellular composition of the microbes (PLFA composition). Recent developments include high-throughput sequencing and microarrays, representing major advances in microbial community analysis. While the diversity of microbes can be determined using DNA-based techniques, microbial activity changes under various conditions. Therefore, the analysis of soil function at any given time requires the analysis of gene expression using RNA-based techniques. Molecular techniques have tremendously advanced our knowledge in the field of soil microbiology, however, the limitations should not be underestimated. This presentation will critically review both the advantages and the limitations of techniques used in soil microbial analysis.

  2. Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

    PubMed Central

    Dias, Armando Cavalcante Franco; Pereira e Silva, Michele de Cassia; Cotta, Simone Raposo; Dini-Andreote, Francisco; Soares, Fábio Lino; Salles, Joana Falcão; Azevedo, João Lúcio; van Elsas, Jan Dirk

    2012-01-01

    Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies. PMID:22941088

  3. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

    NASA Astrophysics Data System (ADS)

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-02-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.

  4. Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana.

    PubMed

    Winterbach, Christiaan W; Whitesell, Carolyn; Somers, Michael J

    2015-01-01

    Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana.

  5. Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana

    PubMed Central

    Winterbach, Christiaan W.; Whitesell, Carolyn; Somers, Michael J.

    2015-01-01

    Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana. PMID:26308859

  6. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area

    PubMed Central

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area. PMID:26902649

  7. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area.

    PubMed

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-02-23

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area.

  8. Post-Hurricane Successional Dynamics in Abundance and Diversity of Canopy Arthropods in a Tropical Rainforest.

    PubMed

    Schowalter, T D; Willig, M R; Presley, S J

    2017-01-03

    We quantified long-term successional trajectories of canopy arthropods on six tree species in a tropical rainforest ecosystem in the Luquillo Mountains of Puerto Rico that experienced repeated hurricane-induced disturbances during the 19-yr study (1991-2009). We expected: 1) differential performances of arthropod species to result in taxon- or guild-specific responses; 2) differences in initial conditions to result in distinct successional responses to each hurricane; and 3) the legacy of hurricane-created gaps to persist despite subsequent disturbances. At least one significant effect of gap, time after hurricane, or their interaction occurred for 53 of 116 analyses of taxon abundance, 31 of 84 analyses of guild abundance, and 21 of 60 analyses of biodiversity (e.g., richness, evenness, dominance, and rarity). Significant responses were ∼60% more common for time after hurricane than for gap creation, indicating that temporal changes in habitat during recovery were of primary importance. Both increases and decreases in abundance or diversity occurred in response to each factor. Guild-level responses were probably driven by changes in the abundance of resources on which they rely. For example, detritivores were most abundant soon after hurricanes when litter resources were elevated, whereas sap-suckers were most abundant in gaps where new foliage growth was the greatest. The legacy of canopy gaps created by Hurricane Hugo persisted for at least 19 yr, despite droughts and other hurricanes of various intensities that caused forest damage. This reinforces the need to consider historical legacies when seeking to understand responses to disturbance.

  9. The distribution and abundance of interstellar C2H

    NASA Technical Reports Server (NTRS)

    Huggins, P. J.; Carlson, W. J.; Kinney, A. L.

    1984-01-01

    C2H(N = 1-0) emission has been extensively observed in a variety of molecular clouds, including: 12 hot, dense, cloud cores, 3 bright-rimmed clouds (in NGC 1977, IC 1396, and IC 1848), and across the extended OMC - 1 cloud. It has also been observed in the circumstellar envelopes IRC + 10216 and AFGL 2688. Abundance analyses of the molecular clouds yield C2H/(C-13)O abundance ratios of about 0.01, with little variation (less than about a factor of 4) either between clouds or across individual clouds. In the Orion plateau source, the C2H abundance is enhanced by less than a factor of 4, relative to the extended cloud. The generally high levels of C2H found in the molecular clouds are not readily accounted for by simple, steady-state chemical models, and suggest, as do earlier observations of atomic carbon, that the carbon chemistry in dense clouds is more active than is commonly assumed.

  10. Fossil Signatures Using Elemental Abundance Distributions and Bayesian Probabilistic Classification

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Storrie-Lombardi, Michael C.

    2004-01-01

    Elemental abundances (C6, N7, O8, Na11, Mg12, Al3, P15, S16, Cl17, K19, Ca20, Ti22, Mn25, Fe26, and Ni28) were obtained for a set of terrestrial fossils and the rock matrix surrounding them. Principal Component Analysis extracted five factors accounting for the 92.5% of the data variance, i.e. information content, of the elemental abundance data. Hierarchical Cluster Analysis provided unsupervised sample classification distinguishing fossil from matrix samples on the basis of either raw abundances or PCA input that agreed strongly with visual classification. A stochastic, non-linear Artificial Neural Network produced a Bayesian probability of correct sample classification. The results provide a quantitative probabilistic methodology for discriminating terrestrial fossils from the surrounding rock matrix using chemical information. To demonstrate the applicability of these techniques to the assessment of meteoritic samples or in situ extraterrestrial exploration, we present preliminary data on samples of the Orgueil meteorite. In both systems an elemental signature produces target classification decisions remarkably consistent with morphological classification by a human expert using only structural (visual) information. We discuss the possibility of implementing a complexity analysis metric capable of automating certain image analysis and pattern recognition abilities of the human eye using low magnification optical microscopy images and discuss the extension of this technique across multiple scales.

  11. Bird diversity and abundance in organic and conventional apple orchards in northern Japan

    PubMed Central

    Katayama, Naoki

    2016-01-01

    Many studies have investigated the benefits of agri-environmental schemes, such as organic farming, on biodiversity conservation in annual systems, but their effectiveness in perennial systems is less well understood, particularly in bird communities in temperate regions of Asia. This study examined the effects of organic farming practices on species richness and abundance of breeding birds in apple orchards in northern Japan. Bird counts were conducted in six pairs of organic and conventional orchards during the breeding season in April and May 2015. The total species richness of birds, estimated by sample- and coverage-based rarefaction and extrapolation curves, was greater in organic orchards than in conventional orchards. Among the three dietary guilds (insectivore, granivore, and omnivore), only insectivorous species were more abundant in organic orchards than in conventional ones. This study offers the first quantitative evidence that organic farming can be beneficial for enhancing the diversity of birds, particularly of insectivores, in fruit orchards in Japan. PMID:27677408

  12. The abundance and age distributions of 500 F stars in the solar neighbourhood

    NASA Technical Reports Server (NTRS)

    Clegg, R. E. S.; Bell, R. A.

    1973-01-01

    The uvby catalog of Perry has been used, in conjunction with theoretical uvby colors and stellar evolutionary tracks, to obtain the metal abundance distribution and age distribution of F and G type dwarf stars within 100 pc of the sun. Eighty-three per cent of stars with spectral type F5-G2 have metal content within a factor of 2.5 of the solar abundance, and only 2% have less than one-quarter the solar abundance. The metal abundance distribution, which contains more metal-rich stars than found in previous investigations of F and G dwarfs, has also been compared with the observed metal abundance distribution of G and K giants and the model galaxy calculations of Truran and Cameron (1971). A comparison of the age distribution with evolutionary calculations implies that the rate of star formation in the galaxy may not have decreased by a large factor in the last 10 billion years.

  13. Patterns of diversity and abundance of carrion insect assemblages in the Natural Park "Hoces del Río Riaza" (central Spain).

    PubMed

    Baz, Arturo; Cifrián, Blanca; Martín-Vega, Daniel

    2014-01-01

    The patterns of diversity and abundance of the carrion insect species in the different habitats of the Natural Park "Hoces del Río Riaza" (central Spain) were studied with the use of carrion-baited traps. Representativeness of the inventories was assessed with the calculation of randomized species richness curves and nonparametric estimators. Coleoptera families, Silphidae and Dermestidae, and Diptera families, Calliphoridae and Muscidae, were dominant in every sampling habitat, but differences in the patterns of diversity and abundance were found. Lusitanian oakwood and riparian forest were the most diverse habitats with high abundance of saprophagous species, whereas more open (i.e., exposed to continuous sunlight during the day) habitats showed lower diversity values and a different species composition and distribution of species abundance, favoring thermophilous species and necrophagous species with high tolerance to different environmental conditions. Differences in the bioclimatical features of the sampled habitats are suggested to explain the composition and diversity of the carrion insect assemblages in different environments.

  14. Distribution and diversity of archaeal communities in selected Chinese soils.

    PubMed

    Cao, Peng; Zhang, Li-Mei; Shen, Ju-Pei; Zheng, Yuan-Ming; Di, Hong J; He, Ji-Zheng

    2012-04-01

    To understand the distribution and diversity of archaea in Chinese soils, the archaeal communities in a series of topsoils and soil profiles were investigated using quantitative PCR, T-RFLP combining sequencing methods. Archaeal 16S rRNA gene copy numbers, ranging from 4.96 × 10(6) to 1.30 × 10(8)  copies g(-1) dry soil, were positively correlated with soil pH, organic carbon and total nitrogen in the topsoils. In the soil profiles, archaeal abundance was positively correlated with soil pH but negatively with depth profile. The relative abundance of archaea in the prokaryotes (sum of bacteria and archaea) ranged from 0.20% to 9.26% and tended to increase along the depth profile. T-RFLP and phylogenetic analyses revealed that the structure of archaeal communities in cinnamon soils, brown soils, and fluvo-aquic soils was similar and dominated by Crenarchaeota group 1.1b and 1.1a. These were different from those in red soils, which were dominated by Crenarchaeota group 1.3 and 1.1c. Canonical correspondence analysis indicated that the archaeal community was primarily influenced by soil pH.

  15. Design for mosquito abundance, diversity, and phenology sampling within the National Ecological Observatory Network

    USGS Publications Warehouse

    Hoekman, D.; Springer, Yuri P; Barker, C.M.; Barrera, R.; Blackmore, M.S.; Bradshaw, W.E.; Foley, D. H.; Ginsberg, Howard; Hayden, M. H.; Holzapfel, C. M.; Juliano, S. A.; Kramer, L. D.; LaDeau, S. L.; Livdahl, T. P.; Moore, C. G.; Nasci, R.S.; Reisen, W.K.; Savage, H. M.

    2016-01-01

    The National Ecological Observatory Network (NEON) intends to monitor mosquito populations across its broad geographical range of sites because of their prevalence in food webs, sensitivity to abiotic factors and relevance for human health. We describe the design of mosquito population sampling in the context of NEON’s long term continental scale monitoring program, emphasizing the sampling design schedule, priorities and collection methods. Freely available NEON data and associated field and laboratory samples, will increase our understanding of how mosquito abundance, demography, diversity and phenology are responding to land use and climate change.

  16. The Abundance and Distribution of Presolar Materials in Cluster IDPS

    NASA Technical Reports Server (NTRS)

    Messenger, Scott; Keller, Lindsay; Nakamura-Messenger, Keiko; Ito, Motoo

    2007-01-01

    Presolar grains and remnants of interstellar organic compounds occur in a wide range of primitive solar system materials, including meteorites, interplanetary dust particles (IDPs), and comet Wild-2 samples. Among the most abundant presolar phases are silicate stardust grains and molecular cloud material. However, these materials have also been susceptible to destruction and alteration during parent body and nebular processing. In addition to their importance as direct samples of remote and ancient astrophysical environments, presolar materials thus provide a measure of how well different primitive bodies have preserved the original solar system starting materials.

  17. Spider fauna of semiarid eastern Colorado agroecosystems: diversity, abundance, and effects of crop intensification.

    PubMed

    Kerzicnik, Lauren M; Peairs, Frank B; Cushing, Paula E; Draney, Michael L; Merrill, Scott C

    2013-02-01

    Spiders are critical predators in agroecosystems. Crop management practices can influence predator density and diversity, which, in turn, can influence pest management strategies. Crop intensification is a sustainable agricultural technique that can enhance crop production although optimizing soil moisture. To date, there is no information on how crop intensification affects natural enemy populations, particularly spiders. This study had two objectives: to characterize the abundance and diversity of spiders in eastern Colorado agroecosystems, and to test the hypothesis that spider diversity and density would be higher in wheat (Triticum aestivum L.) in crop-intensified rotations compared with wheat in conventional rotations. We collected spiders through pitfall, vacuum, and lookdown sampling from 2002 to 2007 to test these objectives. Over 11,000 spiders in 19 families from 119 species were captured from all sampling techniques. Interestingly, the hunting spider guild represented 89% of the spider fauna captured from all sites with the families Gnaphosidae and Lycosidae representing 75% of these spiders. Compared with European agroecosystems, these agroecosystems had greater diversity, which can be beneficial for the biological control of pests. Overall, spider densities were low in these semiarid cropping systems, and crop intensification effects on spider densities were not evident at this scale.

  18. Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes

    PubMed Central

    Delgado, Dolores; Alonso-Blanco, Carlos; Fenoll, Carmen; Mena, Montaña

    2011-01-01

    Background and Aims Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. Methods Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. Key Results and Conclusions Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and

  19. Solid and Aqueous Geochemical Controls on Phylogenetic Diversity and Abundance of Microbial Biofilms

    NASA Astrophysics Data System (ADS)

    Jones, A. A.; Bennett, P. C.

    2015-12-01

    In the subsurface, the vast majority of microorganisms are found in biofilms attached to mineral surfaces. The fickle nature of these environments (chemically and physically) likely causes dynamic ecological shifts in these microbial communities. We used laboratory biofilm reactors (inoculated with a diverse subsurface community) to explore the role of mineralogy as part of a microbe-mineral-water ecosystem under variable pressures (mineralogy, pH, carbon, phosphate). Following multivariate analyses, pH was identified as the key physicochemical property associated with variation in both phylogenetic and taxonomic diversity as well as overall community structure (P<0.05). In particular, the ability of minerals, media, or a combination of the two to buffer metabolically generated acidity impacted community structure under oligotrophic and eutrophic conditions. Additionally, we found that media phosphate limitations were significantly correlated to greater biofilm accumulation (P<0.002), but lower species richness (P<0.001) and Shannon diversity (P<0.001); while mineral-bound phosphate limitations were significantly correlated to lesser biofilm accumulation (P<0.05) but not to species richness or diversity. Carbon (as acetate, lactate, or formate) added to the media was correlated with a significant increase in biofilm accumulation (P<0.04), and overall Shannon diversity (P<0.006), but not significantly correlated with overall species richness. Although variable in magnitude, the effect of surface chemistry on microbial diversity (both phylogenetic and taxonomic) was statistically significant, in all reactors, regardless of environmental pressures. Phylogenetically, surface type (carbonate, silicate, or Al-silicate) controlled ~70-90%, meaning that organisms attached to similar surfaces were significantly more genetically similar. Taxonomy and proportional abundance was significantly sensitive to variations in media chemistry with consistent patterns emerging among

  20. Distribution and abundance of nesting ospreys in the United States

    USGS Publications Warehouse

    Henny, C.J.

    1983-01-01

    Nesting Ospreys (Pandion haliaetus) in the contiguous United States now number about 8,000 pairs. Five regional populations exist (in order of abundance): Atlantic Coast, Florida and Gulf Coast, Pacific Northwest, Western Interior, and Great Lakes. Pesticides severely impacted the populations in the northern portion of the Atlantic Coast (Boston to Cape May) and the Great Lakes, but both are now recovering. During recent years in the west, especially in the Western Interior, reservoirs have been responsible for a range expansion and, perhaps, a population increase. However, a strong fidelity to ancestral breeding areas (short dispersal distance) has slowed the range expansion. Unique introductions to distant reservoirs (from breeding populations) are now being made and followed with intense interest. Ospreys adapted to man, his structures, and many of his habitat changes, but proved sensitive to his chemical pollutants. These characteristics make the Osprey an excellent environmental indicator species.

  1. Climatic controls on the global distribution, abundance, and species richness of mangrove forests

    USGS Publications Warehouse

    Osland, Michael J.; Feher, Laura; Griffith, Kereen; Cavanaugh, Kyle C.; Enwright, Nicholas M.; Day, Richard H.; Stagg, Camille L.; Krauss, Ken W.; Howard, Rebecca J.; Grace, James B.; Rogers, Kerrylee

    2017-01-01

    Mangrove forests are highly productive tidal saline wetland ecosystems found along sheltered tropical and subtropical coasts. Ecologists have long assumed that climatic drivers (i.e., temperature and rainfall regimes) govern the global distribution, structure, and function of mangrove forests. However, data constraints have hindered the quantification of direct climate-mangrove linkages in many parts of the world. Recently, the quality and availability of global-scale climate and mangrove data have been improving. Here, we used these data to better understand the influence of air temperature and rainfall regimes upon the distribution, abundance, and species richness of mangrove forests. Although our analyses identify global-scale relationships and thresholds, we show that the influence of climatic drivers is best characterized via regional range limit-specific analyses. We quantified climatic controls across targeted gradients in temperature and/or rainfall within 14 mangrove distributional range limits. Climatic thresholds for mangrove presence, abundance, and species richness differed among the 14 studied range limits. We identified minimum temperature-based thresholds for range limits in eastern North America, eastern Australia, New Zealand, eastern Asia, eastern South America, and southeast Africa. We identified rainfall-based thresholds for range limits in western North America, western Gulf of Mexico, western South America, western Australia, Middle East, northwest Africa, east central Africa, and west central Africa. Our results show that in certain range limits (e.g., eastern North America, western Gulf of Mexico, eastern Asia), winter air temperature extremes play an especially important role. We conclude that rainfall and temperature regimes are both important in western North America, western Gulf of Mexico, and western Australia. With climate change, alterations in temperature and rainfall regimes will affect the global distribution, abundance, and

  2. The plankton community in Norwegian coastal waters—abundance, composition, spatial distribution and diel variation

    NASA Astrophysics Data System (ADS)

    Bratbak, Gunnar; Jacquet, Stéphan; Larsen, Aud; Pettersson, Lasse H.; Sazhin, Andrey F.; Thyrhaug, Runar

    2011-09-01

    The purpose of the present study was to explore the composition and variation of the pico-, nano- and micro-plankton communities in Norwegian coastal waters and Skagerrak, and the co-occurrence of bacteria and viruses. Samples were collected along three cruise transects from Jæren, Lista and Oksøy on the south coast of Norway and into the North Sea and Skagerrak. We also followed a drifting buoy for 55 h in Skagerrak in order to observe diel variations. Satellite ocean color images (SeaWiFS) of the chlorophyll a (chl a) distribution compared favorably to in situ measurements in open waters, while closer to the shore remote sensing chl a data was overestimated compared to the in situ data. Using light microscopy, we identified 49 micro- and 15 nanoplankton sized phototrophic forms as well as 40 micro- and 12 nanoplankton sized heterotrophic forms. The only picoeukaryote (0.2-2.0 μm) we identified was Resultor micron (Pedinophyceae ). Along the transects a significant variation in the distribution and abundance of different plankton forms were observed, with Synechococcus spp and autotrophic picoeukaryotes as the most notable examples. There was no correlation between viruses and chl a, but between viruses and bacteria, and between viruses and some of the phytoplankton groups, especially the picoeukaryotes. Moreover, there was a negative correlation between nutrients and small viruses (Low Fluorescent Viruses) but a positive correlation between nutrients and large viruses (High Fluorescent Viruses). The abundance of autotrophic picoplankton, bacteria and viruses showed a diel variation in surface waters with higher values around noon and late at night and lower values in the evening. Synechococcus spp were found at 20 m depth 25-45 nautical miles from shore apparently forming a bloom that stretched out for more than 100 nautical miles from Skagerrak and up the south west coast of Norway. The different methods used for assessing abundance, distribution and

  3. A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province

    PubMed Central

    Shi, Chenyan; Liu, Yi; Hu, Xiaomin; Xiong, Jinfeng; Zhang, Bo; Yuan, Zhiming

    2015-01-01

    Mosquitoes as one of the most common but important vectors have the potential to transmit or acquire a lot of viruses through biting, however viral flora in mosquitoes and its impact on mosquito-borne disease transmission has not been well investigated and evaluated. In this study, the metagenomic techniquehas been successfully employed in analyzing the abundance and diversity of viral community in three mosquito samples from Hubei, China. Among 92,304 reads produced through a run with 454 GS FLX system, 39% have high similarities with viral sequences belonging to identified bacterial, fungal, animal, plant and insect viruses, and 0.02% were classed into unidentified viral sequences, demonstrating high abundance and diversity of viruses in mosquitoes. Furthermore, two novel viruses in subfamily Densovirinae and family Dicistroviridae were identified, and six torque tenosus virus1 in family Anelloviridae, three porcine parvoviruses in subfamily Parvovirinae and a Culex tritaeniorhynchus rhabdovirus in Family Rhabdoviridae were preliminarily characterized. The viral metagenomic analysis offered us a deep insight into the viral population of mosquito which played an important role in viral initiative or passive transmission and evolution during the process. PMID:26030271

  4. Bacterial abundance and diversity in pond water supplied with different feeds

    PubMed Central

    Qin, Ya; Hou, Jie; Deng, Ming; Liu, Quansheng; Wu, Chongwei; Ji, Yingjie; He, Xugang

    2016-01-01

    The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions. PMID:27759010

  5. Bacterial abundance and diversity in pond water supplied with different feeds

    NASA Astrophysics Data System (ADS)

    Qin, Ya; Hou, Jie; Deng, Ming; Liu, Quansheng; Wu, Chongwei; Ji, Yingjie; He, Xugang

    2016-10-01

    The abundance and diversity of bacteria in two types of ponds were investigated by quantitative PCR and Illumina MiSeq sequencing. The results revealed that the abundance of bacterial 16S rRNA genes in D ponds (with grass carp fed sudan grass) was significantly lower than that in E ponds (with grass carp fed commercial feed). The microbial communities were dominated by Proteobacteria, Cyanobacteria, Bacteroidetes, and Actinobacteria in both E and D ponds, while the abundance of some genera was significantly different between the two types of ponds. Specifically, some potential pathogens such as Acinetobacter and Aeromonas were found to be significantly decreased, while some probiotics such as Comamonadaceae unclassified and Bacillales unclassified were significantly increased in D ponds. In addition, water quality of D ponds was better than that of E ponds. Temperature, dissolved oxygen and nutrients had significant influence on bacterial communities. The differences in bacterial community compositions between the two types of ponds could be partially explained by the different water conditions.

  6. Diversity of abundance patterns of neutron-capture elements in very metal-poor stars

    NASA Astrophysics Data System (ADS)

    Aoki, Misa; Aoki, Wako; Ishimaru, Yuhri; Wanajo, Shinya

    2014-05-01

    Observations of Very Metal-Poor stars indicate that there are at least two sites to r-process; "weak r-process" and "main r-process". A question is whether these two are well separated or there exists a variation in the r-process. We present the results of abundance analysis of neutron-capture elements in the two Very Metal-Poor stars HD107752 and HD110184 in the Milky Way halo observed with the Subaru Telescope HDS. The abundance patterns show overabundace at light n-capture elements (e.g. Sr, Y), inferring the element yielding of weak r-process, while heavy neutron-capture elements (e.g. Ba, Eu) are deficient; however, the overabundance of light ones is not as significant as that previously found in stars representing the weak r-process (e.g. HD122563; Honda et al. 2006). Our study show diversity in the abundance patterns from light to heavy neutron-capture elements in VMP stars, suggesting a variation in r-process, which may depend on electron fraction of environment.

  7. The diversity and abundance of North American bird assemblages fail to track changing productivity.

    PubMed

    Dobson, LuAnna L; La Sorte, Frank A; Manne, Lisa L; Hawkins, Bradford A

    2015-04-01

    Plant biomass or productivity and the species richness of birds are associated across a range of spatial scales. Species-energy theory is generally assumed to explain these correlations. If true, bird richness should also track productivity temporally, and there should be spatial and temporal relationships between productivity and both bird abundance and bird richness. Using the summer normalized difference vegetation index (NDVI) for 1982-2006 and the North American Breeding Bird Survey, we evaluated the response of avian richness and abundance to interannual changes in plant biomass or productivity. We found positive spatial relationships between richness and NDVI for all 25 years. Temporally, however, richness and NDVI were positively associated at 1579 survey sites and negatively associated at 1627 sites (mean r2 = 0.09). Further, total abundance and NDVI were unrelated spatially (r2 values spanning < 0.01 and 0.03) and weakly related temporally (mean r2 = 0.10). We found no evidence that productivity drives bird richness beyond the spatial correlations, and neither prediction arising from species-energy theory was confirmed. Spatial relationships between productivity and bird richness may thus be largely spurious, arising via covariance between plant biomass or productivity and vegetation structural complexity, and the latter may be driving bird communities. This is consistent with the MacArthurs' classic hypothesis that the vertical profile of foliage drives bird species diversity.

  8. Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting.

    PubMed

    Yin, Yanan; Song, Wen; Gu, Jie; Zhang, Kaiyu; Qian, Xun; Zhang, Xin; Zhang, Yajun; Li, Yang; Wang, Xiaojuan

    2016-12-01

    This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg(-1), i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH4(+)-N, NO3(-)-N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process.

  9. Diversity of abundance patterns of neutron-capture elements in very metal-poor stars

    SciTech Connect

    Aoki, Misa; Ishimaru, Yuhri; Aoki, Wako; Wanajo, Shinya

    2014-05-02

    Observations of Very Metal-Poor stars indicate that there are at least two sites to r-process; “weak r-process” and “main r-process”. A question is whether these two are well separated or there exists a variation in the r-process. We present the results of abundance analysis of neutron-capture elements in the two Very Metal-Poor stars HD107752 and HD110184 in the Milky Way halo observed with the Subaru Telescope HDS. The abundance patterns show overabundace at light n-capture elements (e.g. Sr, Y), inferring the element yielding of weak r-process, while heavy neutron-capture elements (e.g. Ba, Eu) are deficient; however, the overabundance of light ones is not as significant as that previously found in stars representing the weak r-process (e.g. HD122563; Honda et al. 2006). Our study show diversity in the abundance patterns from light to heavy neutron-capture elements in VMP stars, suggesting a variation in r-process, which may depend on electron fraction of environment.

  10. Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems.

    PubMed

    Lynn, Tin Mar; Ge, Tida; Yuan, Hongzhao; Wei, Xiaomeng; Wu, Xiaohong; Xiao, Keqing; Kumaresan, Deepak; Yu, San San; Wu, Jinshui; Whiteley, Andrew S

    2017-04-01

    CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of (14)C ((14)C-MBC) differed among the soils from three ecosystems, accounting for 14.2-20.2% of (14)C-labeled soil organic carbon ((14)C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, (14)C-SOC level, and (14)C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

  11. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    USGS Publications Warehouse

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  12. A glimpse into the deep of the Antarctic Polar Front - Diversity and abundance of abyssal molluscs

    NASA Astrophysics Data System (ADS)

    Jörger, K. M.; Schrödl, M.; Schwabe, E.; Würzberg, L.

    2014-10-01

    Our knowledge of the biodiversity and distribution patterns of benthic deep-sea faunas is still limited, with large parts of the world's abyss unexplored, lacking α-taxonomic data across oceans basins and especially of biogeographic transition zones between oceans. The Antarctic Polar Frontal Zone has been discussed as major biogeographic barrier hindering faunal exchange between Subantarctic and Antarctic provinces and conserving high rates of endemism in the Southern Ocean benthos. In the present study we report first, exploratory α-taxonomy on the malacofauna sampled by means of an epibenthic sledge from four bathyal respectively abyssal stations (2732-4327 m depth) in the vicinity of the Antarctic Polar Front during the SYSTCO II expedition (SYSTem COupling in the Southern Ocean, RV Polarstern cruise ANT XXVIII/3). We identified 58 distinct molluscan taxa based on external morphology ('morphospecies'); of the 33 taxa successfully assigned to described species 94% were previously reported from the Southern Ocean, but 24% exhibit distribution ranges crossing the Polar Front. One North Atlantic scaphopod is reported for the first time in Antarctic waters. Our study supports that the Antarctic Polar Front does not serve as effective barrier preventing gene flow in deep-sea molluscs. The present dataset shows the general characteristics of deep-sea sampling: patchiness in distribution and a high degree of singletons. Overall molluscan abundances were generally low ranging between 3.60 and 24.65 ind./1000 m², but in comparison with equatorial and subtropic abyssal basins, gastropod species richness and abundance were reaching high values similar to high Antarctic stations. Comparison between high productivity and low productivity zones along the Polar Front suggests increased abundances and species richness in high productivity zones. Intensified sampling is needed, however, to outweigh stochastic errors and to evaluate the influence of carbon flux as driving

  13. Diversity, Community Composition and Abundance of Anammox Bacteria in Sediments of the North Marginal Seas of China

    PubMed Central

    Shehzad, Ahmed; Liu, Jiwen; Yu, Min; Qismat, Shakeela; Liu, Jingli; Zhang, Xiao-Hua

    2016-01-01

    Over the past few decades, anammox bacteria have been recognized as key players that contribute significantly to the release of large amounts of nitrogen in the global marine nitrogen cycle. In the present study, the diversity, community composition, and abundance of anammox bacteria from the sediments of four diverse regions in the north marginal seas in China were determined via clone library construction and a quantitative PCR analysis. The clone libraries retrieved by the 16S rRNA gene and Hzo gene markers indicated that “Candidatus Scalindua” was the predominant group throughout the sites examined. The 16S rRNA gene clone libraries revealed exceptional diversity by identifying two potential novel anammox clades, as evidenced by the high sequence similarities between these two clades and known anammox genera, and their unique phylogenetic positions with high bootstrap values. However, their potential roles in the anammox reaction need to be validated. Six novel members of Planctomycetes, divergent from the known genera of anammox bacteria, were also detected. A phylogenetic analysis by Hzo protein sequences revealed the existence of two known genera, i.e., “Candidatus Jettenia” and “Candidatus Anammoxoglobus”, which are rarely captured from marine sediments. Among all ecological parameters investigated, the distribution patterns and composition of anammox bacteria were found to be influenced by salinity, total organic matter, and temperature. The abundance of the anammox bacterial 16S rRNA gene from the sites examined ranged between 3.95×105 and 9.21×105 copies g−1 wet sediment and positively correlated with the median size of the sediment sample. PMID:27180640

  14. Skate assemblage on the eastern Patagonian Shelf and Slope: structure, diversity and abundance.

    PubMed

    Arkhipkin, A; Brickle, P; Laptikhovsky, V; Pompert, J; Winter, A

    2012-04-01

    The eastern Patagonian Shelf and continental slope of the south-west Atlantic Ocean support a high biodiversity and abundance of skates. In this study, meso-scale differences in the assemblages, spatial and seasonal distributions of skates are revealed among six habitat zones of the eastern Patagonian Shelf characterized by distinctive oceanographic conditions. Most skates belonged to temperate fauna, and their abundance was much greater in habitats occupied by temperate waters (north-western outer shelf) or mixed waters (northern slope) than in habitats occupied by sub-Antarctic waters (SASW) (south-eastern outer shelf and southern slope). Sub-Antarctic skates were not abundant on the shelf even in habitats occupied by SASW, occurring mainly in deep areas of the lower continental slope. The majority of temperate skates migrated seasonally, shifting northward in winter and spreading southward with warming waters in summer. Most temperate species had two peaks in female maturity (mainly spring and autumn) and spawned in the same habitats where they fed. It is hypothesized that the high biodiversity and abundance of skates on the Patagonian Shelf and Slope are due to the practical absence of their natural competitors, flatfishes, which occupy similar eco-niches elsewhere.

  15. Abundance, diversity, and latitudinal gradients of southeastern Atlantic and Antarctic abyssal gastropods

    NASA Astrophysics Data System (ADS)

    Schrödl, M.; Bohn, J. M.; Brenke, N.; Rolán, E.; Schwabe, E.

    2011-03-01

    Mollusca are widely used for deriving concepts on deep-sea biology and biodiversity, yet abyssal collections are limited to only a few regions of the world ocean and biased toward the northern Atlantic. The present study compares gastropod molluscs sampled along a transect through the southern Atlantic from the equator to Antarctica. The DIVA I and II expeditions concentrated on the hardly explored Guinea, Angola, and Cape Basins. Of the 145 deep-sea deployments (5025-5656 m depth) analyzed to date, 20 have yielded 68 specimens of benthic gastropods, representing 27 species. Only five abyssal species were previously known, four of them from the northern Atlantic deep sea; the remainder appear to be undescribed. Interestingly, there is no faunal overlap with the nearby Antarctic deep-sea. Most of these DIVA species (63%) are represented by single individuals, or limited to one or two stations. The rarity (i.e. 0.55 specimens m -2 calculated from quantitative corers) and still undetectable patchiness of southeastern Atlantic abyssal gastropods may indicate "source-sink" dynamics, but comparison is needed with thus far hardly explored regional bathyal faunas. The BRENKE-epibenthic sledge (EBS) may be efficient at surveying the abyssal gastropod species richness, but is shown to drastically underestimate true abundances. Low diversity values throughout the three southern Atlantic ocean basins do further challenge earlier estimates of a hyperdiverse global abyssal macrofauna. Comparative EBS data available from the southern hemisphere indicate a gradient from the equatorial Guinea Basin towards higher gastropod abundances and diversity in Antarctica. This is in clear contrast to the paradigm of a globally strongly decreasing marine diversity from lower to higher latitudes, highlighting the importance of further exploring the southern fauna from the tropics to Antarctica.

  16. Distribution and abundance of zooplankton populations in Crater Lake, Oregon

    USGS Publications Warehouse

    Larson, G.L.; McIntire, C.D.; Buktenica, M.W.; Girdner, S.F.; Truitt, R.E.

    2007-01-01

    The zooplankton assemblages in Crater Lake exhibited consistency in species richness and general taxonomic composition, but varied in density and biomass during the period between 1988 and 2000. Collectively, the assemblages included 2 cladoceran taxa and 10 rotifer taxa (excluding rare taxa). Vertical habitat partitioning of the water column to a depth of 200 m was observed for most species with similar food habits and/or feeding mechanisms. No congeneric replacement was observed. The dominant species in the assemblages were variable, switching primarily between periods of dominance of Polyarthra-Keratella cochlearis and Daphnia. The unexpected occurrence and dominance of Asplanchna in 1991 and 1992 resulted in a major change in this typical temporal shift between Polyarthra-K. cochlearis and Daphnia. Following a collapse of the zooplankton biomass in 1993 that was probably caused by predation from Asplanchna, Kellicottia dominated the zooplankton assemblage biomass between 1994 and 1997. The decline in biomass of Kellicottia by 1998 coincided with a dramatic increase in Daphnia biomass. When Daphnia biomass declined by 2000, Keratella biomass increased again. Thus, by 1998 the assemblage returned to the typical shift between Keratella-Polyarthra and Daphnia. Although these observations provided considerable insight about the interannual variability of the zooplankton assemblages in Crater Lake, little was discovered about mechanisms behind the variability. When abundant, kokanee salmon may have played an important role in the disappearance of Daphnia in 1990 and 2000 either through predation, inducing diapause, or both. ?? 2007 Springer Science+Business Media B.V.

  17. Marine Mammal Habitat in Ecuador: Seasonal Abundance and Environmental Distribution

    DTIC Science & Technology

    2010-06-01

    surveys will investigate the distribution of marine mammals inhabiting the oceanic areas between the Ecuadorian mainland and around the Galápagos Islands ...concentrations of chlorophyll off the West coast of the Galápagos Islands . Here, upwelling driven productivity (which is initiated by the subsurface...derived macronutrients) is enhanced by iron inputs derived from the island platform. The confluence of the Equatorial Undercurrent and Peru Current

  18. Diel fluctuations in the abundance and community diversity of coastal bacterioplankton assemblages over a tidal cycle.

    PubMed

    Olapade, Ola A

    2012-01-01

    The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene sequences of unknown bacteria (32% to 73%), however, the operational taxonomic units from members of the α-Proteobacteria, Bacteroidetes, Firmicutes, and Cyanobacteria were also well represented during the four tidal events examined. Comparatively, sequence diversity was highest in OT, lowest in low tide, and very similar between HT and incoming tide. The results indicate that the dynamics of bacterial occurrence and diversity appeared to be more pronounced during HT and OT, further indicative of the ecological importance of several environmental variables including temperature, light intensity, and nutrient availability that are also concurrently fluctuating during these tidal events in marine systems.

  19. Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment

    PubMed Central

    Hargreaves, K. R.; Colvin, H. V.; Patel, K. V.; Clokie, J. J. P.

    2013-01-01

    Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of C. difficile has not previously been explored. In this study, we isolated C. difficile from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of C. difficile exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains. PMID:23913427

  20. Distribution and abundance of Stomoxyini flies (Diptera: Muscidae) in Thailand.

    PubMed

    Changbunjong, Tanasak; Weluwanarak, Thekhawet; Ratanakorn, Parntep; Maneeon, Pattarapon; Ganpanakngan, Manoch; Apiwathnasorn, Chamnarn; Sungvornyothin, Sungsit; Sriwichai, Patchara; Sumruayphol, Suchada; Ruangsittichai, Jiraporn

    2012-11-01

    Stomoxyini flies (Diptera: Muscidae) include species of parasitic flies of medical and veterinary importance. The adult flies feed on the blood of mammals and may transmit several parasites and pathogens. We conducted an entomological survey of Stomoxyini flies from different sites in Thailand. Stomoxyini flies were collected at four major types of sites: zoos, livestock farms, wildlife conservation areas and a national park using vavoua traps between November 2010 and April 2011. A total of 3,314 Stomoxyini flies belonging to the genera Stomoxys, Haematobosca, Haematostoma and Haematobia were collected. Eight species were identified: S. calcitrans (46.6%), S. uruma (26.8%), S. pulla (4.3%), S. indicus (0.7%), S. sitiens (0.1%), H. sanguinolenta (11.2 %), H. austeni (0.5%) and H. irritans exigua (9.8%). The diversity of Stomoxyini flies in the livestock farms was higher than the other sites. Altitude correlated with the number of flies. This study provides information that may be useful for Stomoxyini flies control.

  1. Molecular diversity and distribution of marine fungi across 130 European environmental samples

    PubMed Central

    Richards, Thomas A.; Leonard, Guy; Mahé, Frédéric; del Campo, Javier; Romac, Sarah; Jones, Meredith D. M.; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

    2015-01-01

    Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal ‘OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments. PMID:26582030

  2. Molecular diversity and distribution of marine fungi across 130 European environmental samples.

    PubMed

    Richards, Thomas A; Leonard, Guy; Mahé, Frédéric; Del Campo, Javier; Romac, Sarah; Jones, Meredith D M; Maguire, Finlay; Dunthorn, Micah; De Vargas, Colomban; Massana, Ramon; Chambouvet, Aurélie

    2015-11-22

    Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the diversity and relative abundance of fungi across marine samples taken from six European near-shore sites. We removed very rare fungal operational taxonomic units (OTUs) selecting only OTUs recovered from multiple samples for a detailed analysis. This approach identified a set of 71 fungal 'OTU clusters' that account for 66% of all the sequences assigned to the Fungi. Phylogenetic analyses demonstrated that this diversity includes a significant number of chytrid-like lineages that had not been previously described, indicating that the marine environment encompasses a number of zoosporic fungi that are new to taxonomic inventories. Using the sequence datasets, we identified cases where fungal OTUs were sampled across multiple geographical sites and between different sampling depths. This was especially clear in one relatively abundant and diverse phylogroup tentatively named Novel Chytrid-Like-Clade 1 (NCLC1). For comparison, a subset of the water column samples was also investigated using fluorescent microscopy to examine the abundance of eukaryotes with chitin cell walls. Comparisons of relative abundance of RNA-derived fungal tag sequences and chitin cell-wall counts demonstrate that fungi constitute a low fraction of the eukaryotic community in these water column samples. Taken together, these results demonstrate the phylogenetic position and environmental distribution of 71 lineages, improving our understanding of the diversity and abundance of fungi in marine environments.

  3. Species diversity and distribution patterns of the ants of Amazonian Ecuador.

    PubMed

    Ryder Wilkie, Kari T; Mertl, Amy L; Traniello, James F A

    2010-10-01

    Ants are among the most diverse, abundant and ecologically significant organisms on earth. Although their species richness appears to be greatest in the New World tropics, global patterns of ant diversity and distribution are not well understood. We comprehensively surveyed ant diversity in a lowland primary rainforest in Western Amazonia, Ecuador using canopy fogging, pitfall traps, baits, hand collecting, mini-Winkler devices and subterranean probes to sample ants. A total of 489 ant species comprising 64 genera in nine subfamilies were identified from samples collected in only 0.16 square kilometers. The most species-rich genera were Camponotus, Pheidole, Pseudomyrmex, Pachycondyla, Brachymyrmex, and Crematogaster. Camponotus and Pseudomyrmex were most diverse in the canopy, while Pheidole was most diverse on the ground. The three most abundant ground-dwelling ant genera were Pheidole, Solenopsis and Pyramica. Crematogaster carinata was the most abundant ant species in the canopy; Wasmannia auropunctata was most abundant on the ground, and the army ant Labidus coecus was the most abundant subterranean species. Ant species composition among strata was significantly different: 80% of species were found in only one stratum, 17% in two strata, and 3% in all three strata. Elevation and the number of logs and twigs available as nest sites were significant predictors of ground-dwelling ant species richness. Canopy species richness was not correlated with any ecological variable measured. Subterranean species richness was negatively correlated with depth in the soil. When ant species were categorized using a functional group matrix based on diet, nest-site preference and foraging ecology, the greatest diversity was found in Omnivorous Canopy Nesters. Our study indicates ant species richness is exceptionally high at Tiputini. We project 647-736 ant species in this global hotspot of biodiversity. Considering the relatively small area surveyed, this region of western

  4. Parametric scaling from species relative abundances to absolute abundances in the computation of biological diversity: a first proposal using Shannon's entropy.

    PubMed

    Ricotta, Carlo

    2003-01-01

    Traditional diversity measures such as the Shannon entropy are generally computed from the species' relative abundance vector of a given community to the exclusion of species' absolute abundances. In this paper, I first mention some examples where the total information content associated with a given community may be more adequate than Shannon's average information content for a better understanding of ecosystem functioning. Next, I propose a parametric measure of statistical information that contains both Shannon's entropy and total information content as special cases of this more general function.

  5. Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges

    PubMed Central

    Coma, Rafel; Riemann, Lasse

    2015-01-01

    Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. 15N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of 15N to 14N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology. PMID:26070678

  6. Microbial Diversity and Putative Diazotrophy in High- and Low-Microbial-Abundance Mediterranean Sponges.

    PubMed

    Ribes, Marta; Dziallas, Claudia; Coma, Rafel; Riemann, Lasse

    2015-09-01

    Microbial communities associated with marine sponges carry out nutrient transformations essential for benthic-pelagic coupling; however, knowledge about their composition and function is still sparse. We evaluated the richness and diversity of prokaryotic assemblages associated with three high-microbial-abundance (HMA) and three low-microbial-abundance (LMA) sympatric Mediterranean sponges to address their stability and uniqueness. Moreover, to examine functionality and because an imbalance between nitrogen ingestion and excretion has been observed for some of these species, we sequenced nitrogenase genes (nifH) and measured N2 fixation. The prokaryotic communities in the two sponge types did not differ in terms of richness, but the highest diversity was found in HMA sponges. Moreover, the discrete composition of the communities in the two sponge types relative to that in the surrounding seawater indicated that horizontal transmission and vertical transmission affect the microbiomes associated with the two sponge categories. nifH genes were found in all LMA species and sporadically in one HMA species, and about half of the nifH gene sequences were common between the different sponge species and were also found in the surrounding water, suggesting horizontal transmission. (15)N2-enriched incubations showed that N2 fixation was measurable in the water but was not associated with the sponges. Also, the analysis of the isotopic ratio of (15)N to (14)N in sponge tissue indicated that N2 fixation is not an important source of nitrogen in these Mediterranean sponges. Overall, our results suggest that compositional and functional features differ between the prokaryotic communities associated with HMA and LMA sponges, which may affect sponge ecology.

  7. The Distribution and Abundance of Mercury Methylating Microorganisms in Mid-Atlantic Wetlands

    NASA Astrophysics Data System (ADS)

    Santillan, E. F. U.; Gilmour, C. C.; Schwartz, G.; Christensen, G. A.; King, A. J.; Elias, D. A.

    2015-12-01

    The discovery of the genes responsible for microbial methylmercury production, hgcAB, has led to the identification of novel Hg methylators with diverse metabolisms including Fe and SO42- reducing bacteria, syntrophs, and methanogens. We recently developed DNA probes for hgcA in each group of methylators: Deltaproteobacteria, Firmicutes, and Archaea [Christensen, 2015]. In this study, we use the probes to determine quantity and distribution of hgcA+ organisms in mid-Atlantic marshes and sediments, and in Hg-contaminated wetland soils. We also analyze hgcA distribution over a 28-day soil slurry experiment designed to evaluate the impact of activated carbon on Hg methylation and demethylation [Gilmour, 2015]. Initial soils show Deltaproteobacteria comprise most hgcA+ organisms. Methanogens encompass >45% of the remaining methylators. The addition of SO42- to induce SO42- reducing conditions in slurries caused the number of hgcA+ Deltaproteobacteria to increase and the number of hgcA+ methanogens to decrease to >32%. In soils and slurries, Firmicutes were below detection, suggesting our Firmicute primers are either unrepresentative in natural samples, or that hgcA+ Firmicutes are rare. This observation is interesting as Firmicutes include organisms with divergent metabolisms, and their role in environmental methylation is still unknown. Slurries also show no correlation between hgcA abundance and Hg concentrations. We now plan to explore how hgcA abundance relates to Hg-methylation and electron acceptor availability. Our results offer initial insights into the natural distribution of hgcA, supporting the idea that the distribution of different methylators is related to electron acceptors and redox chemistry. Christensen, G., Wymore, AM, King, A, Pdar, M, Hurt Jur, RA, Santillan, EFU, Gilmour, CC, Brandt, CC, Brown, SD, Palumbo, AV, Elias, DA (2015), A Study of Mercury Methylation Genetics: Qualitative and Quantitative Analysis of hgcAB in Pure Culture, paper presented

  8. Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.

    PubMed

    Carini, Paul; Marsden, Patrick J; Leff, Jonathan W; Morgan, Emily E; Strickland, Michael S; Fierer, Noah

    2016-12-19

    Extracellular DNA from dead microorganisms can persist in soil for weeks to years(1-3). Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide(4). We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.

  9. Abundance and diversity of epibenthic amphipods (Crustacea) from contrasting bathyal habitats

    NASA Astrophysics Data System (ADS)

    Knox, Matthew A.; Hogg, Ian D.; Pilditch, Conrad A.; Lörz, Anne-Nina; Nodder, Scott D.

    2012-04-01

    To investigate relationships between epibenthic macrofauna and bathyal habitat characteristics, we examined the abundance, diversity and community composition of amphipod crustaceans relative to environmental variables on two major bathymetric features of New Zealand - the Chatham Rise and Challenger Plateau. An epibenthic (Brenke) sledge was used to sample depths ranging from 200 to 1200 m. Fifteen stations were sampled on the Chatham Rise, which is an extensive submarine ridge, east of New Zealand, characterised by high productivity in surface waters, associated with the Subtropical Front. Five stations were sampled on the Challenger Plateau, west of New Zealand, a region with a similar depth range, but less topographical relief and lower pelagic productivity relative to the Chatham Rise. Over 12,500 amphipods were recovered and identified. We found high abundance (range: 44-2074 individuals 1000 m-2) and taxonomic richness (27 families) in both regions. Amphipod assemblages at all stations were largely dominated by the same families, particularly the Phoxocephalidae. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. However, the remaining three, more distal, western Challenger Plateau stations were highly differentiated from other stations and from one another, despite being relatively similar habitats. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic-pelagic coupling and emphasising the importance of benthic-pelagic links in bathyal ecosystems.

  10. The diversity and abundance of bacteria inhabiting seafloor lavas positively correlate with rock alteration.

    PubMed

    Santelli, Cara M; Edgcomb, Virginia P; Bach, Wolfgang; Edwards, Katrina J

    2009-01-01

    Young, basaltic ocean crust exposed near mid-ocean ridge spreading centers present a spatially extensive environment that may be exploited by epi- and endolithic microbes in the deep sea. Geochemical energy released during basalt alteration reactions can theoretically support chemosynthesis, contributing to a trophic base for the ocean crust biome. To examine associations between endolithic microorganisms and basalt alteration processes, we compare the phylogenetic diversity, abundance and community structure of bacteria existing in several young, seafloor lavas from the East Pacific Rise at approximately 9 degrees N that are variably affected by oxidative seawater alteration. The results of 16S rRNA gene analyses and real-time, quantitative polymerase chain reaction measurements show that the abundance of prokaryotic communities, dominated by the bacterial domain, positively correlates with the extent of rock alteration--the oldest, most altered basalt harbours the greatest microbial biomass. The bacterial community overlap, structure and species richness relative to alteration state is less explicit, but broadly corresponds to sample characteristics (type of alteration products and general alteration state). Phylogenetic analyses suggest that the basalt biome may contribute to the geochemical cycling of Fe, S, Mn, C and N in the deep sea.

  11. Abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China.

    PubMed

    Song, Zhao-Qi; Wang, Li; Wang, Feng-Ping; Jiang, Hong-Chen; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Li, Wen-Jun

    2013-09-01

    It has been suggested that archaea carrying the accA gene, encoding the alpha subunit of the acetyl CoA carboxylase, autotrophically fix CO2 using the 3-hydroxypropionate/4-hydroxybutyrate pathway in low-temperature environments (e.g., soils, oceans). However, little new information has come to light regarding the occurrence of archaeal accA genes in high-temperature ecosystems. In this study, we investigated the abundance and diversity of archaeal accA gene in hot springs in Yunnan Province, China, using DNA- and RNA-based phylogenetic analyses and quantitative polymerase chain reaction. The results showed that archaeal accA genes were present and expressed in the investigated Yunnan hot springs with a wide range of temperatures (66-96 °C) and pH (4.3-9.0). The majority of the amplified archaeal accA gene sequences were affiliated with the ThAOA/HWCG III [thermophilic ammonia-oxidizing archaea (AOA)/hot water crenarchaeotic group III]. The archaeal accA gene abundance was very close to that of AOA amoA gene, encoding the alpha subunit of ammonia monooxygenase. These data suggest that AOA in terrestrial hot springs might acquire energy from ammonia oxidation coupled with CO2 fixation using the 3-hydroxypropionate/4-hydroxybutyrate pathway.

  12. Diversity, abundance, and consistency of microbial oxygenase expression and biodegradation in a shallow contaminated aquifer

    SciTech Connect

    Yagi, J.M.; Madsen, E.L.

    2009-10-15

    The diversity of Rieske dioxygenase genes and short-term temporal variability in the abundance of two selected dioxygenase gene sequences were examined in a naphthalene-rich, coal tar waste-contaminated subsurface study site. Using a previously published PCR-based approach (S. M. Ni Chadhain, R. S. Norman, K. V. Pesce, J. J. Kukor, and G. J. Zylstra, Appl. Environ. Microbiol. 72: 4078-4087, 2006) a broad suite of genes was detected, ranging from dioxygenase sequences associated with Rhodococcus and Sphingomonas to 32 previously uncharacterized Rieske gene sequence clone groups. The nag genes appeared frequently (20% of the total) in two groundwater monitoring wells characterized by low (similar to 10{sup 2} ppb; similar to 1 {mu} M) ambient concentrations of naphthalene. A quantitative competitive PCR assay was used to show that abundances of nag genes (and archetypal nah genes) fluctuated substantially over a 9-month period. To contrast short-term variation with long-term community stability, in situ community gene expression (dioxygenase mRNA) and biodegradation potential (community metabolism of naphthalene in microcosms) were compared to measurements from 6 years earlier. cDNA sequences amplified from total RNA extracts revealed that nah- and nag-type genes were expressed in situ, corresponding well with structural gene abundances. Despite evidence for short-term (9-month) shifts in dioxygenase gene copy number, agreement in field gene expression (dioxygenase mRNA) and biodegradation potential was observed in comparisons to equivalent assays performed 6 years earlier. Thus, stability in community biodegradation characteristics at the hemidecadal time frame has been documented for these subsurface microbial communities.

  13. High abundance and diversity of iron-reducing bacteria in wet tropical forest soils

    NASA Astrophysics Data System (ADS)

    Dubinsky, E. A.; Brodie, E. L.; Andersen, G. L.; Silver, W. L.; Firestone, M. K.

    2005-12-01

    In wet tropical forests, warm and damp conditions promote rapid oxygen consumption in soils that contain high concentrations of iron oxides. Ferric iron is often the most abundant terminal electron acceptor for bacteria in soil during frequent periods of oxygen depletion. Highly-weathered soils of the wet tropics are likely to support large populations of Fe(III) reducing microorganisms whose activity is consequential to soil mineralogy and geochemistry. We studied the diversity and abundance of Fe(III)-reducing bacteria along a 700 m elevation gradient with variable soil redox conditions in northeast Puerto Rico. Culturable iron-reducers were enumerated, isolated and identified using five different media that contained poorly-crystalline Fe(III) oxides as the terminal electron acceptor. Entire soil microbial communities were characterized along the gradient using high-density 16S rRNA gene microarrays capable of detecting 9000 different bacterial and archaeal taxa and assessing changes in their spatial abundance. Fe(III)-reducing bacteria spanned the Proteobacteria and Firmicutes and included many previously unidentified Fe(III) reducers. Populations of culturable iron reducers numbered 108 to 1010 bacteria per gram soil, some of the highest numbers found in any soils or sediments, and population size increased significantly with elevation. These bacteria were dominated by both unclassified alpha- and gamma proteobacteria not previously known to reduce iron, in addition to delta-proteobacteria, such as the family Geobacteraceae, that are well-known Fe(III) reducers. The activity of this group of bacteria can affect biogeochemical cycles that are linked to iron and fundamental to tropical forest productivity, including phosphorus and carbon cycling.

  14. Diversity and abundance of phyllosphere bacteria are linked to insect herbivory.

    PubMed

    Humphrey, Parris T; Nguyen, Trang T; Villalobos, Martha M; Whiteman, Noah K

    2014-03-01

    Simultaneous or sequential attack by herbivores and microbes is common in plants. Many seed plants exhibit a defence trade-off against chewing herbivorous insects and leaf-colonizing ('phyllosphere') bacteria, which arises from cross-talk between the phytohormones jasmonic acid (JA, induced by many herbivores) and salicylic acid (SA, induced by many bacteria). This cross-talk may promote reciprocal susceptibility in plants between phyllosphere bacteria and insect herbivores. In a population of native bittercress (Cardamine cordifolia, Brassicaceae), we tested whether simulating prior damage with JA or SA treatment induced resistance or susceptibility (respectively) to chewing herbivores. In parallel, we conducted culture-dependent surveys of phyllosphere bacteria to test the hypothesis that damage by chewing herbivores correlates positively with bacterial abundance in leaves. Finally, we tested whether bacterial infection induced susceptibility to herbivory by a major chewing herbivore of bittercress, Scaptomyza nigrita (Drosophilidae). Overall, our results suggest that reciprocal susceptibility to herbivory and microbial attack occurs in bittercress. We found that JA treatment reduced and SA treatment increased S. nigrita herbivory in bittercress in the field. Bacterial abundance was higher in herbivore-damaged vs. undamaged leaves (especially Pseudomonas syringae). However, Pedobacter spp. and Pseudomonas fluorescens infections were negatively associated with herbivory. Experimental Pseudomonas spp. infections increased S. nigrita herbivory in bittercress. Thus, plant defence signalling trade-offs can have important ecological consequences in nature that may be reflected in a positive correlation between herbivory and phyllosphere bacterial abundance and diversity. Importantly, the strength and direction of this association varies within and among prevalent bacterial groups.

  15. Diversity and abundance of invertebrate epifaunal assemblages associated with gorgonians are driven by colony attributes

    NASA Astrophysics Data System (ADS)

    Cúrdia, João; Carvalho, Susana; Pereira, Fábio; Guerra-García, José Manuel; Santos, Miguel N.; Cunha, Marina R.

    2015-06-01

    The present study aimed to explicitly quantify the link between the attributes of shallow-water gorgonian colonies (Octocorallia: Alcyonacea) and the ecological patterns of associated non-colonial epifaunal invertebrates. Based on multiple regression analysis, we tested the contribution of several attributes (colony height, width, and area, fractal dimension as a measure of colony complexity, lacunarity as a measure of the heterogeneity, and "colonial" epibiont cover) to abundance and taxonomic richness of associated assemblages. The results highlight the variation in the response of epifaunal assemblages to the gorgonian colony characteristics. The nature and intensity of the relationships were gorgonian species-dependent and varied from one taxonomic group to another. For both gorgonian species analyzed, the strongest predictor of species richness and abundance of the epifaunal assemblages was "colonial" epibiont cover, possibly due to a trophic effect (direct or indirect enhancement of food availability) combined with the surface available for colonization (species-area effect). Although structural complexity is usually indicated as the main driver for rich and abundant coral-associated assemblages, no significant relationship was observed between fractal dimension and the community descriptors; lacunarity, which reflects the sizes of the inter-branch spaces, was only linked to taxonomic richness in the assemblages associated with Leptogorgia lusitanica. The validity of the paradigm that structural complexity enhances biodiversity may be scale-dependent. In the case of gorgonians, the effect of complexity at the "garden" level may be more relevant than at the individual colony level. This reinforces the need for the conservation of gorgonian aggregation areas as a whole in order to preserve host diversity and size structure.

  16. A landscape analysis of cougar distribution and abundance in Montana, USA.

    PubMed

    Riley, S J; Malecki, R A

    2001-09-01

    Recent growth in the distribution and abundance of cougars (Puma concolor) throughout western North America has created opportunities, challenges, and problems for wildlife managers and raises questions about what factors affect cougar populations. We present an analysis of factors thought to affect cougar distribution and abundance across the broad geographical scales on which most population management decisions are made. Our objectives were to: (1) identify and evaluate landscape parameters that can be used to predict the capability of habitats to support cougars, and (2) evaluate factors that may account for the recent expansion in cougar numbers. Habitat values based on terrain ruggedness and forested cover explained 73% of the variation in a cougar abundance index. Indices of cougar abundance also were spatially and temporally correlated with ungulate abundance. An increase in the number and total biomass of ungulate prey species is hypothesized to account for recent increases in cougars. Cougar populations in Montana are coping with land development by humans when other components of habitat and prey populations are sufficient. Our analysis provides a better understanding of what may have influenced recent growth in cougar distribution and abundance in Montana and, when combined with insights about stakeholder acceptance capacity, offers a basis for cougar management at broad scales. Long-term conservation of cougars necessitates a better understanding of ecosystem functions that affect prey distribution and abundance, more accurate estimates of cougar populations, and management abilities to integrate these components with human values.

  17. Relating species abundance distributions to species-area curves in two Mediterranean-type shrublands

    USGS Publications Warehouse

    Keeley, Jon E.

    2003-01-01

    Based on both theoretical and empirical studies there is evidence that different species abundance distributions underlie different species-area relationships. Here I show that Australian and Californian shrubland communities (at the scale from 1 to 1000 m2) exhibit different species-area relationships and different species abundance patterns. The species-area relationship in Australian heathlands best fits an exponential model and species abundance (based on both density and cover) follows a narrow log normal distribution. In contrast, the species-area relationship in Californian shrublands is best fit with the power model and, although species abundance appears to fit a log normal distribution, the distribution is much broader than in Australian heathlands. I hypothesize that the primary driver of these differences is the abundance of small-stature annual species in California and the lack of annuals in Australian heathlands. Species-area is best fit by an exponential model in Australian heathlands because the bulk of the species are common and thus the species-area curves initially rise rapidly between 1 and 100 m2. Annuals in Californian shrublands generate very broad species abundance distributions with many uncommon or rare species. The power function is a better model in these communities because richness increases slowly from 1 to 100 m2 but more rapidly between 100 and 1000 m2due to the abundance of rare or uncommon species that are more likely to be encountered at coarser spatial scales. The implications of this study are that both the exponential and power function models are legitimate representations of species-area relationships in different plant communities. Also, structural differences in community organization, arising from different species abundance distributions, may lead to different species-area curves, and this may be tied to patterns of life form distribution.

  18. Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia.

    PubMed

    Pyritz, Lennart W; Büntge, Anna B S; Herzog, Sebastian K; Kessler, Michael

    2010-10-01

    Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures.

  19. Effects of Habitat Structure and Fragmentation on Diversity and Abundance of Primates in Tropical Deciduous Forests in Bolivia

    PubMed Central

    Büntge, Anna B. S.; Herzog, Sebastian K.; Kessler, Michael

    2010-01-01

    Habitat structure and anthropogenic disturbance are known to affect primate diversity and abundance. However, researchers have focused on lowland rain forests, whereas endangered deciduous forests have been neglected. We aimed to investigate the relationships between primate diversity and abundance and habitat parameters in 10 deciduous forest fragments southeast of Santa Cruz, Bolivia. We obtained primate data via line-transect surveys and visual and acoustic observations. In addition, we assessed the vegetation structure (canopy height, understory density), size, isolation time, and surrounding forest area of the fragments. We interpreted our results in the context of the historical distribution data for primates in the area before fragmentation and interviews with local people. We detected 5 of the 8 historically observed primate species: Alouatta caraya, Aotus azarae boliviensis, Callithrix melanura, Callicebus donacophilus, and Cebus libidinosus juruanus. Total species number and detection rates decreased with understory density. Detection rates also negatively correlated with forest areas in the surroundings of a fragment, which may be due to variables not assessed, i.e., fragment shape, distance to nearest town. Observations for Alouatta and Aotus were too few to conduct further statistics. Cebus and Callicebus were present in 90% and 70% of the sites, respectively, and their density did not correlate with any of the habitat variables assessed, signaling high ecological plasticity and adaptability to anthropogenic impact in these species. Detections of Callithrix were higher in areas with low forest strata. Our study provides baseline data for future fragmentation studies in Neotropical dry deciduous forests and sets a base for specific conservation measures. PMID:20949116

  20. Microbial Diversity and Lipid Abundance in Microbial Mats from a Sulfidic, Saline, Warm Spring in Utah, USA

    NASA Astrophysics Data System (ADS)

    Gong, J.; Edwardson, C.; Mackey, T. J.; Dzaugis, M.; Ibarra, Y.; Course 2012, G.; Frantz, C. M.; Osburn, M. R.; Hirst, M.; Williamson, C.; Hanselmann, K.; Caporaso, J.; Sessions, A. L.; Spear, J. R.

    2012-12-01

    The microbial diversity of Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake was investigated. The measured pH, temperature, salinity, and sulfide concentration along the flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM to negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were dissected into depth profiles based on the color and texture of the mat layers. Genomic DNA was extracted from each layer, and the 16S rRNA gene was amplified and sequenced on the Roche 454 Titanium platform. Fatty acids were also extracted from the mat layers and analyzed by liquid chromatography and mass spectrometry. The mats at Stinking Springs were classified into roughly two morphologies with respect to their spatial distribution: loose, sometimes floating mats proximal to the spring source; and thicker, well-laminated mats distal to the spring source. Loosely-laminated mats were found in turbulent stream flow environments, whereas well-laminated mats were common in less turbulent sheet flows. Phototrophs, sulfur oxidizers, sulfate reducers, methanogens, other bacteria and archaea were identified by 16S rRNA gene sequences. Diatoms, identified by microscopy and lipid analysis were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were identified and characterized at the two fast flowing sites. These two streamer varieties were dominated by either cyanobacteria or flavobacteria. Overall, our genomic and lipid analysis suggest that the physical and chemical environment is more predictive of the community composition than mat morphology. Site Map

  1. Abundance, diversity, and vitality of mycorrhizae of Scots pine (Pinus sylvestris L.) in lignite recultivation sites.

    PubMed

    Münzenberger, B; Golldack, J; Ullrich, A; Schmincke, B; Hüttl, R F

    2004-07-01

    Scots pine (Pinus sylvestris L.) stands cover large areas in the Lusatian and the Middle German lignite mining districts. Due to adverse chemical substrate conditions, the root systems of the trees are restricted to the ameliorated top-spoil and the organic forest floor layers. To investigate functioning of fine root systems under the prevailing site factors, we studied mycorrhizal colonization rate and frequency as well as mycorrhizal diversity, vitality and growth phases in Scots pine ecosystems along a chronosequence in both mining districts. Mycorrhizal rate was close to 100% in both districts. Mycorrhizal abundance was higher in the organic forest floor layer than the mineral soil layer. In total, 25 morphotypes were recorded. Diversity differed between the districts. The mycorrhizae of Amphinema byssoides, Tuber puberulum, Pinirhiza discolor, Pinirhiza cf. bicolorata and E-type were present in both mining areas. These morphotypes are typical of nutrient-rich soils with high pH values. Compared with the undisturbed sites, vitality of mycorrhizae was very high at the test sites on spoil substrate, correlating with the high growth dynamics of mycorrhizae at recultivation sites. A relatively high carbon flow to the mycorrhizal root systems at these sites seems likely. Thus, mycorrhizal root systems are able to cope with the ameliorated top-spoil and the organic layer. The main reason for the adaptation is the large number of ectomycorrhizal fungal species available in this area where Pinus sylvestris is indigenous.

  2. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

    PubMed Central

    Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J. R.; Sinninghe Damsté, Jaap S.; Villanueva, Laura

    2016-01-01

    Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments. PMID:27812355

  3. Prokaryote diversity and virus abundance in shallow hydrothermal vents of the Mediterranean Sea (Panarea Island) and the Pacific Ocean (north Sulawesi-Indonesia).

    PubMed

    Manini, E; Luna, G M; Corinaldesi, C; Zeppilli, D; Bortoluzzi, G; Caramanna, G; Raffa, F; Danovaro, R

    2008-05-01

    Despite their ubiquitous distribution in tectonically active coastal zones, shallow water hydrothermal vents have been less investigated than deep-sea vents. In the present study, we investigated the role of viral control and fluid emissions on prokaryote abundance, diversity, and community structure (total Archaea, total Bacteria, and sulphate-reducing bacteria) in waters and sediments surrounding the caldera of four different shallow-water hydrothermal vents (three located in the Mediterranean Sea and one in the Pacific Ocean). All vents, independent of their location, generally displayed a significant decrease of benthic prokaryote abundance, as well as its viable fraction, with increasing distance from the vent. Prokaryote assemblages were always dominated by Bacteria. Benthic Archaea accounted for 23-33% of total prokaryote abundance in the Mediterranean Sea and from 13 to 29% in the Pacific Ocean, whereas in the water column they accounted for 25-38%. The highest benthic bacterial ribotype richness was observed in close proximity of the vents (i.e., at 10-cm distance from the emissions), indicating that vent fluids might influence bacterial diversity in surrounding sediments. Virioplankton and viriobenthos abundances were low compared to other marine systems, suggesting that temperature and physical-chemical conditions might influence viral survival in these vent systems. We thus hypothesize that the high bacterial diversity observed in close proximity of the vents is related with the highly variable vent emissions, which could favor the coexistence of several prokaryotic species.

  4. Abundance- and functional-based mechanisms of plant diversity loss with fertilization in the presence and absence of herbivores.

    PubMed

    Yang, Zhongling; Hautier, Yann; Borer, Elizabeth T; Zhang, Chunhui; Du, Guozhen

    2015-09-01

    Nutrient supply and herbivores can regulate plant species composition, biodiversity and functioning of terrestrial ecosystems. Nutrient enrichment frequently increases plant productivity and decreases diversity while herbivores tend to maintain plant diversity in productive systems. However, the mechanisms by which nutrient enrichment and herbivores regulate plant diversity remain unclear. Abundance-based mechanisms propose that fertilization leads to the extinction of rare species due to random loss of individuals of all species. In contrast, functional-based mechanisms propose that species exclusion is based on functional traits which are disadvantageous under fertilized conditions. We tested mechanistic links between fertilization and diversity loss in the presence or absence of consumers using data from a 4-year fertilization and fencing experiment in an alpine meadow. We found that both abundance- and functional-based mechanisms simultaneously affected species loss in the absence of herbivores while only abundance-based mechanisms affected species loss in the presence of herbivores. Our results indicate that an abundance-based mechanism may consistently play a role in the loss of plant diversity with fertilization, and that diversity decline is driven primarily by the loss of rare species regardless of a plant's functional traits and whether or not herbivores are present. Increasing efforts to conserve rare species in the context of ecosystem eutrophication is a central challenge for grazed grassland ecosystems.

  5. Snow-borne nanosized particles: Abundance, distribution, composition, and significance in ice nucleation processes

    NASA Astrophysics Data System (ADS)

    Rangel-Alvarado, Rodrigo Benjamin; Nazarenko, Yevgen; Ariya, Parisa A.

    2015-11-01

    Physicochemical processes of nucleation constitute a major uncertainty in understanding aerosol-cloud interactions. To improve the knowledge of the ice nucleation process, we characterized physical, chemical, and biological properties of fresh snow using a suite of state-of-the-art techniques based on mass spectrometry, electron microscopy, chromatography, and optical particle sizing. Samples were collected at two North American Arctic sites, as part of international campaigns (2006 and 2009), and in the city of Montreal, Canada, over the last decade. Particle size distribution analyses, in the range of 3 nm to 10 µm, showed that nanosized particles are the most numerous (38-71%) in fresh snow, with a significant portion (11 to 19%) less than 100 nm in size. Particles with diameters less than 200 nm consistently exhibited relatively high ice-nucleating properties (on average ranged from -19.6 ± 2.4 to -8.1 ± 2.6°C). Chemical analysis of the nanosized fraction suggests that they contain bioorganic materials, such as amino acids, as well as inorganic compounds with similar characteristics to mineral dust. The implication of nanoparticle ubiquity and abundance in diverse snow ecosystems are discussed in the context of their importance in understanding atmospheric nucleation processes.

  6. Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis.

    PubMed

    Tourna, Maria; Maclean, Paul; Condron, Leo; O'Callaghan, Maureen; Wakelin, Steven A

    2014-06-01

    Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry.

  7. Abundance and Distribution of Diagnostic Carbon Fixation Genes in a Deep-Sea Hydrothermal Gradient Ecosystem

    NASA Astrophysics Data System (ADS)

    Blumenfeld, H. N.; Kelley, D. S.; Girguis, P. R.; Schrenk, M. O.

    2010-12-01

    The walls of deep-sea hydrothermal vent chimneys sustain steep thermal and chemical gradients resulting from the mixing of hot (350°C+) hydrothermal fluids with cold, oxygenated seawater. The chemical disequilibrium generated from this process has the potential to drive numerous chemolithoautotrophic metabolisms, many of which have been demonstrated to be operative in microbial pure cultures. In addition to the well-known Calvin Cycle, at least five additional pathways have been discovered including the Reverse Tricarboxylic Acid Cycle (rTCA), the Reductive Acetyl-CoA pathway, and the 3-hydroxyproprionate pathway. Most of the newly discovered pathways have been found in thermophilic and hyperthermophilic Bacteria and Archaea, which are the well represented in microbial diversity studies of hydrothermal chimney walls. However, to date, little is known about the environmental controls that impact various carbon fixation pathways. The overlap of limited microbial diversity with distinct habitat conditions in hydrothermal chimney walls provides an ideal setting to explore these relationships. Hydrothermal chimney walls from multiple structures recovered from the Juan de Fuca Ridge in the northeastern Pacific were sub-sampled and analyzed using PCR-based assays. Earlier work showed elevated microbial abundances in the outer portions of mature chimney walls, with varying ratios of Archaea to Bacteria from the outer to inner portions of the chimneys. Common phylotypes identified in these regions included Epsilonproteobacteria, Gammaproteobacteria, and Desulfurococcales. Total genomic DNA was extracted from mineralogically distinct niches within these structures and queried for genes coding key regulatory enzymes for each of the well studied carbon fixation pathways. Preliminary results show the occurrence of genes representing rTCA cycle (aclB) and methyl coenzyme A reductase (mcrA) - a proxy for the Reductive Acetyl-CoA Pathway within interior portion of mature

  8. Abundance estimation from multiple photo surveys: confidence distributions and reduced likelihoods for bowhead whales off Alaska.

    PubMed

    Schweder, Tore

    2003-12-01

    Maximum likelihood estimates of abundance are obtained from repeated photographic surveys of a closed stratified population with naturally marked and unmarked individuals. Capture intensities are assumed log-linear in stratum, year, and season. In the chosen model, an approximate confidence distribution for total abundance of bowhead whales, with an accompanying likelihood reduced of nuisance parameters, is found from a parametric bootstrap experiment. The confidence distribution depends on the assumed study protocol. A confidence distribution that is exact (except for the effect of discreteness) is found by conditioning in the unstratified case without unmarked individuals.

  9. Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances

    PubMed Central

    Boulangeat, Isabelle; Gravel, Dominique; Thuiller, Wilfried

    2014-01-01

    Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model’s performance and that the spatial variations of species presence–absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution. PMID:22462813

  10. Species Diversity, Abundance, and Host Preferences of Mosquitoes (Diptera: Culicidae) in Two Different Ecotypes of Madagascar With Recent RVFV Transmission.

    PubMed

    Jean Jose Nepomichene, Thiery Nirina; Elissa, Nohal; Cardinale, Eric; Boyer, Sebastien

    2015-09-01

    Mosquito diversity and abundance were examined in six Madagascan villages in either arid (Toliary II district) or humid (Mampikony district) ecotypes, each with a history of Rift Valley fever virus transmission. Centers for Disease Control and Prevention light traps without CO2 (LT) placed near ruminant parks and animal-baited net trap (NT) baited with either zebu or sheep/goat were used to sample mosquitoes, on two occasions between March 2011 and October 2011. Culex tritaeniorhynchus (Giles) was the most abundant species, followed by Culex antennatus (Becker) and Anopheles squamosus/cydippis (Theobald/de Meillon). These three species comprised more than half of all mosquitoes collected. The NT captured more mosquitoes in diversity and in abundance than the LT, and also caught more individuals of each species, except for An. squamosus/cydippis. Highest diversity and abundance were observed in the humid and warm district of Mampikony. No host preference was highlighted, except for Cx. tritaeniorhynchus presenting a blood preference for zebu baits. The description of species diversity, abundance, and host preference described herein can inform the development of control measures to reduce the risk of mosquito-borne diseases in Madagascar.

  11. Energy gradients and the geographic distribution of local ant diversity.

    PubMed

    Kaspari, Michael; Ward, Philip S; Yuan, May

    2004-08-01

    Geographical diversity gradients, even among local communities, can ultimately arise from geographical differences in speciation and extinction rates. We evaluated three models--energy-speciation, energy-abundance, and area--that predict how geographic trends in net diversification rates generate trends in diversity. We sampled 96 litter ant communities from four provinces: Australia, Madagascar, North America, and South America. The energy-speciation hypothesis best predicted ant species richness by accurately predicting the slope of the temperature diversity curve, and accounting for most of the variation in diversity. The communities showed a strong latitudinal gradient in species richness as well as inter-province differences in diversity. The former vanished in the temperature-diversity residuals, suggesting that the latitudinal gradient arises primarily from higher diversification rates in the tropics. However, inter-province differences in diversity persisted in those residuals--South American communities remained more diverse than those in North America and Australia even after the effects of temperature were removed.

  12. [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA.

    PubMed

    Boyd, Eric S; Hamilton, Trinity L; Swanson, Kevin D; Howells, Alta E; Baxter, Bonnie K; Meuser, Jonathan E; Posewitz, Matthew C; Peters, John W

    2014-11-28

    The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications.

  13. Abundance, diversity, and dynamics of viruses on microorganisms in activated sludge processes.

    PubMed

    Otawa, Kenichi; Lee, Sang Hyon; Yamazoe, Atsushi; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

    2007-01-01

    We examined the abundance of viruses on microorganisms in activated sludge and the dynamics of their community structure. Direct counting with epifluorescence microscopy and pulsed-field gel electrophoresis (PFGE) were applied to 20 samples from 14 full-scale wastewater treatment plants (wwtps) treating municipal, industrial, or animal wastewater. Furthermore, to observe the dynamics of viral community structure over time, a laboratory-scale sequencing batch reactor was operated for 58 days. The concentrations of virus particles in the wwtps, as quantified by epifluorescence microscopy, ranged from 4.2 x 10(7) to 3.0 x 10(9) mL-1. PFGE, improved by the introduction of a higher concentration of Tris-EDTA buffer in the DNA extraction step, was successfully used to profile DNA viruses in the activated sludge. Most of the samples from different wwtps commonly had bands in the 40-70 kb range. In the monitoring of viral DNA size distribution in the laboratory-scale reactor, some bands were observed stably throughout the experimental period, some emerged during the operation, and others disappeared. Rapid emergence and disappearance of two intense bands within 6 days was observed. Our data suggest that viruses--especially those associated with microorganisms--are abundant and show dynamic behavior in activated sludge.

  14. Distribution and abundance of decapod crustacean larvae in the southeastern Bering Sea with emphasis on commercial species. Final report

    SciTech Connect

    Armstrong, D.A.; Incze, L.S.; Wencker, D.L.; Armstrong, J.L.

    1981-01-01

    Contents include: Distribution and abundance of king crab larvae, Paralithodes camtschatica and P. platypus in the southeast Bering Sea; Distribution and abundance of the larvae of tanner crabs in the southeastern Bering Sea; Distribution and abundance of other brachyuran larvae in the southeastern Bering Sea with emphasis on Erimacrus isenbeckii; Distribution and abundance of shrimp larvae in the southeastern Bering Sea with emphasis on pandalid species; Distribution and abundance of hermit crabs (Paguridae) in the southeasternBering Sea; Possible oil impacts on decapod larbae in the southeastern Bering Sea with emphesis on the St. George Basin.

  15. Competition with stone crabs drives juvenile spiny lobster abundance and distribution.

    PubMed

    Behringer, Donald C; Hart, John E

    2017-02-28

    Interspecific competition is assumed to have a strong influence on the population dynamics of competing species, but is not easily demonstrated for mobile species in the wild. In the Florida Keys (USA), anecdotal observations have long pointed to an inverse relationship in abundance of two large decapod crustaceans found co-occurring in hard-bottom habitat, the stone crab Menippe mercenaria and the Caribbean spiny lobster Panulirus argus. We used them to explicitly test whether competition for a renewable resource (shelter) can drive the abundance and distribution of the inferior competitor. We first explored this relationship in shelter competition mesocosm experiments to determine the competitively dominant species. Results showed that stone crabs are clearly the dominant competitors regardless of the number of lobsters present, the presence of co-sheltering species such as the spider crab, Damithrax spinosissimus, or the order of introduction of competitors into the mesocosm. We also found that lobsters use chemical cues from stone crabs to detect and avoid them. We then tested the ramifications of this competitive dominance in the field by manipulating stone crab abundance and then tracking the abundance and distribution of spiny lobsters through time. Increased stone crab abundance immediately resulted in decreased lobster abundance and increased aggregation. The opposite occurred on sites where stone crabs were removed. When we stopped removing stone crabs from these sites, they soon returned and lobster abundance decreased. This study explicitly demonstrated that interspecific competition can drive population dynamics between these species, and ultimately, community composition in these shallow water habitats.

  16. Viral abundance and distribution in mesopelagic and bathypelagic waters of the Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Magagnini, Mirko; Corinaldesi, Cinzia; Monticelli, Luis S.; De Domenico, Emilio; Danovaro, Roberto

    2007-08-01

    Despite the fact that marine viruses have been increasingly investigated in the last decade, knowledge on virus abundance, biomass and distribution in mesopelagic and bathypelagic waters is limited. We report here the results of a large-spatial-scale study (covering more than 3000 km) on the virioplankton distribution in epi-, meso- and bathypelagic waters in 19 areas of the Mediterranean Sea, from the Alboran Sea and Western Mediterranean, to the Tyrrhenian Sea, Sicily Channel and Ionian Sea. Integrated viral abundance in epipelagic waters was significantly higher than in deep-sea waters (on average, 2.4 vs. 0.5×10 12 viruses m -3). However, abundance of viruses in the deep-Mediterranean waters was the highest reported so far for deep seas worldwide (7.0 and 3.1×10 11 viruses m -3 in mesopelagic and bathypelagic waters, respectively) and their biomass accounted for 13-18% of total prokaryotic C biomass. The significant relationship between viral abundance and prokaryotic abundance and production in deep waters suggests that also deep-sea viruses are closely dependent on the abundance and metabolism of their hosts. Moreover, virus to prokaryote (and nucleoid-containing cell (NuCC)) abundance ratio increased with increasing depths suggesting that deep waters may represent optimal environments for viral survival or proliferation. Overall, our results indicate that deep waters may represent a significant reservoir of viruses and open new perspectives for future investigations of viral impact on the functioning of meso-bathypelagic ecosystems.

  17. The Giant Branch of omega Centauri. V. The Calcium Abundance Distribution

    NASA Astrophysics Data System (ADS)

    Norris, John E.; Freeman, K. C.; Mighell, K. J.

    1996-05-01

    We present an unbiased catalog of calcium abundances for 517 red giants brighter that MV ˜ -1 in the chemically inhomogeneous globular cluster ω Centauri. The basic features of the abundance distribution are as follows: (1) few, if any, stars exist on the giant branch of ω Cen with [Ca/H] less than ˜-1.6; (2) there is a well-defined peak in the distribution at [Ca/H] = -1.4, with a long tail stretching up to [Ca/H] ˜-0.3; and (3) the distribution is bimodal with a second smaller peak in the distribution at [Ca/H] = -0.9. The distribution may be well fitted by two components each having a simple closed box abundance distribution and for which the ratio of more metal rich to more metal poor is ˜0.2. We argue that the present data, taken together with the abundance patterns of the s-process elements in this cluster reported by in 1994 by Vanture, Wallerstein, & Brown and in 1995 by Norris & Da Costa, are most convincingly described in terms of the two components representing successive epochs of star formation in the cluster, rather than of their being two independent merging fragments. Examination of the radial distribution of [Ca/H] suggests that there is an abundance gradient in the cluster, consistent with its having been formed in a dissipative manner. The picture emerges of ω Cen having evolved within the Searle-Zinn paradigm of Galactic globular cluster formation, from a gaseous protocloud of mass perhaps as large as ˜108 Msun and initial abundance [Ca/H] ˜ -1.5 on a timescale 1 Gyr, well away from the central region of the forming Galaxy and later coming into dynamical equilibrium with it.

  18. Distribution and abundance of pelagic tunicates in the North Yellow Sea

    NASA Astrophysics Data System (ADS)

    Franco, Pietro; Chen, Hongju; Liu, Guangxing

    2014-10-01

    In this paper, the distribution patterns and abundance of pelagic tunicates in the North Yellow Sea of China during the period 2006-2007 were analyzed. Zooplankton samples were obtained with vertical towing from bottom to surface using a WP2 plankton net (200 μm mesh size; mouth area: 0.25 m2). Five species belonging to two classes were identified: Oikopleura dioica, O. longicauda and Fritillaria borealis belonging to class Appendicularia; Salpa fusiformis and Doliolum denticulatum of class Thaliacea. O. dioica and O. longicauda were the dominant species, occurring in the samples of all four seasons, with different distribution patterns. Their maximum abundance were 1664.7 ind. m-3 (spring) and 1031.7 ind. m-3 (spring) respectively. Following Oikopleura spp. were D. denticulatum, which was found only in autumn with an average abundance of 149.6 ind. m-3, and S. fusiformis, which was detected all the year long except for autumn with low abundance (max. abundance 289.4 ind. m-3 in summer). Only a very small amount of F. borealis was detected in summer samples, with an average abundance of 2.7 ind. m-3. The relationship between tunicates abundances and the environmental factors was analyzed using the stepwise regression model for each species. The variation of appendicularian abundance showed a significant correlation with the surface water temperature and with the concentration of Chl- a. No relationship was found between tunicates abundance and salinity, likely due to the slight changes in surface salinity of the studied area during the four seasons. Salps abundance and that of doliolids were significantly correlated to bottom water temperature, indicating that these two species ( S. fusiformis and D. denticulatum) migrate vertically in the water column. In particular D. denticulatum, known to be a warm water species, showed not only an important correlation with water temperature, but also a spatial distribution connected to the warm currents in the North Yellow

  19. The distribution and abundance of desert tortoises on the Nevada Test Site

    SciTech Connect

    Not Available

    1991-01-01

    This report presents the results of transect studies conducted from 1981--1986 to determine the distribution and abundance of desert tortoises (Gopherus agassizii) on the Nevada Test Site (NTS) and summarizes the current understanding of the distribution of this species on NTS. Seven hundred fifty-nine transect having a total length of 1,190.7 km were walked and 380 sign of tortoises were counted. The abundance of tortoises on NTS is low to very low relative to the other areas within this species' range. Tortoises appear to be more abundant on NTS on the bajadas and foothills of limestone and dolomite mountains than on mountains of volcanic origin. Sign of tortoises were found were 880 to 1600 m and sign was more abundant at higher elevations (>1200 m) than has been reported previously for Nevada. The scale of classification of vegetation associations available for NTS is too large to be useful for predicting tortoise abundance. Tortoises were found only in approximately the southern third of NTS. They probably do not occur in Yucca Flat or anywhere else north of the Control Point. A map of the northern boundary of the range of desert tortoises on NTS is presented and additional studies of the distribution and abundance of tortoises on NTS are recommended. 30 refs., 9 figs., 4 tabs.

  20. Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida.

    PubMed

    D'Antonio, Nicole L; Gilliam, David S; Walker, Brian K

    2016-01-01

    Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km(2)) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and A. cervicornis abundance using high resolution bathymetric data. Acropora cervicornis was distributed throughout the study area, and the Getis-Ord Gi* statistic and Anselin Local Moran's I spatial cluster analysis showed significant clustering along topographic features termed ridge crests. Significant clustering was further supported by the inverse distance weighted surface model. Ordinal logistic regression indicated 1) as distance from a ridge increases, odds of reduced A. cervicornis abundance increases; 2) as topographic elevation increases, odds of increased abundance increases; and 3) as mean depth increases, odds of increased abundance increases. This study provides detailed information on A. cervicornis distribution and abundance at a regional scale and supports modeling its distributions in similar habitats elsewhere throughout the western Atlantic and Caribbean. Acropora cervicornis is frequently observed and in areas an abundant species within the nearshore habitat along the SE FL portion of the Florida Reef Tract (FRT). This study provides a better understanding of local habitat associations thus facilitating appropriate management of the nearshore environment and species conservation. The portion of the FRT between Hillsboro and Port Everglades inlets should be

  1. Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida

    PubMed Central

    Gilliam, David S.; Walker, Brian K.

    2016-01-01

    Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km2) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and A. cervicornis abundance using high resolution bathymetric data. Acropora cervicornis was distributed throughout the study area, and the Getis-Ord Gi* statistic and Anselin Local Moran’s I spatial cluster analysis showed significant clustering along topographic features termed ridge crests. Significant clustering was further supported by the inverse distance weighted surface model. Ordinal logistic regression indicated 1) as distance from a ridge increases, odds of reduced A. cervicornis abundance increases; 2) as topographic elevation increases, odds of increased abundance increases; and 3) as mean depth increases, odds of increased abundance increases. This study provides detailed information on A. cervicornis distribution and abundance at a regional scale and supports modeling its distributions in similar habitats elsewhere throughout the western Atlantic and Caribbean. Acropora cervicornis is frequently observed and in areas an abundant species within the nearshore habitat along the SE FL portion of the Florida Reef Tract (FRT). This study provides a better understanding of local habitat associations thus facilitating appropriate management of the nearshore environment and species conservation. The portion of the FRT between Hillsboro and Port Everglades inlets should be

  2. Abundance and Diversity of Soil Arthropods in the Olive Grove Ecosystem

    PubMed Central

    Gonçalves, Maria Fátima; Pereira, José Alberto

    2012-01-01

    Arthropods are part of important functional groups in soil food webs. Recognizing these arthropods and understanding their function in the ecosystem as well as when they are active is essential to understanding their roles. In the present work, the abundance and diversity of soil arthropods is examined in olive groves in the northeast region of Portugal during the spring. Five classes of arthropods were found: Chilopoda, Malacostraca, Entognatha, Insecta, and Arachnida. Captures were numerically dominated by Collembola within Entognatha, representing 70.9% of total captures. Arachnida and Insecta classes represented about 20.4 and 9.0%, respectively. Among the predatory arthropods, the most representative groups were Araneae and Opiliones from Arachnida, and Formicidae, Carabidae, and Staphylinidae from Insecta. From the Formicidae family, Tetramorium semilaeve (Andre 1883), Tapinoma nigerrimum (Nylander 1856), and Crematogaster scutellaris (Olivier 1792) were the most representative ant species. Arthropods demonstrated preference during the day, with 74% of the total individuals recovered in this period, although richness and similarity were analogous during the day and night. PMID:22943295

  3. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential.

    PubMed

    Becerril-Espinosa, Amayaly; Freel, Kelle C; Jensen, Paul R; Soria-Mercado, Irma E

    2013-04-01

    The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1-38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26-56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98-100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites.

  4. Diversity and abundance of bacteria in an underground oil-storage cavity

    PubMed Central

    Watanabe, Kazuya; Kodama, Yumiko; Kaku, Nobuo

    2002-01-01

    Background Microorganisms inhabiting subterranean oil fields have recently attracted much attention. Since intact groundwater can easily be obtained from the bottom of underground oil-storage cavities without contamination by surface water, studies on such oil-storage cavities are expected to provide valuable information to understand microbial ecology of subterranean oil fields. Results DNA was extracted from the groundwater obtained from an oil-storage cavity situated at Kuji in Iwate, Japan, and 16S rRNA gene (16S rDNA) fragments were amplified by PCR using combinations of universal and Bacteria-specific primers. The sequence analysis of 154 clones produced 31 different bacterial sequence types (a unique clone or group of clones with sequence similarity of > 98). Major sequence types were related to Desulfotomaculum, Acetobacterium, Desulfovibrio, Desulfobacula, Zoogloea and Thiomicrospira denitrificans. The abundance in the groundwater of bacterial populations represented by these major sequence types was assessed by quantitative competitive PCR using specific primers, showing that five rDNA types except for that related to Desulfobacula shared significant proportions (more than 1%) of the total bacterial rDNA. Conclusions Bacteria inhabiting the oil-storage cavity were unexpectedly diverse. A phylogenetic affiliation of cloned 16S rDNA sequences suggests that bacteria exhibiting different types of energy metabolism coexist in the cavity. PMID:12197947

  5. Primary succession changes diversity, abundance and function of soil microorganisms across glacier forelands

    NASA Astrophysics Data System (ADS)

    Kandeler, Ellen; Philippot, Laurent; Tscherko, Dagmar

    2010-05-01

    Primary successional ecosystems, such as glacier forelands, present an ideal opportunity to study the biological colonization of substrates. In a glacier foreland, time is substituted by space by using the distance from the retreating glacier as a proxy for soil age. Since the ice covers of many glaciers have receded over the past century, glacier forelands have released substrates for soil development. Autotrophic colonizers are expected to be important in the initial stages of the primary community assembly. Microbial growth, however, might also come from allochthonous dead organic matter and living invertebrates in these newly formed environments. Recently, a previously unrecognized heterotrophic phase which should allow the initial establishment of functional communities was proposed. Current studies in microbial ecology account for both autotrophic and heterotrophic colonization along primary successional gradients, such as glacier forelands, land lifts, floodplains, landslides and volcanoes. The presentation will give a summary of studies focusing on abundance, diversity and function of soil microorganisms along selected successional stages within the forelands of two glaciers in the Austrian Alps.

  6. Abundance and diversity of soil arthropods in the olive grove ecosystem.

    PubMed

    Gonçalves, Maria Fátima; Pereira, José Alberto

    2012-01-01

    Arthropods are part of important functional groups in soil food webs. Recognizing these arthropods and understanding their function in the ecosystem as well as when they are active is essential to understanding their roles. In the present work, the abundance and diversity of soil arthropods is examined in olive groves in the northeast region of Portugal during the spring. Five classes of arthropods were found: Chilopoda, Malacostraca, Entognatha, Insecta, and Arachnida. Captures were numerically dominated by Collembola within Entognatha, representing 70.9% of total captures. Arachnida and Insecta classes represented about 20.4 and 9.0%, respectively. Among the predatory arthropods, the most representative groups were Araneae and Opiliones from Arachnida, and Formicidae, Carabidae, and Staphylinidae from Insecta. From the Formicidae family, Tetramorium semilaeve (Andre 1883), Tapinoma nigerrimum (Nylander 1856), and Crematogaster scutellaris (Olivier 1792) were the most representative ant species. Arthropods demonstrated preference during the day, with 74% of the total individuals recovered in this period, although richness and similarity were analogous during the day and night.

  7. High fungal diversity and abundance recovered in the deep-sea sediments of the Pacific Ocean.

    PubMed

    Xu, Wei; Pang, Ka-Lai; Luo, Zhu-Hua

    2014-11-01

    Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10(6) to 5.23 × 10(7)copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.

  8. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential

    PubMed Central

    Becerril-Espinosa, Amayaly; Freel, Kelle C.; Jensen, Paul R.

    2015-01-01

    The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1–38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26–56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98–100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites. PMID:23229438

  9. Abundance, diversity and antibiotics resistance pattern of Vibrio spp. in coral ecosystem of Kurusadai island.

    PubMed

    Haldar, Soumya; Mody, Kalpana H; Jha, Bhavanath

    2011-04-01

    The abundance and species diversity of Vibrio associated with coral reef ecosystem of Kurusadai island, Tamil Nadu, India were evaluated. A total of twelve sampling locations including different live and dead coral surfaces, surrounding water and rock surface (negative control) were selected for the present study. Total viable and TCBS counts were found to be higher in dead coral as compared to that of live coral. Out of total 21 species of Vibrio isolated, 13 were identified up to species level based on biochemical tests and 16S rRNA gene sequence homology, while remaining 8 isolates did not show homology up to species level with any of the sequences available in the NCBI database. Moreover, these unidentified Vibrio spp. exhibited intra-species variation. This study indicated association of hitherto unknown Vibrio species with coral reef ecosystem of Kurusadai island. Assuming that only resistant bacteria can grow in the coral environment, susceptibility against a total of 20 antibiotics was evaluated. All the isolates exhibited resistance towards more than 6 antibiotics. Interestingly, none of the identified bacteria were previously reported to be of coral pathogen reflecting the healthy nature of the ecosystem. However, a continuous monitoring of the region will be prerequisite to envisage the role of these bacteria on the health status of the coral ecosystem.

  10. Modeled distribution and abundance of a pelagic seabird reveal trends in relation to fisheries

    USGS Publications Warehouse

    Renner, Martin; Parrish, Julia K.; Piatt, John F.; Kuletz, Kathy J.; Edwards, Ann E.; Hunt, George L.

    2013-01-01

    The northern fulmar Fulmarus glacialis is one of the most visible and widespread seabirds in the eastern Bering Sea and Aleutian Islands. However, relatively little is known about its abundance, trends, or the factors that shape its distribution. We used a long-term pelagic dataset to model changes in fulmar at-sea distribution and abundance since the mid-1970s. We used an ensemble model, based on a weighted average of generalized additive model (GAM), multivariate adaptive regression splines (MARS), and random forest models to estimate the pelagic distribution and density of fulmars in the waters of the Aleutian Archipelago and Bering Sea. The most important predictor variables were colony effect, sea surface temperature, distribution of fisheries, location, and primary productivity. We calculated a time series from the ratio of observed to predicted values and found that fulmar at-sea abundance declined from the 1970s to the 2000s at a rate of 0.83% (± 0.39% SE) per annum. Interpolating fulmar densities on a spatial grid through time, we found that the center of fulmar distribution in the Bering Sea has shifted north, coinciding with a northward shift in fish catches and a warming ocean. Our study shows that fisheries are an important, but not the only factor, shaping fulmar distribution and abundance trends in the eastern Bering Sea and Aleutian Islands.

  11. Distribution and abundance of fish larvae in the northern Ionian Sea (Eastern Mediterranean)

    NASA Astrophysics Data System (ADS)

    Granata, Antonia; Cubeta, Annaluce; Minutoli, Roberta; Bergamasco, Alessandro; Guglielmo, Letterio

    2011-09-01

    The purpose of this paper was to study the spatial distribution, abundance and composition of fish larvae in the northern Ionian Sea. Samples were collected to the 600 m depth with an electronic multinet BIONESS during the "INTERREG Italia-Grecia" oceanographic cruise carried out in March 2000 off the Apulian Italian coast. A total of 46 species of teleost early stages were collected, belonging to 38 genera and 22 families. Over 52% of the larvae identified were mesopelagic species, almost 27% were demersal and about 21% pelagic. A total of 307 myctophids, 69 clupeids and 61 gadid post-larvae dominated the community. Benthosema glaciale (mean 6.1 mm SL) was the most abundant species (21.6%), the most frequent in the samples (28.8%), and dominant in the whole study area (mean 1.4 ind/100 m3). Particular attention was given to the horizontal and vertical distribution and abundance of the three dominant post-larval species: Benthosema glaciale, Sprattus sprattus sprattus and Notoscopelus elongatus. The Pearson coefficient ( R = 0.734) showed a high correlation between total zooplankton and fish larval assemblages in terms of spatial distribution abundance values. Regarding the vertical distribution of fish larvae, Sorensen's index ( S = 0.69) showed that fish larvae and total zooplankton abundance peaks co-occurred along the water column.

  12. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  13. Diversity and Abundance of Ammonia-Oxidizing Archaea in Hydrothermal Vent Chimneys of the Juan de Fuca Ridge▿ †

    PubMed Central

    Wang, Shufang; Xiao, Xiang; Jiang, Lijing; Peng, Xiaotong; Zhou, Huaiyang; Meng, Jun; Wang, Fengping

    2009-01-01

    The abundance and diversity of archaeal ammonia monooxygenase subunit A (amoA) genes from hydrothermal vent chimneys at the Juan de Fuca Ridge were investigated. The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments. PMID:19395559

  14. Effects of transgenic cry1Ie maize on non-lepidopteran pest abundance, diversity and community composition.

    PubMed

    Guo, Jingfei; He, Kanglai; Bai, Shuxiong; Zhang, Tiantao; Liu, Yunjun; Wang, Fuxin; Wang, Zhenying

    2016-12-01

    Non-lepidopteran pests are exposed to, and may be influenced by, Bt toxins when feeding on Bt maize that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt). In order to assess the potential effects of transgenic cry1Ie maize on non-lepidopteran pest species and ecological communities, a 2-year field study was conducted to compare the non-lepidopteran pest abundance, diversity and community composition between transgenic cry1Ie maize (Event IE09S034, Bt maize) and its near isoline (Zong 31, non-Bt maize) by whole plant inspections. Results showed that Bt maize had no effects on non-lepidopteran pest abundance and diversity (Shannon-Wiener diversity index, Simpson's diversity index, species richness, and Pielou's index). There was a significant effect of year and sampling time on those indices analyzed. Redundancy analysis indicated maize type, sampling time and year totally explained 20.43 % of the variance in the non-lepidopteran pest community composition, but no association was presented between maize type (Bt maize and non-Bt maize) and the variance. Nonmetric multidimensional scaling analysis showed that sampling time and year, rather than maize type had close relationship with the non-lepidopteran pest community composition. These results corroborated the hypothesis that, at least in the short-term, the transgenic cry1Ie maize had negligible effects on the non-lepidopteran pest abundance, diversity and community composition.

  15. Mosquito species diversity and abundance in relation to land use in a riceland agroecosystem in Mwea, Kenya.

    PubMed

    Muturi, Ephantus J; Shililu, Josephat; Jacob, Benjamin; Gu, Weidong; Githure, John; Novak, Robert

    2006-06-01

    We conducted an entomological survey to determine the mosquito species diversity and abundance in relation to land use in the Mwea rice scheme, Kenya. Adult mosquitoes were collected by indoor spraying of houses and outdoors by CDC light traps in three villages representing planned (Mbuinjeru) and unplanned (Kiamachiri) rice agroecosystems and a non-irrigated agroecosystem (Murinduko). During the 12-month sampling period, a total of 98,708 mosquitoes belonging to five genera and 25 species were collected. The five most common species collected during this study were Anopheles arabiensis Patton (52.5%), Culex quinquefasciatus Say (36.7%), Anopheles pharoensis Theobald (5.2%), Anopheles coustani Laveran (1.4%), and Anopheles funestus Giles (1.3%). Anopheles arabiensis, Cx quinquefasciatus, and An. pharoensis were more abundant in rice agroecosystems than in the non-irrigated agroecosystem, and in planned than in the unplanned rice agroecosystems. In contrast, An. funestus was more abundant in the non-irrigated agroecosystem. The mosquito species diversity (H) and evenness (E(H)) in the non-irrigated agroecosystem (Shannon diversity Index, H = 1.507, EH = 0.503) was significantly higher than in the rice agroecosystems (H) = 0.968, E(H) = 0.313, unplanned; and H= 1.040, E(H) = 0.367 planned). Results of lag cross correlation analysis revealed a strong relationship between rainfall and the abundance of An. arabiensis, and C. quinquefasciatus in the non-irrigated agroecosystem but not in the rice agroecosystems. It is inferred from the data that different levels of habitat perturbations with regard to rice cultivation have different effects on mosquito diversity and abundance. This provides an understanding of how mosquito diversity is impacted by different habitat management and rice cropping strategies.

  16. Pelagic nekton abundance and distribution in the northern Sacramento–San Joaquin Delta, California

    USGS Publications Warehouse

    Feyrer, Frederick; Slater, Steven B.; Portz, Donald E.; Odom, Darren; Morgan-King, Tara L.; Brown, Larry R.

    2017-01-01

    Knowledge of the habitats occupied by species is fundamental for the development of effective conservation and management actions. The collapse of pelagic fish species in the Sacramento–San Joaquin Delta, California, has triggered a need to better understand factors that drive their distribution and abundance. A study was conducted in summer–fall 2014 in an attempt to identify physical and biological habitat conditions that drive the abundance and distribution of pelagic species in the northern region of the system. The study was conducted in the three largest channels in the northern Sacramento–San Joaquin Delta by dimension, volume, and flow capacity. The pelagic community was dominated by three nonnative species, Siberian prawn Exopalaemon modestus, which comprised 56% of the total number of organisms, and two fish species, Threadfin Shad Dorosoma petenense and Mississippi Silversides Menidia audens, which together comprised 43% of the total number of organisms. Total fish and total shrimp abundance were sensitive to the most extreme values of turbidity and temperature encountered and positively associated with total zooplankton biomass. The results suggested that habitat conditions in terminal channels, historically a common feature on the landscape, support higher abundances of pelagic species and zooplankton than open-ended channels. These results provide resource managers with useful information on the habitat associations of pelagic species and on how the future distribution and abundance of pelagic species will likely change in response to climate or other ecological factors.

  17. [Diversity and distribution of crustaceans and echinoderms and their relation with sedimentation levels in coral reefs].

    PubMed

    Vázquez-Domínguez, Ella

    2003-03-01

    Seven reef formations were studied in South Caicos, Turks & Caicos, to determine the species richness, patterns of diversity and patterns of distribution of crustaceans and echinoderms, and to evaluate the relationship between these parameters and the degree of sedimentation of the different sites. The reefs showed a gradient from a high sedimentation level, almost totally covered by algae, to places with no sediment particles deposited over the corals. Sites were classified as with high, low or null sedimentation, and species richness, abundance, diversity, spatial distribution of species and similarity among sites were estimated. No unique pattern was found: for crustaceans as well as for echinoderms, the site with the highest diversity value and high equitability, presumably associated to the environmental heterogeneity of this reef formation, showed null sedimentation and an uniform and random pattern of distribution, crustaceans and echinoderms respectively. The two sites with the lowest diversity for both animal groups, although with different sedimentation levels, showed the lowest equitability value and were the only sites with an aggregated pattern of distribution. The next sites in diversity for crustaceans were those with high sedimentation, probably because most species present inhabit empty conchs, in the sediment, or among seagrass. For the echinoderms, on the contrary, the intermediate sites in diversity had low sedimentation; the habitat requirements for these species (inside sponges, over the corals or among rocks) may have determined this result. The sites with lowest diversity had high sedimentation levels. In these, crustaceans showed the lowest equitability values and an aggregated spatial distribution, while the community of echinoderms was dominated by one single species. Although only general descriptions can be elucidated with the present results, knowledge about the basic population characteristics and natural history of these reef

  18. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  19. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    NASA Astrophysics Data System (ADS)

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-12-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m‑3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]‑1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5.

  20. Diversity, abundance and activity of ammonia-oxidizing microorganisms in fine particulate matter

    PubMed Central

    Gao, Jing-Feng; Fan, Xiao-Yan; Pan, Kai-Ling; Li, Hong-Yu; Sun, Li-Xin

    2016-01-01

    Increasing ammonia emissions could exacerbate air pollution caused by fine particulate matter (PM2.5). Therefore, it is of great importance to investigate ammonia oxidation in PM2.5. This study investigated the diversity, abundance and activity of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB) and complete ammonia oxidizers (Comammox) in PM2.5 collected in Beijing-Tianjin-Hebei megalopolis, China. Nitrosopumilus subcluster 5.2 was the most dominant AOA. Nitrosospira multiformis and Nitrosomonas aestuarii were the most dominant AOB. Comammox were present in the atmosphere, as revealed by the occurrence of Candidatus Nitrospira inopinata in PM2.5. The average cell numbers of AOA, AOB and Ca. N. inopinata were 2.82 × 104, 4.65 × 103 and 1.15 × 103 cell m−3 air, respectively. The average maximum nitrification rate of PM2.5 was 0.14 μg (NH4+-N) [m3 air·h]−1. AOA might account for most of the ammonia oxidation, followed by Comammox, while AOB were responsible for a small part of ammonia oxidation. Statistical analyses showed that Nitrososphaera subcluster 4.1 was positively correlated with organic carbon concentration, and Nitrosomonas eutropha showed positive correlation with ammonia concentration. Overall, this study expanded our knowledge concerning AOA, AOB and Comammox in PM2.5 and pointed towards an important role of AOA and Comammox in ammonia oxidation in PM2.5. PMID:27941955

  1. Diversity and abundance of deep-sea Isopoda along the Southern Polar Front: Results from the SYSTCO I and II expeditions

    NASA Astrophysics Data System (ADS)

    Meyer-Löbbecke, A.; Brandt, A.; Brix, S.

    2014-10-01

    For the investigation of the diversity and composition of deep-sea Isopoda in the Polar Front of the Southern Ocean two expeditions were performed, ANtartic benthic DEEP-sea biodiversity: colonization history and recent community patterns-SYSTem COupling (ANDEEP-SYSTCO I, 2007/2008) and SYSTCO II (2012). Samples were taken in the Atlantic sector of the Southern Polar Front (52°S) within a depth range between 2752 and 4327 m using an epibenthic sledge. From nine stations, located in four different geographic areas, a total of 107 species from 476 specimens were identified, 99% belonged to the suborder Asellota. Haploniscidae was the most dominant family in terms of abundance, followed by Munnopsidae and Desmosomatidae. However, Munnopsidae were the most diverse followed by Desmosomatidae and Haploniscidae. The majority of species (53%) did not occur frequently indicating a patchy distribution; only one species, Haploniscus spinifer Hansen, 1916, was found at almost all stations comprising more than 10% of all sampled specimens. Isopod abundance was generally low in the Polar Front compared to other regions of the Southern Ocean, like the Weddell Sea. Diversity strongly varied between stations even within the same sampling area, it was highest around a depth of 3000 m with 48 species found at station 13-16 at 0°E. Surface chl a concentration, received from satellite images as a measure for food supply, was compared with isopod abundance and diversity, however, no clear pattern could be observed. Analysis of the species composition of Isopoda revealed in general terms that deep-sea stations within the same depth range build one cluster. Also the sampling year, the geographic area or salinity turned out to be possible factors affecting species composition. The deep-sea area along the Southern Polar Front is characterized by low numbers of specimens but shelters a relatively high level of isopod diversity with species also known from other regions of the Atlantic.

  2. Environmental correlates of species rank – abundance distributions in global drylands

    PubMed Central

    Ulrich, Werner; Soliveres, Santiago; Thomas, Andrew D.; Dougill, Andrew J.; Maestre, Fernando T.

    2016-01-01

    Theoretical models predict lognormal species abundance distributions (SADs) in stable and productive environments, with log-series SADs in less stable, dispersal driven communities. We studied patterns of relative species abundances of perennial vascular plants in global dryland communities to: i) assess the influence of climatic and soil characteristics on the observed SADs, ii) infer how environmental variability influences relative abundances, and iii) evaluate how colonisation dynamics and environmental filters shape abundance distributions. We fitted lognormal and log-series SADs to 91 sites containing at least 15 species of perennial vascular plants. The dependence of species relative abundances on soil and climate variables was assessed using general linear models. Irrespective of habitat type and latitude, the majority of the SADs (70.3%) were best described by a lognormal distribution. Lognormal SADs were associated with low annual precipitation, higher aridity, high soil carbon content, and higher variability of climate variables and soil nitrate. Our results do not corroborate models predicting the prevalence of log-series SADs in dryland communities. As lognormal SADs were particularly associated with sites with drier conditions and a higher environmental variability, we reject models linking lognormality to environmental stability and high productivity conditions. Instead our results point to the prevalence of lognormal SADs in heterogeneous environments, allowing for more evenly distributed plant communities, or in stressful ecosystems, which are generally shaped by strong habitat filters and limited colonisation. This suggests that drylands may be resilient to environmental changes because the many species with intermediate relative abundances could take over ecosystem functioning if the environment becomes suboptimal for dominant species. PMID:27330404

  3. EMBATTLED BIVALVES: BIOGEOGRAPHIC DISTRIBUTIONS AND ABUNDANCES FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

    EPA Science Inventory

    As part of an EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change, we have synthesized in a web-based tool, the Coastal Biogeographic Risk Analysis Tool (CBRAT), the biogeographic distributions and abundances of bivalves, found in dept...

  4. Factors determining the distribution and abundance of Dreissena polymorpha in lakes, dam reserviors and channels

    SciTech Connect

    Karatayev, A.

    1995-06-01

    This article addresses the several factors affecting the distribution and abundance of Dreissena polymorphia in bodies of water. Factors covered include: (1) salinity, (2) oxygen level, (3) temperature, (4) substrate, (5) depth, and (6) water chemistry. The analysis of the data allowed the specification of limiting or optimal concentrations of the principle abiotic parameters.

  5. BIVALVE BIOGEOGRAPHIC DISTRIBUTIONS, ABUNDANCES, AND CLIMATE VULNERABILITY FROM THE BEAUFORT SEA TO THE GULF OF CALIFORNIA

    EPA Science Inventory

    As part of an U.S. EPA/USGS project to predict the relative vulnerability of near-coastal species to climate change along the Pacific Coast, we have synthesized the biogeographic distributions and abundances of bivalves found in depths <200 m. We have included the twelve &ldqu...

  6. A determination of the thick disk chemical abundance distribution: Implications for galaxy evolution

    NASA Technical Reports Server (NTRS)

    Gilmore, Gerard; Wyse, Rosemary F. G.; Jones, Bryn J.

    1995-01-01

    We present a determination of the thick disk iron abundance distribution obtained from an in situ sample of F/G stars. These stars are faint, 15 less than or approximately = V less than or approximately = 18, selected on the basis of color, being a subset of the larger survey of Gilmore and Wyse designed to determine the properties of the stellar populations several kiloparsecs from the Sun. The fields studied in the present paper probe the iron abundance distribution of the stellar populations of the galaxy at 500-3000 pc above the plane, at the solar Galactocentric distance. The derived chemical abundance distributions are consistent with no metallicity gradients in the thick disk over this range of vertical distance, and with an iron abundance distribution for the thick disk that has a peak at -0.7 dex. The lack of a vertical gradient argues against slow, dissipational settling as a mechanism for the formation of the thick disk. The photometric and metallicity data support a turn-off of the thick disk that is comparable in age to the metal-rich globular clusters, or greater than or approximately = 12 Gyr, and are consistent with a spread to older ages.

  7. Critical metals in manganese nodules from the Cook Islands EEZ, abundances and distributions

    USGS Publications Warehouse

    Hein, James R.; Spinardi, Francesca; Okamoto, Nobuyuki; Mizell, Kira; Thorburn, Darryl; Tawake, Akuila

    2015-01-01

    Compiled data from a series of four cruises by the Japan International Cooperation Agency and the Mining agency of Japan from 1985 to 2000 were used to generate a map that defines the statistical distribution of nodule abundance throughout the EEZ, except the Manihiki Plateau. The abundance distribution map shows a belt of high nodule abundance (19–45 kg/m2) that starts in the southeast corner of the EEZ, runs northwest, and also bifurcates into a SW trending branch. Small, isolated areas contain abundances of nodules of up to 58 kg/m2. Six ~ 20,000 km2 areas of particularly high abundance were chosen to represent potential exploration areas, and maps for metal concentration were generated to visualize metal distribution and to extrapolate estimated metal tonnages within the six sites and the EEZ as a whole. Grades for Mn, Cu, and Ni are low in CIs nodules in areas of high abundance; however, Ti, Co, and REY show high contents where nodule abundances are high. Of the six areas identified to represent a range of metal contents, one at the northern end of the N-S abundance main belt optimizes the most metals and would yield the highest dry metric tons for Mn (61,002,292), Ni (1,247,834), Mo (186,166), V (356,247), W (30,215), and Zr (195,323). When compared with the Clarion–Clipperton Zone, the CIs nodules show higher nodule abundances (> 25 kg/m2 over ~ 123,844 km2), and are more enriched in the green-tech, high-tech, and energy metals Co, Ti, Te, Nb, REY, Pt, and Zr. The CIs EEZ shows a significant resource potential for these critical metals due to their high prices, high demand, and the high nodule abundance, which will allow for a smaller footprint for a 20-year mine site and therefore smaller environmental impact.

  8. Insights into global diatom distribution and diversity in the world’s ocean

    PubMed Central

    Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

    2016-01-01

    Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron. We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered. PMID:26929361

  9. Insights into global diatom distribution and diversity in the world's ocean.

    PubMed

    Malviya, Shruti; Scalco, Eleonora; Audic, Stéphane; Vincent, Flora; Veluchamy, Alaguraj; Poulain, Julie; Wincker, Patrick; Iudicone, Daniele; de Vargas, Colomban; Bittner, Lucie; Zingone, Adriana; Bowler, Chris

    2016-03-15

    Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically important groups of phytoplankton. They are considered to be particularly important in nutrient-rich coastal ecosystems and at high latitudes, but considerably less so in the oligotrophic open ocean. The Tara Oceans circumnavigation collected samples from a wide range of oceanic regions using a standardized sampling procedure. Here, a total of ∼12 million diatom V9-18S ribosomal DNA (rDNA) ribotypes, derived from 293 size-fractionated plankton communities collected at 46 sampling sites across the global ocean euphotic zone, have been analyzed to explore diatom global diversity and community composition. We provide a new estimate of diversity of marine planktonic diatoms at 4,748 operational taxonomic units (OTUs). Based on the total assigned ribotypes, Chaetoceros was the most abundant and diverse genus, followed by Fragilariopsis, Thalassiosira, and Corethron We found only a few cosmopolitan ribotypes displaying an even distribution across stations and high abundance, many of which could not be assigned with confidence to any known genus. Three distinct communities from South Pacific, Mediterranean, and Southern Ocean waters were identified that share a substantial percentage of ribotypes within them. Sudden drops in diversity were observed at Cape Agulhas, which separates the Indian and Atlantic Oceans, and across the Drake Passage between the Atlantic and Southern Oceans, indicating the importance of these ocean circulation choke points in constraining diatom distribution and diversity. We also observed high diatom diversity in the open ocean, suggesting that diatoms may be more relevant in these oceanic systems than generally considered.

  10. The distribution and diversity of benthic macroinvertebrate fauna in Pondicherry mangroves, India

    PubMed Central

    2013-01-01

    Background Species distribution, abundance and diversity of mangrove benthic macroinvertebrate fauna and the relationships to environmental conditions are important parts of understanding the structure and function of mangrove ecosystems. In this study seasonal variation in the distribution of macrobenthos and related environmental parameters were explored at four mangrove stations along the Pondicherry coast of India, from September 2008 to July 2010. Multivariate statistical analyses, including cluster analysis, principal component analysis and non-multidimensional scales plot were employed to help define trophic status, water quality and benthic characteristic at the four monitoring stations. Results Among the 528 samples collected over 168 ha of mangrove forest 76 species of benthic macroinvertebrate fauna were identified. Macrofauna were mainly composed of deposit feeders, dominated numerically by molluscs and crustaceans. Statistical analyses yielded the following descriptors of benthic macroinvertebrate fauna species distribution: densities between 140–1113 ind. m-2, dominance 0.17-0.50, diversity 1.80-2.83 bits ind-1, richness 0.47-0.74 and evenness 0.45-0.72, equitability 0.38-0.77, berger parker 0.31-0.77 and fisher alpha 2.46-5.70. Increases of species diversity and abundance were recorded during the post monsoon season at station 1 and the lowest diversity was recorded at station 2 during the monsoon season. The pollution indicator organisms Cassidula nucleus, Melampus ceylonicus, Sphaerassiminea minuta were found only at the two most polluted regions, i.e. stations 3 and 4. Benthic macroinvertebrate fauna abundances were inversely related to salinity at the four stations, Based on Bray-Curtis similarity through hierarchical clustering implemented in PAST, it was possible to define three distinct benthic assemblages at the stations. Conclusions From a different multivariate statistical analysis of the different environmental parameters regarding

  11. Does interference competition with wolves limit the distribution and abundance of coyotes?

    PubMed

    Berger, Kim Murray; Gese, Eric M

    2007-11-01

    Interference competition with wolves Canis lupus is hypothesized to limit the distribution and abundance of coyotes Canis latrans, and the extirpation of wolves is often invoked to explain the expansion in coyote range throughout much of North America. We used spatial, seasonal and temporal heterogeneity in wolf distribution and abundance to test the hypothesis that interference competition with wolves limits the distribution and abundance of coyotes. From August 2001 to August 2004, we gathered data on cause-specific mortality and survival rates of coyotes captured at wolf-free and wolf-abundant sites in Grand Teton National Park (GTNP), Wyoming, USA, to determine whether mortality due to wolves is sufficient to reduce coyote densities. We examined whether spatial segregation limits the local distribution of coyotes by evaluating home-range overlap between resident coyotes and wolves, and by contrasting dispersal rates of transient coyotes captured in wolf-free and wolf-abundant areas. Finally, we analysed data on population densities of both species at three study areas across the Greater Yellowstone Ecosystem (GYE) to determine whether an inverse relationship exists between coyote and wolf densities. Although coyotes were the numerically dominant predator, across the GYE, densities varied spatially and temporally in accordance with wolf abundance. Mean coyote densities were 33% lower at wolf-abundant sites in GTNP, and densities declined 39% in Yellowstone National Park following wolf reintroduction. A strong negative relationship between coyote and wolf densities (beta = -3.988, P < 0.005, r(2) = 0.54, n = 16), both within and across study sites, supports the hypothesis that competition with wolves limits coyote populations. Overall mortality of coyotes resulting from wolf predation was low, but wolves were responsible for 56% of transient coyote deaths (n = 5). In addition, dispersal rates of transient coyotes captured at wolf-abundant sites were 117% higher

  12. Distribution and abundance of saltcedar and Russian olive in the western United States

    USGS Publications Warehouse

    Nagler, Pamela L.; Glenn, Edward P.; Jarnevich, Catherine S.; Shafroth, Patrick B.

    2011-01-01

    Over the past century, two introduced Eurasian trees, saltcedar (Tamarix spp.) and Russian olive (Elaeagnus angustifolia) have become wide spread on western United States of American (U.S.) rivers. This paper reviews the literature on the following five key areas related to their distribution and abundance in the western United States: (1) the history of introduction, planting, and spread of saltcedar and Russian olive; (2) their current distribution; (3) their current abundance; (4) factors controlling their current distribution and abundance; and (5) models that have been developed to predict their future distribution and abundance. Saltcedar and Russian olive are now the third and fourth most frequently occurring woody riparian plants and the second and fifth most abundant species (out of 42 native and non-native species) along rivers in the western United States. Currently there is not a precise estimate of the areas that these species occupy in the entire West. Climatic variables are important determinants of their distribution and abundance. For example, saltcedar is limited by its sensitivity to hard freezes, whereas Russian olive appears to have a chilling requirement for bud break and seed germination, and can presumably survive colder winter temperatures. Either species can be dominant, co-dominant or sub-dominant relative to native species on a given river system. A number of environmental factors such as water availability, soil salinity, degree of stream flow regulation, and fire frequency can influence the abundance of these species relative to native species. Numerous studies suggest that both species have spread on western rivers primarily through a replacement process, whereby stress-tolerant species have moved into expanded niches that are no longer suitable for mesic native pioneer species. Better maps of current distribution and rigorous monitoring of distributional changes though time can help to resolve differences in predictions of potential

  13. Bacterial diversity and distribution in the holocene sediments of a northern temperate lake.

    PubMed

    Nelson, David M; Ohene-Adjei, Samuel; Hu, Feng Sheng; Cann, Isaac K O; Mackie, Roderick I

    2007-08-01

    Sediments contain an abundance of microorganisms. However, the diversity and distribution of microorganisms associated with sediments are poorly understood, particularly in lacustrine environments. We used banding patterns from denaturing gradient gel electrophoresis (DGGE) and 16S rDNA sequences to assess the structure of bacterial communities in the Holocene sediments of a meromictic lake in Minnesota. Cluster analysis of the DGGE banding patterns indicates that the early- and middle-Holocene samples group separately from the late-Holocene samples. About 79% of the recovered bacterial sequences cluster with the alpha-, beta-, delta-, epsilon-, and gamma- Proteobacteriaceae and Firmicutes. The remaining approximately 21% lack cultured representatives. The taxonomic lineages of bacteria differ statistically among the early-, middle-, and late-Holocene samples, although the difference is smallest between early- and middle-Holocene samples. Early- and middle-Holocene samples are dominated by epsilon-Proteobacteriaceae, and late-Holocene samples are dominated by sequences from uncultured subphyla. We only recovered delta-Proteobacteriaceae in late-Holocene sediments and alpha- and gamma- Proteobacteriaceae in late- and middle-Holocene sediments. Diversity estimates derived from early-, middle-, and late-Holocene clone libraries indicate that the youngest (late-Holocene) samples had significantly greater bacterial diversity than the oldest (early-Holocene) samples, and the middle-Holocene samples contained intermediate levels of diversity. The observed patterns of diversity may be caused by increased bacterial niche-partitioning in younger sediments that contain a greater abundance of labile organic matter than older sediments.

  14. DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms

    PubMed Central

    Feng, Bang; Xu, Jianping; Wu, Gang; Zeng, Nian-Kai; Li, Yan-Chun; Tolgor, Bau; Kost, Gerhard W.; Yang, Zhu L.

    2012-01-01

    The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions. PMID:22629418

  15. Spatio-temporal variations in the diversity and abundance of commercially important Decapoda and Stomatopoda in subtropical Hong Kong waters

    NASA Astrophysics Data System (ADS)

    Lui, Karen K. Y.; Ng, Jasmine S. S.; Leung, Kenneth M. Y.

    2007-05-01

    In subtropical Hong Kong, western waters (WW) are strongly influenced by the freshwater input from the Pearl River estuary, especially during summer monsoon, whereas eastern waters (EW) are predominantly influenced by oceanic currents throughout the year. Such hydrographical differences may lead to spatio-temporal differences in biodiversity of benthic communities. This study investigated the diversity and abundance of commercially important decapods and stomatopods in EW (i.e. Tolo Harbour and Channel) and WW (i.e. Tuen Mun and Lantau Island) of Hong Kong using monthly trawl surveys (August 2003-May 2005). In total, 22 decapod and nine stomatopod species were recorded. The penaeid Metapenaeopsis sp. and stomatopod Oratosquillina interrupta were the most abundant and dominant crustaceans in EW and WW, respectively. Both univariate and multivariate analyses showed that WW supported significantly higher abundance, biomass and diversity of crustaceans than EW, although there were significant between-site and within-site variations in community structure. Higher abundance and biomass of crustaceans were recorded in summer than winter. Such spatio-temporal variations could be explained by differences in the hydrography, environmental conditions and anthropogenic impacts between the two areas. Temporal patterns in the abundance-biomass comparison curves and negative W-statistics suggest that the communities have been highly disturbed in both areas, probably due to anthropogenic activities such as bottom trawling and marine pollution.

  16. Megafaunal communities in rapidly warming fjords along the West Antarctic Peninsula: hotspots of abundance and beta diversity.

    PubMed

    Grange, Laura J; Smith, Craig R

    2013-01-01

    Glacio-marine fjords occur widely at high latitudes and have been extensively studied in the Arctic, where heavy meltwater inputs and sedimentation yield low benthic faunal abundance and biodiversity in inner-middle fjords. Fjord benthic ecosystems remain poorly studied in the subpolar Antarctic, including those in extensive fjords along the West Antarctic Peninsula (WAP). Here we test ecosystem predictions from Arctic fjords on three subpolar, glacio-marine fjords along the WAP. With seafloor photographic surveys we evaluate benthic megafaunal abundance, community structure, and species diversity, as well as the abundance of demersal nekton and macroalgal detritus, in soft-sediment basins of Andvord, Flandres and Barilari Bays at depths of 436-725 m. We then contrast these fjord sites with three open shelf stations of similar depths. Contrary to Arctic predictions, WAP fjord basins exhibited 3 to 38-fold greater benthic megafaunal abundance than the open shelf, and local species diversity and trophic complexity remained high from outer to inner fjord basins. Furthermore, WAP fjords contained distinct species composition, substantially contributing to beta and gamma diversity at 400-700 m depths along the WAP. The abundance of demersal nekton and macroalgal detritus was also substantially higher in WAP fjords compared to the open shelf. We conclude that WAP fjords are important hotspots of benthic abundance and biodiversity as a consequence of weak meltwater influences, low sedimentation disturbance, and high, varied food inputs. We postulate that WAP fjords differ markedly from their Arctic counterparts because they are in earlier stages of climate warming, and that rapid warming along the WAP will increase meltwater and sediment inputs, deleteriously impacting these biodiversity hotspots. Because WAP fjords also provide important habitat and foraging areas for Antarctic krill and baleen whales, there is an urgent need to develop better understanding of the

  17. Megafaunal Communities in Rapidly Warming Fjords along the West Antarctic Peninsula: Hotspots of Abundance and Beta Diversity

    PubMed Central

    Grange, Laura J.; Smith, Craig R.

    2013-01-01

    Glacio-marine fjords occur widely at high latitudes and have been extensively studied in the Arctic, where heavy meltwater inputs and sedimentation yield low benthic faunal abundance and biodiversity in inner-middle fjords. Fjord benthic ecosystems remain poorly studied in the subpolar Antarctic, including those in extensive fjords along the West Antarctic Peninsula (WAP). Here we test ecosystem predictions from Arctic fjords on three subpolar, glacio-marine fjords along the WAP. With seafloor photographic surveys we evaluate benthic megafaunal abundance, community structure, and species diversity, as well as the abundance of demersal nekton and macroalgal detritus, in soft-sediment basins of Andvord, Flandres and Barilari Bays at depths of 436–725 m. We then contrast these fjord sites with three open shelf stations of similar depths. Contrary to Arctic predictions, WAP fjord basins exhibited 3 to 38-fold greater benthic megafaunal abundance than the open shelf, and local species diversity and trophic complexity remained high from outer to inner fjord basins. Furthermore, WAP fjords contained distinct species composition, substantially contributing to beta and gamma diversity at 400–700 m depths along the WAP. The abundance of demersal nekton and macroalgal detritus was also substantially higher in WAP fjords compared to the open shelf. We conclude that WAP fjords are important hotspots of benthic abundance and biodiversity as a consequence of weak meltwater influences, low sedimentation disturbance, and high, varied food inputs. We postulate that WAP fjords differ markedly from their Arctic counterparts because they are in earlier stages of climate warming, and that rapid warming along the WAP will increase meltwater and sediment inputs, deleteriously impacting these biodiversity hotspots. Because WAP fjords also provide important habitat and foraging areas for Antarctic krill and baleen whales, there is an urgent need to develop better understanding of the

  18. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation.

    PubMed

    Leloup, Julie; Fossing, Henrik; Kohls, Katharina; Holmkvist, Lars; Borowski, Christian; Jørgensen, Bo Barker

    2009-05-01

    In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

  19. [FeFe]-Hydrogenase Abundance and Diversity along a Vertical Redox Gradient in Great Salt Lake, USA

    PubMed Central

    Boyd, Eric S.; Hamilton, Trinity L.; Swanson, Kevin D.; Howells, Alta E.; Baxter, Bonnie K.; Meuser, Jonathan E.; Posewitz, Matthew C.; Peters, John W.

    2014-01-01

    The use of [FeFe]-hydrogenase enzymes for the biotechnological production of H2 or other reduced products has been limited by their sensitivity to oxygen (O2). Here, we apply a PCR-directed approach to determine the distribution, abundance, and diversity of hydA gene fragments along co-varying salinity and O2 gradients in a vertical water column of Great Salt Lake (GSL), UT. The distribution of hydA was constrained to water column transects that had high salt and relatively low O2 concentrations. Recovered HydA deduced amino acid sequences were enriched in hydrophilic amino acids relative to HydA from less saline environments. In addition, they harbored interesting variations in the amino acid environment of the complex H-cluster metalloenzyme active site and putative gas transfer channels that may be important for both H2 transfer and O2 susceptibility. A phylogenetic framework was created to infer the accessory cluster composition and quaternary structure of recovered HydA protein sequences based on phylogenetic relationships and the gene contexts of known complete HydA sequences. Numerous recovered HydA are predicted to harbor multiple N- and C-terminal accessory iron-sulfur cluster binding domains and are likely to exist as multisubunit complexes. This study indicates an important role for [FeFe]-hydrogenases in the functioning of the GSL ecosystem and provides new target genes and variants for use in identifying O2 tolerant enzymes for biotechnological applications. PMID:25464382

  20. Quantifying quagga mussel veliger abundance and distribution in Copper Basin Reservoir (California) using acoustic backscatter.

    PubMed

    Anderson, Michael A; Taylor, William D

    2011-11-01

    Quagga mussels (Dreissena bugensis) have been linked to oligotrophication of lakes, alteration of aquatic food webs, and fouling of infrastructure associated with water supply and power generation, causing potentially billions of dollars in direct and indirect damages. Understanding their abundance and distribution is key in slowing their advance, assessing their potential impacts, and evaluating effectiveness of control strategies. Volume backscatter strength (Sv) measurements at 201- and 430-kHz were compared with quagga mussel veliger and zooplankton abundances determined from samples collected using a Wisconsin closing net from the Copper Basin Reservoir on the Colorado River Aqueduct. The plankton within the lower portion of the water column (>18 m depth) was strongly dominated by D-shaped quagga mussel veligers, comprising up to 95-99% of the community, and allowed direct empirical measurement of their mean backscattering cross-section. The upper 0-18 m of the water column contained a smaller relative proportion of veligers based upon net sampling. The difference in mean volume backscatter strength at these two frequencies was found to decrease with decreasing zooplankton abundance (r(2) = 0.94), allowing for correction of Sv due to the contribution of zooplankton and the determination of veliger abundance in the reservoir. Hydroacoustic measurements revealed veligers were often present at high abundances (up to 100-200 ind L(-1)) in a thin 1-2 m layer at the thermocline, with considerable patchiness in their distribution observed along a 700 m transect on the reservoir. Under suitable conditions, hydroacoustic measurements can rapidly provide detailed information on the abundance and distribution of quagga mussel veligers over large areas with high horizontal and vertical resolution.

  1. The Composition of Comet C/2012 K1 (PanSTARRS) and the Distribution of Primary Volatile Abundances among Comets

    NASA Astrophysics Data System (ADS)

    Roth, Nathan X.; Gibb, Erika L.; Bonev, Boncho P.; DiSanti, Michael A.; Mumma, Michael J.; Villanueva, Geronimo L.; Paganini, Lucas

    2017-04-01

    On 2014 May 22 and 24 we characterized the volatile composition of the dynamically new Oort cloud comet C/2012 K1 (PanSTARRS) using the long-slit, high resolution (λ/Δλ ≈ 25,000) near-infrared echelle spectrograph (NIRSPEC) at the 10 m Keck II telescope on Maunakea, Hawaii. We detected fluorescent emission from six primary volatiles (H2O, HCN, CH4, C2H6, CH3OH, and CO). Upper limits were derived for C2H2, NH3, and H2CO. We report rotational temperatures, production rates, and mixing ratios (relative to water). Compared with median abundance ratios for primary volatiles in other sampled Oort cloud comets, trace gas abundance ratios in C/2012 K1 (PanSTARRS) for CO and HCN are consistent, but CH3OH and C2H6 are enriched while H2CO, CH4, and possibly C2H2 are depleted. When placed in context with comets observed in the near-infrared to date, the data suggest a continuous distribution of abundances of some organic volatiles (HCN, C2H6, CH3OH, CH4) among the comet population. The level of “enrichment” or “depletion” in a given comet does not necessarily correlate across all molecules sampled, suggesting that chemical diversity among comets may be more complex than the simple organics-enriched, organics-normal, and organics-depleted framework.

  2. Distribution, abundance, and habitat associations of a large bivalve (Panopea generosa) in a eutrophic, fjord estuary

    USGS Publications Warehouse

    Mcdonald, P. Sean; Essington, Timothy E.; Davis, Jonathan P.; Galloway, Aaron W.E.; Stevick, Bethany C.; Jensen, Gregory C.; Vanblaricom, Glenn R.; Armstrong, David A.

    2015-01-01

    Marine bivalves are important ecosystem constituents and frequently support valuable fisheries. In many nearshore areas, human disturbance—including declining habitat and water quality—can affect the distribution and abundance of bivalve populations, and complicate ecosystem and fishery management assessments. Infaunal bivalves, in particular, are frequently cryptic and difficult to detect; thus, assessing potential impacts on their populations requires suitable, scalable methods for estimating abundance and distribution. In this study, population size of a common benthic bivalve (the geoduck Panopea generosa) is estimated with a Bayesian habitat-based model fit to scuba and tethered camera data in Hood Canal, a fjord basin in Washington state. Densities declined more than two orders of magnitude along a north—south gradient, concomitant with patterns of deepwater dissolved oxygen, and intensity and duration of seasonal hypoxia. Across the basin, geoducks were most abundant in loose, unconsolidated, sand substrate. The current study demonstrates the utility of using scuba, tethered video, and habitat models to estimate the abundance and distribution of a large infaunal bivalve at a regional (385-km2) scale.

  3. Seasonal Abundance, Spatial Distribution, Spawning and Growth of Astropecten irregularis (Echinodermata: Asteroidea)

    NASA Astrophysics Data System (ADS)

    Freeman, S. M.; Richardson, C. A.; Seed, R.

    2001-07-01

    Seasonal trends in the abundance, spatial distribution, spawning and growth of a population of Astropecten irregularis inhabiting the coastal waters of North Wales are described. Population densities of A. irregularis varied seasonally with starfish attaining their maximum and minimum abundances in summer and winter respectively. Changes in their spatial distribution strongly suggests that A. irregularis migrates offshore into deeper waters during the winter months probably to avoid strong onshore wave surges. High population densities of starfish which occur during the summer months may be associated with spawning aggregations or the availability of suitable prey species; a smaller peak in starfish abundance occurred during autumn 1997 coinciding with the settlement of the bivalve Spisula subtruncata and the cumacean Diastylis rugosa , prey species which are readily consumed by A. irregularis. Astropecten irregularis spawned during late spring-early summer, but thereafter the gonad somatic index remained at a low level until late autumn; the index increased throughout winter and starfish attained peak reproductive condition by late spring. Small starfish (arm length <24 mm), showed little evidence of reproductive development. Limited recruitment of A. irregularis (<8 mm) occurred during October-November 1996, and the integration of this small cohort into the main population occurred within one year. Locomotory activity and burrowing depth of starfish maintained in laboratory aquaria correlated with changes in seawater temperature; activity was largely inhibited and burrowing depth significantly increased at temperatures <8 °C. Seawater temperature is probably an important factor regulating the abundance and distribution of A. irregularis in coastal waters.

  4. Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

    USGS Publications Warehouse

    Pooler, P.S.; Smith, D.R.

    2005-01-01

    We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

  5. Elemental Abundance Distributions in Basalt Clays and Meteorites: Is It a Biosignature?

    NASA Technical Reports Server (NTRS)

    Fisk, M. R.; Storrie-Lombardi, M. C.; Joseph, J.

    2005-01-01

    Volcanic glass altered by microorganisms exhibits distinctive textures differing significantly from abiotic alteration [1-4]. We have previously presented morphological evidence of bioweathering in sub-oceanic basalt glass [5] and olivine [6], and noted similar alterations in Nakhla [7]. We have also introduced an autonomous Bayesian probabilistic classification methodology to identify biotic and abiotic alteration in sub-oceanic basalts using elemental abundance data [8]. We now present data from multiple sub-oceanic sites addressing the more general question of utilizing elemental abundance distribution in clays as a valid biosignature for the exploration of putative clay alteration products in meteorites.

  6. Distribution-abundance relationship for passerines breeding in Tunisian oases: test of the sampling hypothesis.

    PubMed

    Selmi, Slaheddine; Boulinier, Thierry

    2004-05-01

    The positive relationship between local abundance and distribution of species is a widely recognized pattern in community ecology. However, it has been suggested that this relationship can simply be an artefact of sampling because locally rare species are less detectable then locally abundant ones, and hence their distribution can easily be underestimated. Here, we use count data to investigate the relationship between distribution and abundance of passerines breeding in a sample of oases from southern Tunisia, and we provide a test of the sampling artefact hypothesis. In particular, we checked for a difference in detection probability between localized and widespread species, and we tested if increasing the sampling effort affects the significance of the relationship. A significant positive relationship between the average local abundance of passerine species and the proportion of occupied oases was found. The use of a capture-recapture approach allowed us to estimate and to compare the detection probabilities of localized and widespread species subsets. We found that localized species were locally less detectable than widespread species, which is consistent with the main assumption of the sampling artefact hypothesis. However, increasing the detection probability of species by conducting more counts did not affect the significance of the relationship, which did not give support to the sampling artefact hypothesis. Our work implies that sampling contributed to the distribution-abundance relationship we found, but that it is unlikely that such a relationship could entirely be explained by an artefact of sampling. It also underlines the insight that can be gained by using probabilistic approaches of estimating species number and detection probability when attempting to disentangle sampling from ecological effects in community ecology studies.

  7. Do abundance distributions and species aggregation correctly predict macroecological biodiversity patterns in tropical forests?

    PubMed Central

    Wiegand, Thorsten; Lehmann, Sebastian; Huth, Andreas; Fortin, Marie‐Josée

    2016-01-01

    Abstract Aim It has been recently suggested that different ‘unified theories of biodiversity and biogeography’ can be characterized by three common ‘minimal sufficient rules’: (1) species abundance distributions follow a hollow curve, (2) species show intraspecific aggregation, and (3) species are independently placed with respect to other species. Here, we translate these qualitative rules into a quantitative framework and assess if these minimal rules are indeed sufficient to predict multiple macroecological biodiversity patterns simultaneously. Location Tropical forest plots in Barro Colorado Island (BCI), Panama, and in Sinharaja, Sri Lanka. Methods We assess the predictive power of the three rules using dynamic and spatial simulation models in combination with census data from the two forest plots. We use two different versions of the model: (1) a neutral model and (2) an extended model that allowed for species differences in dispersal distances. In a first step we derive model parameterizations that correctly represent the three minimal rules (i.e. the model quantitatively matches the observed species abundance distribution and the distribution of intraspecific aggregation). In a second step we applied the parameterized models to predict four additional spatial biodiversity patterns. Results Species‐specific dispersal was needed to quantitatively fulfil the three minimal rules. The model with species‐specific dispersal correctly predicted the species–area relationship, but failed to predict the distance decay, the relationship between species abundances and aggregations, and the distribution of a spatial co‐occurrence index of all abundant species pairs. These results were consistent over the two forest plots. Main conclusions The three ‘minimal sufficient’ rules only provide an incomplete approximation of the stochastic spatial geometry of biodiversity in tropical forests. The assumption of independent interspecific placements is most

  8. Diversity and distribution of winter phytoplankton in the Arabian Gulf and the Sea of Oman

    NASA Astrophysics Data System (ADS)

    Polikarpov, Igor; Saburova, Maria; Al-Yamani, Faiza

    2016-05-01

    The spatial distribution of the phytoplankton (diversity, composition, and cell abundance) was described in relation to local environmental conditions across the Arabian Gulf, the Strait of Hormuz, and the Sea of Oman based on data of ROPME cruise of winter 2006. The 376 phytoplankton taxa identified in these waters represented a diverse composition of species with a prevalence of dinoflagellates and diatoms. Three peaks in the phytoplankton abundance were recorded throughout the studied area associated with diatom-dominated phytoplankton blooms in the central and northwestern part of the Arabian Gulf and in the Sea of Oman and the adjacent waters. The studied area was divided into three main regions by cluster analysis based on differences in the phytoplankton composition and concentration. The Sea of Oman and the Strait of Hormuz were occupied by highly abundant, strongly diatom-dominated phytoplankton assemblage. The Arabian Gulf was divided into two main regions along a diagonal northwest-southeast axis, with rather diatom-dominated phytoplankton assemblage off the south and along the Iranian coast but with flagellate-dominated phytoplankton of the north and along the Arabian coast. The distance-based linear modeling revealed a significant relationship between the phytoplankton composition and water masses as indexed by salinity. Our results demonstrated that abundance and composition of winter phytoplankton were related to water circulation pattern in the Arabian Gulf and the Sea of Oman.

  9. Abundance, diversity, and feeding behavior of coral reef butterflyfishes at Lord Howe Island

    PubMed Central

    Pratchett, Morgan S; Hoey, Andrew S; Cvitanovic, Christopher; Hobbs, Jean-Paul A; Fulton, Christopher J

    2014-01-01

    Endemic species are assumed to have a high risk of extinction because their restricted geographic range is often associated with low abundance and high ecological specialization. This study examines the abundance of Chaetodon butterflyfishes at Lord Howe Island in the south-west Pacific, and compares interspecific differences in local abundance to the feeding behavior and geographic range of these species. Contrary to expected correlations between abundance and geographic range, the single most abundant species of butterflyfish was Chaetodon tricinctus, which is endemic to Lord Howe Island and adjacent reefs; densities of C. tricinctus (14.1 ± 2.1 SE fish per 200m2) were >3 times higher than the next most abundant butterflyfish (Chaetodon melannotus), and even more abundant than many other geographically widespread species. Dietary breadth for the five dominant butterflyfishes at Lord Howe Island was weakly and generally negative correlated with abundance. The endemic C. tricinctus was a distinct outlier in this relationship, though our extensive feeding observations suggest some issues with the measurements of dietary breadth for this species. Field observations revealed that all bites taken on benthic substrates by C. tricinctus were from scleractinian corals, but adults rarely, if ever, took bites from the benthos, suggesting that they may be feeding nocturnally and/or using mid-water prey, such as plankton. Alternatively, the energetic demands of C. tricinctus may be fundamentally different to other coral-feeding butterflyfishes. Neither dietary specialization nor geographic range accounts for interspecific variation in abundance of coral reef butterflyfishes at Lord Howe Island, while much more work on the foraging behavior and population dynamics of C. tricinctus will be required to understand its’ abundance at this location. PMID:25478152

  10. Distribution and Molecular Diversity of Arborescent Gossypium Species.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mexico is a center of diversity of Gossypium. As currently circumscribed, arborescent Gossypium species (Section Erioxylum) are widely distributed in dry deciduous forests located from the central state of Sinaloa at the north of its range to the eastern state of Oaxaca in the south. However, extens...

  11. Abundance and size distribution of sublittoral meiobenthos along estuarine salinity gradients

    NASA Astrophysics Data System (ADS)

    Yamamuro, Masumi

    2000-10-01

    Abundance and size distribution of the sublittoral meiobenthos in the upper 3 cm of the sediment were surveyed in the eutrophic, estuarine lagoons, Lakes Nakaumi and Shinji, Japan. Samples were taken in late spring from 10 stations located along salinity gradients. The density of meiobenthos was at a minimum in the intermediate salinity zone. Nematodes in L. Shinji were significantly larger in size than in L. Nakaumi, due to the size reduction of marine species in the latter. The biomass of co-existing bivalves, which would contribute more food supply to the meiobenthic fauna, did not affect the abundance and size of meiobenthos. It was suggested that the salinity gradient was the most influential factor on the abundance and size structure of meiobenthos in estuarine lagoons where salinity is fairly constant.

  12. Microplastic abundance, distribution and composition along a latitudinal gradient in the Atlantic Ocean.

    PubMed

    Kanhai, La Daana K; Officer, Rick; Lyashevska, Olga; Thompson, Richard C; O'Connor, Ian

    2017-02-15

    Microplastics in the world's oceans are a global concern due to the potential threat they pose to marine organisms. This study investigated microplastic abundance, distribution and composition in the Atlantic Ocean on a transect from the Bay of Biscay to Cape Town, South Africa. Microplastics were sampled from sub-surface waters using the underway system of the RV Polarstern. Potential microplastics were isolated from samples and FT-IR spectroscopy was used to identify polymer types. Of the particles analysed, 63% were rayon and 37% were synthetic polymers. The majority of microplastics were identified as polyesters (49%) and blends of polyamide or acrylic/polyester (43%). Overall, fibres (94%) were predominant. Average microplastic abundance in the Atlantic Ocean was 1.15±1.45particlesm(-3). Of the 76 samples, 14 were from the Benguela upwelling and there was no statistically significant difference in microplastic abundance between upwelled and non-upwelled sites.

  13. Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

    NASA Astrophysics Data System (ADS)

    Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

    2013-12-01

    Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

  14. [Diversity and abundance of echinoderms from the reef lagoon at Cahuita National Park, Caribbean from Costa Rica].

    PubMed

    Bolaños, Natalie; Bourg, Amandine; Gómez, Javier; Alvarado, Juan José

    2005-12-01

    A total of 15 species of echinoderms (one asteroid, seven ophiuroids, five echinoids and two holothurians) were recorded at the Cahuita National Park reef lagoon, between September and October 2003, using a 1 m2 quadrant. The sites with coral substrate and algae were the most diverse, while those with seagrass and sand were the least. Ophiuroids were the most abundant group with 170 individuals, asteroids were the least abundant. Adding other studies and reports of echinoderms to this study, a total of 23 species have been found at Cahuita National Park, which is the most diverse area on the Caribbean of Costa Rica. We report nine new echinoderm records for Costa Rica's Caribbean.

  15. Effects of urbanization on the distribution and abundance of amphibians and invasive species in southern California streams

    USGS Publications Warehouse

    Riley, S.P.D.; Busteed, G.T.; Kats, L.B.; Vandergon, T.L.; Lee, L.F.S.; Dagit, R.G.; Kerby, J.L.; Fisher, R.N.; Sauvajot, R.M.

    2005-01-01

    Urbanization negatively affects natural ecosystems in many ways, and aquatic systems in particular. Urbanization is also cited as one of the potential contributors to recent dramatic declines in amphibian populations. From 2000 to 2002 we determined the distribution and abundance of native amphibians and exotic predators and characterized stream habitat and invertebratecommunities in 35 streams in an urbanized landscape north of Los Angeles (U.S.A.). We measured watershed development as the percentage of area within each watershed occupied by urban land uses. Streams in more developed watersheds often had exotic crayfish (Procambarus clarkii) and fish, and had fewer native species such as California newts (Taricha torosa) and California treefrogs (Hyla cadaverina). These effects seemed particularly evident above 8% development, a result coincident with other urban stream studies that show negative impacts beginning at 10-15% urbanization. For Pacific treefrogs (H. regilla), the most widespread native amphibian, abundance was lower in the presence of exotic crayfish, although direct urbanization effects were not found. Benthic macroinvertebrate communities were also less diverse in urban streams, especially for sensitive species. Faunal community changes in urban streams may be related to changes in physical stream habitat, such as fewer pool and more run habitats and increased water depth and flow, leading to more permanent streams. Variation in stream permanence was particularly evident in 2002, a dry year when many natural streams were dry but urban streams were relatively unchanged. Urbanization has significantly altered stream habitat in this region and may enhance invasion by exotic species and negatively affect diversity and abundance of native amphibians. ??2005 Society for Conservation Biology.

  16. Understanding the Nature of Stellar Chemical Abundance Distributions in Nearby Stellar Systems

    NASA Astrophysics Data System (ADS)

    Lee, Duane Morris

    Since stars retain signatures of their galactic origins in their chemical compositions, we can exploit the chemical abundance distributions that we observe in stellar systems to put constraints on the nature of their progenitors. In this thesis, I present results from three projects aimed at understanding how high resolution spectroscopic observations of nearby stellar systems might be interpreted. The first project presents one possible explanation for the origin of peculiar abundance distributions observed in ultra-faint dwarf satellites of the Milky Way. The second project explores to what extent the distribution of chemical elements in the stellar halo can be used to trace Galactic accretion history from the birth of the Galaxy to the present day. Finally, a third project focuses on developing an input optimization algorithm for the second project to produce better estimates of halo accretion histories. In conclusion, I propose some other new ways to use statistical models and techniques along with chemical abundance distribution data to uncover galactic histories.

  17. Spatial Distribution and Variations of Dust Abundances in the Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Paradis, Déborah; Reach, W. T.; Bernard, J.; Block, M.; Engelbracht, C. W.; Gordon, K.; Hora, J. L.; Indebetouw, R.; Kawamura, A.; Meade, M.; Meixner, M.; Sewilo, M.; Vijh, U. P.; Volk, K.

    2009-05-01

    The Large Magellanic Cloud (LMC) is the nearest galaxy external to the Milky Way, located at a distance of about 55 kpc. As opposed to the situation in the Galaxy, where studies of the infrared emission from dust in the interstellar medium (ISM) suffer from significant confusion along the line of sight, the favorable viewing angle for the LMC offers a direct view to the processes taking place in the diffuse ISM. The LMC has a lower metallicity than that of our Galaxy, estimated to 1/2-1/3 of the solar metallicity. Using the data obtained with the Spitzer Space telescope as part of the Surveying the Agents of a Galaxy's Evolution (SAGE) Legacy survey, we have studied the variations of the dust composition and abundance across the LMC. We traced maps of the relative abundance of Polycyclic Aromatic Hydrocarbons (PAH) and Very Small Grains (VSG), compared to Big Grains (BG). PAH are more abundant in the old stellar bar and close to molecular clouds, whereas the main source of VSG is located around 30-Doradus (brightest region of the LMC) and at the center of the bar. Morever the VSG relative abundance follows the distribution of the HII regions quite well, contrary to the PAH distribution. PAH and VSG could have a different origin or might have been subjected to different processing in the ISM. VSG abundance could trace the active star formation sites and PAH abundance could represent quiescent environments. We think that VSG could result from BG destruction in grain-grain collisions, due to turbulent motions. PAH could come from VSG shattering in some regions and could also be injected into the ISM during the AGB mass loss.

  18. Distribution and abundance of Larvaceans in the Southern Ocean between 30 and 80°E

    NASA Astrophysics Data System (ADS)

    Lindsay, M. C. M.; Williams, G. D.

    2010-05-01

    Larvaceans are gelatinous zooplankton that inhabit most oceans, coastal waters and estuaries, and are thought to be important grazers of the ocean's primary production. To date there is little known about larvaceans in the Southern Ocean and their ecological role. This paper details a Larvacean survey conducted during the BROKE-West voyage (Jan-Mar 2006) to the southwest Indian Ocean sector of the East Antarctic margin between 30 and 80°E and 60 and 70°S. Larvacean abundances were quantified from three sampling devices: a ring net with 150-μm mesh and cross-sectional area of 0.8 m 2; a Rectangular Mid-Water Trawl (RMT1) with 300-μm mesh and a nominal cross-sectional area of 1 m 2; and a Continuous Plankton Recorder (CPR) with a 270-μm mesh and a 1.6-cm 2 cross-sectional area. The samples collected from the ring net were identified to the species level using stereo dissecting microscopes and scanning electron microscopy (SEM). The survey revealed two species: Oikopleura gaussica and Fritillaria drygalski. The abundance of both species increased from <1 ind. m -3 to 5.8 ind. m -3 as the survey progressed from west to east and decreased from 5.8 ind. m -3 in the north to 2 ind. m -3 in the south until the shelf region and marginal sea-ice zone where abundances increased to 4 ind. m -3. Statistically significant relationships were identified between abundance and latitude in samples from the RMT1 and Ring net. There was also a relationship between the larvacean abundance from the RMT1 and longitude. Although larvacean distribution and abundance patterns appeared to agree with the large-scale oceanographic boundaries of the survey area, there were no statistically significant relationships between larvacean abundance and any physical oceanography parameters.

  19. Abundance and distribution of feral pigs at Hakalau Forest National Wildlife Refuge, 2010-2013

    USGS Publications Warehouse

    Hess, Steven C.; Leopold, Christina R.; Kendall, Steven J.

    2013-01-01

    The Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex has intensively managed feral pigs (Sus scrofa) and monitored feral pig presence with surveys of all managed areas since 1988. Results of all available data regarding pig management activities through 2004 were compiled and analyzed, but no further analyses had been conducted since then. The objective of this report was to analyze recent feral ungulate surveys at the Hakalau Forest Unit to determine current pig abundance and distribution. Activity indices for feral pigs, consisting of the presence of fresh or intermediate sign at 422 stations, each with approximately 20 sample plots, were compiled for years 2010–2013. A calibrated model based on the number of pigs removed from one management unit and concurrent activity surveys was applied to estimate pig abundance in other management units. Although point estimates appeared to decrease from 489.1 (±105.6) in 2010 to 407.6 (±88.0) in 2013, 95% confidence intervals overlapped, indicating no significant change in pig abundance within all management units. Nonetheless, there were significant declines in pig abundance over the four-year period within management units 1, 6, and 7. Areas where pig abundance remained high include the southern portion of Unit 2. Results of these surveys will be useful for directing management actions towards specific management units.

  20. Habitat characteristics predicting distribution and abundance patterns of scallops in D'Entrecasteaux Channel, Tasmania.

    PubMed

    Mendo, Tania; Lyle, Jeremy M; Moltschaniwskyj, Natalie A; Tracey, Sean R; Semmens, Jayson M

    2014-01-01

    Habitat characteristics greatly influence the patterns of distribution and abundance in scallops, providing structure for the settlement of spat and influencing predation risk and rates of survival. Establishing scallop-habitat relationships is relevant to understanding the ecological processes that regulate scallop populations and to managing critical habitats. This information is particularly relevant for the D'Entrecasteaux Channel, south-eastern Tasmania (147.335 W, 43.220 S), a region that has supported significant but highly variable scallop production over many years, including protracted periods of stock collapse. Three species of scallops are present in the region; the commercial scallop Pecten fumatus, the queen scallop Equichlamys bifrons, and the doughboy scallop Mimachlamys asperrima. We used dive surveys and Generalized Additive Modelling to examine the relationship between the distribution and abundance patterns of each species and associated habitat characteristics. The aggregated distribution of each species could be predicted as a function of sediment type and species-specific habitat structural components. While P. fumatus was strongly associated with finer sediments and E. bifrons with coarse grain sediments, M. asperrima had a less selective association, possibly related to its ability to attach on a wide range of substrates. Other habitat characteristics explaining P. fumatus abundance were depth, Asterias amurensis abundance, shell and macroalgae cover. Equichlamys bifrons was strongly associated with macroalgae and seagrass cover, whereas M. asperrima abundance was greatly explained by sponge cover. The models define a set of relationships from which plausible hypotheses can be developed. We propose that these relationships are mediated by predation pressure as well as the specific behavioural characteristics of each species. The findings also highlight the specific habitat characteristics that are relevant for spatial management and habitat

  1. Habitat Characteristics Predicting Distribution and Abundance Patterns of Scallops in D’Entrecasteaux Channel, Tasmania

    PubMed Central

    Mendo, Tania; Lyle, Jeremy M.; Moltschaniwskyj, Natalie A.; Tracey, Sean R.; Semmens, Jayson M.

    2014-01-01

    Habitat characteristics greatly influence the patterns of distribution and abundance in scallops, providing structure for the settlement of spat and influencing predation risk and rates of survival. Establishing scallop-habitat relationships is relevant to understanding the ecological processes that regulate scallop populations and to managing critical habitats. This information is particularly relevant for the D’Entrecasteaux Channel, south-eastern Tasmania (147.335 W, 43.220 S), a region that has supported significant but highly variable scallop production over many years, including protracted periods of stock collapse. Three species of scallops are present in the region; the commercial scallop Pecten fumatus, the queen scallop Equichlamys bifrons, and the doughboy scallop Mimachlamys asperrima. We used dive surveys and Generalized Additive Modelling to examine the relationship between the distribution and abundance patterns of each species and associated habitat characteristics. The aggregated distribution of each species could be predicted as a function of sediment type and species-specific habitat structural components. While P. fumatus was strongly associated with finer sediments and E. bifrons with coarse grain sediments, M. asperrima had a less selective association, possibly related to its ability to attach on a wide range of substrates. Other habitat characteristics explaining P. fumatus abundance were depth, Asterias amurensis abundance, shell and macroalgae cover. Equichlamys bifrons was strongly associated with macroalgae and seagrass cover, whereas M. asperrima abundance was greatly explained by sponge cover. The models define a set of relationships from which plausible hypotheses can be developed. We propose that these relationships are mediated by predation pressure as well as the specific behavioural characteristics of each species. The findings also highlight the specific habitat characteristics that are relevant for spatial management and

  2. Distribution, abundance, and resting microhabitat of burbot on Julian's Reef, southwestern Lake Michigan

    USGS Publications Warehouse

    Edsall, Thomas A.; Kennedy, Gregory W.; Horns, William H.

    1993-01-01

    We used a remotely operated submersible vehicle equipped with a color video camera to videotape the lake bed and document the distribution and abundance of burbot Lota lota on a 156-hectare portion of Julian's Reef in southwestern Lake Michigan. The substrates and bathymetry of the study area had been mapped recently by side-scan sonar. Burbot density determined from videotapes covering 6,900 m2 of lake bed at depths of 23-41 m averaged 139 individuals/ hectare (range, 0-571/hectare). This density was substantially higher than the highest burbot density (59-95/hectare) reported in the literature. Burbot were present on the lake bed at depths of 23-36 m, but were most abundant near the crest of the reef at 23-28 m, where the water temperature was 8-13°C, their preferred summer temperature range. Substrates in that temperature range on the reef were bedrock, bedrock ridges, and bedrock and rubble. Burbot were most abundant on the bedrock and rubble. Small fish and macroinvertebrates typically eaten by burbot elsewhere in western Lake Michigan were distributed on the reef according to their summer preferred temperatures and were not seen in abundance where burbot density was highest. We saw no lake trout Salvelinus namaycush on Julian's Reef, although large numbers of juvenile lake trout have been stocked there annually and temperatures on the reef were in the preferred summer temperature range for lake trout.

  3. Distribution, abundance, and resting microhabitat of burbot on Julian's Reef, southwestern Lake Michigan

    USGS Publications Warehouse

    Edsall, Thomas A.; Kennedy, Gregory W.; Horns, William H.

    1993-01-01

    We used a remotely operated submersible vehicle equipped with a color video camera to videotape the lake bed and document the distribution and abundance of burbot Lota lotaon a 156-hectare portion of Julian's Reef in southwestern Lake Michigan. The substrates and bathymetry of the study area had been mapped recently by side-scan sonar. Burbot density determined from videotapes covering 6,900 m2 of lake bed at depths of 23–41 m averaged 139 individuals/ hectare (range, 0–571/hectare). This density was substantially higher than the highest burbot density (59–95/hectare) reported in the literature. Burbot were present on the lake bed at depths of 23–36 m, but were most abundant near the crest of the reef at 23–28 m, where the water temperature was 8–13°C, their preferred summer temperature range. Substrates in that temperature range on the reef were bedrock, bedrock ridges, and bedrock and rubble. Burbot were most abundant on the bedrock and rubble. Small fish and macroinvertebrates typically eaten by burbot elsewhere in western Lake Michigan were distributed on the reef according to their summer preferred temperatures and were not seen in abundance where burbot density was highest. We saw no lake trout Salvelinus namaycush on Julian's Reef, although large numbers of juvenile lake trout have been stocked there annually and temperatures on the reef were in the preferred summer temperature range for lake trout.

  4. Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China

    PubMed Central

    Wang, Shaojun; Chen, Han Y. H.; Tan, Yan; Fan, Huan; Ruan, Honghua

    2016-01-01

    Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon’s and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability. PMID:26857390

  5. Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat

    PubMed Central

    Ballaud, Flore; Dufresne, Alexis; Francez, André-Jean; Colombet, Jonathan; Sime-Ngando, Télesphore; Quaiser, Achim

    2016-01-01

    Viruses impact microbial activity and carbon cycling in various environments, but their diversity and ecological importance in Sphagnum-peatlands are unknown. Abundances of viral particles and prokaryotes were monitored bi-monthly at a fen and a bog at two different layers of the peat surface. Viral particle abundance ranged from 1.7 x 106 to 5.6 x 108 particles mL-1, and did not differ between fen and bog but showed seasonal fluctuations. These fluctuations were positively correlated with prokaryote abundance and dissolved organic carbon, and negatively correlated with water-table height and dissolved oxygen. Using shotgun metagenomics we observed a shift in viral diversity between winter/spring and summer/autumn, indicating a seasonal succession of viral communities, mainly driven by weather-related environmental changes. Based on the seasonal asynchrony between viral and microbial diversity, we hypothesize a seasonal shift in the active microbial communities associated with a shift from lysogenic to lytic lifestyles. Our results suggest that temporal variations of environmental conditions rather than current habitat differences control the dynamics of virus-host interactions in Sphagnum-dominated peatlands. PMID:26779149

  6. Valuing the recreational benefits of wetland adaptation to climate change: a trade-off between species' abundance and diversity.

    PubMed

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations.

  7. Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China.

    PubMed

    Wang, Shaojun; Chen, Han Y H; Tan, Yan; Fan, Huan; Ruan, Honghua

    2016-02-09

    Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon's and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability.

  8. Valuing the Recreational Benefits of Wetland Adaptation to Climate Change: A Trade-off Between Species' Abundance and Diversity

    NASA Astrophysics Data System (ADS)

    Faccioli, Michela; Riera Font, Antoni; Torres Figuerola, Catalina M.

    2015-03-01

    Climate change will further exacerbate wetland deterioration, especially in the Mediterranean region. On the one side, it will accelerate the decline in the populations and species of plants and animals, this resulting in an impoverishment of biological abundance. On the other one, it will also promote biotic homogenization, resulting in a loss of species' diversity. In this context, different climate change adaptation policies can be designed: those oriented to recovering species' abundance and those aimed at restoring species' diversity. Based on the awareness that knowledge about visitors' preferences is crucial to better inform policy makers and secure wetlands' public use and conservation, this paper assesses the recreational benefits of different adaptation options through a choice experiment study carried out in S'Albufera wetland (Mallorca). Results show that visitors display positive preferences for an increase in both species' abundance and diversity, although they assign a higher value to the latter, thus suggesting a higher social acceptability of policies pursuing wetlands' differentiation. This finding acquires special relevance not only for adaptation management in wetlands but also for tourism planning, as most visitors to S'Albufera are tourists. Thus, given the growing competition to attract visitors and the increasing demand for high environmental quality and unique experiences, promoting wetlands' differentiation could be a good strategy to gain competitive advantage over other wetland areas and tourism destinations.

  9. Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea.

    PubMed

    Xu, Dapeng; Jiao, Nianzhi; Ren, Rui; Warren, Alan

    2016-09-30

    Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75-m depth. The communities of microbial eukaryotes were clustered into shallow-, middle-, and deep-water groups according to the depth from which they were collected, indicating a depth-related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50-m deep, being most abundant near the sea floor where they contributed ca. 64-97% and 40-74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area.

  10. [Distribution and abundance of fish community in the littoral area of "Los Petenes" Biosphere Reserve, Campeche, Mexico].

    PubMed

    Muñoz-Rojas, Sandra; Ayala-Pérez, Luis Amado; Sosa-López, Atahualpa; Villalobos-Zapata, Guillermo Jorge

    2013-03-01

    "Los Petenes" Biosphere Reserve (RBLP) is a critical habitat for many aquatic and terrestrial species. It has the biggest and better conserved seagrass beds, and it represents an important habitat for food, protection and breeding of aquatic organisms, and a temporal refuge for migratory species. The objective of this study was to describe the ichthyofauna diversity in the littoral coastal area of the RBLP, to identify the ecological dominant species, and to analyze the abundance of the fish community and its temporal and spatial changes, and their relationship with some environmental variables. Monthly fish samples were obtained with the aid of trawl nets, from 24 samplings sites distributed along the reserve, between May 2009 and April 2010. The trawl net was operated 288 times and 21 795 individuals with 279.5kg of weight were collected. A total of 46 fish species grouped in 34 genera and 23 families were identified. In a spatial scale, the abundance showed the next ranges: 0.018-0.094ind./m2; 0.249-1.072 g/m2 and 9.75-19.32g/ind.; the diversity indexes obtained were: H'n=1.46-2.15, J'=0.45-0.71 and D'=2.08-3.92. In a temporal scale, the abundance and diversity ranged between: 0.026-0.066ind./m2; 0.342-0.764g/m2 and 6.49-22.98g/ind.; H'n=1.76-2.08; J'=0.52-0.64 and D'=3.07-4.18. Eleven dominant species were identified with a representation of the 94.39% in number of individuals, and 89.66% in weight of the total catch. From the total, eight species had economic or commercial importance, especially Lagodon rhomboides and Haemulon plumierii. The cluster analyses identified four fish associations; these results are discussed in order to identify relationships between habitat-species. Finally, the canonical correspondence analysis evidenced an association between H. plumierii with salinity and dissolved solids. The RBLP has high habitat diversity and its fish community has developed strategies to use all the spatial and temporal conditions and to satisfy the needs

  11. Impact of Grassland Reseeding, Herbicide Spraying and Ploughing on Diversity and Abundance of Soil Arthropods

    PubMed Central

    Liu, Wei; Zhang, Junling; Norris, Stuart L.; Murray, Philip J.

    2016-01-01

    In order to determine the interactive effect of reseeding, herbicide spraying and ploughing on soil fauna communities, we conducted a grassland reseeding experiment combined with pre-reseed management to examine how with the whole reseeding process affects soil faunal composition. Sampling occasions and exact treatments were as follows: (1) before chemical herbicide spray; (2) after spray but before ploughing; (3) after ploughing but before reseeding; and (4) after 1 year of recovery. Our results demonstrate that, Acari and Collembola were the two soil fauna taxa with the highest abundance and accounted for around 96% of the relative total abundance among the various managements. Herbicide application tended to increase soil invertebrate abundance. Conversely, subsequent ploughing significantly reduced soil invertebrate abundance and had an obvious negative effect on soil primary and secondary decomposers, which were mainly due to the variations of Acari (especially Oribatida) and Coleoptera group abundance. Moreover, reseeding also reduced the individual number of the groups mentioned above, and favored those predators with a larger body size and individual weight. After 1 year recovery, Collembola abundance recovered to the pre-treatment levels, while with Arthropod and Acari groups were still fluctuating. PMID:27555863

  12. Impact of Grassland Reseeding, Herbicide Spraying and Ploughing on Diversity and Abundance of Soil Arthropods.

    PubMed

    Liu, Wei; Zhang, Junling; Norris, Stuart L; Murray, Philip J

    2016-01-01

    In order to determine the interactive effect of reseeding, herbicide spraying and ploughing on soil fauna communities, we conducted a grassland reseeding experiment combined with pre-reseed management to examine how with the whole reseeding process affects soil faunal composition. Sampling occasions and exact treatments were as follows: (1) before chemical herbicide spray; (2) after spray but before ploughing; (3) after ploughing but before reseeding; and (4) after 1 year of recovery. Our results demonstrate that, Acari and Collembola were the two soil fauna taxa with the highest abundance and accounted for around 96% of the relative total abundance among the various managements. Herbicide application tended to increase soil invertebrate abundance. Conversely, subsequent ploughing significantly reduced soil invertebrate abundance and had an obvious negative effect on soil primary and secondary decomposers, which were mainly due to the variations of Acari (especially Oribatida) and Coleoptera group abundance. Moreover, reseeding also reduced the individual number of the groups mentioned above, and favored those predators with a larger body size and individual weight. After 1 year recovery, Collembola abundance recovered to the pre-treatment levels, while with Arthropod and Acari groups were still fluctuating.

  13. Fishing drives declines in fish parasite diversity and has variable effects on parasite abundance.

    PubMed

    Wood, Chelsea L; Sandin, Stuart A; Zgliczynski, Brian; Guerra, Ana Sofía; Micheli, Fiorenza

    2014-07-01

    Despite the ubiquity and ecological importance of parasites, relatively few studies have assessed their response to anthropogenic environmental change. Heuristic models have predicted both increases and decreases in parasite abundance in response to human disturbance, with empirical support for both. However, most studies focus on one or a few selected parasite species. Here, we assess the abundance of parasites of seven species of coral reef fishes collected from three fished and three unfished islands of the Line Islands archipelago in the central equatorial Pacific. Because we chose fish hosts that spanned different trophic levels, taxonomic groups, and body sizes, we were able to compare parasite responses across a broad cross section of the total parasite community in the presence and absence of fishing, a major human impact on marine ecosystems. We found that overall parasite species richness was substantially depressed on fished islands, but that the response of parasite abundance varied among parasite taxa: directly transmitted parasites were significantly more abundant on fished than on unfished islands, while the reverse was true for trophically transmitted parasites. This probably arises because trophically transmitted parasites require multiple host species, some of which are the top predators most sensitive to fishing impacts. The increase in directly transmitted parasites appeared to be due to fishing-driven compensatory increases in the abundance of their hosts. Together, these results provide support for the predictions of both heuristic models, and indicate that the direction of fishing's impact on parasite abundance is mediated by parasite traits, notably parasite transmission strategies.

  14. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  15. Juvenile Salmonid and Baitfish Distribution, Abundance and Prey Resources in Selected Areas of Grays Harbor, Washington

    DTIC Science & Technology

    1981-09-01

    size. 14i 188 The density-size distributions of the two species in freshwater also affect the degree of interspecific competition and pressure for...that physiological changes associated with smoltification, changes in population abundance or avail- = ability of food resources, or interspecific ... competition could have 52 depressed growth, but he was unable to offer direct evidence to support or refute any of these alternative hypotheses

  16. Lutzomyia longipalpis Presence and Abundance Distribution at Different Micro-spatial Scales in an Urban Scenario.

    PubMed

    Santini, María Soledad; Utgés, María Eugenia; Berrozpe, Pablo; Manteca Acosta, Mariana; Casas, Natalia; Heuer, Paola; Salomón, O Daniel

    2015-01-01

    The principal objective of this study was to assess a modeling approach to Lu. longipalpis distribution in an urban scenario, discriminating micro-scale landscape variables at microhabitat and macrohabitat scales and the presence from the abundance of the vector. For this objective, we studied vectors and domestic reservoirs and evaluated different environmental variables simultaneously, so we constructed a set of 13 models to account for micro-habitats, macro-habitats and mixed-habitats. We captured a total of 853 sandflies, of which 98.35% were Lu. longipalpis. We sampled a total of 197 dogs; 177 of which were associated with households where insects were sampled. Positive rK39 dogs represented 16.75% of the total, of which 47% were asymptomatic. Distance to the border of the city and high to medium density vegetation cover ended to be the explanatory variables, all positive, for the presence of sandflies in the city. All variables in the abundance model ended to be explanatory, trees around the trap, distance to the stream and its quadratic, being the last one the only one with negative coefficient indicating that the maximum abundance was associated with medium values of distance to the stream. The spatial distribution of dogs infected with L. infantum showed a heterogeneous pattern throughout the city; however, we could not confirm an association of the distribution with the variables assessed. In relation to Lu. longipalpis distribution, the strategy to discriminate the micro-spatial scales at which the environmental variables were recorded allowed us to associate presence with macrohabitat variables and abundance with microhabitat and macrohabitat variables. Based on the variables associated with Lu. longipalpis, the model will be validated in other cities and environmental surveillance, and control interventions will be proposed and evaluated in the microscale level and integrated with socio-cultural approaches and programmatic and village (mesoscale

  17. Lutzomyia longipalpis Presence and Abundance Distribution at Different Micro-spatial Scales in an Urban Scenario

    PubMed Central

    Santini, María Soledad; Utgés, María Eugenia; Berrozpe, Pablo; Manteca Acosta, Mariana; Casas, Natalia; Heuer, Paola; Salomón, O. Daniel

    2015-01-01

    The principal objective of this study was to assess a modeling approach to Lu. longipalpis distribution in an urban scenario, discriminating micro-scale landscape variables at microhabitat and macrohabitat scales and the presence from the abundance of the vector. For this objective, we studied vectors and domestic reservoirs and evaluated different environmental variables simultaneously, so we constructed a set of 13 models to account for micro-habitats, macro-habitats and mixed-habitats. We captured a total of 853 sandflies, of which 98.35% were Lu. longipalpis. We sampled a total of 197 dogs; 177 of which were associated with households where insects were sampled. Positive rK39 dogs represented 16.75% of the total, of which 47% were asymptomatic. Distance to the border of the city and high to medium density vegetation cover ended to be the explanatory variables, all positive, for the presence of sandflies in the city. All variables in the abundance model ended to be explanatory, trees around the trap, distance to the stream and its quadratic, being the last one the only one with negative coefficient indicating that the maximum abundance was associated with medium values of distance to the stream. The spatial distribution of dogs infected with L. infantum showed a heterogeneous pattern throughout the city; however, we could not confirm an association of the distribution with the variables assessed. In relation to Lu. longipalpis distribution, the strategy to discriminate the micro-spatial scales at which the environmental variables were recorded allowed us to associate presence with macrohabitat variables and abundance with microhabitat and macrohabitat variables. Based on the variables associated with Lu. longipalpis, the model will be validated in other cities and environmental surveillance, and control interventions will be proposed and evaluated in the microscale level and integrated with socio-cultural approaches and programmatic and village (mesoscale

  18. Distribution of known macrozooplankton abundance and biomass in the global ocean

    NASA Astrophysics Data System (ADS)

    Moriarty, R.; Buitenhuis, E. T.; Le Quéré, C.; Gosselin, M.-P.

    2013-07-01

    Macrozooplankton are an important link between higher and lower trophic levels in the oceans. They serve as the primary food for fish, reptiles, birds and mammals in some regions, and play a role in the export of carbon from the surface to the intermediate and deep ocean. Little, however, is known of their global distribution and biomass. Here we compiled a dataset of macrozooplankton abundance and biomass observations for the global ocean from a collection of four datasets. We harmonise the data to common units, calculate additional carbon biomass where possible, and bin the dataset in a global 1 × 1 degree grid. This dataset is part of a wider effort to provide a global picture of carbon biomass data for key plankton functional types, in particular to support the development of marine ecosystem models. Over 387 700 abundance data and 1330 carbon biomass data have been collected from pre-existing datasets. A further 34 938 abundance data were converted to carbon biomass data using species-specific length frequencies or using species-specific abundance to carbon biomass data. Depth-integrated values are used to calculate known epipelagic macrozooplankton biomass concentrations and global biomass. Global macrozooplankton biomass, to a depth of 350 m, has a mean of 8.4 μg C L-1, median of 0.2 μg C L-1 and a standard deviation of 63.5 μg C L-1. The global annual average estimate of macrozooplankton biomass in the top 350 m, based on the median value, is 0.02 Pg C. There are, however, limitations on the dataset; abundance observations have good coverage except in the South Pacific mid-latitudes, but biomass observation coverage is only good at high latitudes. Biomass is restricted to data that is originally given in carbon or to data that can be converted from abundance to carbon. Carbon conversions from abundance are restricted by the lack of information on the size of the organism and/or the absence of taxonomic information. Distribution patterns of global

  19. Monitoring change in the abundance and distribution of insects using butterflies and other indicator groups.

    PubMed

    Thomas, J A

    2005-02-28

    Conservative estimates suggest that 50-90% of the existing insect species on Earth have still to be discovered, yet the named insects alone comprise more than half of all known species of organism. With such poor baseline knowledge, monitoring change in insect diversity poses a formidable challenge to scientists and most attempts to generalize involve large extrapolations from a few well-studied taxa. Butterflies are often the only group for which accurate measures of change can be obtained. Four schemes, used successfully to assess change in British butterflies, that are increasingly being applied across the world are described: Red Data Books (RDB) list the best judgements of experts of the conservation status of species in their field of expertise; mapping schemes plot the changing distributions of species at scales of 1-100 km2; transect monitoring schemes generate time series of changes in abundance in sample populations of species on fixed sites across the UK; and occasional surveys measure the number, boundaries and size of all populations of a (usually RDB) species at intervals of 10-30 years. All schemes describe consistent patterns of change, but if they are to be more generally useful, it is important to understand how well butterflies are representative of other taxa. Comparisons with similarly measured changes in native bird and plant species suggest that butterflies have declined more rapidly that these other groups in Britain; it should soon be possible to test whether this pattern exists elsewhere. It is also demonstrated that extinction rates in British butterflies are similar to those in a range of other insect groups over 100 years once recording bias is accounted for, although probably lower than in aquatic or parasitic taxa. It is concluded that butterflies represent adequate indicators of change for many terrestrial insect groups, but recommended that similar schemes be extended to other popular groups, especially dragonflies, bumblebees

  20. Monitoring change in the abundance and distribution of insects using butterflies and other indicator groups

    PubMed Central

    Thomas, J.A

    2005-01-01

    Conservative estimates suggest that 50–90% of the existing insect species on Earth have still to be discovered, yet the named insects alone comprise more than half of all known species of organism. With such poor baseline knowledge, monitoring change in insect diversity poses a formidable challenge to scientists and most attempts to generalize involve large extrapolations from a few well-studied taxa. Butterflies are often the only group for which accurate measures of change can be obtained. Four schemes, used successfully to assess change in British butterflies, that are increasingly being applied across the world are described: Red Data Books (RDB) list the best judgements of experts of the conservation status of species in their field of expertise; mapping schemes plot the changing distributions of species at scales of 1–100 km2; transect monitoring schemes generate time series of changes in abundance in sample populations of species on fixed sites across the UK; and occasional surveys measure the number, boundaries and size of all populations of a (usually RDB) species at intervals of 10–30 years. All schemes describe consistent patterns of change, but if they are to be more generally useful, it is important to understand how well butterflies are representative of other taxa. Comparisons with similarly measured changes in native bird and plant species suggest that butterflies have declined more rapidly that these other groups in Britain; it should soon be possible to test whether this pattern exists elsewhere. It is also demonstrated that extinction rates in British butterflies are similar to those in a range of other insect groups over 100 years once recording bias is accounted for, although probably lower than in aquatic or parasitic taxa. It is concluded that butterflies represent adequate indicators of change for many terrestrial insect groups, but recommended that similar schemes be extended to other popular groups, especially dragonflies

  1. Changes in the distribution and abundance of albatrosses in the eastern Bering Sea: 1975-2010

    NASA Astrophysics Data System (ADS)

    Kuletz, Kathy J.; Renner, Martin; Labunski, Elizabeth A.; Hunt, George L.

    2014-11-01

    A number of marine species are showing poleward shifts in their distributions in response to climate warming. Three albatross species frequent the Bering Sea, the Laysan (Phoebastria immutabilis), the black-footed (Phoebastria nigripes), and the endangered short-tailed albatross (Phoebastria albatrus). To determine if albatrosses changed their distribution or abundance in the eastern Bering Sea between 1975 and 2010, we examined at-sea survey data using the North Pacific Pelagic Seabird Database. Within our study area, all three species of albatross occurred most frequently in the waters of the Aleutian Islands. In the eastern Bering Sea, all three species were most abundant near the shelf break, and in particular in the vicinity of the major submarine canyons in the shelf slope. Starting in the 1990s, population densities increased for all three albatross species, with a marked increase in the 2000s. In the 2000s, there was also an increase in the frequency at which albatrosses were recorded in the central and northern Bering Sea. Both black-footed and short-tailed albatrosses shifted the centers of their Bering Sea distributions northward. The Laysan albatross center of distribution shifted southward due to increased numbers along the southern shelf break, but densities also increased northward. We suggest that the observed changes in distribution and abundance of the three albatross species in the eastern Bering Sea may have been responses to an increase in the availability of squid, their primary prey, there. Additionally, the expansion of the distribution of the short-tailed albatross in the eastern Bering Sea may represent the reclamation of its previous range, now that the population is beginning to recover from near extinction caused by over harvesting. We suggest that predicted increases in ocean temperatures and northward movement of prey could result in albatrosses and other marine apex predators foraging farther north along the Bering Sea shelf and

  2. Comparison of five modelling techniques to predict the spatial distribution and abundance of seabirds

    USGS Publications Warehouse

    O'Connell, Allan F.; Gardner, Beth; Oppel, Steffen; Meirinho, Ana; Ramírez, Iván; Miller, Peter I.; Louzao, Maite

    2012-01-01

    Knowledge about the spatial distribution of seabirds at sea is important for conservation. During marine conservation planning, logistical constraints preclude seabird surveys covering the complete area of interest and spatial distribution of seabirds is frequently inferred from predictive statistical models. Increasingly complex models are available to relate the distribution and abundance of pelagic seabirds to environmental variables, but a comparison of their usefulness for delineating protected areas for seabirds is lacking. Here we compare the performance of five modelling techniques (generalised linear models, generalised additive models, Random Forest, boosted regression trees, and maximum entropy) to predict the distribution of Balearic Shearwaters (Puffinus mauretanicus) along the coast of the western Iberian Peninsula. We used ship transect data from 2004 to 2009 and 13 environmental variables to predict occurrence and density, and evaluated predictive performance of all models using spatially segregated test data. Predicted distribution varied among the different models, although predictive performance varied little. An ensemble prediction that combined results from all five techniques was robust and confirmed the existence of marine important bird areas for Balearic Shearwaters in Portugal and Spain. Our predictions suggested additional areas that would be of high priority for conservation and could be proposed as protected areas. Abundance data were extremely difficult to predict, and none of five modelling techniques provided a reliable prediction of spatial patterns. We advocate the use of ensemble modelling that combines the output of several methods to predict the spatial distribution of seabirds, and use these predictions to target separate surveys assessing the abundance of seabirds in areas of regular use.

  3. Distribution and abundance of western gray whales during a seismic survey near Sakhalin Island, Russia.

    PubMed

    Yazvenko, S B; McDonald, T L; Blokhin, S A; Johnson, S R; Meier, S K; Melton, H R; Newcomer, M W; Nielson, R M; Vladimirov, V L; Wainwright, P W

    2007-11-01

    Exxon Neftegas Limited, operator of the Sakhalin-1 consortium, is developing oil and gas reserves on the continental shelf off northeast Sakhalin Island, Russia. DalMorNefteGeofizika (DMNG), on behalf of the Sakhalin-1 consortium, conducted a 3-D seismic survey of the Odoptu license area during 17 August-9 September 2001. A portion of the primary known feeding area of the endangered western gray whale (Eschrichtius robustus) is located adjacent to the seismic block. The data presented here were collected as part of daily monitoring to determine if there was any measurable effect of the seismic survey on the distribution and abundance of western gray whales. Mitigation and monitoring program included aerial surveys conducted between 19 July and 19 November using the methodology outlined by the Southern California High Energy Seismic Survey team (HESS). These surveys provided documentation of the distribution, abundance and bottom feeding activity of western gray whales in relation to seismic survey sounds. From an operations perspective, the aerial surveys provided near real-time data on the location of whales in and outside the feeding area, and documented whether whales were displaced out of an area normally used as feeding habitat. The objectives of this study were to assess (a) temporal changes in the distribution and abundance of gray whales in relation to seismic survey, and (b) the influence of seismic survey, environmental factors, and other variables on the distribution and abundance of gray whales within their preferred feeding area adjacent to Piltun Bay. Multiple regression analysis revealed a limited redistribution of gray whales southward within the Piltun feeding area when the seismic survey was fully operational. A total of five environmental and other variables unrelated to seismic survey (date and proxies of depth, sea state and visibility) and one seismic survey-related variable (seg3d, i.e., received sound energy accumulated over 3 days) had

  4. Abundance and Distribution Characteristics of Microplastics in Surface Seawaters of the Incheon/Kyeonggi Coastal Region.

    PubMed

    Chae, Doo-Hyeon; Kim, In-Sung; Kim, Seung-Kyu; Song, Young Kyoung; Shim, Won Joon

    2015-10-01

    Microplastics in marine environments are of emerging concern due to their widespread distribution, their ingestion by various marine organisms, and their roles as a source and transfer vector of toxic chemicals. However, our understanding of their abundance and distribution characteristics in surface seawater (SSW) remains limited. We investigated microplastics in the surface microlayer (SML) and the SSW at 12 stations near-shore and offshore of the Korean west coast, Incheon/Kyeonggi region. Variation between stations, sampling media, and sampling methods were compared based on abundances, size distribution, and composition profiles of microsized synthetic polymer particles. The abundance of microplastics was greater in the SML (152,688 ± 92,384 particles/m(3)) than in SSW and showed a significant difference based on the sampling method for SSWs collected using a hand net (1602 ± 1274 particles/m(3)) and a zooplankton trawl net (0.19 ± 0.14 particles/m(3)). Ship paint particles (mostly alkyd resin polymer) accounted for the majority of microplastics detected in both SML and SSWs, and increased levels were observed around the voyage routes of large vessels. This indicates that polymers with marine-based origins become an important contributor to microplastics in coastal SSWs of this coastal region.

  5. Vertical distribution and diel patterns of zooplankton abundance and biomass at Conch Reef, Florida Keys (USA)

    PubMed Central

    Heidelberg, Karla B.; O'Neil, Keri L.; Bythell, John C.; Sebens, Kenneth P.

    2010-01-01

    Zooplankton play an important role in the trophic dynamics of coral reef ecosystems. Detailed vertical and temporal distribution and biomass of zooplankton were evaluated at four heights off the bottom and at six times throughout the diel cycle over a coral reef in the Florida Keys (USA). Zooplankton abundance averaged 4396 ± 1949 SD individuals m−3, but temporal and spatial distributions varied for individual zooplankton taxa by time of day and by height off the bottom. Copepods comprised 93–96% of the abundance in the samples. Taxon-based zooplankton CHN values paired with abundance data were used to estimate biomass. Average daily biomass ranged from 3.1 to 21.4 mg C m−3 and differed by both height off the bottom and by time of day. While copepods were the numerically dominant organisms, their contribution to biomass was only 35% of the total zooplankton biomass. Our findings provide important support for the new emerging paradigm of how zooplankton are distributed over reefs. PMID:20046854

  6. Abundance and distribution of immature mosquitoes in urban rivers proximate to their larval habitats.

    PubMed

    Ma, Minghai; Huang, Minsheng; Leng, Peien

    2016-11-01

    Whether ecological restoration of polluted urban rivers would provide suitable breeding habitats for some mosquitoes was not clear yet. It was therefore important to determine how altered river conditions influence mosquito ecology. Monthly data on water quality and larval density were obtained to determine the effects of river systems on the distribution and abundance of immature mosquitoes in two coastal cities in Eastern China. In total, 5 species within two genera of mosquitoes were collected and identified in habitat with vegetation from three positive rivers. Culex pipiens pallens was the most abundant and widely distributed species. A new species (Culex fuscanus) was reported in certain districts. Physico-chemical parameters of river water were important, but not the only, set of influences on immature mosquito breeding. Aquatic vegetation could increase the likelihood of mosquito breeding while artificial aeration might prevent the approach of mosquitoes. Slow-moving water might be a new potential marginal habitat type for some Culex and Aedes albopictus. Variation of river system with ecological restoration might influence the abundance and distribution of immature mosquitoes.

  7. Distribution and abundance of predators that affect duck production--prairie pothole region

    USGS Publications Warehouse

    Sargeant, A.B.; Greenwood, R.J.; Sovada, M.A.; Shaffer, T.L.

    1993-01-01

    During 1983-88, the relative abundance of 18 species and species-groups of mammalian and avian predators affecting duck production in the prairie pothole region was determined in 33 widely scattered study areas ranging in size from 23-26 km2. Accounts of each studied species and species-group include habitat and history, population structure and reported densities, and information on distribution and abundance from the present study. Index values of undetected, scarce, uncommon, common, or numerous were used to rate abundance of nearly all species in each study area. Principal survey methods were livetrapping of striped skunks (Mephitis mephitis) and Franklin's ground squirrels (Spermophilus franklinii), systematic searches for carnivore tracks in quarter sections (0.65 km2), daily records of sightings of individual predator species, and systematic searches for occupied nests of tree-nesting avian predators. Abundances of predators in individual areas were studied 1-3 years.The distribution and abundance of predator species throughout the prairie pothole region have undergone continual change since settlement of the region by Europeans in the late 1800's. Predator populations in areas we studied differed markedly from those of pristine times. The changes occurred from habitat alterations, human-inflicted mortality of predators, and interspecific relations among predator species. Indices from surveys of tracks revealed a decline in the abundance of red foxes (Vulpes vulpes) and an albeit less consistent decline in the abundance of raccoons (Procyon lotor) with an increase in the abundance of coyotes (Canis latrans). Records of locations of occupied nests revealed great horned owls (Bubo virginianus) and red-tailed hawks (Buteo jamaicensis) tended to nest 0.5 km apart, and American crows (Corvus brachyrhynchos) tended to avoid nesting 0.5 km of nests of red-tailed hawks. Excluding large gulls, for which no measurements of abundance were obtained, the number of

  8. Diversity and abundance of forest frogs (Anura: Leptodactylidae) before and after Hurricane Georges in the Cordillera Central of Puerto Rico

    USGS Publications Warehouse

    Vilella, F.J.; Fogarty, J.H.

    2005-01-01

    Caribbean hurricanes often impact terrestrial vertebrates in forested environments. On 21 September 1998, Hurricane Georges impacted Puerto Rico with sustained winds in excess of 166 km/hr, causing damage to forests of the island's principal mountain range; the Cordillera Central. We estimated forest frog abundance and diversity from call counts conducted along marked transects before and after Hurricane Georges in two forests reserves of the Cordillera Central (Maricao and Guilarte). We used distance sampling to estimate density of Eleutherodactylus coqui and recorded counts of other species. After the hurricane, the abundance of E. coqui increased in both reserves compared to prehurricane levels while abundance of other frog species decreased. In Maricao, relative abundance of E. richmondi (P = 0.013) and E. brittoni (P = 0.034) were significantly lower after the hurricane. Moreover, species richness and evenness of the Maricao and Guilarte frog assemblages declined after the hurricane. Our results on abundance patterns of the forest frog assemblages of Maricao and Guilarte Forests were similar to those reported from the Luquillo Experimental Forest after Hurricane Hugo in September 1989. Long-term demographic patterns of the forest frog assemblages in the Cordillera Central may be associated with changes due to the ecological succession in post-hurricane forests. Copyright 2005 College of Arts and Sciences.

  9. Landscape models of brook trout abundance and distribution in lotic habitat with field validation

    USGS Publications Warehouse

    McKenna, James E.; Johnson, James H.

    2011-01-01

    Brook trout Salvelinus fontinalis are native fish in decline owing to environmental changes. Predictions of their potential distribution and a better understanding of their relationship to habitat conditions would enhance the management and conservation of this valuable species. We used over 7,800 brook trout observations throughout New York State and georeferenced, multiscale landscape condition data to develop four regionally specific artificial neural network models to predict brook trout abundance in rivers and streams. Land cover data provided a general signature of human activity, but other habitat variables were resistant to anthropogenic changes (i.e., changing on a geological time scale). The resulting models predict the potential for any stream to support brook trout. The models were validated by holding 20% of the data out as a test set and by comparison with additional field collections from a variety of habitat types. The models performed well, explaining more than 90% of data variability. Errors were often associated with small spatial displacements of predicted values. When compared with the additional field collections (39 sites), 92% of the predictions were off by only a single class from the field-observed abundances. Among “least-disturbed” field collection sites, all predictions were correct or off by a single abundance class, except for one where brown trout Salmo trutta were present. Other degrading factors were evident at most sites where brook trout were absent or less abundant than predicted. The most important habitat variables included landscape slope, stream and drainage network sizes, water temperature, and extent of forest cover. Predicted brook trout abundances were applied to all New York streams, providing a synoptic map of the distribution of brook trout habitat potential. These fish models set benchmarks of best potential for streams to support brook trout under broad-scale human influences and can assist with planning and

  10. Vertical and horizontal distributions of microbial abundances and enzymatic activities in propylene-glycol-affected soils.

    PubMed

    Biró, Borbála; Toscano, Giuseppe; Horváth, Nikoletta; Matics, Heléna; Domonkos, Mónika; Scotti, Riccardo; Rao, Maria A; Wejden, Bente; French, Helen K

    2014-01-01

    The natural microbial activity in the unsaturated soil is vital for protecting groundwater in areas where high loads of biodegradable contaminants are supplied to the surface, which usually is the case for airports using aircraft de-icing fluids (ADF) in the cold season. Horizontal and vertical distributions of microbial abundance were assessed along the western runway of Oslo Airport (Gardermoen, Norway) to monitor the effect of ADF dispersion with special reference to the component with the highest chemical oxygen demand (COD), propylene glycol (PG). Microbial abundance was evaluated by several biondicators: colony-forming units (CFU) of some physiological groups (aerobic and anaerobic heterotrophs and microscopic fungi), most probable numbers (MPN) of PG degraders, selected catabolic enzymatic activities (fluorescein diacetate (FDA) hydrolase, dehydrogenase, and β-glucosidase). High correlations were found between the enzymatic activities and microbial counts in vertical soil profiles. All microbial abundance indicators showed a steep drop in the first meter of soil depth. The vertical distribution of microbial abundance can be correlated by a decreasing exponential function of depth. The horizontal trend of microbial abundance (evaluated as total aerobic CFU, MPN of PG-degraders, and FDA hydrolase activity) assessed in the surface soil at an increasing distance from the runway is correlated negatively with the PG and COD loads, suggesting the relevance of other chemicals in the modulation of microbial growth. The possible role of potassium formate, component of runway de-icers, has been tested in the laboratory by using mixed cultures of Pseudomonas spp., obtained by enrichment with a selective PG medium from soil samples taken at the most contaminated area near the runway. The inhibitory effect of formate on the growth of PG degraders is proven by the reduction of biomass yield on PG in the presence of formate.

  11. Distribution and relative abundance of fishes in littoral areas of Chief Joseph Reservoir, Columbia River

    USGS Publications Warehouse

    Gadomski, Dena M.; Venditti, David A.; Robinson, T. Craig; Beeman, John W.; Maule, Alec G.

    2004-01-01

    We surveyed fish assemblages in littoral areas of Chief Joseph Reservoir of the upper Columbia River to aid in understanding this ecosystem. Fish distributions and abundances were examined during April-July 1999 in relation to environmental conditions in the reservoir. We also compared the fish assemblages in Chief Joseph reservoir in 1999 to a past study conducted during 1974-1975, and to assemblages in other areas of the Columbia River. During 67 hr of electrofishing and 78 beach seine hauls in Chief Joseph Reservoir, 7460 fishes representing 8 families were collected. The majority of the catch was native – northern pikeminnow; redside shiners; longnose, bridgelip, and largescale suckers; and sculpins. The most abundant introduced species was walleye, and one species, rainbow trout, was mostly of net-pen origin. Larger sizes of suckers and northern pikeminnow were most abundant in the upper reservoir, likely due to upstream spawning migrations. The lower reservoir contained greater abundances of smaller fishes, and this area had lower flows, smaller substrates, and more complex shorelines that offered these fishes refugia. Only adult suckers displayed significant differences in abundances related to substrate. The relative abundances of species appeared to have changed since the 1970s, when the dominant fishes were northern pikeminnow, peamouth, largescale suckers, and walleye. Fish assemblage differences between Chief Joseph Reservoir and lower Columbia River reservoirs were also evident due to the morphology of the reservoir, its more northerly location, and the lack of fish passage facilities at Chief Joseph Dam. Our study is one of the few descriptions of fishes in the upper Columbia Rivers.

  12. Predicting probability of occurrence and factors affecting distribution and abundance of three Ozark endemic crayfish species at multiple spatial scales

    USGS Publications Warehouse

    Nolen, Matthew S.; Magoulick, Daniel D.; DiStefano, Robert J.; Imhoff, Emily M.; Wagner, Brian K.

    2014-01-01

    We found that a range of environmental variables were important in predicting crayfish distribution and abundance at multiple spatial scales and their importance was species-, response variable- and scale dependent. We would encourage others to examine the influence of spatial scale on species distribution and abundance patterns.

  13. Species richness, distribution and genetic diversity of Caenorhabditis nematodes in a remote tropical rainforest

    PubMed Central

    2013-01-01

    Background In stark contrast to the wealth of detail about C. elegans developmental biology and molecular genetics, biologists lack basic data for understanding the abundance and distribution of Caenorhabditis species in natural areas that are unperturbed by human influence. Methods Here we report the analysis of dense sampling from a small, remote site in the Amazonian rain forest of the Nouragues Natural Reserve in French Guiana. Results Sampling of rotting fruits and flowers revealed proliferating populations of Caenorhabditis, with up to three different species co-occurring within a single substrate sample, indicating remarkable overlap of local microhabitats. We isolated six species, representing the highest local species richness for Caenorhabditis encountered to date, including both tropically cosmopolitan and geographically restricted species not previously isolated elsewhere. We also documented the structure of within-species molecular diversity at multiple spatial scales, focusing on 57 C. briggsae isolates from French Guiana. Two distinct genetic subgroups co-occur even within a single fruit. However, the structure of C. briggsae population genetic diversity in French Guiana does not result from strong local patterning but instead presents a microcosm of global patterns of differentiation. We further integrate our observations with new data from nearly 50 additional recently collected C. briggsae isolates from both tropical and temperate regions of the world to re-evaluate local and global patterns of intraspecific diversity, providing the most comprehensive analysis to date for C. briggsae population structure across multiple spatial scales. Conclusions The abundance and species richness of Caenorhabditis nematodes is high in a Neotropical rainforest habitat that is subject to minimal human interference. Microhabitat preferences overlap for different local species, although global distributions include both cosmopolitan and geographically restricted

  14. Large-Scale Geographic Variation in Distribution and Abundance of Australian Deep-Water Kelp Forests

    PubMed Central

    Marzinelli, Ezequiel M.; Williams, Stefan B.; Babcock, Russell C.; Barrett, Neville S.; Johnson, Craig R.; Jordan, Alan; Kendrick, Gary A.; Pizarro, Oscar R.; Smale, Dan A.; Steinberg, Peter D.

    2015-01-01

    Despite the significance of marine habitat-forming organisms, little is known about their large-scale distribution and abundance in deeper waters, where they are difficult to access. Such information is necessary to develop sound conservation and management strategies. Kelps are main habitat-formers in temperate reefs worldwide; however, these habitats are highly sensitive to environmental change. The kelp Ecklonia radiate is the major habitat-forming organism on subtidal reefs in temperate Australia. Here, we provide large-scale ecological data encompassing the latitudinal distribution along the continent of these kelp forests, which is a necessary first step towards quantitative inferences about the effects of climatic change and other stressors on these valuable habitats. We used the Autonomous Underwater Vehicle (AUV) facility of Australia’s Integrated Marine Observing System (IMOS) to survey 157,000 m2 of seabed, of which ca 13,000 m2 were used to quantify kelp covers at multiple spatial scales (10–100 m to 100–1,000 km) and depths (15–60 m) across several regions ca 2–6° latitude apart along the East and West coast of Australia. We investigated the large-scale geographic variation in distribution and abundance of deep-water kelp (>15 m depth) and their relationships with physical variables. Kelp cover generally increased with latitude despite great variability at smaller spatial scales. Maximum depth of kelp occurrence was 40–50 m. Kelp latitudinal distribution along the continent was most strongly related to water temperature and substratum availability. This extensive survey data, coupled with ongoing AUV missions, will allow for the detection of long-term shifts in the distribution and abundance of habitat-forming kelp and the organisms they support on a continental scale, and provide information necessary for successful implementation and management of conservation reserves. PMID:25693066

  15. Distribution of viral abundance in the reef environment of Key Largo, Florida.

    PubMed

    Paul, J H; Rose, J B; Jiang, S C; Kellogg, C A; Dickson, L

    1993-03-01

    The distribution of viral and microbial abundance in the Key Largo, Fla., reef environment was measured. Viral abundance was measured by transmission electron microscope direct counts and plaque titer on specific bacterial hosts in water and sediment samples from Florida Bay (Blackwater Sound) and along a transect from Key Largo to the outer edge of the reef tract in Key Largo Sanctuary. Water column viral direct counts were highest in Blackwater Sound of Florida Bay (1.2 x 10(7) viruses per ml), decreased to the shelf break (1.7 x 10(6) viruses per ml), and were inversely correlated with salinity (r = -0.97). Viral direct counts in sediment samples ranged from 1.35 x 10(8) to 5.3 x 10(8)/cm(3) of sediment and averaged nearly 2 orders of magnitude greater than counts in the water column. Viral direct counts (both sediment and water column measurements) exceeded plaque titers on marine bacterial hosts (Vibrio natriegens and others) by 7 to 8 orders of magnitude. Water column viral abundance did not correlate with bacterial direct counts or chlorophyll a measurements, and sediment viral parameters did not correlate with water column microbial, viral, or salinity data. Coliphage, which are indicators of fecal pollution, were detected in two water column samples and most sediment samples, yet their concentrations were relatively low (<2 to 15/liter for water column samples, and <2 to 108/cm(3) of sediment). Our findings indicate that viruses are abundant in the Key Largo environment, particularly on the Florida Bay side of Key Largo, and that processes governing their distribution in the water column (i.e., salinity and freshwater input) are independent of those governing their distribution in the sediment environment.

  16. Do Stacked Species Distribution Models Reflect Altitudinal Diversity Patterns?

    PubMed Central

    Mateo, Rubén G.; Felicísimo, Ángel M.; Pottier, Julien; Guisan, Antoine; Muñoz, Jesús

    2012-01-01

    The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed. PMID

  17. Distribution of known macrozooplankton abundance and biomass in the global ocean

    NASA Astrophysics Data System (ADS)

    Moriarty, R.; Buitenhuis, E. T.; Le Quéré, C.; Gosselin, M.-P.

    2012-04-01

    Macrozooplankton are an important link between higher and lower trophic levels in the oceans. They serve as the primary food for fish, reptiles, birds and mammals in some regions, and play a role in the export of carbon from the surface to the intermediate and deep ocean. Little, however, is known of their global distribution and biomass. Here we compiled a dataset of macrozooplankton abundance and biomass observations for the global ocean from a collection of four datasets. We harmonise the data to common units, calculate additional carbon biomass where possible, and bin the dataset in a global 1 × 1 degree grid. This dataset is part of a wider effort to provide a global picture of carbon biomass data for key plankton functional types, in particular to support the development of marine ecosystem models. Over 387 700 abundance data and 1330 carbon biomass data have been collected from pre-existing datasets. A further 34 938 abundance data were converted to carbon biomass data using species-specific length frequencies or using species-specific abundance to carbon biomass data. Depth-integrated values are used to calculate known epipelagic macrozooplankton biomass concentrations and global biomass. Global macrozooplankton biomass has a mean of 8.4 μg C l-1, median of 0.15 μg C l-1 and a standard deviation of 63.46 μg C l-1. The global annual average estimate of epipelagic macrozooplankton, based on the median value, is 0.02 Pg C. Biomass is highest in the tropics, decreasing in the sub-tropics and increasing slightly towards the poles. There are, however, limitations on the dataset; abundance observations have good coverage except in the South Pacific mid latitudes, but biomass observation coverage is only good at high latitudes. Biomass is restricted to data that is originally given in carbon or to data that can be converted from abundance to carbon. Carbon conversions from abundance are restricted in the most part by the lack of information on the size of the

  18. Abundance, distribution and size structure of Diadema antillarum (Echinodermata: Diadematidae) in South Eastern Cuban coral reefs.

    PubMed

    Martín Blanco, F; González Sansón, G; Pina Amargós, F; Clero Alonso, L

    2010-06-01

    The 1983-1984 mass mortality event of Diadema antillarum affected more than 93% of the total Caribbean population. Although there are no records about the status of Diadema populations before and after die-off on Cuban reefs, anecdotal information suggests that populations were struck. We analyzed spatial variation in the abundance and size structure of D. antillarum in 22 reefs sites in Jardines de la Reina, from June 2004 to September 2005. Counts of Diadema were performed in five 30x2 m transects at each sampling site and sampling time, and test diameters were measured in September 2005 at the same fore reefs. Abundances were higher at reef crests (mean densities 0.08-2.18 ind./m2), while reef slope populations reached a maximum site level of 0.13 ind./m2 at only one site and showed values up to three orders of magnitude lower than those from reef crests. Highest abundance occurred at the west margin of major channels between keys where larval recruitment seems to be favored by local oceanographic features and facilitated by the abundance of Echinometra lucunter. The size frequency distribution of D. antillarum indicates that recruitment began to be noticeable three years before September 2005, suggesting these populations were depleted in the past and they are recovering now.

  19. At-sea distribution and abundance of seabirds off southern California: A 20-year comparison

    USGS Publications Warehouse

    Mason, J.W.; McChesney, G.J.; McIver, W.R.; Carter, H.R.; Takekawa, J.Y.; Golightly, R.T.; Ackerman, J.T.; Orthmeyer, D.L.; Perry, W.M.; Yee, J.L.; Pierson, M.O.; McCrary, M.D.

    2007-01-01

    We conducted aerial at-sea and coastal surveys to examine the distribution and abundance of seabirds off southern California, from Cambria, California, to the Mexican border. From May 1999-January 2002, we flew 102 d, covered >54,640 km of transect lines, and conducted nine complete surveys of southern California in January, May, and September. We identified 54 species comprising 12 families and counted >135,000 individuals. Seabird densities were greater along island and mainland coastlines than at sea and were usually greatest in January surveys. Densities were greatest at sea near the northern Channel Islands in January and north of Point Conception in May, and lowest in the southwestern portion of the Southern California Bight in all survey months. On coastal transects, seabird densities were greatest along central and southern portions of the mainland coastline from Point Arguello to Mexico. We estimated that 981,000 ?? 144,000 (x?? ?? SE) seabirds occurred in the study area in January, 862,000 ?? 95,000 in May, and 762,000 ?? 72,000 in September. California Gulls (Larus californicus), Western Grebes (Aechmophorus occidentalis), and Cassin's Auklets (Ptychoramphus aleuticus) were most abundant in January surveys at sea, whereas Sooty and Short-tailed shearwaters (Puffinus griseus and P. tenuirostris), phalaropes (Phalaropus spp.), and Western Gulls (Larus. occidentalis) were most abundant in May and September surveys. On coastal transects, California Gulls, Western Grebes, Western Gulls, and Surf Scoters (Melanitta perspicillata) were most abundant in January; Western Grebes, Western Gulls, Surf Scoters, and Brown Pelicans (Pelecanus occidentalis) were most abundant in May; and Sooty Shearwaters, Short-tailed Shearwaters, Western Gulls, Western Grebes, Brown Pelicans, and Heermann's Gulls (Larus heermanni) were most abundant in September. Compared to historical seabird densities collected in the same area two decades ago (1975-1978 and 1980-1983), abundance

  20. Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice.

    PubMed

    Yuan, Hongzhao; Ge, Tida; Chen, Xiangbi; Liu, Shoulong; Zhu, Zhenke; Wu, Xiaohong; Wei, Wenxue; Whiteley, Andrew Steven; Wu, Jinshui

    2015-11-01

    Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator

  1. Anopheles larval abundance and diversity in three rice agro-village complexes Mwea irrigation scheme, central Kenya

    PubMed Central

    2010-01-01

    Background The diversity and abundance of Anopheles larvae has significant influence on the resulting adult mosquito population and hence the dynamics of malaria transmission. Studies were conducted to examine larval habitat dynamics and ecological factors affecting survivorship of aquatic stages of malaria vectors in three agro-ecological settings in Mwea, Kenya. Methods Three villages were selected based on rice husbandry and water management practices. Aquatic habitats in the 3 villages representing planned rice cultivation (Mbui Njeru), unplanned rice cultivation (Kiamachiri) and non-irrigated (Murinduko) agro-ecosystems were sampled every 2 weeks to generate stage-specific estimates of mosquito larval densities, relative abundance and diversity. Records of distance to the nearest homestead, vegetation coverage, surface debris, turbidity, habitat stability, habitat type, rice growth stage, number of rice tillers and percent Azolla cover were taken for each habitat. Results Captures of early, late instars and pupae accounted for 78.2%, 10.9% and 10.8% of the total Anopheles immatures sampled (n = 29,252), respectively. There were significant differences in larval abundance between 3 agro-ecosystems. The village with 'planned' rice cultivation had relatively lower Anopheles larval densities compared to the villages where 'unplanned' or non-irrigated. Similarly, species composition and richness was higher in the two villages with either 'unplanned' or limited rice cultivation, an indication of the importance of land use patterns on diversity of larval habitat types. Rice fields and associated canals were the most productive habitat types while water pools and puddles were important for short periods during the rainy season. Multiple logistic regression analysis showed that presence of other invertebrates, percentage Azolla cover, distance to nearest homestead, depth and water turbidity were the best predictors for Anopheles mosquito larval abundance. Conclusion

  2. Distribution and abundance of marine bird and pinniped populations within Port Foster, Deception Island, Antarctica

    NASA Astrophysics Data System (ADS)

    Kendall, Katrina A.; Ruhl, Henry A.; Wilson, Robert C.

    2003-06-01

    Seabirds and pinnipeds were surveyed during four cruises from March 1999 to November 2000 at Port Foster, Deception Island, Antarctica. Abundances and distributions of three species of pinnipeds, Arctocephalus gazella (Antarctic fur seals), Leptonychotes weddelli (Weddell seals), and Lobodon carcinophagus (crabeater seals), and 11 species of marine birds were documented within Port Foster. A. gazella was the dominant pinniped within Port Foster; its abundance has increased since the 1986/87 austral summer season. A. gazella were concentrated at the entrance to Port Foster. More pinnipeds were observed during the austral summer than during the spring. The most dominant seabird, Pygoscelis antarctica (chinstrap penguin), was concentrated along the rocky cliffs behind the beaches where A. gazella hauled out. Larus dominicanus (kelp gull) and Daption capense (cape petrel) were the most dominant flying seabirds. All other seabird species were more widely distributed around Port Foster than P. antarctica. There was no clear trend in abundances of seabirds over the study period. It is possible that the protected area of Port Foster provides refuge for vagrants of colonies along the outer periphery of the island and as a stopover point for migrating species.

  3. Salinity-driven shifts in the activity, diversity, and abundance of anammox bacteria of estuarine and coastal wetlands

    NASA Astrophysics Data System (ADS)

    Jiang, Xiaofen; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Gao, Juan; Li, Xiaofei; Wang, Rong; Yu, Chendi; Lin, Xianbiao

    2017-02-01

    Anaerobic ammonium oxidation (anammox) plays a significant role in nitrogen removal in estuarine and coastal wetlands. However, the effects of changing salinity on anammox activity and anammox bacterial dynamics in these environments are not well understood. In this study, serial incubation experiments with a salinity gradient (0-40) were conducted to explore the responses of anammox bacterial activity, diversity and abundance to the changing salinity in the intertidal wetland of the Yangtze Estuary. Results show that activity and abundance of anammox bacteria firstly increased with the increase of salinity, but they were physiologically stressed by high-level salinity (>30) in a short-term incubation (<10 days). However, the treatment with salinity of 5 showed the maximal anammox activity and anammox bacterial abundance after a long-term incubation (60-120 days). In addition, Kuenenia (Kuenenia stuttgartiensis), Scalindua (Scalindua wagner, marina, and brodae), and three unknown anammox-like groups were observed, and anammox bacterial diversity increased along the salinity gradient. Anammox community structure varied slightly within the first 10-day incubation, but the dominant anammox bacterial group shifted from Kuenenia to Scalindua with increasing salinity after the long-term incubation. Overall, this study demonstrates the effects of salinity on anammox bacterial community and anammox activity, and suggests the importance of salinity in regulating the anammox process in estuarine and coastal wetlands with frequent salinity fluctuation.

  4. The diversity and abundance of bacteria and oxygenic phototrophs in saline biological desert crusts in Xinjiang, northwest China.

    PubMed

    Li, Ke; Liu, Ruyin; Zhang, Hongxun; Yun, Juanli

    2013-07-01

    Although microorganisms, particularly oxygenic phototrophs, are known as the major players in the biogeochemical cycles of elements in desert soil ecosystems and have received extensive attention, still little is known about the effects of salinity on the composition and abundances of microbial community in desert soils. In this study, the diversity and abundance of bacteria and oxygenic phototrophs in biological desert crusts from Xinjiang province, which were under different salinity conditions, were investigated by using clone library and quantitative PCR (qPCR). The 16S rRNA gene phylogenetic analysis showed that cyanobacteria, mainly Microcoleus vagnitus of the order Oscillatoriales, were predominant in the low saline crusts, while other phototrophs, such as diatom, were the main microorganism group responsible for the oxygenic photosynthesis in the high saline crusts. Furthermore, the higher salt content in crusts may stimulate the growth of other bacteria, including Deinococcus-Thermus, Bacteroidetes, and some subdivisions of Proteobacteria (β-, γ-, and δ-Proteobacteria). The cpcBA-IGS gene analysis revealed the existence of novel M. vagnitus strains in this area. The qPCR results showed that the abundance of oxygenic phototrophs was significantly higher under lower saline condition than that in the higher saline crusts, suggesting that the higher salinity in desert crusts could suppress the numbers of total bacteria and phototrophic bacteria but did highly improve the diversity of salt-tolerant bacteria.

  5. Checklist, diversity and distribution of testate amoebae in Chile.

    PubMed

    Fernández, Leonardo D; Lara, Enrique; Mitchell, Edward A D

    2015-10-01

    Bringing together more than 170 years of data, this study represents the first attempt to construct a species checklist and analyze the diversity and distribution of testate amoebae in Chile, a country that encompasses the southwestern region of South America, countless islands and part of the Antarctic. In Chile, known diversity includes 416 testate amoeba taxa (64 genera, 352 infrageneric taxa), 24 of which are here reported for the first time. Species-accumulation plots show that in Chile, the number of testate amoeba species reported has been continually increasing since the mid-19th century without leveling off. Testate amoebae have been recorded in 37 different habitats, though they are more diverse in peatlands and rainforest soils. Only 11% of species are widespread in continental Chile, while the remaining 89% of the species exhibit medium or short latitudinal distribution ranges. Also, species composition of insular Chile and the Chilean Antarctic territory is a depauperated subset of that found in continental Chile. Nearly, the 10% of the species reported here are endemic to Chile and many of them are distributed only within the so-called Chilean biodiversity hotspot (ca. 25° S-47° S). These findings are here thoroughly discussed in a biogeographical and evolutionary context.

  6. Soft-sediment crustacean diversity and distribution along the Portuguese continental shelf

    NASA Astrophysics Data System (ADS)

    Sampaio, Leandro; Mamede, Renato; Ricardo, Fernando; Magalhães, Luísa; Rocha, Hélder; Martins, Roberto; Dauvin, Jean-Claude; Rodrigues, Ana Maria; Quintino, Victor

    2016-11-01

    This study analyzed the crustacean diversity, distribution and relationship with environmental factors in the western and the southern Portuguese continental shelf, between 10 and 200 m depth. A total of 10,639 specimens belonging to 242 taxa from 90 families were identified, mostly amphipods (55.8% of the total taxa). The mysid Gastrosaccus spinifer and the amphipods Socarnes erythrophthalmus and Cheirocratus sundevallii were the most abundant and the amphipods Ampelisca brevicornis, Leucothoe incisa and Autonoe spiniventris were the most frequent species. The highest abundance and diversity was found in coarser sediments with up to 306 individuals per 0.1 m2. Alpha diversity ranged from 1 to 28 sp./0.1 m2. Moreover, this study confirmed six previously doubtful first records and added an additional 19 new records to the Portuguese fauna. The results also confirmed the Portuguese coast as a transition zone of mixed Atlantic and Mediterranean faunas and exposed a noticeable North African and Macaronesian influence. A multivariate analysis based on the abundance of crustaceans revealed six affinity groups characterized by: (a) C. sundevallii, Guernea (Guernea) coalita and Sarsinebalia cristoboi on very coarse sands; (b) G. spinifer, Nototropis falcatus and Pontocrates arenarius on coarse sands; (c) Othomaera othonis, Processa modica modica and Animoceradocus semiserratus on heterogeneous medium sands; (d) A. brevicornis, Urothoe pulchella and Necalianassa truncata on fine sands; (e) Ampelisca pectenata, Bodotria scorpioides and Astacilla dilatata on heterogeneous fine sands and (f) Callianassa subterranea, Ampelisca tenuicornis and Ampelisca typica on muddy fine sands. Sediment grain-size and depth were the variables best related to the benthic crustacean spatial distribution patterns along the Portuguese continental shelf.

  7. Bison grazing increases arthropod abundance and diversity in a tallgrass prairie.

    PubMed

    Moran, Matthew D

    2014-10-01

    How grazing-induced ecosystem changes by ungulates indirectly affect other consumers is a question of great interest. I investigated the effect of grazing by American Bison (Bos bison L.) on an arthropod community in tallgrass prairie. Grazing increased the abundance of arthropods, an increase that was present in both herbivorous and carnivorous assemblages, but not in detritivores. The increase in herbivores and reduction in plant biomass from grazing resulted in an arthropod herbivore load almost three times higher in grazed plots compared with controls. Among herbivores, the sap-feeding insect guild was dramatically more abundant, while chewing herbivores were not affected. Herbivorous and carnivorous arthropod richness was higher in grazed plots, although the response was strongest among herbivores. Arthropod abundance on individual grasses and forbs was significantly higher in grazed areas, while plant type had no effect on abundance, indicating that the change was ecosystem-wide and not simply in response to a reduction in grass biomass from grazing. The response of arthropods to grazing was strongest in the early part of the growing season. Published research shows that ungulate grazing, although decreasing available biomass to other consumers, enhances plant quality by increasing nitrogen level in plants. The arthropod results of this study suggest higher plant quality outweighs the potential negative competitive effects of plant biomass removal, although other activities of bison could not be ruled out as the causative mechanism. Because arthropods are extremely abundant organisms in grasslands and a food source for other consumers, bison may represent valuable management tools for maintaining biodiversity.

  8. Review of factors affecting the distribution and abundance of waterfowl in shallow-water habitats of Chesapeake Bay

    USGS Publications Warehouse

    Perry, M.C.; Deller, A.S.

    1996-01-01

    Long-term trends of waterfowl populations in Chesapeake Bay demonstrate the importance of shallow-water habitats for waterfowl species. Although recent increases in field feeding by geese and swans lessened the importance of shallow-water areas for these species, most duck species depend almost exclusively on shallow-water habitats. Many factors influenced the distribution and abundance of waterfowl in shallow-water habitats. Habitat degradation resulted in the decline in numbers of most duck species and a change in distribution of some species. Increased numbers of mallards (Anas platyrhynchos) in recent decades probably resulted from release programs conducted by the Maryland Department of Natural Resources and private individuals. Studies of food habits since 1885 showed a decline in submerged-aquatic vegetation in the diet of some species, such as the canvasback (Aythya valisineria ), and an increase in the proportions of invertebrates in the diet. Diversity of food organisms for many waterfowl species has declined. Surveys of vegetation and invertebrates in the Chesapeake Bay generally reflect a degradation of shallow-water habitat. Human population increases in the Chesapeake Bay watershed directly and indirectly affected waterfowl distribution and abundance. The increase of exotic plant and invertebrate species in the bay, in most cases, benefited waterfowl populations. Increased contaminants have reduced the quality and quantity of habitat, although serious attempts to reverse this trend are underway. The use of shallow-water habitats by humans for fishing, hunting, boating, and other recreational and commercial uses reduced the use of shallow-water habitats by waterfowl. Humans can lessen the adverse influences on the valuable shallow-water habitats by restricting human population growth near these habitats and improving the water quality of the bay tributaries. Other affirmative actions that will improve these areas for waterfowl include greater

  9. Fitting statistical distributions to sea duck count data: implications for survey design and abundance estimation

    USGS Publications Warehouse

    Zipkin, Elise F.; Leirness, Jeffery B.; Kinlan, Brian P.; O'Connell, Allan F.; Silverman, Emily D.

    2014-01-01

    Determining appropriate statistical distributions for modeling animal count data is important for accurate estimation of abundance, distribution, and trends. In the case of sea ducks along the U.S. Atlantic coast, managers want to estimate local and regional abundance to detect and track population declines, to define areas of high and low use, and to predict the impact of future habitat change on populations. In this paper, we used a modified marked point process to model survey data that recorded flock sizes of Common eiders, Long-tailed ducks, and Black, Surf, and White-winged scoters. The data come from an experimental aerial survey, conducted by the United States Fish & Wildlife Service (USFWS) Division of Migratory Bird Management, during which east-west transects were flown along the Atlantic Coast from Maine to Florida during the winters of 2009–2011. To model the number of flocks per transect (the points), we compared the fit of four statistical distributions (zero-inflated Poisson, zero-inflated geometric, zero-inflated negative binomial and negative binomial) to data on the number of species-specific sea duck flocks that were recorded for each transect flown. To model the flock sizes (the marks), we compared the fit of flock size data for each species to seven statistical distributions: positive Poisson, positive negative binomial, positive geometric, logarithmic, discretized lognormal, zeta and Yule–Simon. Akaike’s Information Criterion and Vuong’s closeness tests indicated that the negative binomial and discretized lognormal were the best distributions for all species for the points and marks, respectively. These findings have important implications for estimating sea duck abundances as the discretized lognormal is a more skewed distribution than the Poisson and negative binomial, which are frequently used to model avian counts; the lognormal is also less heavy-tailed than the power law distributions (e.g., zeta and Yule–Simon), which are

  10. Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

    PubMed Central

    Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  11. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  12. Impact of copper on the abundance and diversity of sulfate-reducing prokaryotes in two chilean marine sediments.

    PubMed

    Besaury, Ludovic; Ouddane, Baghdad; Pavissich, Juan Pablo; Dubrulle-Brunaud, Carole; González, Bernardo; Quillet, Laurent

    2012-10-01

    We studied the abundance and diversity of the sulfate-reducing prokaryotes (SRPs) in two 30-cm marine chilean sediment cores, one with a long-term exposure to copper-mining residues, the other being a non-exposed reference sediment. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and showed that SRPs are sensitive to high copper concentrations, as the mean number of SRPs all along the contaminated sediment was two orders of magnitude lower than in the reference sediment. SRP diversity was analyzed by using the dsrB-sequences-based PCR-DGGE method and constructing gene libraries for dsrB-sequences. Surprisingly, the diversity was comparable in both sediments, with dsrB sequences belonging to Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae, SRP families previously described in marine sediments, and to a deep branching dsrAB lineage. The hypothesis of the presence of horizontal transfer of copper resistance genes in the microbial population of the polluted sediment is discussed.

  13. Abundance and diversity of ammonia-oxidizing bacteria in relation to ammonium in a chinese shallow eutrophic urban lake

    PubMed Central

    Qiu, Shanlian; Chen, Guoyuan; Zhou, Yiyong

    2010-01-01

    The measures of most-probable-number and restriction fragment length polymorphism analysis were used to analyze the abundance and diversity of ammonia-oxidizing bacteria in sediment of a Chinese shallow eutrophic urban lake (Lake Yuehu). Among the 5 sampling sites, ammonia concentration in interstitial water was positively proportional not only to the content of organic matter, but also to ammonia-oxidizing bacteria numbers (at a magnitude of 105 cells g-1 dry weight) in sediment significantly. Furthermore, the diversity of ammonia-oxidizing bacteria were determined by means of PCR primers targeting the amoA gene with five gene libraries created and restriction pattern analysis. The 13 restriction patterns were recorded with 4 ones being common among all sampling sites. The 8 restriction patterns including 4 unique ones were found at the site with the highest NH4+ concentrations in interstitial water, while, there were only common patterns without unique ones at the site with the lowest NH4+ concentrations in interstitial water. Phylogenetic analysis showed that the amoA fragments retrieved belong to Nitrosomonas oligotropha & ureae lineage, N. europaea lineage, N. communis lineage and Nitrosospira lineage, most of which were affiliated with the genus Nitrosomonas. The N. oligotropha & ureae-like bacteria were the dominant species. Thus, the abundance and diversity of sediment AOB is closely linked to ammonium status in eutrophic lakes. PMID:24031484

  14. Abundance, trends and distribution of baleen whales off Western Alaska and the central Aleutian Islands

    NASA Astrophysics Data System (ADS)

    Zerbini, Alexandre N.; Waite, Janice M.; Laake, Jeffrey L.; Wade, Paul R.

    2006-11-01

    Large whales were extensively hunted in coastal waters off Alaska, but current distribution, population sizes and trends are poorly known. Line transect surveys were conducted in coastal waters of the Aleutian Islands and the Alaska Peninsula in the summer of 2001-2003. Abundances of three species were estimated by conventional and multiple covariate distance sampling (MCDS) methods. Time series of abundance estimates were used to derive rates of increase for fin whales ( Balaenoptera physalus) and humpback whales ( Megaptera novaeangliae). Fin whales occurred primarily from the Kenai Peninsula to the Shumagin Islands, but were abundant only near the Semidi Islands and Kodiak. Humpback whales were found from the Kenai Peninsula to Umnak Island and were more abundant near Kodiak, the Shumagin Islands and north of Unimak Pass. Minke whales ( B. acutorostrata) occurred primarily in the Aleutian Islands, with a few sightings south of the Alaska Peninsula and near Kodiak Island. Humpback whales were observed in large numbers in their former whaling grounds. In contrast, high densities of fin whales were not observed around the eastern Aleutian Islands, where whaling occurred. Average abundance estimates (95% CI) for fin, humpback and minke whales were 1652 (1142-2389), 2644 (1899-3680), and 1233 (656-2315), respectively. Annual rates of increase were estimated at 4.8% (95% CI=4.1-5.4%) for fin and 6.6% (5.2-8.6%) for humpback whales. This study provides the first estimate of the rate of increase of fin whales in the North Pacific Ocean. The estimated trends are consistent with those of other recovering baleen whales. There were no sightings of blue or North Pacific right whales, indicating the continued depleted status of these species.

  15. Probabilisitc Geobiological Classification Using Elemental Abundance Distributions and Lossless Image Compression in Recent and Modern Organisms

    NASA Technical Reports Server (NTRS)

    Storrie-Lombardi, Michael C.; Hoover, Richard B.

    2005-01-01

    Last year we presented techniques for the detection of fossils during robotic missions to Mars using both structural and chemical signatures[Storrie-Lombardi and Hoover, 2004]. Analyses included lossless compression of photographic images to estimate the relative complexity of a putative fossil compared to the rock matrix [Corsetti and Storrie-Lombardi, 2003] and elemental abundance distributions to provide mineralogical classification of the rock matrix [Storrie-Lombardi and Fisk, 2004]. We presented a classification strategy employing two exploratory classification algorithms (Principal Component Analysis and Hierarchical Cluster Analysis) and non-linear stochastic neural network to produce a Bayesian estimate of classification accuracy. We now present an extension of our previous experiments exploring putative fossil forms morphologically resembling cyanobacteria discovered in the Orgueil meteorite. Elemental abundances (C6, N7, O8, Na11, Mg12, Ai13, Si14, P15, S16, Cl17, K19, Ca20, Fe26) obtained for both extant cyanobacteria and fossil trilobites produce signatures readily distinguishing them from meteorite targets. When compared to elemental abundance signatures for extant cyanobacteria Orgueil structures exhibit decreased abundances for C6, N7, Na11, All3, P15, Cl17, K19, Ca20 and increases in Mg12, S16, Fe26. Diatoms and silicified portions of cyanobacterial sheaths exhibiting high levels of silicon and correspondingly low levels of carbon cluster more closely with terrestrial fossils than with extant cyanobacteria. Compression indices verify that variations in random and redundant textural patterns between perceived forms and the background matrix contribute significantly to morphological visual identification. The results provide a quantitative probabilistic methodology for discriminating putatitive fossils from the surrounding rock matrix and &om extant organisms using both structural and chemical information. The techniques described appear applicable

  16. Distribution and relative abundance of forest birds in relation to burn severity in southeastern Arizona

    USGS Publications Warehouse

    Kirkpatrick, C.; Conway, C.J.; Jones, P.B.

    2006-01-01

    The frequency of wild and prescribed fires in montane forests of the southwestern United States has increased after a century of fire suppression and subsequent fuels accumulation. To assess the effects of recent fires (median time since fire = 6 yr) on the montane forest bird community, we surveyed birds in 8 Sky Island mountain ranges in southeastern Arizona, USA, and examined how the distribution (i.e., presence-absence) of 65 species and relative abundance of 16 species correlated with evidence of severe and less severe fire at >1,500 survey points. We detected associations between fire and bird presence-absence for 17% of the 65 species analyzed and between fire and bird relative abundance for 25% of the 16 species analyzed. Most species (73%) were positively associated with burned areas and displayed stronger associations (i.e., more extreme odds ratios) with survey points that had evidence of severe as opposed to less severe fire. Positive associations with severe fire were strong (>3 to 1 odds) for western wood-pewee (Contopus sordidulus) and house wren (Troglodytes aedon), and negative associations with severe fire were strong for warbling vireo (Vireo gilvus) and red-breasted nuthatch (Sitta canadensis). Although recent fires appear to have had a positive effect on the distribution and relative abundance of several montane forest bird species in the region, these species are not the open-woodland birds that we would have expected to have benefited from fire based on previous research. Nevertheless, our results confirm associations between fire and bird presence-absence and relative abundance reported previously for 7 species of birds. Our results also provide new information for Grace's warbler (Dendroica graciae) and greater pewee (C. pertinax), 2 species for which fire data were formerly lacking. Managers can use these data to make and test predictions about the effects of future fires, both severe and less severe, on montane forest birds in the

  17. [Latitudinal and bathymetric distribution of the most abundant and frequent species in the shrimp bycatch from the Gulf of California, Mexico].

    PubMed

    Rábago-Quiroz, Carlos Hiram; López-Martínez, Juana; Valdez-Holguín, José Eduardo; Nevárez Martínez, Manuel O

    2011-03-01

    The Gulf of California is one of the most mega-diverse regions in the world, for which few fishery information is available. We present here latitudinal and bathymetric distribution of the most abundant and frequent bycatch species from the Gulf of California. The samples were obtained from a total of 111 hauls taken during seven research cruises of the closed shrimp season (2002-2005-2007), and also, from research cruises made at depths up to 90 m. Due to the high variety species in this experimental shrimp bycatch, only those with highest biological value index (BVI) were selected. A total of fifteen species had the highest BVI and represented about 60% of the total abundance. A total of 16 508 organisms were analyzed, representing 243 fish, crustacean, mollusk and echinoderm species. Fish were the most abundant, being the most frequent species: Urobatis halleri, Synodus scituliceps, Diplectrum pacificum, Haemulopsis nitidus and Eucinostomus argenteus. A wide latitudinal distribution of these species along the study area, as well as a bathymetric distribution from 9 to 67 m depth, was observed. Two of these species were found at 325 m depth. Due to the wide bathymetric distribution obtained, total abundances and sizes for each species by depth strata should be determined, and one can assume that deeper than 25 m, the capture of these species decreases, and these areas can be used as natural repopulation areas, for depths where they are mainly captured by the commercial shrimp fishery.

  18. Diversity and distribution of unicellular opisthokonts along the European coast analysed using high-throughput sequencing.

    PubMed

    Del Campo, Javier; Mallo, Diego; Massana, Ramon; de Vargas, Colomban; Richards, Thomas A; Ruiz-Trillo, Iñaki

    2015-09-01

    The opisthokonts are one of the major super groups of eukaryotes. It comprises two major clades: (i) the Metazoa and their unicellular relatives and (ii) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here, we begin to address this gap by analysing high-throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyse the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of choanoflagellates in coastal waters as well as a relevant representation of the ichthyosporeans and the uncultured marine opisthokonts (MAOP). Furthermore, we describe a new lineage of marine fonticulids (MAFO) that appears to be abundant in sediments. Taken together, our work points to a greater potential ecological role for unicellular opisthokonts than previously appreciated in marine environments, both in water column and sediments, and also provides evidence of novel opisthokont phylogenetic lineages. This study highlights the importance of high-throughput sequencing approaches to unravel the diversity and distribution of both known and novel eukaryotic lineages.

  19. Distribution and diversity of holothuroids (Echinodermata) on Cascadia Basin and Tufts Abyssal Plain

    NASA Astrophysics Data System (ADS)

    Carney, Robert S.; Carey, Andrew G.

    1982-05-01

    The pattern of diversity, species composition, and inter-sample similarity of the holothuroid fauna was examined for 95 beam trawl samples from below 2000 m on the Cascadia Basin and Tufts Abyssal Plain off Oregon, U.S.A. Abundance as inferred from catch size, diversity, species composition, and zonation all showed major change over the sampled area where there was a depth change. Where depth remained relatively constant across the floor of Cascadia Basin, faunal changes were minor in spite of progressive isolation from land. Overall bathymetric patterns of zonation and diversity were basically like those found for other faunal groups in the deep-sea depth. The distribution of minor species indicated that the holothuroid fauna at the base of the continental slope, the apron of Astoria Fan, and near Cascadia Channel might be slightly different from that at similar depths elsewhere in the sampled area. The marked uniformity of the holothuroid fauna across the basin floor appeared to be restricted to epifaunal sediment-feeding species. Infaunal forms were more abundant at the slope base, similar to previous findings for the macro-infauna.

  20. Plant diversity moderates drought stress in grasslands: Implications from a large real-world study on (13)C natural abundances.

    PubMed

    Klaus, Valentin H; Hölzel, Norbert; Prati, Daniel; Schmitt, Barbara; Schöning, Ingo; Schrumpf, Marion; Solly, Emily F; Hänsel, Falk; Fischer, Markus; Kleinebecker, Till

    2016-10-01

    Land-use change and intensification play a key role in the current biodiversity crisis. The resulting species loss can have severe effects on ecosystem functions and services, thereby increasing ecosystem vulnerability to climate change. We explored whether land-use intensification (i.e. fertilization intensity), plant diversity and other potentially confounding environmental factors may be significantly related to water use (i.e. drought stress) of grassland plants. Drought stress was assessed using δ(13)C abundances in aboveground plant biomass of 150 grassland plots across a gradient of land-use intensity. Under water shortage, plants are forced to increasingly take up the heavier (13)C due to closing stomata leading to an enrichment of (13)C in biomass. Plants were sampled at the community level and for single species, which belong to three different functional groups (one grass, one herb, two legumes). Results show that plant diversity was significantly related to the δ(13)C signal in community, grass and legume biomass indicating that drought stress was lower under higher diversity, although this relation was not significant for the herb species under study. Fertilization, in turn, mostly increased drought stress as indicated by more positive δ(13)C values. This effect was mostly indirect by decreasing plant diversity. In line with these results, we found similar patterns in the δ(13)C signal of the organic matter in the topsoil, indicating a long history of these processes. Our study provided strong indication for a positive biodiversity-ecosystem functioning relationship with reduced drought stress at higher plant diversity. However, it also underlined a negative reinforcing situation: as land-use intensification decreases plant diversity in grasslands, this might subsequently increases drought sensitivity. Vice-versa, enhancing plant diversity in species-poor agricultural grasslands may moderate negative effects of future climate change.

  1. Hierarchical spatial models for predicting pygmy rabbit distribution and relative abundance

    USGS Publications Warehouse

    Wilson, T.L.; Odei, J.B.; Hooten, M.B.; Edwards, T.C.

    2010-01-01

    Conservationists routinely use species distribution models to plan conservation, restoration and development actions, while ecologists use them to infer process from pattern. These models tend to work well for common or easily observable species, but are of limited utility for rare and cryptic species. This may be because honest accounting of known observation bias and spatial autocorrelation are rarely included, thereby limiting statistical inference of resulting distribution maps. We specified and implemented a spatially explicit Bayesian hierarchical model for a cryptic mammal species (pygmy rabbit Brachylagus idahoensis). Our approach used two levels of indirect sign that are naturally hierarchical (burrows and faecal pellets) to build a model that allows for inference on regression coefficients as well as spatially explicit model parameters. We also produced maps of rabbit distribution (occupied burrows) and relative abundance (number of burrows expected to be occupied by pygmy rabbits). The model demonstrated statistically rigorous spatial prediction by including spatial autocorrelation and measurement uncertainty. We demonstrated flexibility of our modelling framework by depicting probabilistic distribution predictions using different assumptions of pygmy rabbit habitat requirements. Spatial representations of the variance of posterior predictive distributions were obtained to evaluate heterogeneity in model fit across the spatial domain. Leave-one-out cross-validation was conducted to evaluate the overall model fit. Synthesis and applications. Our method draws on the strengths of previous work, thereby bridging and extending two active areas of ecological research: species distribution models and multi-state occupancy modelling. Our framework can be extended to encompass both larger extents and other species for which direct estimation of abundance is difficult. ?? 2010 The Authors. Journal compilation ?? 2010 British Ecological Society.

  2. Soil compaction and organic matter affect conifer seedling nonmycorrhizal and ectomycorrhizal root tip abundance and diversity. Forest Service research paper

    SciTech Connect

    Amaranthus, M.P.; Page-Dumroese, D.; Harvey, A.; Cazares, E.; Bednar, L.F.

    1996-05-01

    Three levels of organic matter removal (bole only; bole and crowns; and bole, crowns, and forest floor) and three levels of mechanical soil compaction (no compaction, moderate compaction, and severe soil compaction) were studied as they influence Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) and western white pine (Pinus monticola Dougl. ex D. Don) seedlings following outplanting. Moderate and severe soil compaction significantly reduced nonmycorrhizal root tip abundance on both Douglas-fir and western white pine seedlings (p less than or equal to 0.05). Ectomycorrhizal root tip abundance was significantly reduced on Douglas-fir seedlings in severely compacted areas with bole and crowns and bole, crowns, and forest floor removed. Ectomycorrhizal diversity also was significantly reduced on Douglas-fir seedlings in all severely compacted areas.

  3. Influence of Trap Height and Bait Type on Abundance and Species Diversity of Cerambycid Beetles Captured in Forests of East-Central Illinois.

    PubMed

    Schmeelk, Thomas C; Millar, Jocelyn G; Hanks, Lawrence M

    2016-08-01

    We assessed how height of panel traps above the forest floor, and the type of trap bait used, influenced the abundance and diversity of cerambycid beetles caught in forested areas of east-central Illinois. Panel traps were suspended from branches of hardwood trees at three heights above the ground: understory (∼1.5 m), lower canopy (∼6 m), and midcanopy (∼12 m). Traps were baited with either a multispecies blend of synthesized cerambycid pheromones or a fermenting bait mixture. Traps captured a total of 848 beetles of 50 species in the cerambycid subfamilies Cerambycinae, Lamiinae, Lepturinae, and Parandrinae, and one species in the closely related family Disteniidae. The species caught in highest numbers was the cerambycine Anelaphus pumilus (Newman), represented by 349 specimens. The 17 most abundant species (mean ± 1 SD: 45 ± 80 specimens per species) included 12 cerambycine and five lamiine species. Of these most abundant species, 13 (77%) were attracted to traps baited with the pheromone blend. Only the cerambycine Eburia quadrigeminata (Say) was attracted by the fermenting bait. Three species were captured primarily in understory traps, and another five species primarily in midcanopy traps. Variation among cerambycid species in their vertical distribution in forests accounted for similar overall abundances and species richness across trap height treatments. These findings suggest that trapping surveys of native communities of cerambycids, and quarantine surveillance for newly introduced exotic species, would be optimized by including a variety of trap baits and distributing traps across vertical strata of forests.

  4. Red Squirrel Middens Influence Abundance but Not Diversity of Other Vertebrates

    PubMed Central

    Posthumus, Erin E.; Koprowski, John L.; Steidl, Robert J.

    2015-01-01

    Some animals modify the environment in ways that can influence the resources available to other species. Because red squirrels (Tamiasciurus hudsonicus) create large piles of conifer-cone debris (middens) in which they store cones, squirrels concentrate resources that might affect biodiversity locally. To determine whether other animals are attracted to midden sites beyond their affinity for the same resources that attract red squirrels, we assessed associations between middens, mammals, and birds at population and community levels. We surveyed 75 middens where residency rates of red squirrels varied during the previous five years; sampling along this residency gradient permitted us to evaluate the influence of resources at middens beyond the influence of a resident squirrel. At each location, we quantified vegetation, landscape structure, abundance of conifer cones, and midden structure, and used capture–recapture, distance sampling, and remote cameras to quantify presence, abundance, and species richness of mammals and birds. Red squirrels and the resources they concentrated at middens influenced mammals and birds at the population scale and to a lesser extent at the community scale. At middens with higher residency rates of red squirrels, richness of medium and large mammals increased markedly and species richness of birds increased slightly. After accounting for local forest characteristics, however, only species richness of medium-to-large mammals was associated with a red squirrel being resident during surveys. In areas where red squirrels were resident during surveys or in areas with greater amounts of resources concentrated by red squirrels, abundances of two of four small mammal species and two of four bird species increased. We conclude that the presence of this ecosystem modifier and the resources it concentrates influence abundance of some mammals and birds, which may have implications for maintaining biodiversity across the wide geographic range

  5. Red squirrel middens influence abundance but not diversity of other vertebrates.

    PubMed

    Posthumus, Erin E; Koprowski, John L; Steidl, Robert J

    2015-01-01

    Some animals modify the environment in ways that can influence the resources available to other species. Because red squirrels (Tamiasciurus hudsonicus) create large piles of conifer-cone debris (middens) in which they store cones, squirrels concentrate resources that might affect biodiversity locally. To determine whether other animals are attracted to midden sites beyond their affinity for the same resources that attract red squirrels, we assessed associations between middens, mammals, and birds at population and community levels. We surveyed 75 middens where residency rates of red squirrels varied during the previous five years; sampling along this residency gradient permitted us to evaluate the influence of resources at middens beyond the influence of a resident squirrel. At each location, we quantified vegetation, landscape structure, abundance of conifer cones, and midden structure, and used capture-recapture, distance sampling, and remote cameras to quantify presence, abundance, and species richness of mammals and birds. Red squirrels and the resources they concentrated at middens influenced mammals and birds at the population scale and to a lesser extent at the community scale. At middens with higher residency rates of red squirrels, richness of medium and large mammals increased markedly and species richness of birds increased slightly. After accounting for local forest characteristics, however, only species richness of medium-to-large mammals was associated with a red squirrel being resident during surveys. In areas where red squirrels were resident during surveys or in areas with greater amounts of resources concentrated by red squirrels, abundances of two of four small mammal species and two of four bird species increased. We conclude that the presence of this ecosystem modifier and the resources it concentrates influence abundance of some mammals and birds, which may have implications for maintaining biodiversity across the wide geographic range

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

    PubMed Central

    Fortel, Laura; Henry, Mickaël; Guilbaud, Laurent; Guirao, Anne Laure; Kuhlmann, Michael; Mouret, Hugues; Rollin, Orianne; Vaissière, Bernard E.

    2014-01-01

    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

  7. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    PubMed

    Miranda, Lilibeth N; Hutchison, Keith; Grossman, Arthur R; Brawley, Susan H

    2013-01-01

    Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1) to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2) determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3) to determine how the microbial community associated with a laboratory strain (P.um.1) established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1) were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads). The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7). The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria) were also abundant. Sphingobacteria (Bacteroidetes) and Flavobacteria (Bacteroidetes) had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes), was abundant. Lewinella (as 66 OTUs) was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had unexpected

  8. Abundance, diversity and functional gene expression of denitrifier communities in adjacent riparian and agricultural zones.

    PubMed

    Dandie, Catherine E; Wertz, Sophie; Leclair, Caissie L; Goyer, Claudia; Burton, David L; Patten, Cheryl L; Zebarth, Bernie J; Trevors, Jack T

    2011-07-01

    Lands under riparian and agricultural management differ in soil properties, water content, plant species and nutrient content and are therefore expected to influence denitrifier communities, denitrification and nitrous oxide (N(2) O) emissions. Denitrifier community abundance, denitrifier community structure, denitrification gene expression and activity were quantified on three dates in a maize field and adjacent riparian zone. N(2) O emissions were greater in the agricultural zone, whereas complete denitrification to N(2) was greater in the riparian zone. In general, the targeted denitrifier community abundance did not change between agricultural and riparian zones. However, nosZ gene expression was greater in the riparian zone than the agricultural zone. The community structure of nirS-gene-bearing denitrifiers differed in June only, whereas the nirK-gene-bearing community structure differed significantly between the riparian and the agricultural zones at all dates. The nirK-gene-bearing community structure was correlated with soil pH, while no significant correlations were found between nirS-gene-bearing community structure and soil environmental variables or N(2) O emissions, denitrification or denitrifier enzyme activity. The results suggested for the nirK and nirS-gene-bearing communities different factors control abundance vs. community structure. The nirK-gene-bearing community structure was also more responsive than the nirS-gene-bearing community structure to change between the two ecosystems.

  9. Life history, diversity and distribution: A study of Japanese pteridophytes

    USGS Publications Warehouse

    Guo, Q.; Kato, Masako; Ricklefs, R.E.

    2003-01-01

    Many studies address the relationships between diversity or distribution and attributes of the physical environment. However, how these relationships are connected to variation in life history is poorly understood. This is particularly true in the case of pteridophytes. Japanese ferns and their allies comprise one of the best-known pteridophyte floras in the world. We analyzed ca 600 species of Japanese pteridophytes for which there is detailed information on distribution, reproduction, and chromosome number. Species richness was greatest in groups with a single reproductive mode (sexual, followed by apogamous), but distribution was greatest in species groups with multiple reproductive modes: sexual plus either sterile (irregular in meiosis) or apogamous. Geographical ranges varied greatly among species with small chromosome numbers but were uniformly small among species having high chromosome numbers. Seasonally green (mostly summer green) species had significantly larger distribution ranges than evergreen species. Endemic species had higher proportions of apogamy and sterility than non-endemic species. Seasonally green species had significantly larger distributional ranges, and a smaller proportion of species with apogamous reproduction, than evergreen species. There was no clear relationship between distribution and spore size, either among endemic species, non-endemic species, or all species combined. There was no relationship between spore size and chromosome number when all species were combined. However, positive relationships were detected within three of the nine largest genera, suggesting potential phylogenetic effects. We concluded that habitat availability, rather than dispersability, may be the limiting factor for the distribution of pteridophytes in Japan.

  10. Constraining the Galactic potential via action-based distribution functions for mono-abundance stellar populations

    NASA Astrophysics Data System (ADS)

    Ting, Yuan-Sen; Rix, Hans-Walter; Bovy, Jo; van de Ven, Glenn

    2013-09-01

    We present a rigorous and practical way of constraining the Galactic potential based on the phase-space information for many individual stars. Such an approach is needed to dynamically model the data from ongoing spectroscopic surveys of the Galaxy and in the future Gaia. This approach describes the orbit distribution of stars by a family of parametrized distribution function (DF) proposed by McMillan and Binney, which are based on actions. We find that these parametrized DFs are flexible enough to capture well the observed phase-space distributions of individual abundance-selected Galactic subpopulations of stars (`mono-abundance populations') for a disc-like gravitational potential, which enables independent dynamical constraints from each of the Galactic mono-abundance populations. We lay out a statistically rigorous way to constrain the Galactic potential parameters by constructing the joint likelihood of potential and DF parameters, and subsequently marginalizing over the DF parameters. This approach explicitly incorporates the spatial selection function inherent to all Galactic surveys, and can account for the uncertainties of the individual position-velocity observations. On that basis, we study the precision of the parameters of the Galactic potential that can be reached with various sample sizes and realistic spatial selection functions. By creating mock samples from the DF, we show that, even under a restrictive and realistic spatial selection function, given a two-parameter gravitational potential, one can recover the true potential parameters to a few per cent with sample sizes of a few thousands. The assumptions of axisymmetry, of DFs that are smooth in the actions and of no time variation remain important limitations in our current study.

  11. Distribution and abundance of nonnative fishes in streams of the western United States

    USGS Publications Warehouse

    Schade, C.B.; Bonar, Scott A.

    2005-01-01

    This report presents data from one of the largest standardized stream surveys conducted in he western United States, which shows that one of every four individual fish in streams of 12 western states are nonnative. The states surveyed included Arizona, California, Colorado, Idaho, Montana, Nevada, North Dakota, Oregon, South Dakota, Utah, Washington, and Wyoming. The most widely distributed and abundant nonnative fishes in the western USA were brook trout Salvelinus fontinalis, brown trout Salmo trutta, rainbow trout Oncorhynchus mykiss, common carp Cyprinus carpio, smallmouth bass Micropterus dolomieu, largemouth bass M. salmoides, green sunfish Lepomis cyanellus, fathead minnow Pimephales promelas, yellow perch Percaflavescens, yellow bullhead Ameiurus natalis, cutthroat trout O. clarkii, western mosquitofish Gambusia affinis, golden shiner Notemigonus crysoleucas, channel catfish Ictalurus punctatus, and red shiner Cyprinella lutrensis. The greatest abundance and distribution of nonnative fishes was in interior states, and the most common nonnatives were introduced for angling. Nonnative fishes were widespread in pristine to highly disturbed streams influenced by all types of land use practices. We present ranges in water temperature, flow, stream order, riparian cover, human disturbance, and other environmental conditions where the 10 most common introduced species were found. Of the total western U.S. stream length bearing fish, 50.1% contained nonnative fishes while 17.9% contained physical environment that was ranked highly or moderately disturbed by humans. Introduced fishes can adversely affect stream communities, and they are much more widespread in western U.S. streams than habitat destruction. The widespread distribution and high relative abundance of nonnative fishes and their documented negative effects suggest their management and control should elicit at least as much attention as habitat preservation in the protection of native western U.S. stream

  12. Iron and Titanium Abundance and Maturity Degree Distribution on the Lunar Nearside

    NASA Astrophysics Data System (ADS)

    Shkuratov, Yurij G.; Kaydash, Vadym G.; Opanasenko, Nickolaj V.

    1999-02-01

    New digital images of the lunar nearside albedos at 0.42, 0.65, 0.75, and 0.95 μm derived from telescopic data were used to map the abundance and distribution of iron, titanium, and maturity degree on the lunar nearside. Developing the approach by P. Luceyet al.(1995,Science268, 1150), a method of separating contributions of the Fe and Ti abundance and maturity degree to spectral properties of the lunar surface is presented. The main objective of the method is an analysis of the 3D correlation diagram of optical characteristics of regolith material with the aim of choosing a coordinate system providing the best correlations of these characteristics with Fe and Ti abundance (data for the Surveyor, Luna, and Apollo landing sites) and with maturity degree (laboratory measurements of lunar samples by E. Fischer and C. Pieters (e.g., 1996,J. Geophys. Res.101, 2225). To find the coordinates, a geometrical optics model of light scattering in particulate media enabling to calculate the absorption coefficient from albedo measurements is used. An analysis of the correlation diagram FeO-TiO2provides two maps characterizing optical types of the lunar nearside. In particular, the maps show that the basalts of Mare Serenitatis and Mare Tranquillitatis are not widely extended on the lunar nearside. The maturity degree, parameterIs/FeO, was also mapped. Regions withIs/FeO≤50 are young craters surrounded by ray systems, whereas the conditionIs/FeO≥70 corresponds to regions associated with Copernicus ejecta, western boundaries of Mare Tranquillitatis and Mare Serenitatis, and a portion of the south highland. The new map of FeO distribution on the lunar nearside was used to study a correlation between iron content and distribution of remanent magnetism over the lunar surface. The relationship obtained has a reverse behavior: the lower the iron content, the higher the magnetism.

  13. Distribution of diverse nitrogen fixers in the global ocean

    NASA Astrophysics Data System (ADS)

    Monteiro, F. M.; Follows, M. J.; Dutkiewicz, S.

    2010-09-01

    We employ a global three-dimensional model to simulate diverse phytoplanktonic diazotrophs (nitrogen fixers) in the oceans. In the model, the structure of the marine phytoplankton community self-assembles from a large number of potentially viable physiologies. Amongst them, analogs of Trichodesmium, unicellular diazotrophs and diatom-diazotroph associations (DDA) are successful and abundant. The simulated biogeography and nitrogen fixation rates of the modeled diazotrophs compare favorably with a compilation of published observations, which includes both traditional and molecular measurements of abundance and activity of marine diazotrophs. In the model, the diazotroph analogs occupy warm subtropical and tropical waters, with higher concentrations and nitrogen fixation rates in the tropical Atlantic Ocean and the Arabian Sea/Northern Indian Ocean, and lower values in the tropical and subtropical South Pacific Ocean. The three main diazotroph types typically co-exist in the model, although Trichodesmium analogs dominate the diazotroph population in much of the North and tropical Atlantic Ocean and the Arabian Sea, while unicellular-diazotroph analogs dominate in the South Atlantic, Pacific and Indian oceans. This pattern reflects the relative degree of nutrient limitation by iron or phosphorus. The model suggests in addition that unicellular diazotrophs could add as much new nitrogen to the global ocean as Trichodesmium.

  14. Local Abundance Patterns of Noctuid Moths in Olive Orchards: Life-History Traits, Distribution Type and Habitat Interactions

    PubMed Central

    Pérez-Guerrero, Sergio; Redondo, Alberto José; Yela, José Luis

    2011-01-01

    Local species abundance is related to range size, habitat characteristics, distribution type, body size, and life-history variables. In general, habitat generalists and polyphagous species are more abundant in broad geographical areas. Underlying this, local abundance may be explained from the interactions between life-history traits, chorological pattern, and the local habitat characteristics. The relationship within taxa between life-history traits, distribution area, habitat characteristics, and local abundance of the noctuid moth (Lepidoptera: Noctuidae) assemblage in an olive orchard, one of the most important agro-ecosystems in the Mediterranean basin, was analyzed. A total of 66 species were detected over three years of year-round weekly samplings using the light-trap method. The life-history traits examined and the distribution type were found to be related to the habitat-species association, but none of the biological strategies defined from the association to the different habitats were linked with abundance. In contrast to general patterns, dispersal ability and number of generations per year explained differences in abundance. The relationships were positive, with opportunistic taxa that have high mobility and several generations being locally more abundant. In addition, when the effect of migrant species was removed, the distribution type explained abundance differences, with Mediterranean taxa (whose baricenter is closer to the studied area) being more abundant. PMID:21529251

  15. Aspherical abundance distribution of ejecta from neutrino-driven core collapse supernova

    NASA Astrophysics Data System (ADS)

    Fujimoto, Shin-Ichiro; Kotake, Kei; Hashimoto, Masa-Aki; Ono, Masaomi; Ohnishi, Naofumi

    2010-08-01

    We examine explosive nucleosynthesis during a delayed neutrino-driven, supernova explosion aided by standing accretion shock instability, based on two-dimensional hydrodynamic simulations of the explosion of a 15Msolar progenitor. We find that abundance pattern of the supernova ejecta is similar to that of the solar system, for cases with high explosion energies of ~=1051 ergs. Aspherical distribution of Fe, Si, and O, which is observed in a nearby core-collapse SN remnant such as Cas A, is obtained in spite of the explosion of the non-rotating, spherical progenitor.

  16. Spatial Distribution of CO Isotopologue Abundance Ratios in the Center of NGC 1068

    NASA Astrophysics Data System (ADS)

    Taniguchi, A.; Kohno, K.; Tamura, Y.; Izumi, T.; Takano, S.; Nakajima, T.; Tosaki, T.

    2015-12-01

    We present an initial result of the spatial distribution of [12CO]/[13CO] and [C16O]/[C18O] abundance ratios in the central ˜1 kpc region of the nearby Seyfert 2 galaxy NGC 1068 observed with ALMA Cycle 0. With non-LTE analyses, both ratios are found to be different between the central circumnuclear disk (CND) and surrounding starburst ring (the Ring). The very high (˜300-1000) value may reflects the difference of chemical evolution and environment at the Ring.

  17. roAp stars: surface lithium abundance distribution and magnetic field configuration

    NASA Astrophysics Data System (ADS)

    Polosukhina, N.; Shulyak, D.; Shavrina, A.; Lyashko, D.; Drake, N. A.; Glagolevski, Yu.; Kudryavtsev, D.; Smirnova, M.

    2014-08-01

    High-resolution spectra obtained with the 6m BTA telescope, Russia, and with HARPS and VLT/UVES telescopes at ESO, Chile, were used for Doppler Imaging analysis of two roAp stars, HD 12098 and HD 60435, showing strong and variable Li resonance line in their spectra. We found that Li has highly inhomogeneous distribution on the surfaces of these stars. We compared our results with previously obtained Doppler Imaging mapping of two CP2 stars, HD 83368 and HD 3980, and discuss the correlation between the position of the high Li-abundance spots and magnetic field.

  18. Diversity and Spatial-Temporal Distribution of Soil Macrofauna Communities Along Elevation in the Changbai Mountain, China.

    PubMed

    Yin, Xiuqin; Qiu, Lili; Jiang, Yunfeng; Wang, Yeqiao

    2017-03-23

    The understanding of patterns of vertical variation and diversity of flora and fauna along elevational change has been well established over the past century. However, it is unclear whether there is an elevational distribution pattern for soil fauna. This study revealed the diversity and spatial-temporal distribution of soil macrofauna communities in different vegetation zones from forest to alpine tundra along elevation of the Changbai Mountain, China. The abundance, richness, and Shannon-Wiener diversity index of soil macrofauna communities were compared in four distinguished vegetation zones including the coniferous and broadleaved mixed forest zone, the coniferous forest zone, the subalpine dwarf birch (Betula ermanii) forest zone, and the alpine tundra zone. Soil macrofauna were extracted in May, July, and September of 2009. In each season, the abundance and richness of the soil macrofauna decreased with the ascending elevation. The Shannon-Wiener diversity indices of the soil macrofauna were higher in the vegetation zones of lower elevation than of higher elevation. Significant differences were observed in the abundance, richness, and Shannon-Wiener diversity index for the studied vegetation zones. Soil macrofauna congregated mainly to the litter layer in the low-elevation areas and in the 0-5 cm soil layer of the higher elevation areas. The results emphasized that the diversity of soil macrofauna communities decreased as the elevation increased and possess the distinct characteristics of zonation in the mountain ecosystem. The diversity and distribution of soil macrofauna communities were influenced by mean annual precipitation, altitude, annual radiation quantity, and mean annual temperature.

  19. Variations in the abundance and structural diversity of microbes forming biofilms in a thermally stressed coral reef system.

    PubMed

    Mahmoud, Huda

    2015-11-30

    Little information is known about biofilm formation in the thermally stressed coral reef systems north of the Arabian Gulf. The current study investigates the abundance and diversity of marine microbes involved in biofilm formation and their succession over a period of 14 weeks (May-August 2007) at temperatures exceeding 32 °C. The results showed variations in microbial numbers and the development of more stable biofilm communities as the biofilms aged. The culture-dependent technique and microscopic examination of the developed biofilms showed the dominance of key species known for their role in precipitating CaCO3 such as Vibrio and in facilitating coral larvae settlement and metamorphosis such as Pseudoalteromonas, Bacillariophyceae and Rhodophyceae. The results revealed biofilm formations with microbial diversities that have the potential to support the larval settlement and metamorphism of marine organisms and to consolidate and stabilize biofilms via the process of calcification in the thermally stressed coral reef system considered herein.

  20. Geographic distribution of haplotype diversity at the bovine casein locus

    PubMed Central

    Jann, Oliver C; Ibeagha-Awemu, Eveline M; Özbeyaz, Ceyhan; Zaragoza, Pilar; Williams, John L; Ajmone-Marsan, Paolo; Lenstra, Johannes A; Moazami-Goudarzi, Katy; Erhardt, Georg

    2004-01-01

    The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A2-CSN3*AI/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed. PMID:15040901

  1. Shifts in abundance and diversity of mobile genetic elements after the introduction of diverse pesticides into an on-farm biopurification system over the course of a year.

    PubMed

    Dealtry, Simone; Holmsgaard, Peter N; Dunon, Vincent; Jechalke, Sven; Ding, Guo-Chun; Krögerrecklenfort, Ellen; Heuer, Holger; Hansen, Lars H; Springael, Dirk; Zühlke, Sebastian; Sørensen, Søren J; Smalla, Kornelia

    2014-07-01

    Biopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (intI1, intI2) and genes encoding resistance to sulfonamides (sul1, sul2) and streptomycin (aadA) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1 trfA gene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1β and a decrease in the abundance of IncP-1ε over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1β plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides.

  2. Shifts in Abundance and Diversity of Mobile Genetic Elements after the Introduction of Diverse Pesticides into an On-Farm Biopurification System over the Course of a Year

    PubMed Central

    Dealtry, Simone; Holmsgaard, Peter N.; Dunon, Vincent; Jechalke, Sven; Ding, Guo-Chun; Krögerrecklenfort, Ellen; Heuer, Holger; Hansen, Lars H.; Springael, Dirk; Zühlke, Sebastian; Sørensen, Søren J.

    2014-01-01

    Biopurification systems (BPS) are used on farms to control pollution by treating pesticide-contaminated water. It is assumed that mobile genetic elements (MGEs) carrying genes coding for enzymes involved in degradation might contribute to the degradation of pesticides. Therefore, the composition and shifts of MGEs, in particular, of IncP-1 plasmids carried by BPS bacterial communities exposed to various pesticides, were monitored over the course of an agricultural season. PCR amplification of total community DNA using primers targeting genes specific to different plasmid groups combined with Southern blot hybridization indicated a high abundance of plasmids belonging to IncP-1, IncP-7, IncP-9, IncQ, and IncW, while IncU and IncN plasmids were less abundant or not detected. Furthermore, the integrase genes of class 1 and 2 integrons (intI1, intI2) and genes encoding resistance to sulfonamides (sul1, sul2) and streptomycin (aadA) were detected and seasonality was revealed. Amplicon pyrosequencing of the IncP-1 trfA gene coding for the replication initiation protein revealed high IncP-1 plasmid diversity and an increase in the abundance of IncP-1β and a decrease in the abundance of IncP-1ε over time. The data of the chemical analysis showed increasing concentrations of various pesticides over the course of the agricultural season. As an increase in the relative abundances of bacteria carrying IncP-1β plasmids also occurred, this might point to a role of these plasmids in the degradation of many different pesticides. PMID:24771027

  3. Effects of initial moisture content of Korean traditional wheat-based fermentation starter nuruk on microbial abundance and diversity.

    PubMed

    Bal, Jyotiranjan; Yun, Suk-Hyun; Yeo, Soo-Hwan; Kim, Jung-Mi; Kim, Beom-Tae; Kim, Dae-Hyuk

    2017-03-01

    The brewing of makgeolli, one of Korea's most popular alcoholic beverages that is gaining popularity globally, is facilitated by nuruk, a traditional Korean cereal starter. The nuruk microbiome greatly influences the fermentation process as well as the nutritional, hygienic, and aromatic qualities of the product. This study is a continuation of our efforts to examine nuruk biodiversity at a depth previously unattainable. In this study, microfloral dynamics in wheat-based nuruk C, composed of traditional ingredients such as barley, green gram, and wheat and fermented under various internal moisture contents of 20% (C20), 26% (C26), and 30% (C30), was evaluated using 454 pyrosequencing during the 30-day fermentation process. Rarefaction analysis and alpha diversity parameters indicated adequate sampling. C20 showed the greatest fungal richness and diversity, C20 and C26 exhibited similar bacterial richness and diversity, while C30 had low fungal and bacterial richness. Fungal taxonomic assignments revealed that the initial moisture content caused selective enrichment of Aspergillus candidus with a decreasing trend during fermentation, whereas Saccharomycetales sp. exhibited increasing relative abundance with increasing moisture content from day 6 of the fermentation process. Depending on initial moisture level, changes in bacterial communities were also observed in the genera Streptomyces, Bacillus, and Staphylococcus, with decreasing trends whereas Saccharopolyspora exhibited a sigmoidal trend with the highest abundance in C26. These findings demonstrate the possible impact of initial moisture content of nuruk on microfloral richness, diversity, and dynamics; this study is thus a step toward our ultimate goal of enhancing the quality of nuruk.

  4. Abundance, distribution, and isotopic composition of particulate black carbon in the northern Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Yang, Weifeng; Guo, Laodong

    2014-11-01

    There exists increasing evidence supporting the important role of black carbon in global carbon cycles. Particulate black carbon (PBC) is allochthonous and has distinct reactivities compared to the bulk particulate organic carbon (tot-POC) in marine environments. However, the abundance, geochemical behavior of PBC and its importance in oceanic carbon budget remain poorly understood. Here we report the abundance, distribution, and stable isotopic signatures of BC derived from the chemo-thermal oxidation (CTO-375) method (BCCTO) in the Gulf of Mexico. Our results show that BCCTO abundance decreased from shelf to basin, and more than a half of riverine BCCTO could be removed over the shelf. Moreover, BCCTO is much more refractory compared to the tot-POC and has δ13C values lower than those of BC-excluded POC. These results highlight the significance of PBC in marine carbon cycles and potentially suggest the need for a new end-member term in quantifying POC sources in the ocean.

  5. Distribution and abundance of American eels in the White Oak River estuary, North Carolina

    USGS Publications Warehouse

    Hightower, J.E.; Nesnow, C.

    2006-01-01

    Apparent widespread declines in abundance of Anguilla rostrata (American eel) have reinforced the need for information regarding its life history and status. We used commercial eel pots and crab (peeler) pots to examine the distribution, condition, and abundance of American eels within the White Oak River estuary, NC, during summers of 2002-2003. Catch of American eels per overnight set was 0.35 (SE = 0.045) in 2002 and 0.49 (SE = 0.044) in 2003. There was not a significant linear relationship between catch per set and depth in 2002 (P = 0.31, depth range 0.9-3.4 m) or 2003 (P = 0.18, depth range 0.6-3.4 m). American eels from the White Oak River were in good condition, based on the slope of a length-weight relationship (3.41) compared to the median slope (3.15) from other systems. Estimates of population density from grid sampling in 2003 (300 mm and larger: 4.0-13.8 per ha) were similar to estimates for the Hudson River estuary, but substantially less than estimates from other (smaller) systems including tidal creeks within estuaries. Density estimates from coastal waters can be used with harvest records to examine whether overfishing has contributed to the recent apparent declines in American eel abundance.

  6. Diversity and abundance of the arsenite oxidase gene aioA in geothermal areas of Tengchong, Yunnan, China.

    PubMed

    Jiang, Zhou; Li, Ping; Jiang, Dawei; Wu, Geng; Dong, Hailiang; Wang, Yanhong; Li, Bing; Wang, Yanxin; Guo, Qinghai

    2014-01-01

    A total of 12 samples were collected from the Tengchong geothermal areas of Yunnan, China, with the goal to assess the arsenite (AsIII) oxidation potential of the extant microbial communities as inferred by the abundance and diversity of the AsIII oxidase large subunit gene aioA relative to geochemical context. Arsenic concentrations were higher (on average 251.68 μg/L) in neutral or alkaline springs than in acidic springs (on average 30.88 μg/L). aioA abundance ranged from 1.63 × 10(1) to 7.08 × 10(3) per ng of DNA and positively correlated with sulfide and the ratios of arsenate (AsV):total dissolved arsenic (AsTot). Based on qPCR estimates of bacterial and archaeal 16S rRNA gene abundance, aioA-harboring organisms comprised as much as ~15% of the total community. Phylogenetically, the major aioA sequences (270 total) in the acidic hot springs (pH 3.3-4.4) were affiliated with Aquificales and Rhizobiales, while those in neutral or alkaline springs (pH 6.6-9.1) were inferred to be primarily bacteria related to Thermales and Burkholderiales. Interestingly, aioA abundance at one site greatly exceeded bacterial 16S rRNA gene abundance, suggesting these aioA genes were archaeal even though phylogenetically these aioA sequences were most similar to the Aquificales. In summary, this study described novel aioA sequences in geothermal features geographically far removed from those in the heavily studied Yellowstone geothermal complex.

  7. Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes

    PubMed Central

    Mahnert, Alexander; Vaishampayan, Parag; Probst, Alexander J.; Auerbach, Anna; Moissl-Eichinger, Christine; Venkateswaran, Kasthuri; Berg, Gabriele

    2015-01-01

    Cleanrooms have been considered microbially-reduced environments and are used to protect human health and industrial product assembly. However, recent analyses have deciphered a rather broad diversity of microbes in cleanrooms, whose origin as well as physiological status has not been fully understood. Here, we examined the input of intact microbial cells from a surrounding built environment into a spacecraft assembly cleanroom by applying a molecular viability assay based on propidium monoazide (PMA). The controlled cleanroom (CCR) was characterized by ~6.2*103 16S rRNA gene copies of intact bacterial cells per m2 floor surface, which only represented 1% of the total community that could be captured via molecular assays without viability marker. This was in contrast to the uncontrolled adjoining facility (UAF) that had 12 times more living bacteria. Regarding diversity measures retrieved from 16S rRNA Illumina-tag analyzes, we observed, however, only a minor drop in the cleanroom facility allowing the conclusion that the number but not the diversity of microbes is strongly affected by cleaning procedures. Network analyses allowed tracking a substantial input of living microbes to the cleanroom and a potential enrichment of survival specialists like bacterial spore formers and archaeal halophiles and mesophiles. Moreover, the cleanroom harbored a unique community including 11 exclusive genera, e.g., Haloferax and Sporosarcina, which are herein suggested as indicators of cleanroom environments. In sum, our findings provide evidence that archaea are alive in cleanrooms and that cleaning efforts and cleanroom maintenance substantially decrease the number but not the diversity of indoor microbiomes. PMID:26273838

  8. Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes.

    PubMed

    Mahnert, Alexander; Vaishampayan, Parag; Probst, Alexander J; Auerbach, Anna; Moissl-Eichinger, Christine; Venkateswaran, Kasthuri; Berg, Gabriele

    2015-01-01

    Cleanrooms have been considered microbially-reduced environments and are used to protect human health and industrial product assembly. However, recent analyses have deciphered a rather broad diversity of microbes in cleanrooms, whose origin as well as physiological status has not been fully understood. Here, we examined the input of intact microbial cells from a surrounding built environment into a spacecraft assembly cleanroom by applying a molecular viability assay based on propidium monoazide (PMA). The controlled cleanroom (CCR) was characterized by ~6.2*103 16S rRNA gene copies of intact bacterial cells per m2 floor surface, which only represented 1% of the total community that could be captured via molecular assays without viability marker. This was in contrast to the uncontrolled adjoining facility (UAF) that had 12 times more living bacteria. Regarding diversity measures retrieved from 16S rRNA Illumina-tag analyzes, we observed, however, only a minor drop in the cleanroom facility allowing the conclusion that the number but not the diversity of microbes is strongly affected by cleaning procedures. Network analyses allowed tracking a substantial input of living microbes to the cleanroom and a potential enrichment of survival specialists like bacterial spore formers and archaeal halophiles and mesophiles. Moreover, the cleanroom harbored a unique community including 11 exclusive genera, e.g., Haloferax and Sporosarcina, which are herein suggested as indicators of cleanroom environments. In sum, our findings provide evidence that archaea are alive in cleanrooms and that cleaning efforts and cleanroom maintenance substantially decrease the number but not the diversity of indoor microbiomes.

  9. Optical constants using two particle size distributions: On-going laboratory efforts to quantitatively address clay abundance on Mars

    NASA Astrophysics Data System (ADS)

    Roush, T. L.; Bishop, J. L.; Brown, A. J.; Blake, D.; Bristow, T.

    2013-12-01

    Data obtained at visible and near-infrared wavelengths by OMEGA on MarsExpress and CRISM on MRO provide definitive evidence for the presence of phyllosilicates and other hydrated phases on Mars. A diverse range of both Fe/Mg-OH and Al-OH-bearing phyllosilicates were identified including the smectites, nontronite, saponite, and montmorillonite. In order to constrain the abundances of these phyllosilicates spectral analyses of mixtures of pure end-members are needed. We report on the final stages of our on-going effort to enable the quantitative evaluation of the abundance of hydrated-hydroxylated silicates when they are contained in mixtures. We include several two component mixtures of hydrated/hydroxylated silicates with each other and with two analogs for other martian materials: pyroxene (enstatite) and palagonitic soil (an alteration product of basaltic glass). For the hydrated-hydroxylated silicates we include saponite and montmorillonite (Mg- and Al- rich smectites). We prepared three size separates of each end-member for study: 20-45, 63-90, and 125-150 μm. We used scanning electron microscope images to characterize the grain size distribution, of each sample. Using the grain size distribution, we have derived initial estimates of the optical constants of these materials and compare them to values estimated for the same samples, but using the mean particle size of the sieve fraction. We discuss the results of our calculations for these materials and their implications for modeling the physical mixtures and eventual comparison to Martian spectra.

  10. Vertical distribution of picoeukaryotic diversity in the Sargasso Sea.

    PubMed

    Not, Fabrice; Gausling, Rudolf; Azam, Farooq; Heidelberg, John F; Worden, Alexandra Z

    2007-05-01

    Eukaryotic molecular diversity within the picoplanktonic size-fraction has primarily been studied in marine surface waters. Here, the vertical distribution of picoeukaryotic diversity was investigated in the Sargasso Sea from euphotic to abyssal waters, using size-fractionated samples (< 2 microm). 18S rRNA gene clone libraries were used to generate sequences from euphotic zone samples (deep chlorophyll maximum to the surface); the permanent thermocline (500 m); and the pelagic deep-sea (3000 m). Euphotic zone and deep-sea data contrasted strongly, the former displaying greater diversity at the first-rank taxon level, based on 232 nearly full-length sequences. Deep-sea sequences belonged almost exclusively to the Alveolata and Radiolaria, while surface samples also contained known and putative photosynthetic groups, such as unique Chlorarachniophyta and Chrysophyceae sequences. Phylogenetic analyses placed most Alveolata and Stramenopile sequences within previously reported 'environmental' clades, i.e. clades within the Novel Alveolate groups I and II (NAI and NAII), or the novel Marine Stramenopiles (MAST). However, some deep-sea NAII formed distinct, bootstrap supported clades. Stramenopiles were recovered from the euphotic zone only, although many MAST are reportedly heterotrophic, making the observed distribution a point for further investigation. An unexpectedly high proportion of radiolarian sequences were recovered. From these, five environmental radiolarian clades, RAD-I to RAD-V, were identified. RAD-IV and RAD-V were composed of Taxopodida-like sequences, with the former solely containing Sargasso Sea sequences, although from all depth zones sampled. Our findings highlight the vast diversity of these protists, most of which remain uncultured and of unknown ecological function.

  11. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region.

  12. The abundance and seasonal distribution of Culex mosquitoes in Iowa during 1995-97.

    PubMed

    Lee, J H; Rowley, W A

    2000-12-01

    The abundance and seasonal distribution of Culex mosquitoes were monitored by measuring oviposition activity during the summers of 1995, 1996, and 1997. Five species of culicine mosquitoes laid egg rafts in ovitraps. Egg rafts of 4 Culex species-Cx. restuans (54.98%), Cx. pipiens (25.41%), Cx. salinarius (12.18%), and Cx. tarsalis (0.14%)-constituted more than 92% of the total egg rafts collected. Culiseta inornata (0.1%) was the only other species to lay viable egg rafts in the ovitraps. A small percentage (7.19%) of egg rafts did not hatch; thus identification was not possible. Compared with New Jersey light trap data in a nearby area, the abundance of Cx. tarsalis and Cs. inornata was markedly underestimated with ovitraps. These data may also reflect differences in the specific location of the 2 trap sites