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Sample records for abundance community composition

  1. Effects of landscape anthropization on mosquito community composition and abundance

    NASA Astrophysics Data System (ADS)

    Ferraguti, Martina; Martínez-de La Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-07-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control.

  2. Effects of landscape anthropization on mosquito community composition and abundance

    PubMed Central

    Ferraguti, Martina; Martínez-de la Puente, Josué; Roiz, David; Ruiz, Santiago; Soriguer, Ramón; Figuerola, Jordi

    2016-01-01

    Anthropogenic landscape transformation has an important effect on vector-borne pathogen transmission. However, the effects of urbanization on mosquito communities are still only poorly known. Here, we evaluate how land-use characteristics are related to the abundance and community composition of mosquitoes in an area with endemic circulation of numerous mosquito-borne pathogens. We collected 340 829 female mosquitoes belonging to 13 species at 45 localities spatially grouped in 15 trios formed by 1 urban, 1 rural and 1 natural area. Mosquito abundance and species richness were greater in natural and rural areas than in urban areas. Environmental factors including land use, vegetation and hydrological characteristics were related to mosquito abundance and community composition. Given the differing competences of each species in pathogen transmission, these results provide valuable information on the transmission potential of mosquito-borne pathogens that will be of great use in public and animal health management by allowing, for instance, the identification of the priority areas for pathogen surveillance and vector control. PMID:27373794

  3. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    NASA Astrophysics Data System (ADS)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

  4. 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

  5. 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.

  6. 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.

  7. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities.

    PubMed

    Smith, Renee J; Paterson, James S; Sibley, Cally A; Hutson, John L; Mitchell, James G

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices.

  8. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

    PubMed Central

    Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  9. 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.

  10. 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.

  11. 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.

  12. Habitat selection determines abundance, richness and species composition of beetles in aquatic communities.

    PubMed

    Binckley, Christopher A; Resetarits, William J

    2005-09-22

    Distribution and abundance patterns at the community and metacommunity scale can result from two distinct mechanisms. Random dispersal followed by non-random, site-specific mortality (species sorting) is the dominant paradigm in community ecology, while habitat selection provides an alternative, largely unexplored, mechanism with different demographic consequences. Rather than differential mortality, habitat selection involves redistribution of individuals among habitat patches based on perceived rather than realized fitness, with perceptions driven by past selection. In particular, habitat preferences based on species composition can create distinct patterns of positive and negative covariance among species, generating more complex linkages among communities than with random dispersal models. In our experiments, the mere presence of predatory fishes, in the absence of any mortality, reduced abundance and species richness of aquatic beetles by up to 80% in comparison with the results from fishless controls. Beetle species' shared habitat preferences generated distinct patterns of species richness, species composition and total abundance, matching large-scale field patterns previously ascribed to random dispersal and differential mortality. Our results indicate that landscape-level patterns of distribution and species diversity can be driven to a large extent by habitat selection behaviour, a critical, but largely overlooked, mechanism of community and metacommunity assembly.

  13. 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.

  14. 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

  15. 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

  16. Composition of fungal soil communities varies with plant abundance and geographic origin

    PubMed Central

    Reininger, Vanessa; Martinez-Garcia, Laura B.; Sanderson, Laura; Antunes, Pedro M.

    2015-01-01

    Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities. We also assessed whether these plants showed different symbiotic relationships with soil biota through their roots. We characterized the plant community and collected roots to investigate fungal communities using 454 pyrosequencing and assessed arbuscular mycorrhizal colonization and enemy-induced lesions. Differences in fungal communities were considered based on the assessment of α- and β diversity depending on plant ‘abundance’ and ‘origin’. Plant abundance and origin determined the fungal community. Fungal richness was higher for native abundant as opposed to relatively rare native plant species. However, this was not observed for exotics of contrasting abundance. Regardless of their origin, β diversity was higher for rare than for abundant species. Abundant exotics in the community, which happen to be grasses, were the least mycorrhizal whereas rare natives were most susceptible to enemy attack. Our results suggest that compared with exotics, the relative abundance of remnant native plant species in our old-field site is still linked to the structure of belowground fungal communities. In contrast, exotic species may act as a disturbing agent contributing towards the homogenization of soil fungal communities, potentially changing feedback interactions. PMID:26371291

  17. Environmental controls on fungal community composition and abundance over 3 years in native and degraded shrublands.

    PubMed

    Glinka, Clare; Hawkes, Christine V

    2014-11-01

    Soil fungal communities have high local diversity and turnover, but the relative contribution of environmental and regional drivers to those patterns remains poorly understood. Local factors that contribute to fungal diversity include soil properties and the plant community, but there is also evidence for regional dispersal limitation in some fungal communities. We used different plant communities with different soil conditions and experimental manipulations of both vegetation and dispersal to distinguish among these factors. Specifically, we compared native shrublands with former native shrublands that had been disturbed or converted to pasture, resulting in soils progressively more enriched in carbon and nutrients. We tested the role of vegetation via active removal, and we manipulated dispersal by adding living soil inoculum from undisturbed native sites. Soil fungi were tracked for 3 years, with samples taken at ten time points from June 2006 to June 2009. We found that soil fungal abundance, richness, and community composition responded primarily to soil properties, which in this case were a legacy of plant community degradation. In contrast, dispersal had no effect on soil fungi. Temporal variation in soil fungi was partly related to drought status, yet it was much broader in native sites compared to pastures, suggesting some buffering due to the increased soil resources in the pasture sites. The persistence of soil fungal communities over 3 years in this study suggests that soil properties can act as a strong local environmental filter. Largely persistent soil fungal communities also indicate the potential for strong biotic resistance and soil legacies, which presents a challenge for both the prediction of how fungi respond to environmental change and our ability to manipulate fungi in efforts such as ecosystem restoration.

  18. Microbial abundance and community composition influence production performance in a low-temperature petroleum reservoir.

    PubMed

    Li, Guoqiang; Gao, Peike; Wu, Yunqiang; Tian, Huimei; Dai, Xuecheng; Wang, Yansen; Cui, Qingfeng; Zhang, Hongzuo; Pan, Xiaoxuan; Dong, Hanping; Ma, Ting

    2014-05-06

    Enhanced oil recovery using indigenous microorganisms has been successfully applied in the petroleum industry, but the role of microorganisms remains poorly understood. Here, we investigated the relationship between microbial population dynamics and oil production performance during a water flooding process coupled with nutrient injection in a low-temperature petroleum reservoir. Samples were collected monthly over a two-year period. The microbial composition of samples was determined using 16S rRNA gene pyrosequencing and real-time quantitative polymerase chain reaction analyses. Our results indicated that the microbial community structure in each production well microhabitat was dramatically altered during flooding with eutrophic water. As well as an increase in the density of microorganisms, biosurfactant producers, such as Pseudomonas, Alcaligenes, Rhodococcus, and Rhizobium, were detected in abundance. Furthermore, the density of these microorganisms was closely related to the incremental oil production. Oil emulsification and changes in the fluid-production profile were also observed. In addition, we found that microbial community structure was strongly correlated with environmental factors, such as water content and total nitrogen. These results suggest that injected nutrients increase the abundance of microorganisms, particularly biosurfactant producers. These bacteria and their metabolic products subsequently emulsify oil and alter fluid-production profiles to enhance oil recovery.

  19. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    NASA Astrophysics Data System (ADS)

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.

  20. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils

    PubMed Central

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-01

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils. PMID:26739424

  1. Abundance, composition and activity of denitrifier communities in metal polluted paddy soils.

    PubMed

    Liu, Yuan; Liu, Yongzhuo; Zhou, Huimin; Li, Lianqing; Zheng, Jinwei; Zhang, Xuhui; Zheng, Jufeng; Pan, Genxing

    2016-01-07

    Denitrification is one of the most important soil microbial processes leading to the production of nitrous oxide (N2O). The potential changes with metal pollution in soil microbial community for N2O production and reduction are not well addressed. In this study, topsoil samples were collected both from polluted and non-polluted rice paddy fields and denitrifier communities were characterized with molecular fingerprinting procedures. All the retrieved nirK sequences could be grouped into neither α- nor β- proteobacteria, while most of the nosZ sequences were affiliated with α-proteobacteria. The abundances of the nirK and nosZ genes were reduced significantly in the two polluted soils. Thus, metal pollution markedly affected composition of both nirK and nosZ denitrifiers. While the total denitrifying activity and N2O production rate were both reduced under heavy metal pollution of the two sites, the N2O reduction rate showed no significant change. These findings suggest that N2O production activity could be sensitive to heavy metal pollution, which could potentially lead to a decrease in N2O emission in polluted paddies. Therefore, metal pollution could have potential impacts on soil N transformation and thus on N2O emission from paddy soils.

  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. Cell abundance and microbial community composition along a complete oil sand mining and reclamation process

    NASA Astrophysics Data System (ADS)

    Lappé, M.; Schneider, B.; Kallmeyer, J.

    2012-12-01

    (~0.37 mmol/L), whereas in the MFTs nitrate concentrations are much lower (~0.04 mmol/L). In some MFT samples sulphate appears to be the most abundant electron acceptor (up to 94 mmol/L) but no hydrogen sulphide could be detected. High cell counts in root-bearing layers might be related to a supply with otherwise unavailable nutrients, especially phosphorus. Another plausible explanation is that the cells are brought in the sand with the peat-mineral mix, because it seems that the mix contains a significant amount of roots. Samples with low amounts or no roots showed lower cell abundances. Sand and MFTs also differ in the microbial community composition. Molecular analysis of bacterial isolates of samples with different oil content show that β-Proteobacteria dominate the cultivable bacterial population in substrates with a high residual content of oil, whereas in the low oil content sand they play a minor role. The data of corresponding metagenomic analyses confirm these results. In MFTs β-Proteobacteria make up about 80% of the total bacterial population. The surprisingly stable cell abundance indicates that microbial processes take place throughout the entire production process. Rising cell numbers in root-bearing horizons show that a plant cover fosters microbial abundance and diversity, helping to restore full ecosystem functionality.

  4. 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.

  5. In-feed administered sub-therapeutic chlortetracycline alters community composition and structure but not the abundance of community resistance determinants in the fecal flora of the rat.

    PubMed

    Brooks, S P J; Kheradpir, E; McAllister, M; Kwan, J; Burgher-McLellan, K; Kalmokoff, M

    2009-08-01

    The impact of continuous sub-therapeutic chlortetracycline on community structure, composition and abundance of tetracycline resistance genes in the rat fecal community was investigated. Rats were fed a standard diet containing chlortetracycline at 15 microg g(-1) diet for 28 days, followed by 30 microg g(-1) diet to completion of the study on day-56. These levels are similar to those administered to swine during the grow-out phase. Sub-therapeutic chlortetracycline affected the fecal community as determined through change in the cultivable anaerobic community and through molecular-based analyses including denaturing gradient gel electrophoresis profiles of the variable 2-3 region community 16S rRNA genes over time and through comparative sequence analysis of 16S rRNA gene community libraries. Significant decreases in fecal phylotype diversity occurred in response to sub-therapeutic chlortetracycline, although total bacterial output remained constant over the entire feeding trial. Chlortetracycline at 15 microg g(-1) diet resulted in significant change in community composition, but only modest change to the fecal community structure in terms of the distribution of individual phylotypes among the major fecal lineages. Chlortetracycline at 30 microg g(-1) diet significantly altered the distribution of phylotypes among the major fecal lineages shifting the overall community such that Gram-negative phylotypes aligning within the phylum Bacteroidetes became the dominant lineage (>60% of total community). While chlortetracycline impacted both fecal community structure and composition, there was no significant effect on the abundance of community tetracycline resistance genes [tet(Q), tet(W), tet(O)] or on the emergence of a new putative tetracycline resistance gene identified within the fecal community. While sub-therapeutic chlortetracycline provides sufficient selective pressure to significantly alter the fecal community, the primary outcome appears to be the

  6. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    PubMed

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant.

  7. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

    PubMed

    Liu, Yuan; Liu, Yongzhuo; Ding, Yuanjun; Zheng, Jinwei; Zhou, Tong; Pan, Genxing; Crowley, David; Li, Lianqing; Zheng, Jufeng; Zhang, Xuhui; Yu, Xinyan; Wang, Jiafang

    2014-01-01

    While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.

  8. Community composition, abundance and biomass of zooplankton in Zhangzi Island waters, Northern Yellow Sea

    NASA Astrophysics Data System (ADS)

    Yin, Jiehui; Zhang, Guangtao; Li, Chaolun; Wang, Shiwei; Zhao, Zengxia; Wan, Aiyong

    2016-12-01

    Samples were collected monthly from the sea area around Zhangzi Island, northern Yellow Sea, from July 2009 to June 2010. Vertical net towing was used to examine spatial and temporal variability in zooplankton abundance and biomass. Overall, Calanus sinicus and Saggita crassa were the dominant species found during the study period, while the amphipod Themisto gracilipes was dominant in winter and spring. Vast numbers of the ctenophore species of the genus Beroe were found in October and November. It was not possible to count them, but they constituted a large portion of the total zooplankton biomass. Zooplankton species diversity was highest in October, and species evenness was highest in April. Zooplankton abundance (non-jellyfish) and biomass were highest in June and lowest in August, with annual averages of 131.3 ind./m³ and 217.5 mg/m³, respectively. Water temperature may be responsible for the variations in zooplankton abundance and biomass. Beroe biomass was negatively correlated with other zooplankton abundance. Longterm investigations will be carried out to learn more about the influence of the environment on zooplankton assemblages.

  9. Abundance of antibiotics, antibiotic resistance genes and bacterial community composition in wastewater effluents from different Romanian hospitals.

    PubMed

    Szekeres, Edina; Baricz, Andreea; Chiriac, Cecilia Maria; Farkas, Anca; Opris, Ocsana; Soran, Maria-Loredana; Andrei, Adrian-Stefan; Rudi, Knut; Balcázar, Jose Luis; Dragos, Nicolae; Coman, Cristian

    2017-03-24

    Antimicrobial resistance represents a growing and significant public health threat, which requires a global response to develop effective strategies and mitigate the emergence and spread of this phenomenon in clinical and environmental settings. We investigated, therefore, the occurrence and abundance of several antibiotics and antibiotic resistance genes (ARGs), as well as bacterial community composition in wastewater effluents from different hospitals located in the Cluj County, Romania. Antibiotic concentrations ranged between 3.67 and 53.05 μg L(-1), and the most abundant antibiotic classes were β-lactams, glycopeptides, and trimethoprim. Among the ARGs detected, 14 genes confer resistance to β-lactams, aminoglycosides, chloramphenicol, macrolide-lincosamide-streptogramin B (MLSB) antibiotics, sulfonamides, and tetracyclines. Genes encoding quaternary ammonium resistance and a transposon-related element were also detected. The sulI and qacEΔ1 genes, which confer resistance to sulfonamides and quaternary ammonium, had the highest relative abundance with values ranging from 5.33 × 10(-2) to 1.94 × 10(-1) and 1.94 × 10(-2) to 4.89 × 10(-2) copies/16 rRNA gene copies, respectively. The dominant phyla detected in the hospital wastewater samples were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Among selected hospitals, one of them applied an activated sludge and chlorine disinfection process before releasing the effluent to the municipal collector. This conventional wastewater treatment showed moderate removal efficiency of the studied pollutants, with a 55-81% decrease in antibiotic concentrations, 1-3 order of magnitude lower relative abundance of ARGs, but with a slight increase of some potentially pathogenic bacteria. Given this, hospital wastewaters (raw or treated) may contribute to the spread of these emerging pollutants in the receiving environments. To the best of our knowledge, this study quantified for the first time

  10. 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

  11. Physical and biological control of protistan community composition, distribution and abundance in the seasonal ice zone of the Southern Ocean between 30 and 80°E

    NASA Astrophysics Data System (ADS)

    Davidson, Andrew T.; Scott, Fiona J.; Nash, Geraldine V.; Wright, Simon W.; Raymond, Ben

    2010-05-01

    Protists are critical components of the Antarctic marine ecosystem as they comprise most of the living carbon and are the base of the Antarctic food web. They are also key determinants of vertical carbon flux and mediate draw-down of atmospheric CO 2 by the ocean. The community composition, abundance and distribution of marine protists (phytoplankton and protozoa) was studied during the Baseline Research on Oceanography, Krill and the Environment-West (BROKE-West) survey, in the seasonal ice zone during the 2005-2006 austral summer between 30°E and 80°E. Light and electron microscopy were used to determine the protistan composition and abundance in samples obtained at 30 sites from surface waters and at 26 sites from the depth of the maximum in situ chlorophyll fluorescence (Chl max). Cluster analysis was used to identify 5 groups of sample sites at the surface and 5 at the Chl max that were of similar protist composition and abundance. The physical characteristics, taxonomic composition, indicator taxa, and taxonomic diversity were determined for each group. In the southwest, a bloom of colonial Phaeocystis antarctica dominated the protistan community composition and biomass amongst the receding ice, but this was replaced by the flagellate life stage/s of this haptophyte in waters to the north. In the southeast, a diatom bloom had the highest diversity of protist taxa observed during the survey and centric diatoms dominated the biomass. Outside these blooms, grazing by krill probably reduced the composition and abundance of large diatoms and autotrophic dinoflagellates in coastal to mid-inshore waters. Only in offshore waters did large diatoms and dinoflagellates increase in abundance and diversity, despite low concentrations of iron and silicate at many of these sites. This increase was probably due to reduced top-down control by krill and other large zooplankton. Large diatoms dominated in offshore waters, despite other coincident studies showing that the

  12. Decadal changes in zooplankton abundance and phenology of Long Island Sound reflect interacting changes in temperature and community composition.

    PubMed

    Rice, Edward; Stewart, Gillian

    2016-09-01

    Between 1939 and 1982, several surveys indicated that zooplankton in Long Island Sound, NY (LIS) appeared to follow an annual cycle typical of the Mid-Atlantic coast of North America. Abundance peaked in both early spring and late summer and the peaks were similar in magnitude. In recent decades, this cycle appeared to have shifted. Only one large peak tended to occur, and summer copepod abundance was consistently reduced by ∼60% from 1939 to 1982 levels. In other Mid-Atlantic coastal systems such a dramatic shift has been attributed to the earlier appearance of ctenophores, particularly Mnemiopsis leidyi, during warmer spring months. However, over a decade of surveys in LIS have consistently found near-zero values in M. leidyi biomass during spring months. Our multiple linear regression model indicates that summer M. leidyi biomass during this decade explains <25% of the variation in summer copepod abundance. During these recent, warmer years, summer copepod community shifts appear to explain the loss of copepod abundance. Although Acartia tonsa in 2010-2011 appeared to be present all year long, it was no longer the dominant summer zooplankton species. Warmer summers have been associated with an increase in cyanobacteria and flagellates, which are not consumed efficiently by A. tonsa. This suggests that in warming coastal systems multiple environmental and biological factors interact and likely underlie dramatic alterations to copepod phenology, not single causes.

  13. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany.

    PubMed

    Opitz, Sebastian; Küsel, Kirsten; Spott, Oliver; Totsche, Kai Uwe; Herrmann, Martina

    2014-10-01

    We followed the abundance and compared the diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the groundwater of two superimposed pristine limestone aquifers located in the Hainich region (Thuringia, Germany) over 22 months. Groundwater obtained from the upper aquifer (12 m depth) was characterized by low oxygen saturation (0-20%) and low nitrate concentrations (0-20 μM), contrasting with 50-80% oxygen saturation and 40-200 μM nitrate in the lower aquifer (48 m and 88 m depth). Quantitative PCR targeting bacterial and archaeal amoA and 16S rRNA genes suggested a much higher ammonia oxidizer fraction in the lower aquifer (0.4-7.8%) compared with the upper aquifer (0.01-0.29%). In both aquifers, AOB communities were dominated by one phylotype related to Nitrosomonas ureae, while AOA communities were more diverse. Multivariate analysis of amoA DGGE profiles revealed a stronger temporal variation of AOA and AOB community composition in the upper aquifer, pointing to a stronger influence of surface environments. Parallel fluctuations of AOA, AOB, and total microbial abundance suggested that hydrological factors (heavy rain falls, snow melt) rather than specific physicochemical parameters were responsible for the observed community dynamics.

  14. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    PubMed Central

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  15. Emergence of Algal Blooms: The Effects of Short-Term Variability in Water Quality on Phytoplankton Abundance, Diversity, and Community Composition in a Tidal Estuary

    PubMed Central

    Egerton, Todd A.; Morse, Ryan E.; Marshall, Harold G.; Mulholland, Margaret R.

    2014-01-01

    Algal blooms are dynamic phenomena, often attributed to environmental parameters that vary on short timescales (e.g., hours to days). Phytoplankton monitoring programs are largely designed to examine long-term trends and interannual variability. In order to better understand and evaluate the relationships between water quality variables and the genesis of algal blooms, daily samples were collected over a 34 day period in the eutrophic Lafayette River, a tidal tributary within Chesapeake Bay’s estuarine complex, during spring 2006. During this period two distinct algal blooms occurred; the first was a cryptomonad bloom and this was followed by a bloom of the mixotrophic dinoflagellate, Gymnodinium instriatum. Chlorophyll a, nutrient concentrations, and physical and chemical parameters were measured daily along with phytoplankton abundance and community composition. While 65 phytoplankton species from eight major taxonomic groups were identified in samples and total micro- and nano-phytoplankton cell densities ranged from 5.8 × 106 to 7.8 × 107 cells L−1, during blooms, cryptomonads and G. instriatum were 91.6% and 99.0%, respectively, of the total phytoplankton biomass during blooms. The cryptomonad bloom developed following a period of rainfall and concomitant increases in inorganic nitrogen concentrations. Nitrate, nitrite and ammonium concentrations 0 to 5 days prior were positively lag-correlated with cryptomonad abundance. In contrast, the G. insriatum bloom developed during periods of low dissolved nitrogen concentrations and their abundance was negatively correlated with inorganic nitrogen concentrations. PMID:27694775

  16. Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons

    PubMed Central

    Wallisch, Stefanie; Gril, Tjasa; Dong, Xia; Welzl, Gerd; Bruns, Christian; Heath, Ester; Engel, Marion; Suhadolc, Marjetka; Schloter, Michael

    2014-01-01

    Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and

  17. Effects of different compost amendments on the abundance and composition of alkB harboring bacterial communities in a soil under industrial use contaminated with hydrocarbons.

    PubMed

    Wallisch, Stefanie; Gril, Tjasa; Dong, Xia; Welzl, Gerd; Bruns, Christian; Heath, Ester; Engel, Marion; Suhadolc, Marjetka; Schloter, Michael

    2014-01-01

    Alkane degrading microorganisms play an important role for the bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the abundance and diversity of bacteria harboring the alkane monooxygenase gene (alkB) in an oil-contaminated soil originated from an industrial zone in Celje, Slovenia (Technosol). Soil without any amendments (control soil) and soil amended with two composts differing in their maturation stage and nutrient availability, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12, and 36 weeks of incubation. As expected the addition of compost stimulated the degradation of alkanes in the investigated soil shortly after the addition. By using quantitative real-time PCR higher number of alkB genes were detected in soil samples amended with compost compared to the control soils. To get an insight into the composition of alkB harboring microbial communities, we performed next generation sequencing of amplicons of alkB gene fragment. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soils with stronger effects of the less maturated, nutrient poor compost. The phylogenetic analysis of communities suggested that the addition of compost stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost. AlkB harboring γ-proteobacteria like Shewanella or Hydrocarboniphaga as well as α-proteobacteria of the genus Agrobacterium responded also positively to the addition of compost to soil. The amendment of the less maturated, nutrient poor compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla) mainly at the early sampling time points. Our data indicates that compost amendments significantly change abundance and diversity pattern of alkB harboring microbes in Technosol and

  18. MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data

    PubMed Central

    Noune, Christopher; Hauxwell, Caroline

    2017-01-01

    Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of ‘meta-barcode’ data. This approach relies on comparison of amplicon sequences of ‘barcode’ regions from a population with public-domain databases of reference sequences. However, for many organisms relevant ‘barcode’ regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, ‘MetaGaAP,’ was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom ‘barcode’ regions of less than 30 polymorphisms within the span of a single ‘read’, amplification and sequencing of the ‘barcode’, generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes. The pipeline and workflow were validated in a ‘wild type’ Alphabaculovirus isolate, Helicoverpa armigera single nucleopolyhedrovirus (HaSNPV-AC53) and a tissue-culture derived strain (HaSNPV-AC53-T2). The approach was validated by comparison of polymorphisms in amplicons and shotgun data, and by comparison of predicted dominant and co-dominant genotypes with Sanger sequences. The computational power required to generate and search the database effectively limits the number of polymorphisms that can be included in a barcode to 30 or less. The approach can be used in quantitative analysis of the ecology and pathology of non-model organisms. PMID:28218638

  19. Relative resource abundance explains butterfly biodiversity in island communities.

    PubMed

    Yamamoto, Naoaki; Yokoyama, Jun; Kawata, Masakado

    2007-06-19

    Ecologists have long been intrigued by the factors that control the pattern of biodiversity, i.e., the distribution and abundance of species. Previous studies have demonstrated that coexisting species partition their resources and/or that the compositional similarity between communities is determined by environmental factors, lending support to the niche-assembly model. However, no attempt has been made to test whether the relative amount of resources that reflects relative niche space controls relative species abundance in communities. Here, we demonstrate that the relative abundance of butterfly species in island communities is significantly related to the relative biomasses of their host plants but not to the geographic distance between communities. In the studied communities, the biomass of particular host plant species positively affected the abundance of the butterfly species that used them, and consequently, influenced the relative abundance of the butterfly communities. This indicated that the niche space of butterflies (i.e., the amount of resources) strongly influences butterfly biodiversity patterns. We present this field evidence of the niche-apportionment model that propose that the relative amount of niche space explains the pattern of the relative abundance of the species in communities.

  20. Climate change effects on soil microarthropod abundance and community structure

    SciTech Connect

    Kardol, Paul; Reynolds, W. Nicholas; Norby, Richard J; Classen, Aimee T

    2011-01-01

    Long-term ecosystem responses to climate change strongly depend on how the soil subsystem and its inhabitants respond to these perturbations. Using open-top chambers, we studied the response of soil microarthropods to single and combined effects of ambient and elevated atmospheric [CO{sub 2}], ambient and elevated temperatures and changes in precipitation in constructed old-fields in Tennessee, USA. Microarthropods were assessed five years after treatments were initiated and samples were collected in both November and June. Across treatments, mites and collembola were the most dominant microarthropod groups collected. We did not detect any treatment effects on microarthropod abundance. In November, but not in June, microarthropod richness, however, was affected by the climate change treatments. In November, total microarthropod richness was lower in dry than in wet treatments, and in ambient temperature treatments, richness was higher under elevated [CO{sub 2}] than under ambient [CO{sub 2}]. Differential responses of individual taxa to the climate change treatments resulted in shifts in community composition. In general, the precipitation and warming treatments explained most of the variation in community composition. Across treatments, we found that collembola abundance and richness were positively related to soil moisture content, and that negative relationships between collembola abundance and richness and soil temperature could be explained by temperature-related shifts in soil moisture content. Our data demonstrate how simultaneously acting climate change factors can affect the structure of soil microarthropod communities in old-field ecosystems. Overall, changes in soil moisture content, either as direct effect of changes in precipitation or as indirect effect of warming or elevated [CO{sub 2}], had a larger impact on microarthropod communities than did the direct effects of the warming and elevated [CO{sub 2}] treatments. Moisture-induced shifts in soil

  1. PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 2. Plankton community composition and abundance

    PubMed Central

    Petitpas, Christian M.; Turner, Jefferson T.; Deeds, Jonathan R.; Keafer, Bruce A.; McGillicuddy, Dennis J.; Milligan, Peter J.; Shue, Vangie; White, Kevin D.; Anderson, Donald M.

    2015-01-01

    As part of the Gulf of Maine Toxicity (GOMTOX1) project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin levels in various plankton size fractions, and the community composition of potential grazers of A. fundyense in plankton size fractions during blooms of this toxic dinoflagellate in the coastal Gulf of Maine and on Georges Bank in spring and summer of 2007, 2008, and 2010. PSP toxins and A. fundyense cells were found throughout the sampled water column (down to 50 m) in the 20–64 μm size fractions. While PSP toxins were widespread throughout all size classes of the zooplankton grazing community, the majority of the toxin was measured in the 20–64 μm size fraction. A. fundyense cellular toxin content estimated from field samples was significantly higher in the coastal Gulf of Maine than on Georges Bank. Most samples containing PSP toxins in the present study had diverse assemblages of grazers. However, some samples clearly suggested PSP toxin accumulation in several different grazer taxa including tintinnids, heterotrophic dinoflagellates of the genus Protoperidinium, barnacle nauplii, the harpacticoid copepod Microsetella norvegica, the calanoid copepods Calanus finmarchicus and Pseudocalanus spp., the marine cladoceran Evadne nordmanni, and hydroids of the genus Clytia. Thus, a diverse assemblage of zooplankton grazers accumulated PSP toxins through food-web interactions. This raises the question of whether PSP toxins pose a potential human health risk not only from nearshore bivalve shellfish, but also potentially from fish and other upper-level consumers in zooplankton-based pelagic food webs. PMID:26236112

  2. PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 2. Plankton community composition and abundance.

    PubMed

    Petitpas, Christian M; Turner, Jefferson T; Deeds, Jonathan R; Keafer, Bruce A; McGillicuddy, Dennis J; Milligan, Peter J; Shue, Vangie; White, Kevin D; Anderson, Donald M

    2014-05-01

    As part of the Gulf of Maine Toxicity (GOMTOX) project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin levels in various plankton size fractions, and the community composition of potential grazers of A. fundyense in plankton size fractions during blooms of this toxic dinoflagellate in the coastal Gulf of Maine and on Georges Bank in spring and summer of 2007, 2008, and 2010. PSP toxins and A. fundyense cells were found throughout the sampled water column (down to 50 m) in the 20-64 μm size fractions. While PSP toxins were widespread throughout all size classes of the zooplankton grazing community, the majority of the toxin was measured in the 20-64 μm size fraction. A. fundyense cellular toxin content estimated from field samples was significantly higher in the coastal Gulf of Maine than on Georges Bank. Most samples containing PSP toxins in the present study had diverse assemblages of grazers. However, some samples clearly suggested PSP toxin accumulation in several different grazer taxa including tintinnids, heterotrophic dinoflagellates of the genus Protoperidinium, barnacle nauplii, the harpacticoid copepod Microsetella norvegica, the calanoid copepods Calanus finmarchicus and Pseudocalanus spp., the marine cladoceran Evadne nordmanni, and hydroids of the genus Clytia. Thus, a diverse assemblage of zooplankton grazers accumulated PSP toxins through food-web interactions. This raises the question of whether PSP toxins pose a potential human health risk not only from nearshore bivalve shellfish, but also potentially from fish and other upper-level consumers in zooplankton-based pelagic food webs.

  3. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  4. Abundance of introduced species at home predicts abundance away in herbaceous communities.

    PubMed

    Firn, Jennifer; Moore, Joslin L; MacDougall, Andrew S; Borer, Elizabeth T; Seabloom, Eric W; HilleRisLambers, Janneke; Harpole, W Stanley; Cleland, Elsa E; Brown, Cynthia S; Knops, Johannes M H; Prober, Suzanne M; Pyke, David A; Farrell, Kelly A; Bakker, John D; O'Halloran, Lydia R; Adler, Peter B; Collins, Scott L; D'Antonio, Carla M; Crawley, Michael J; Wolkovich, Elizabeth M; La Pierre, Kimberly J; Melbourne, Brett A; Hautier, Yann; Morgan, John W; Leakey, Andrew D B; Kay, Adam; McCulley, Rebecca; Davies, Kendi F; Stevens, Carly J; Chu, Cheng-Jin; Holl, Karen D; Klein, Julia A; Fay, Philip A; Hagenah, Nicole; Kirkman, Kevin P; Buckley, Yvonne M

    2011-03-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  5. The decoupling of abundance and species richness in lizard communities.

    PubMed

    Nimmo, Dale G; James, Simon G; Kelly, Luke T; Watson, Simon J; Bennett, Andrew F

    2011-05-01

    1. Patterns of species richness often correlate strongly with measures of energy. The more individuals hypothesis (MIH) proposes that this relationship is facilitated by greater resources supporting larger populations, which are less likely to become extinct. Hence, the MIH predicts that community abundance and species richness will be positively related. 2. Recently, Buckley & Jetz (2010, Journal of Animal Ecology, 79, 358-365) documented a decoupling of community abundance and species richness in lizard communities in south-west United States, such that richer communities did not contain more individuals. They predicted, as a consequence of the mechanisms driving the decoupling, a more even distribution of species abundances in species-rich communities, evidenced by a positive relationship between species evenness and species richness. 3. We found a similar decoupling of the relationship between abundance and species richness for lizard communities in semi-arid south-eastern Australia. However, we note that a positive relationship between evenness and richness is expected because of the nature of the indices used. We illustrate this mathematically and empirically using data from both sets of lizard communities. When we used a measure of evenness, which is robust to species richness, there was no relationship between evenness and richness in either data set. 4. For lizard communities in both Australia and the United States, species dominance decreased as species richness increased. Further, with the iterative removal of the first, second and third most dominant species from each community, the relationship between abundance and species richness became increasingly more positive. 5. Our data support the contention that species richness in lizard communities is not directly related to the number of individuals an environment can support. We propose an alternative hypothesis regarding how the decoupling of abundance and richness is accommodated; namely, an inverse

  6. Zooplankton species composition, abundance and biomass on the eastern Bering Sea shelf during summer: The potential role of water-column stability and nutrients in structuring the zooplankton community

    NASA Astrophysics Data System (ADS)

    Coyle, Kenneth O.; Pinchuk, Alexei I.; Eisner, Lisa B.; Napp, Jeffrey M.

    2008-08-01

    The southeastern Bering Sea sustains one of the largest fisheries in the United States, as well as wildlife resources that support valuable tourist and subsistence economies. The fish and wildlife populations in turn are sustained by a food web linking primary producers to apex predators through the zooplankton community. Recent shifts in climate toward warmer conditions may threaten these resources by altering productivity and trophic relationships in the ecosystem on the southeastern Bering Sea shelf. We examined the zooplankton community near the Pribilof Islands and on the middle shelf of the southeastern Bering Sea in summer of 1999 and 2004 to document differences and similarities in species composition, abundance and biomass by region and year. Between August 1999 and August 2004, the summer zooplankton community of the middle shelf shifted from large to small species. Significant declines were observed in the biomass of large scyphozoans ( Chrysaora melanaster), large copepods ( Calanus marshallae), arrow worms ( Sagitta elegans) and euphausiids ( Thysanoessa raschii, T. inermis) between 1999 and 2004. In contrast, significantly higher densities of the small copepods ( Pseudocalanus spp., Oithona similis) and small hydromedusae ( Euphysa flammea) were observed in 2004 relative to 1999. Stomach analyses of young-of-the-year (age 0) pollock ( Theragra chalcogramma) from the middle shelf indicated a dietary shift from large to small copepods in 2004 relative to 1999. The shift in the zooplankton community was accompanied by a 3-fold increase in water-column stability in 2004 relative to 1999, primarily due to warmer water above the thermocline, with a mean temperature of 7.3 °C in 1999 and 12.6 °C in 2004. The elevated water-column stability and warmer conditions may have influenced the zooplankton composition by lowering summer primary production and selecting for species more tolerant of a warm, oligotrophic environment. A time series of temperature from

  7. Local and Landscape Drivers of Parasitoid Abundance, Richness, and Composition in Urban Gardens.

    PubMed

    Burks, Julia M; Philpott, Stacy M

    2017-03-08

    Urbanization negatively affects biodiversity, yet some urban habitat features can support diversity. Parasitoid wasps, an abundant and highly diverse group of arthropods, can inhabit urban areas and do well in areas with higher host abundance, floral resources, or local or landscape complexity. Parasitoids provide biological control services in many agricultural habitats, yet few studies have examined diversity and abundance of parasitoids in urban agroecosystems to understand how to promote conservation and function. We examined the local habitat and landscape drivers of parasitoid abundance, superfamily and family richness, and parasitoid composition in urban gardens in the California central coast. Local factors included garden size, ground cover type, herbaceous plant species, and number of trees and shrubs. Landscape characteristics included land cover and landscape diversity around gardens. We found that garden size, mulch cover, and urban cover within 500 m of gardens predicted increases in parasitoid abundance within gardens. The height of herbaceous vegetation and tree and shrub richness predicted increases in superfamily and family richness whereas increases in urban cover resulted in declines in parasitoid richness. Abundance of individual superfamilies and families responded to a wide array of local and landscape factors, sometimes in opposite ways. Composition of parasitoid communities responded to changes in garden size, herbaceous plant cover, and number of flowers. Thus, both local scale management and landscape planning may impact the abundance, diversity, and community composition of parasitoids in urban gardens, and may result in differences in the effectiveness of parasitoids in biological control.

  8. Host densities as determinants of abundance in parasite communities

    PubMed Central

    Arneberg, P.; Skorping, A.; Grenfell, B.; Read, A. F.

    1998-01-01

    Several epidemiological models predict a positive relationship between host population density and abundance of directly transmitted macroparasites. Here, we generalize these, and test the prediction by a comparative study. We used data on communities of gastrointestinal strongylid nematodes from 19 mammalian species, representing examination of 6670 individual hosts. We studied both the average abundance of all strongylid nematodes within a host species, and the two components of abundance, prevalence and intensity. The effects of host body weight, diet, fecundity and age at maturity and parasite body size were controlled for directly, and the phylogenetically independent contrast method was used to control for confounding factors more generally. Host population density and average parasite abundance were strongly positively correlated within mammalian taxa, and across all species when the effects of host body weight were controlled for. Controlling for other variables did not change this. Even when looking at single parasite species occurring in several host species, abundance was highest in the host species with the highest population density. Prevalence and intensity showed similar patterns. These patterns provide the first macroecological evidence consistent with the prediction that transmission rates depend on host population density in natural parasite communities.

  9. Composition, Cognition, Creativity, and Community

    ERIC Educational Resources Information Center

    Moberg, Eric Michael; Kobylarz, Philip

    2015-01-01

    The purpose of this study was to examine the intersection between and among creativity, cognition, composition, and community. Researchers studied hundreds of adult students from several California community colleges and private universities by means of surveys, observations, and interviews to augment an extensive historical literature review.…

  10. Changes in composition and abundance of functional groups of arctic fungi in response to long-term summer warming

    PubMed Central

    Semenova, Tatiana A.; Morgado, Luis N.; Welker, Jeffrey M.

    2016-01-01

    We characterized fungal communities in dry and moist tundra and investigated the effect of long-term experimental summer warming on three aspects of functional groups of arctic fungi: richness, community composition and species abundance. Warming had profound effects on community composition, abundance, and, to a lesser extent, on richness of fungal functional groups. In addition, our data show that even within functional groups, the direction and extent of response to warming tend to be species-specific and we recommend that studies on fungal communities and their roles in nutrient cycling take into account species-level responses. PMID:27881760

  11. Historical variability in past phytoplankton abundance and composition in Doubtful Sound, New Zealand

    NASA Astrophysics Data System (ADS)

    Schüller, Susanne E.; Allison, Mead A.; Bianchi, Thomas S.; Tian, Feng; Savage, Candida

    2013-10-01

    Doubtful Sound, New Zealand, provides an exceptional opportunity to study a 'baseline' coastal ecosystem with an intact watershed. We present the first data on historical changes in phytoplankton abundance and community composition for three sites in Doubtful Sound using sediment records. Profiles of sedimentary concentrations of β-carotene (a proxy of total algal abundance, 0.021-1.345 mmol g organic carbon-1) and carotenoids were generally depleted, indicating low autochthonous production. Phytoplankton pigments and diatom frustules in Doubtful Sound indicate that diatoms have been prevalent for at least the last ca. 350 years; however, the relative importance of marine and freshwater diatoms has varied through time. Further, the timing of change in phytoplankton biomass and community composition differed among the sites within Doubtful Sound. This finding highlights the need to use multiple sites and complementary biomarkers when studying historical changes in phytoplankton communities in complex ecosystems with strong physicochemical gradients such as fjords.

  12. Nutrient availability modifies species abundance and community structure of Fucus-associated littoral benthic fauna.

    PubMed

    Korpinen, Samuli; Jormalainen, Veijo; Pettay, Esko

    2010-01-01

    The brown alga Fucus vesiculosus is a foundation species in the Baltic Sea littoral, hosting a rich faunal community. We compared the species composition and diversity of invertebrate macrofauna living on F. vesiculosus between sites differing in their eutrophication status and exposure to waves at three different times during a season. We determined the size, nitrogen and phlorotannin content of the alga. The invertebrate community differed substantially between sites near fish farms and those in more pristine environment. Snails and bivalves were more abundant on the Fucus stands near fish farms than on control stands, where crustaceans were more abundant. The abundance of molluscs decreased with the increasing shore exposure, while gammaridean amphipods dominated on the exposed shores. Abundance of several taxa increased during the proceeding growing season. The density of the most important herbivore of F. vesiculosus, Idotea balthica, varied 100-fold during the season being the lowest in June and the highest in August when the generation born in the summer started to feed on Fucus. Thus, the diversity and composition of Fucus-associated invertebrate fauna varies both with environmental conditions of the stand and seasonally. Although the negative effects of eutrophication on distribution and abundance of Fucus stands are well documented, a moderate increase of nutrients was found to increase the species richness of Fucus-associated fauna in early summer.

  13. The abundance and isotopic composition of water in eucrites

    NASA Astrophysics Data System (ADS)

    Barrett, T. J.; Barnes, J. J.; TartèSe, R.; Anand, M.; Franchi, I. A.; Greenwood, R. C.; Charlier, B. L. A.; Grady, M. M.

    2016-06-01

    Volatile elements play a key role in the dynamics of planetary evolution. Extensive work has been carried out to determine the abundance, distribution, and source(s) of volatiles in planetary bodies such as the Earth, Moon, and Mars. A recent study showed that the water in apatite from eucrites has similar hydrogen isotopic compositions compared to water in terrestrial rocks and carbonaceous chondrites, suggesting that water accreted very early in the inner solar system given the ancient crystallization ages (~4.5 Ga) of eucrites. Here, the measurements of water (reported as equivalent H2O abundances) and the hydrogen isotopic composition (δD) of apatite from five basaltic eucrites and one cumulate eucrite are reported. Apatite H2O abundances range from ~30 to ~3500 ppm and are associated with a weighted average δD value of -34 ± 67‰. No systematic variations or correlations are observed in H2O abundance or δD value with eucrite geochemical trend or metamorphic grade. These results extend the range of previously published hydrogen isotope data for eucrites and confirm the striking homogeneity in the H-isotopic composition of water in eucrites, which is consistent with a common source for water in the inner solar system.

  14. 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.

  15. Urban greenness influences airborne bacterial community composition.

    PubMed

    Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

    2016-11-15

    Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

  16. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  17. Factors affecting Culicoides species composition and abundance in avian nests.

    PubMed

    Martínez-de la Puente, J; Merino, S; Tomás, G; Moreno, J; Morales, J; Lobato, E; Talavera, S; Sarto I Monteys, V

    2009-08-01

    Mechanisms affecting patterns of vector distribution among host individuals may influence the population and evolutionary dynamics of vectors, hosts and the parasites transmitted. We studied the role of different factors affecting the species composition and abundance of Culicoides found in nests of the blue tit (Cyanistes caeruleus). We identified 1531 females and 2 males of 7 different Culicoides species in nests, with C. simulator being the most abundant species, followed by C. kibunensis, C. festivipennis, C. segnis, C. truncorum, C. pictipennis and C. circumscriptus. We conducted a medicationxfumigation experiment randomly assigning bird's nests to different treatments, thereby generating groups of medicated and control pairs breeding in fumigated and control nests. Medicated pairs were injected with the anti-malarial drug Primaquine diluted in saline solution while control pairs were injected with saline solution. The fumigation treatment was carried out using insecticide solution or water for fumigated and control nests respectively. Brood size was the main factor associated with the abundance of biting midges probably because more nestlings may produce higher quantities of vector attractants. In addition, birds medicated against haemoparasites breeding in non-fumigated nests supported a higher abundance of C. festivipennis than the rest of the groups. Also, we found that the fumigation treatment reduced the abundance of engorged Culicoides in both medicated and control nests, thus indicating a reduction of feeding success produced by the insecticide. These results represent the first evidence for the role of different factors in affecting the Culicoides infracommunity in wild avian nests.

  18. The Abundance and Isotopic Composition of Hg in Extraterrestrial Materials

    NASA Technical Reports Server (NTRS)

    Lauretta, D. S.

    2004-01-01

    During the past three year grant period we made excellent progress in our study of the abundances and isotopic compositions of Hg and other volatile trace elements in extraterrestrial materials. As part of my startup package I received funds to construct a state-of-the-art experimental facility to study gas-solid reaction kinetics. Much of our effort was spent developing the methodology to measure the abundance and isotopic composition of Hg at ultratrace levels in solid materials. In our first study, the abundance and isotopic composition of Hg was determined in bulk samples of the Murchison (CM) and Allende (CV) carbonaceous chondrites. We have continued our study of mercury in primitive meteorites and expanded the suite of meteorites to include other members of the CM and CV chondrite group as well as CI and CO chondrites. Samples of the CI chondrite Orgueil, the CM chondrites Murray, Nogoya, and Cold Bokkeveld, the CO chondrites Kainsaz, Omans, and Isna, and the CV chondrites Vigarano, Mokoia, and Grosnaja were tested. We have developed a thermal analysis ICP-MS technique and applied it to the study of a suite of thermally labile elements (Zn, As, Se, Cd, In, Sn, Sb, Te, Hg, Au, Tl, Pb, and Bi) in geologic materials as well.

  19. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  20. Bacterial diversity and community composition from seasurface to subseafloor

    PubMed Central

    Walsh, Emily A; Kirkpatrick, John B; Rutherford, Scott D; Smith, David C; Sogin, Mitchell; D'Hondt, Steven

    2016-01-01

    We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment. PMID:26430855

  1. Tropical Secondary Forest Management Influences Frugivorous Bat Composition, Abundance and Fruit Consumption in Chiapas, Mexico

    PubMed Central

    Vleut, Ivar; Levy-Tacher, Samuel Israel; de Boer, Willem Frederik; Galindo-González, Jorge; Vazquez, Luis-Bernardo

    2013-01-01

    Most studies on frugivorous bat assemblages in secondary forests have concentrated on differences among successional stages, and have disregarded the effect of forest management. Secondary forest management practices alter the vegetation structure and fruit availability, important factors associated with differences in frugivorous bat assemblage structure, and fruit consumption and can therefore modify forest succession. Our objective was to elucidate factors (forest structural variables and fruit availability) determining bat diversity, abundance, composition and species-specific abundance of bats in (i) secondary forests managed by Lacandon farmers dominated by Ochroma pyramidale, in (ii) secondary forests without management, and in (iii) mature rain forests in Chiapas, Southern Mexico. Frugivorous bat species diversity (Shannon H’) was similar between forest types. However, bat abundance was highest in rain forest and O. pyramidale forests. Bat species composition was different among forest types with more Carollia sowelli and Sturnira lilium captures in O. pyramidale forests. Overall, bat fruit consumption was dominated by early-successional shrubs, highest late-successional fruit consumption was found in rain forests and more bats consumed early-successional shrub fruits in O. pyramidale forests. Ochroma pyramidale forests presented a higher canopy openness, tree height, lower tree density and diversity of fruit than secondary forests. Tree density and canopy openness were negatively correlated with bat species diversity and bat abundance, but bat abundance increased with fruit abundance and tree height. Hence, secondary forest management alters forests’ structural characteristics and resource availability, and shapes the frugivorous bat community structure, and thereby the fruit consumption by bats. PMID:24147029

  2. Tropical secondary forest management influences frugivorous bat composition, abundance and fruit consumption in Chiapas, Mexico.

    PubMed

    Vleut, Ivar; Levy-Tacher, Samuel Israel; de Boer, Willem Frederik; Galindo-González, Jorge; Vazquez, Luis-Bernardo

    2013-01-01

    Most studies on frugivorous bat assemblages in secondary forests have concentrated on differences among successional stages, and have disregarded the effect of forest management. Secondary forest management practices alter the vegetation structure and fruit availability, important factors associated with differences in frugivorous bat assemblage structure, and fruit consumption and can therefore modify forest succession. Our objective was to elucidate factors (forest structural variables and fruit availability) determining bat diversity, abundance, composition and species-specific abundance of bats in (i) secondary forests managed by Lacandon farmers dominated by Ochroma pyramidale, in (ii) secondary forests without management, and in (iii) mature rain forests in Chiapas, Southern Mexico. Frugivorous bat species diversity (Shannon H') was similar between forest types. However, bat abundance was highest in rain forest and O. pyramidale forests. Bat species composition was different among forest types with more Carollia sowelli and Sturnira lilium captures in O. pyramidale forests. Overall, bat fruit consumption was dominated by early-successional shrubs, highest late-successional fruit consumption was found in rain forests and more bats consumed early-successional shrub fruits in O. pyramidale forests. Ochroma pyramidale forests presented a higher canopy openness, tree height, lower tree density and diversity of fruit than secondary forests. Tree density and canopy openness were negatively correlated with bat species diversity and bat abundance, but bat abundance increased with fruit abundance and tree height. Hence, secondary forest management alters forests' structural characteristics and resource availability, and shapes the frugivorous bat community structure, and thereby the fruit consumption by bats.

  3. Insights into Abundant Rumen Ureolytic Bacterial Community Using Rumen Simulation System

    PubMed Central

    Jin, Di; Zhao, Shengguo; Wang, Pengpeng; Zheng, Nan; Bu, Dengpan; Beckers, Yves; Wang, Jiaqi

    2016-01-01

    Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. PMID:27446045

  4. Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR.

    PubMed

    Stokell, Joshua R; Hamp, Timothy J; Steck, Todd R

    2016-08-01

    Changes in the composition of microbial communities are often examined using high-throughput sequencing (HTS). Here we analyzed bar-coded Illumina sequencing data from a previous work describing the microbial community found in the sputum of a cystic fibrosis patient by itself or in combination with qPCR to measure the absolute abundance of Pseudomonas aeruginosa and Burkholderia multivorans. Through this comparison we were able to determine the computational analysis accuracy of sequencing data to measure the relative abundance of specific taxa. While no correlation was found between relative abundance and absolute abundance of P. aeruginosa or B. multivorans, we did find conclusions derived from HTS data alone differed from those derived from a combination of HTS and qPCR. Our results highlight the importance of using qPCR with HTS when characterizing organisms in microbial communities having a dominant taxon.

  5. The Abundance and Isotopic Composition of Hg in Extraterrestrial Materials

    NASA Technical Reports Server (NTRS)

    Blum, J. D.; Klaue, Bjorn

    2005-01-01

    During the three year grant period we made excellent progress in our study of the abundances and isotopic compositions of Hg and other volatile trace elements in extraterrestrial materials. At the time the grant started, our collaborating PI, Dante Lauretts, was a postdoctoral research associate working with Peter Buseck at Arizona State University. The work on chondritic Hg was done in collaboration with Dante Lauretta and Peter Buseck and this study was published in Lauretta et a1 (2001a). In July, 2001 Dante Lauretta accepted a position as an Assistant Professor in the Lunar and Planetary Laboratory at the University of Arizona. His funding was transferred and this grant has supported much of his research activities during his first two years at the U of A. Several other papers are in preparation and will be published soon. We presented papers on this topic at Goldschmidt Conferences, the Lunar and Planetary Science Conferences, and the Annual Meetings of the Meteoritical Society. The work done under this grant has spurred several new directions of inquiry, which we are still pursuing. Included in this paper are the studies of bulk abundances and isotopic compositions of metreoritic Mercury, and the development of a thermal analysis ICP-MS technique applied to thermally liable elements.

  6. 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.

  7. FORAGE FISH AND ZOOPLANKTON COMMUNITY COMPOSITION IN WESTERN LAKE SUPERIOR

    EPA Science Inventory

    We assessed the abundance, size, and species composition of the fish and zooplankton communities of western Lake Superior during 1996 and 1997. Data were analyzed for 3 ecoregions (Duluth-Superior (1), Apostle Islands (2), Minnesota coast (3) differing in lake bathymetry, phsiodo...

  8. Phytoplankton community composition in nearshore coastal waters of Louisiana

    EPA Science Inventory

    Phytoplankton community compositions within near-shore coastal and estuarine waters of Louisiana were characterized by relative abundance, biovolume, and taxonomic identification to genus and species when possible. The range of total nitrogen was 0.5 to 1.3 mg L-1 and total phos...

  9. Pest management systems affect composition but not abundance of phytoseiid mites (Acari: Phytoseiidae) in apple orchards.

    PubMed

    Szabó, Árpád; Pénzes, Béla; Sipos, Péter; Hegyi, Tamás; Hajdú, Zsuzsanna; Markó, Viktor

    2014-04-01

    We examined the faunal composition and abundance of phytoseiid mites (Acari: Phytoseiidae) in apple orchards under different pest management systems in Hungary. A total of 30 apple orchards were surveyed, including abandoned and organic orchards and orchards where integrated pest management (IPM) or broad spectrum insecticides (conventional pest management) were applied. A total of 18 phytoseiid species were found in the canopy of apple trees. Species richness was greatest in the organic orchards (mean: 3.3 species/400 leaves) and the least in the conventional orchards (1.4), with IPM (2.1) and abandoned (2.7) orchards showing intermediate values. The phytoseiid community's Rényi diversity displayed a similar pattern. However, the total phytoseiid abundance in the orchards with different pest management systems did not differ, with abundance varying between 1.8 and 2.6 phytoseiids/10 leaves. Amblyseius andersoni, Euseius finlandicus, and Typhlodromus pyri were the three most common species. The relative abundance of A. andersoni increased with the pesticide load of the orchards whereas the relative abundance of E. finlandicus decreased. The abundance of T. pyri did not change in the apple orchards under different pest management strategies; regardless of the type of applied treatment, they only displayed greater abundance in five of the orchards. The remaining 15 phytoseiid species only occurred in small numbers, mostly from the abandoned and organic orchards. We identified a negative correlation between the abundance of T. pyri and the other phytoseiids in the abandoned and organic orchards. However, we did not find any similar link between the abundance of A. andersoni and E. finlandicus.

  10. Long-term changes in species composition and relative abundances of sharks at a provisioning site.

    PubMed

    Brunnschweiler, Juerg M; Abrantes, Kátya G; Barnett, Adam

    2014-01-01

    Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark

  11. Nearshore Pelagic Microbial Community Abundance Affects Recruitment Success of Giant Kelp, Macrocystis pyrifera

    PubMed Central

    Morris, Megan M.; Haggerty, John M.; Papudeshi, Bhavya N.; Vega, Alejandro A.; Edwards, Matthew S.; Dinsdale, Elizabeth A.

    2016-01-01

    Marine microbes mediate key ecological processes in kelp forest ecosystems and interact with macroalgae. Pelagic and biofilm-associated microbes interact with macroalgal propagules at multiple stages of recruitment, yet these interactions have not been described for Macrocystis pyrifera. Here we investigate the influence of microbes from coastal environments on recruitment of giant kelp, M. pyrifera. Through repeated laboratory experiments, we tested the effects of altered pelagic microbial abundance on the settlement and development of the microscopic propagules of M. pyrifera during recruitment. M. pyrifera zoospores were reared in laboratory microcosms exposed to environmental microbial communities from seawater during the complete haploid stages of the kelp recruitment cycle, including zoospore release, followed by zoospore settlement, to gametophyte germination and development. We altered the microbial abundance states differentially in three independent experiments with repeated trials, where microbes were (a) present or absent in seawater, (b) altered in community composition, and (c) altered in abundance. Within the third experiment, we also tested the effect of nearshore versus offshore microbial communities on the macroalgal propagules. Distinct pelagic microbial communities were collected from two southern California temperate environments reflecting contrasting intensity of human influence, the nearshore Point Loma kelp forest and the offshore Santa Catalina Island kelp forest. The Point Loma kelp forest is a high impacted coastal region adjacent to the populous San Diego Bay; whereas the kelp forest at Catalina Island is a low impacted region of the Channel Islands, 40 km offshore the southern California coast, and is adjacent to a marine protected area. Kelp gametophytes reared with nearshore Point Loma microbes showed lower survival, growth, and deteriorated morphology compared to gametophytes with the offshore Catalina Island microbial community

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Avian community composition of kopjes in a heterogeneous landscape.

    PubMed

    Trager, Matthew; Mistry, Shahroukh

    2003-05-01

    We examined avian communities of kopjes (naturally occurring insular rock outcrops) in grassland and thorn tree woodland habitats in the Seronera region of Serengeti National Park, northwestern Tanzania. Although kopjes cover a small proportion of the Park's area, they provide resources that are uncommon in the Serengeti landscape and are known to host diverse, yet poorly documented, biotic communities. The primary objectives of this study were (1) to compare avian communities of kopjes with those of their surrounding habitat matrixes; (2) to compare the avian communities among kopjes; and (3) to determine the effects of kopje characteristics (e.g., size, vegetation cover, level of human disturbance and matrix type) on avian diversity and community composition. The avian communities of kopjes differed significantly from those of the matrixes in species composition and guild characteristics. Rare species, frugivorous species and nectarivorous species were more abundant on kopjes, whereas there were more ground-feeding species in matrix sites. Species richness was positively correlated with the area of kopjes covered by tall vegetation (5+ m), but neither total habitat area nor total vegetation cover significantly affected avian diversity. The surrounding habitat type, the fruiting phenology of Ficus and Commiphora trees and the level of human disturbance also influenced the presence and abundance of individual species and accounted for differences in community composition among kopjes. Our results show that kopjes support unique avian assemblages comprising many species that are otherwise rare in Serengeti, and consequently that kopjes may be local hotspots of avian diversity in the region.

  17. Predators alter community organization of coral reef cryptofauna and reduce abundance of coral mutualists

    NASA Astrophysics Data System (ADS)

    Stier, A. C.; Leray, M.

    2014-03-01

    Coral reefs are the most diverse marine systems in the world, yet our understanding of the processes that maintain such extraordinary diversity remains limited and taxonomically biased toward the most conspicuous species. Cryptofauna that live deeply embedded within the interstitial spaces of coral reefs make up the majority of reef diversity, and many of these species provide important protective services to their coral hosts. However, we know very little about the processes governing the diversity and composition of these less conspicuous but functionally important species. Here, we experimentally quantify the role of predation in driving the community organization of small fishes and decapods that live embedded within Pocillopora eydouxi, a structurally complex, reef-building coral found widely across the Indo-Pacific. We use surveys to describe the natural distribution of predators, and then, factorially manipulate two focal predator species to quantify the independent and combined effects of predator density and identity on P. eydouxi-dwelling cryptofauna. Predators reduced abundance (34 %), species richness (20 %), and modified species composition. Rarefaction revealed that observed reductions in species richness were primarily driven by changes in abundance. Additionally, the two predator species uniquely affected the beta diversity and composition of the prey assemblage. Predators reduced the abundance and modified the composition of a number of mutualist fishes and decapods, whose benefit to the coral is known to be both diversity- and density-dependent. We predict that the density and identity of predators present within P. eydouxi may substantially alter coral performance in the face of an increased frequency and intensity of natural and anthropogenic stressors.

  18. Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers.

    PubMed

    Drury, Bradley; Rosi-Marshall, Emma; Kelly, John J

    2013-03-01

    In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization.

  19. Shifts in Campylobacter species abundance may reflect general microbial community shifts in periodontitis progression

    PubMed Central

    Henne, Karsten; Fuchs, Felix; Kruth, Sebastian; Horz, Hans-Peter; Conrads, Georg

    2014-01-01

    Background Oral Campylobacter species have been found to be associated with periodontitis progression. While the etiological significance of Campylobacter rectus is quite established, the association of C. gracilis, C. concisus, and C. curvus with health or disease remains contradictory. Objectives This study hypothesizes that the proportion of species within the Campylobacter genus rather than the absolute abundance of a single species is a suitable indicator for periodontitis progression. Design Subgingival plaque from 90 periodontitis patients and gingival sulcus fluid of 32 healthy individuals were subjected to a newly developed nested PCR approach, in which all Campylobacter spp. were amplified simultaneously. The resulting mixture of 16S-rRNA-gene-amplicons were separated by single-stranded conformation polymorphism (SSCP) gel electrophoresis, followed by sequencing and identification of excised bands and relative quantification of band intensities. In all samples, the abundance of selected periodontitis marker species was determined based on DNA hybridization on a microarray. Results The highly prevalent Campylobacter community was composed of varying proportions of C. rectus, C. gracilis, C. concisus, and C. curvus. Cluster analysis based on SSCP-banding pattern resulted in distinct groups which in turn coincided with significant differences in abundance of established periodontitis marker species (Tannerella forsythia, Porphyromonas gingivalis, and Fusobacterium nucleatum) and progression. Conclusions The shift in the Campylobacter community composition seems to display the general microbial community shift during clinical progression in a simplified manner. The focus on members of the Campylobacter in this study suggests that this genus can be an indicator of ecological changes in the subgingival oral microflora. PMID:25412608

  20. Microbial abundance and composition influence litter decomposition response to environmental change.

    PubMed

    Allison, Steven D; Lu, Ying; Weihe, Claudia; Goulden, Michael L; Martiny, Adam C; Treseder, Kathleen K; Martiny, Jennifer B H

    2013-03-01

    Rates of ecosystem processes such as decomposition are likely to change as a result of human impacts on the environment. In southern California, climate change and nitrogen (N) deposition in particular may alter biological communities and ecosystem processes. These drivers may affect decomposition directly, through changes in abiotic conditions, and indirectly through changes in plant and decomposer communities. To assess indirect effects on litter decomposition, we reciprocally transplanted microbial communities and plant litter among control and treatment plots (either drought or N addition) in a grassland ecosystem. We hypothesized that drought would reduce decomposition rates through moisture limitation of decomposers and reductions in plant litter quality before and during decomposition. In contrast, we predicted that N deposition would stimulate decomposition by relieving N limitation of decomposers and improving plant litter quality. We also hypothesized that adaptive mechanisms would allow microbes to decompose litter more effectively in their native plot and litter environments. Consistent with our first hypothesis, we found that drought treatment reduced litter mass loss from 20.9% to 15.3% after six months. There was a similar decline in mass loss of litter inoculated with microbes transplanted from the drought treatment, suggesting a legacy effect of drought driven by declines in microbial abundance and possible changes in microbial community composition. Bacterial cell densities were up to 86% lower in drought plots and at least 50% lower on litter derived from the drought treatment, whereas fungal hyphal lengths increased by 13-14% in the drought treatment. Nitrogen effects on decomposition rates and microbial abundances were weaker than drought effects, although N addition significantly altered initial plant litter chemistry and litter chemistry during decomposition. However, we did find support for microbial adaptation to N addition with N

  1. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    PubMed

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence.

  2. Composition and abundance of stink bugs (Heteroptera: Pentatomidae) in corn.

    PubMed

    Tillman, P Glynn

    2010-12-01

    The species composition and abundance of stink bugs (Heteroptera: Pentatomidae) in corn, Zea mays L., was determined in this on-farm study in Georgia. Seven species of phytophagous stink bugs were found on corn with the predominant species being Nezara viridula (L.) and Euschistus servus (Say). All developmental stages of these two pests were found, indicating they were developing on the corn crop. The remaining five species, Oebalus pugnax pugnax (F.), Euschistus quadrator (Rolston), Euschistus tristigmus (Say), Euschistus ictericus (L.), and Acrosternum hilare (Say), were found in relatively low numbers. Adult N. viridula were parasitized by the tachinid parasitoid Trichopoda pennipes (F.). There was a pronounced edge effect in distribution of stink bugs in corn. Population dynamics of N. viridula and E. servus were different on early and late-planted corn. Oviposition by females of both stink bug species occurred in mid-to-late-May and again mid-to-late-June in corn, regardless of planting date. In early planted fields, if stink bug females oviposited on corn in mid-July, the resulting nymphs did not survive to the adult stage in corn because ears were close to physiological maturity and leaves were senescing. Density of stink bug adults in early planted corn was relatively low throughout the growing season. In late-planted corn, females of both stink bug species consistently laid eggs in mid-to-late-July on corn with developing ears. This habitat favored continued nymph development, and the resulting adult population reached high levels. These results indicate that corn management practices play a key role in the ecology of stink bugs in corn agroecosystems and provide information for designing management strategies to suppress stink bugs in farmscapes with corn.

  3. Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses

    PubMed Central

    Warshan, Denis; Bay, Guillaume; Nahar, Nurun; Wardle, David A; Nilsson, Marie-Charlotte; Rasmussen, Ulla

    2016-01-01

    Dinitrogen (N2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, Pleurozium schreberi and Hylocomium splendens) represents the main pathway of biological N input into N-depleted boreal forests. Little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of N2-fixation. Using specific nifH primers targeting four major cyanobacterial clusters and quantitative PCR, we investigated how community composition, abundance and nifH expression varied by moss species and over the growing seasons. We evaluated N2-fixation rates across nine forest sites in June and September and explored the abundance and nifH expression of individual cyanobacterial clusters when N2-fixation is highest. Our results showed temporal and host-dependent variations of cyanobacterial community composition, nifH gene abundance and expression. N2-fixation was higher in September than June for both moss species, explained by higher nifH gene expression of individual clusters rather than higher nifH gene abundance or differences in cyanobacterial community composition. In most cases, ‘Stigonema cluster' made up less than 29% of the total cyanobacterial community, but accounted for the majority of nifH gene expression (82–94% of total nifH expression), irrespective of sampling date or moss species. Stepwise multiple regressions showed temporal variations in N2-fixation being greatly explained by variations in nifH expression of the ‘Stigonema cluster'. These results suggest that Stigonema is potentially the most influential N2-fixer in symbiosis with boreal forest feather mosses. PMID:26918665

  4. Indirect effects of predators control herbivore richness and abundance in a benthic eelgrass (Zostera marina) mesograzer community.

    PubMed

    Amundrud, Sarah L; Srivastava, Diane S; O'Connor, Mary I

    2015-07-01

    Herbivore communities can be sensitive to changes in predator pressure (top-down effects) and resource availability (bottom-up effects) in a wide range of systems. However, it remains unclear whether such top-down and bottom-up effects reflect direct impacts of predators and/or resources on herbivores, or are indirect, reflecting altered interactions among herbivore species. We quantified direct and indirect effects of bottom-up and top-down processes on an eelgrass (Zostera marina) herbivore assemblage. In a field experiment, we factorially manipulated water column nutrients (with Osmocote(™) slow-release fertilizer) and predation pressure (with predator exclusion cages) and measured the effects on herbivore abundance, richness and beta diversity. We examined likely mechanisms of community responses by statistically exploring the response of individual herbivore species to trophic manipulations. Predators increased herbivore richness and total abundance, in both cases through indirect shifts in community composition. Increases in richness occurred through predator suppression of common gammarid amphipod species (Monocorophium acherusicum and Photis brevipes), permitting the inclusion of rarer gammarid species (Aoroides columbiae and Pontogeneia rostrata). Increased total herbivore abundance reflected increased abundance of a caprellid amphipod species (Caprella sp.), concurrent with declines in the abundance of other common species. Furthermore, predators decreased beta diversity by decreasing variability in Caprella sp. abundance among habitat patches. Osmocote(™) fertilization increased nutrient concentrations locally, but nutrients dissipated to background levels within 3 m of the fertilizer. Nutrient addition weakly affected the herbivore assemblage, not affecting richness and increasing total abundance by increasing one herbivore species (Caprella sp.). Nutrient addition did not affect beta diversity. We demonstrated that assemblage-level effects of

  5. Plant community diversity and native plant abundance decline with increasing abundance of an exotic annual grass

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Exotic plants are generally considered a serious problem in wildlands around the globe. However, some argue that the impacts of exotic plants have been exaggerated and that biodiversity and other important plant community characteristics are commonly improved with invasion. Thus, disagreement exis...

  6. Abundance and Composition of Epiphytic Bacterial and Archaeal Ammonia Oxidizers of Marine Red and Brown Macroalgae

    PubMed Central

    Trias, Rosalia; García-Lledó, Arantzazu; Sánchez, Noemí; López-Jurado, José Luis; Hallin, Sara

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are important for nitrogen cycling in marine ecosystems. Little is known about the diversity and abundance of these organisms on the surface of marine macroalgae, despite the algae's potential importance to create surfaces and local oxygen-rich environments supporting ammonia oxidation at depths with low dissolved oxygen levels. We determined the abundance and composition of the epiphytic bacterial and archaeal ammonia-oxidizing communities on three species of macroalgae, Osmundaria volubilis, Phyllophora crispa, and Laminaria rodriguezii, from the Balearic Islands (western Mediterranean Sea). Quantitative PCR of bacterial and archaeal 16S rRNA and amoA genes was performed. In contrast to what has been shown for most other marine environments, the macroalgae's surfaces were dominated by bacterial amoA genes rather than those from the archaeal counterpart. On the basis of the sequences retrieved from AOB and AOA amoA gene clone libraries from each algal species, the bacterial ammonia-oxidizing communities were related to Nitrosospira spp. and to Nitrosomonas europaea and only 6 out of 15 operational taxonomic units (OTUs) were specific for the host species. Conversely, the AOA diversity was higher (43 OTUs) and algal species specific, with 17 OTUs specific for L. rodriguezii, 3 for O. volubilis, and 9 for P. crispa. Altogether, the results suggest that marine macroalgae may exert an ecological niche for AOB in marine environments, potentially through specific microbe-host interactions. PMID:22081571

  7. 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.

  8. Fuel breaks affect nonnative species abundance in Californian plant communities

    USGS Publications Warehouse

    Merriam, K.E.; Keeley, J.E.; Beyers, J.L.

    2006-01-01

    We evaluated the abundance of nonnative plants on fuel breaks and in adjacent untreated areas to determine if fuel treatments promote the invasion of nonnative plant species. Understanding the relationship between fuel treatments and nonnative plants is becoming increasingly important as federal and state agencies are currently implementing large fuel treatment programs throughout the United States to reduce the threat of wildland fire. Our study included 24 fuel breaks located across the State of California. We found that nonnative plant abundance was over 200% higher on fuel breaks than in adjacent wildland areas. Relative nonnative cover was greater on fuel breaks constructed by bulldozers (28%) than on fuel breaks constructed by other methods (7%). Canopy cover, litter cover, and duff depth also were significantly lower on fuel breaks constructed by bulldozers, and these fuel breaks had significantly more exposed bare ground than other types of fuel breaks. There was a significant decline in relative nonnative cover with increasing distance from the fuel break, particularly in areas that had experienced more numerous fires during the past 50 years, and in areas that had been grazed. These data suggest that fuel breaks could provide establishment sites for nonnative plants, and that nonnatives may invade surrounding areas, especially after disturbances such as fire or grazing. Fuel break construction and maintenance methods that leave some overstory canopy and minimize exposure of bare ground may be less likely to promote nonnative plants. ?? 2006 by the Ecological Society of America.

  9. 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.

  10. Chemical Compositions and Abundance Anomalies in Stellar Coronae ADP 99

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy; Oliversen, Ronald J. (Technical Monitor)

    2003-01-01

    Progress has been made using both EUVE (Extreme Ultraviolet Explorer) and ASCA (Advanced Satellite for Cosmology and Astrophysics) data and a new postdoctoral scientist has now been hired. Stars studied to date include YY Gem (dMe binary), xi Boo A (intermediate activity G8 V), xi UMa (more active G quadruple system) HR1099 (K1 IV + G5 V) RS CVn-like, AU Mic (dMe). In addition to a paper that concentrated on abundancies in HR1099, a paper was recently submitted on the coronal abundances of AR(tilde)Lac that revealed an interesting pattern of overabundances of very low FIP elements (Al and Ca) compared to the low FIP elements Si, Mg and Fe. Two papers are nearing completion on methods of analysis and on the abundances in the corona of AU(tilde)Mic. Additionally, two invited conference proceedings papers are being published on this work. The main conclusion of the study to date is that our existing ideas of coronal abundance anomalies need complete revision. The solar-like FIP effect is replaced by a pattern than appears to enhance high FIP elements rather than low FIP elements in very active stars. The archival studies we are undertaking now are revealing some key details of these patterns, and are beginning to map out the anomalies as a function of spectral type, a key goal of this study.

  11. Stormwater runoff drives viral community composition changes in inland freshwaters

    PubMed Central

    Williamson, Kurt E.; Harris, Jamie V.; Green, Jasmin C.; Rahman, Faraz; Chambers, Randolph M.

    2014-01-01

    Storm events impact freshwater microbial communities by transporting terrestrial viruses and other microbes to freshwater systems, and by potentially resuspending microbes from bottom sediments. The magnitude of these impacts on freshwater ecosystems is unknown and largely unexplored. Field studies carried out at two discrete sites in coastal Virginia (USA) were used to characterize the viral load carried by runoff and to test the hypothesis that terrestrial viruses introduced through stormwater runoff change the composition of freshwater microbial communities. Field data gathered from an agricultural watershed indicated that primary runoff can contain viral densities approximating those of receiving waters. Furthermore, viruses attached to suspended colloids made up a large fraction of the total load, particularly in early stages of the storm. At a second field site (stormwater retention pond), RAPD-PCR profiling showed that the viral community of the pond changed dramatically over the course of two intense storms while relatively little change was observed over similar time scales in the absence of disturbance. Comparisons of planktonic and particle-associated viral communities revealed two completely distinct communities, suggesting that particle-associated viruses represent a potentially large and overlooked portion of aquatic viral abundance and diversity. Our findings show that stormwater runoff can quickly change the composition of freshwater microbial communities. Based on these findings, increased storms in the coastal mid-Atlantic region predicted by most climate change models will likely have important impacts on the structure and function of local freshwater microbial communities. PMID:24672520

  12. Relative Abundance of and Composition within Fungal Orders Differ between Cheatgrass (Bromus tectorum) and Sagebrush (Artemisia tridentata)-Associated Soils

    PubMed Central

    Weber, Carolyn F.; King, Gary M.; Aho, Ken

    2015-01-01

    Nonnative Bromus tectorum (cheatgrass) is decimating sagebrush steppe, one of the largest ecosystems in the Western United States, and is causing regional-scale shifts in the predominant plant-fungal interactions. Sagebrush, a native perennial, hosts arbuscular mycorrhizal fungi (AMF), whereas cheatgrass, a winter annual, is a relatively poor host of AMF. This shift is likely intertwined with decreased carbon (C)-sequestration in cheatgrass-invaded soils and alterations in overall soil fungal community composition and structure, but the latter remain unresolved. We examined soil fungal communities using high throughput amplicon sequencing (ribosomal large subunit gene) in the 0–4 cm and 4–8 cm depth intervals of six cores from cheatgrass- and six cores from sagebrush-dominated soils. Sagebrush core surfaces (0–4 cm) contained higher nitrogen and total C than cheatgrass core surfaces; these differences mirrored the presence of glomalin related soil proteins (GRSP), which has been associated with AMF activity and increased C-sequestration. Fungal richness was not significantly affected by vegetation type, depth or an interaction of the two factors. However, the relative abundance of seven taxonomic orders was significantly affected by vegetation type or the interaction between vegetation type and depth. Teloschistales, Spizellomycetales, Pezizales and Cantharellales were more abundant in sagebrush libraries and contain mycorrhizal, lichenized and basal lineages of fungi. Only two orders (Coniochaetales and Sordariales), which contain numerous economically important pathogens and opportunistic saprotrophs, were more abundant in cheatgrass libraries. Pleosporales, Agaricales, Helotiales and Hypocreales were most abundant across all libraries, but the number of genera detected within these orders was as much as 29 times lower in cheatgrass relative to sagebrush libraries. These compositional differences between fungal communities associated with cheatgrass- and

  13. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  14. Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers

    PubMed Central

    Drury, Bradley; Rosi-Marshall, Emma

    2013-01-01

    In highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances of Deltaproteobacteria, Desulfococcus, Dechloromonas, and Chloroflexi sequences and increases in abundances of Nitrospirae and Sphingobacteriales sequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization. PMID:23315724

  15. Chemical Compositions and Abundance Anomalies in Stellar Coronae ADP99

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    We have been investigating different statistical methods for analysing the metal abundances of sources with low S/N. A Bayesian technique has been developed that determines the most probable line-to-continuum ratio in the source, thereby leading to the metallicity. This method is a promising approach with which to mine the ASCA archive. Some of this work has now been published in conference proceedings. The flavour of the project has changed very slightly in the last year owing to the increasing availability of several good quality Chandra HETG and LETG spectra for stars for which we had reduced and analysed ASCA data. The Chandra grating spectra in principle provide a means of calibrating the results from the low resolution ASCA spectra and we have started some work toward that goal. One paper concerning abundance ratios in active stars is appearing shortly in conference proceedings and is being readied for publication in a main-stream astrophysical journal. This paper demonstrates for the first time that abundance anomalies cannot be categorized simply in terms of First Ionization Potential (FIP) or inverse-FIP based effects. Different Ne enhancements are found in different star types but a link between enhancement factors and stellar properties is not obvious. The publication noted as in preparation in an earlier report, finding strong Ne enhancements in active stars, is now published. These results will again be used to "calibrate" low resolution results for which line ratio techniques cannot be employed.

  16. Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

    PubMed

    Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

  17. Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

    NASA Astrophysics Data System (ADS)

    Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

    2015-04-01

    In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

  18. Seasonal composition and activity of sulfate-reducing prokaryotic communities in seagrass bed sediments

    EPA Science Inventory

    Sulfate-reducing prokaryotes (SRP) play a key role in the carbon and nutrient cycles of coastal marine, vegetated ecosystems, but the interactions of SRP communities with aquatic plants remain little studied. The abundance, activity, and community composition of SRP was studied i...

  19. The activated sludge ecosystem contains a core community of abundant organisms.

    PubMed

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal.

  20. 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.

  1. Remembrance of things past: modelling the relationship between species' abundances in living communities and death assemblages.

    PubMed

    Olszewski, Thomas D

    2012-02-23

    Accumulations of dead skeletal material are a valuable archive of past ecological conditions. However, such assemblages are not equivalent to living communities because they mix the remains of multiple generations and are altered by post-mortem processes. The abundance of a species in a death assemblage can be quantitatively modelled by successively integrating the product of an influx time series and a post-mortem loss function (a decay function with a constant half-life). In such a model, temporal mixing increases expected absolute dead abundance relative to average influx as a linear function of half-life and increases variation in absolute dead abundance values as a square-root function of half-life. Because typical abundance distributions of ecological communities are logarithmically distributed, species' differences in preservational half-life would have to be very large to substantially alter species' abundance ranks (i.e. make rare species common or vice-versa). In addition, expected dead abundances increase at a faster rate than their range of variation with increased time averaging, predicting greater consistency in the relative abundance structure of death assemblages than their parent living community.

  2. The activated sludge ecosystem contains a core community of abundant organisms

    PubMed Central

    Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

    2016-01-01

    Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

  3. 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

  4. Spatial-Temporal Survey and Occupancy-Abundance Modeling To Predict Bacterial Community Dynamics in the Drinking Water Microbiome

    PubMed Central

    Pinto, Ameet J.; Schroeder, Joanna; Lunn, Mary; Sloan, William

    2014-01-01

    ABSTRACT Bacterial communities migrate continuously from the drinking water treatment plant through the drinking water distribution system and into our built environment. Understanding bacterial dynamics in the distribution system is critical to ensuring that safe drinking water is being supplied to customers. We present a 15-month survey of bacterial community dynamics in the drinking water system of Ann Arbor, MI. By sampling the water leaving the treatment plant and at nine points in the distribution system, we show that the bacterial community spatial dynamics of distance decay and dispersivity conform to the layout of the drinking water distribution system. However, the patterns in spatial dynamics were weaker than those for the temporal trends, which exhibited seasonal cycling correlating with temperature and source water use patterns and also demonstrated reproducibility on an annual time scale. The temporal trends were driven by two seasonal bacterial clusters consisting of multiple taxa with different networks of association within the larger drinking water bacterial community. Finally, we show that the Ann Arbor data set robustly conforms to previously described interspecific occupancy abundance models that link the relative abundance of a taxon to the frequency of its detection. Relying on these insights, we propose a predictive framework for microbial management in drinking water systems. Further, we recommend that long-term microbial observatories that collect high-resolution, spatially distributed, multiyear time series of community composition and environmental variables be established to enable the development and testing of the predictive framework. PMID:24865557

  5. Chemical Compositions and Abundance Anomalies in Stellar Coronae ADP 99

    NASA Technical Reports Server (NTRS)

    Oliversen, Ronald J. (Technical Monitor); Drake, Jeremy

    2004-01-01

    New atomic data for tackling some of our spectra have been investigated by co-I Laming (NRL), including the effects of recombination on spectral line fluxes that are not included in, for example, the CHIANTI database models. Promising new progress has been made with modelling some of the recent abundance anomaly results in terms of Alven wave-driven separation of neutrals and ions in the upper chromosphere. The problems that existing models have is that they cannot simultaneously explain the low-FIP enhanced solar-like coronae and the high-FIP rich active coronae of RS CVn-like stars. The Alven wave model shows promise with both of these scenarios, with the fractionation or suppression of low-FIP ions depending on the characteristics of the chromosphere. This work is currently in the writing up stage. In summary, the work to-date is making good progress in mapping abundance anomalies as a function of spectral type and activity level. We are also making good progress with modelling that we will be able to test with our observational results. With one more year of effort, we'anticipate that the bulk of the work described above can be published, together with outstanding key studies on anomalies among the different active binaries.

  6. Temporal changes in mosquito abundance (Culex pipiens), avian malaria prevalence and lineage composition

    PubMed Central

    2013-01-01

    Background Knowledge on the temporal dynamics of host/vector/parasite interactions is a pre-requisite to further address relevant questions in the fields of epidemiology and evolutionary ecology of infectious diseases. In studies of avian malaria, the natural history of Plasmodium parasites with their natural mosquito vectors, however, is mostly unknown. Methods Using artificial water containers placed in the field, we monitored the relative abundance of parous females of Culex pipiens mosquitoes during two years (2010–2011), in a population in western Switzerland. Additionally, we used molecular tools to examine changes in avian malaria prevalence and Plasmodium lineage composition in female C. pipiens caught throughout one field season (April-August) in 2011. Results C. pipiens relative abundance varied both between years and months, and was associated with temperature fluctuations. Total Plasmodium prevalence was high and increased from spring to summer months (13.1-20.3%). The Plasmodium community was composed of seven different lineages including P. relictum (SGS1, GRW11 and PADOM02 lineages), P. vaughani (lineage SYAT05) and other Plasmodium spp. (AFTRU5, PADOM1, COLL1). The most prevalent lineages, P. vaughani (lineage SYAT05) and P. relictum (lineage SGS1), were consistently found between years, although they had antagonistic dominance patterns during the season survey. Conclusions Our results suggest that the time window of analysis is critical in evaluating changes in the community of avian malaria lineages infecting mosquitoes. The potential determinants of the observed changes as well as their implications for future prospects on avian malaria are discussed. PMID:24499594

  7. Composition of epiphytic bacterial communities differs on petals and leaves.

    PubMed

    Junker, R R; Loewel, C; Gross, R; Dötterl, S; Keller, A; Blüthgen, N

    2011-11-01

    The epiphytic bacterial communities colonising roots and leaves have been described for many plant species. In contrast, microbiologists have rarely considered flowers of naturally growing plants. We identified bacteria isolated from the surface of petals and leaves of two plant species, Saponaria officinalis (Caryophyllaceae) and Lotus corniculatus (Fabaceae). The bacterial diversity was much lower on petals than on leaves of the same plants. Moreover, the bacterial communities differed strongly in composition: while Pseudomonadaceae and Microbacteriaceae were the most abundant families on leaves, Enterobacteriaceae dominated the floral communities. We hypothesise that antibacterial floral volatiles trigger the low diversity on petals, which is supported by agar diffusion assays using substances emitted by flowers and leaves of S. officinalis. These results suggest that bacteria should be included in the interpretation of floral traits, and possible effects of bacteria on pollination are proposed and discussed.

  8. Fungicide Effects on Fungal Community Composition in the Wheat Phyllosphere

    PubMed Central

    Karlsson, Ida; Friberg, Hanna; Steinberg, Christian; Persson, Paula

    2014-01-01

    The fungicides used to control diseases in cereal production can have adverse effects on non-target fungi, with possible consequences for plant health and productivity. This study examined fungicide effects on fungal communities on winter wheat leaves in two areas of Sweden. High-throughput 454 sequencing of the fungal ITS2 region yielded 235 operational taxonomic units (OTUs) at the species level from the 18 fields studied. It was found that commonly used fungicides had moderate but significant effect on fungal community composition in the wheat phyllosphere. The relative abundance of several saprotrophs was altered by fungicide use, while the effect on common wheat pathogens was mixed. The fungal community on wheat leaves consisted mainly of basidiomycete yeasts, saprotrophic ascomycetes and plant pathogens. A core set of six fungal OTUs representing saprotrophic species was identified. These were present across all fields, although overall the difference in OTU richness was large between the two areas studied. PMID:25369054

  9. Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

    PubMed Central

    Trogisch, Stefan; Both, Sabine; Scholten, Thomas; Bruelheide, Helge; Buscot, François

    2013-01-01

    Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition. PMID:23826151

  10. Helium and neon abundances and compositions in cometary matter.

    PubMed

    Marty, Bernard; Palma, Russell L; Pepin, Robert O; Zimmermann, Laurent; Schlutter, Dennis J; Burnard, Peter G; Westphal, Andrew J; Snead, Christopher J; Bajt, Sasa; Becker, Richard H; Simones, Jacob E

    2008-01-04

    Materials trapped and preserved in comets date from the earliest history of the solar system. Particles captured by the Stardust spacecraft from comet 81P/Wild 2 are indisputable cometary matter available for laboratory study. Here we report measurements of noble gases in Stardust material. Neon isotope ratios are within the range observed in "phase Q," a ubiquitous, primitive organic carrier of noble gases in meteorites. Helium displays 3He/4He ratios twice those in phase Q and in Jupiter's atmosphere. Abundances per gram are surprisingly large, suggesting implantation by ion irradiation. The gases are probably carried in high-temperature igneous grains similar to particles found in other Stardust studies. Collectively, the evidence points to gas acquisition in a hot, high ion-flux nebular environment close to the young Sun.

  11. Helium and Neon Abundances and Compositions in Cometary Matter

    SciTech Connect

    Marty, B; Palma, R L; Pepin, R O; Zimmmermann, L; Schlutter, D J; Burnard, P G; Westphal, A J; Snead, C J; Bajt, S; Becker, R H; Simones, J E

    2007-10-15

    Materials trapped and preserved in comets date from the earliest history of the solar system. Particles captured by the Stardust spacecraft from comet Wild 2 are indisputable cometary matter available for laboratory study. Here they report measurements of noble gases in Stardust material. neon isotope ratios are within the range observed in 'phase Q', a ubiquitous, primitive organic carrier of noble gases in meteorites. Helium displays {sup 3}He/{sup 4}He ratios twice those in phase Q and in Jupiter's atmosphere. Abundances per gram are surprisingly large, suggesting implantation by ion irradiation. The gases are carried in high temperature igneous grains similar to particles found in other Stardust studies. Collectively the evidence points to gas acquisition in a hot, high ion flux nebular environment close to the young Sun.

  12. Species-abundance--seed-size patterns within a plant community affected by grazing disturbance.

    PubMed

    Wu, Gao-lin; Shang, Zhan-huan; Zhu, Yuan-jun; Ding, Lu-ming; Wang, Dong

    2015-04-01

    Seed size has been advanced as a key factor that influences the dynamics of plant communities, but there are few empirical or theoretical predictions of how community dynamics progress based on seed size patterns. Information on the abundance of adults, seedlings, soil seed banks, seed rains, and the seed mass of 96 species was collected in alpine meadows of the Qinghai-Tibetan Plateau (China), which had different levels of grazing disturbance. The relationships between seed-mass-abundance patterns for adults, seedlings, the soil seed bank, and seed rain in the plant community were evaluated using regression models. Results showed that grazing levels affected the relationship between seed size and abundance properties of adult species, seedlings, and the soil seed bank, suggesting that there is a shift in seed-size--species-abundance relationships as a response to the grazing gradient. Grazing had no effect on the pattern of seed-size-seed-rain-abundance at four grazing levels. Grazing also had little effect on the pattern of seed-size--species-abundance and pattern of seed-size--soil-seed-bank-abundance in meadows with no grazing, light grazing, and moderate grazing), but there was a significant negative effect in meadows with heavy grazing. Grazing had little effect on the pattern of seed-size--seedling-abundance with no grazing, but had significant negative effects with light, moderate, and heavy grazing, and the |r| values increased with grazing levels. This indicated that increasing grazing pressure enhanced the advantage of smaller-seeded species in terms of the abundances of adult species, seedlings, and soil seed banks, whereas only the light grazing level promoted the seed rain abundance of larger-seeded species in the plant communities. This study suggests that grazing disturbances are favorable for increasing the species abundance for smaller-seeded species but not for the larger-seeded species in an alpine meadow community. Hence, there is a clear

  13. 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.

  14. The community ecology of pathogens: coinfection, coexistence and community composition.

    PubMed

    Seabloom, Eric W; Borer, Elizabeth T; Gross, Kevin; Kendig, Amy E; Lacroix, Christelle; Mitchell, Charles E; Mordecai, Erin A; Power, Alison G

    2015-04-01

    Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host-pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two-pathogen susceptible-infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species-diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.

  15. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

    PubMed Central

    Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Lange, Anja; Westendorf, Astrid M.; Seifert, Marc; Küppers, Ralf

    2017-01-01

    The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities. PMID:28114391

  16. Mosquitoes of Zika Forest, Uganda: species composition and relative abundance.

    PubMed

    Kaddumukasa, M A; Mutebi, J-P; Lutwama, J J; Masembe, C; Akol, A M

    2014-01-01

    Mosquito collections were conducted in Zika Forest near Entebbe, Uganda, from July 2009 through June 2010 using CO2-baited light traps, ovitraps, and human-baited catches. In total, 163,790 adult mosquitoes belonging to 12 genera and 58 species were captured. Of these, 22 species (38%) were captured in Zika Forest for the first time. All the new records found in the forest in this study had previously been captured in other regions of Uganda, implying that they are native to the country and do not represent new introductions. More than 20 species previously collected in Zika Forest were not detected in our collections, and this may suggest a change in the mosquito fauna during the past 40 yr or variation in species composition from year to year. Arboviruses of public health importance have previously been isolated from >50% of the 58 mosquito species captured in Zika Forest, which suggests ahigh potential for transmission and maintenance of a wide range of arboviruses in Zika Forest.

  17. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    PubMed

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p < 0.001) increases in the abundance of the GP PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial

  18. 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.

  19. Consideration of species community composition in statistical ...

    EPA Pesticide Factsheets

    Diseases are increasing in marine ecosystems, and these increases have been attributed to a number of environmental factors including climate change, pollution, and overfishing. However, many studies pool disease prevalence into taxonomic groups, disregarding host species composition when comparing sites or assessing environmental impacts on patterns of disease presence. We used simulated data under a known environmental effect to assess the ability of standard statistical methods (binomial and linear regression, ANOVA) to detect a significant environmental effect on pooled disease prevalence with varying species abundance distributions and relative susceptibilities to disease. When one species was more susceptible to a disease and both species only partially overlapped in their distributions, models tended to produce a greater number of false positives (Type I error). Differences in disease risk between regions or along an environmental gradient tended to be underestimated, or even in the wrong direction, when highly susceptible taxa had reduced abundances in impacted sites, a situation likely to be common in nature. Including relative abundance as an additional variable in regressions improved model accuracy, but tended to be conservative, producing more false negatives (Type II error) when species abundance was strongly correlated with the environmental effect. Investigators should be cautious of underlying assumptions of species similarity in susceptib

  20. 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

  1. Analysis of microbial community composition in a lab-scale membrane distillation bioreactor

    PubMed Central

    Zhang, Q; Shuwen, G; Zhang, J; Fane, AG; Kjelleberg, S; Rice, SA; McDougald, D

    2015-01-01

    Aims Membrane distillation bioreactors (MDBR) have potential for industrial applications where wastewater is hot or waste heat is available, but the role of micro-organisms in MDBRs has never been determined, and thus was the purpose of this study. Methods and Results Microbial communities were characterized by bacterial and archaeal 16S and eukaryotic 18S rRNA gene tag-encoded pyrosequencing of DNA obtained from sludge. Taxonomy-independent analysis revealed that bacterial communities had a relatively low richness and diversity, and community composition strongly correlated with conductivity, total nitrogen and bound extracellular polymeric substances (EPS). Taxonomy-dependent analysis revealed that Rubrobacter and Caldalkalibacillus were abundant members of the bacterial community, but no archaea were detected. Eukaryotic communities had a relatively high richness and diversity, and both changes in community composition and abundance of the dominant genus, Candida, correlated with bound EPS. Conclusions Thermophilic MDBR communities were comprised of a low diversity bacterial community and a highly diverse eukaryotic community with no archea detected. Communities exhibited low resilience to changes in operational parameters. Specifically, retenatate nutrient composition and concentration was strongly correlated with the dominant species. Significance and Impact of the Study This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. PMID:25604265

  2. PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 1. Toxin levels

    PubMed Central

    Deeds, Jonathan R.; Petitpas, Christian M.; Shue, Vangie; White, Kevin D.; Keafer, Bruce A.; McGillicuddy, Dennis J.; Milligan, Peter J.; Anderson, Donald M.; Turner, Jefferson T.

    2014-01-01

    As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX)1 project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20–64, 64–100, 100–200, 200–500, and > 500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May–August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94% ± 4%) of total PSP toxicity was contained in the 20–64 μm size fraction; (2) when further analyzed by depth, the 20–64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7% ± 5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7% ± 4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3% ± 0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (< 1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled. PMID:25076816

  3. PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010: 1. Toxin levels.

    PubMed

    Deeds, Jonathan R; Petitpas, Christian M; Shue, Vangie; White, Kevin D; Keafer, Bruce A; McGillicuddy, Dennis J; Milligan, Peter J; Anderson, Donald M; Turner, Jefferson T

    2014-05-01

    As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX) project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20-64, 64-100, 100-200, 200-500, and > 500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May-August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94% ± 4%) of total PSP toxicity was contained in the 20-64 μm size fraction; (2) when further analyzed by depth, the 20-64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7% ± 5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7% ± 4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3% ± 0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (< 1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled.

  4. Daytime warming lowers community temporal stability by reducing the abundance of dominant, stable species.

    PubMed

    Yang, Zhongling; Zhang, Qian; Su, Fanglong; Zhang, Chunhui; Pu, Zhichao; Xia, Jianyang; Wan, Shiqiang; Jiang, Lin

    2017-01-01

    Daytime warming and nighttime warming have the potential to influence plant community structure and ecosystem functions. However, their impacts on ecological stability remain largely unexplored. We conducted an eight-year field experiment to compare the effects of daytime and nighttime warming on the temporal stability of a temperate steppe in northern China. Our results showed that the cover and stability of dominant species, stability of subordinate species, and compensatory dynamics among species strongly influenced community-level stability. However, daytime, but not nighttime, warming significantly reduced community temporal stability mainly through the reduction in the abundance of dominant, stable species. These findings demonstrate the differential effects of daytime and nighttime warming on community stability and emphasize the importance of understanding the changes of dominant species for accurately predicting community dynamics under climate warming.

  5. Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition.

    PubMed

    Ma, Wai K; Farrell, Richard E; Siciliano, Steven D

    2011-01-01

    Nitrous oxide (N(2)O) is a greenhouse gas with a global warming potential far exceeding that of CO(2). Soil N(2)O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N(2)O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N(2)O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and [Formula: see text] pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N(2)O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N(2)O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N(2)O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N(2)O emission.

  6. Nitrous Oxide Emissions from Ephemeral Wetland Soils are Correlated with Microbial Community Composition

    PubMed Central

    Ma, Wai K.; Farrell, Richard E.; Siciliano, Steven D.

    2011-01-01

    Nitrous oxide (N2O) is a greenhouse gas with a global warming potential far exceeding that of CO2. Soil N2O emissions are a product of two microbially mediated processes: nitrification and denitrification. Understanding the effects of landscape on microbial communities, and the subsequent influences of microbial abundance and composition on the processes of nitrification and denitrification are key to predicting future N2O emissions. The objective of this study was to examine microbial abundance and community composition in relation to N2O associated with nitrification and denitrification processes over the course of a growing season in soils from cultivated and uncultivated wetlands. The denitrifying enzyme assay and N15O3− pool dilution methods were used to compare the rates of denitrification and nitrification and their associated N2O emissions. Functional gene composition was measured with restriction fragment length polymorphism profiles and abundance was measured with quantitative polymerase chain reaction. The change in denitrifier nitrous oxide reductase gene (nosZ) abundance and community composition was a good predictor of net soil N2O emission. However, neither ammonia oxidizing bacteria ammonia monooxygenase (bacterial amoA) gene abundance nor composition predicted nitrification-associated-N2O emissions. Alternative strategies might be necessary if bacterial amoA are to be used as predictive in situ indicators of nitrification rate and nitrification-associated-N2O emission. PMID:21712943

  7. 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

  8. 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

  9. Composite stellar populations and element by element abundances in the Milky Way bulge and elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Tang, Baitian; Worthey, Guy; Davis, A. Bianca

    2014-12-01

    This paper explores the integrated-light characteristics of the Milky Way (MW) bulge and to what extent they match those of elliptical galaxies in the local Universe. We model composite stellar populations with realistic abundance distribution functions (ADFs), tracking the trends of individual elements as a function of overall heavy element abundance as actually observed in MW bulge stars. The resultant predictions for absorption feature strengths from the MW bulge mimic elliptical galaxies better than solar neighbourhood stars do, but the MW bulge does not match elliptical galaxies, either. Comparing bulge versus elliptical galaxies, Fe, Ti, and Mg trend about the same for both but C, Na, and Ca seem irreconcilably different. Exploring the behaviour of abundance compositeness leads to the concepts of `red lean' where a narrower ADF appears more metal rich than a wide one, and `red spread' where the spectral difference between wide and narrow ADFs increases as the ADF peak is moved to more metal-rich values. Tests on the systematics of recovering abundance, abundance pattern, and age from composite stellar populations using single stellar population models were performed. The chemical abundance pattern was recovered adequately, though a few minor systematic effects were uncovered. The prospects of measuring the width of the ADF of an old stellar population were investigated and seem bright using UV to IR photometry.

  10. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

  11. Antibacterial Compounds-Macrolactin Alters the Soil Bacterial Community and Abundance of the Gene Encoding PKS

    PubMed Central

    Yuan, Jun; Zhao, Mengli; Li, Rong; Huang, Qiwei; Rensing, Christopher; Raza, Waseem; Shen, Qirong

    2016-01-01

    Macrolactin produced by many soil microbes has been shown to be an efficient antibacterial agent against many bacterial pathogens. However, studies examining the effect of macrolactin on both the soil bacterial community and the intrinsic bacterial species that harbor genes responsible for the production of this antibiotic have not been conducted so far. In this study, a mixture of macrolactin was isolated from the liquid culture of Bacillus amyloliquefaciens NJN-6, and applied to the soil once a week for four weeks. 16S rRNA Illumina MiSeq sequencing showed that continuous application of macrolactin reduced the α-diversity of the soil bacterial community and thereby changed the relative abundance of microbes at both the phylum and genus level. The relative abundance of Proteobacteria and Firmicutes was significantly increased along with a significant decrease in the relative abundance of Acidobacteria. However, the application of macrolactins had an insignificant effect on the total numbers of bacteria. Further, the native gene responsible for the production of macrolactin, the gene encoding polyketide synthase was reduced in copy number after the application of macrolactin. The results of this study suggested that a bactericide from a microbial source could decrease the diversity of the soil bacterial community and change the bacterial community structure. Moreover, the populations of the intrinsic bacterial species which harbor genes responsible for macrolactin production were inhibited when the external source antibiotic was applied. PMID:27965639

  12. Shifts in the abundance and community structure of soil ammonia oxidizers in a wet sclerophyll forest under long-term prescribed burning.

    PubMed

    Long, Xi-En; Chen, Chengrong; Xu, Zhihong; He, Ji-Zheng

    2014-02-01

    Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles.

  13. Hunting or habitat? Drivers of waterbird abundance and community structure in agricultural wetlands of southern India.

    PubMed

    Ramachandran, Ramesh; Kumar, Ajith; Gopi Sundar, Kolla S; Bhalla, Ravinder Singh

    2017-02-28

    The relative impacts of hunting and habitat on waterbird community were studied in agricultural wetlands of southern India. We surveyed wetlands to document waterbird community, and interviewed hunters to document hunting intensity, targeted species, and the motivations for hunting. Our results show that hunting leads to drastic declines in waterbird diversity and numbers, and skew the community towards smaller species. Hunting intensity, water spread, and vegetation cover were the three most important determinants of waterbird abundance and community structure. Species richness, density of piscivorous species, and medium-sized species (31-65 cm) were most affected by hunting. Out of 53 species recorded, 47 were hunted, with a preference for larger birds. Although illegal, hunting has increased in recent years and is driven by market demand. This challenges the widely held belief that waterbird hunting in India is a low intensity, subsistence activity, and undermines the importance of agricultural wetlands in waterbird conservation.

  14. 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

  15. 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

  16. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  17. 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

  18. Temporal variation in copepod abundance and composition in a strong, persistent coastal upwelling zone

    NASA Astrophysics Data System (ADS)

    Fontana, Rachel E.; Elliott, Meredith L.; Largier, John L.; Jahncke, Jaime

    2016-03-01

    Zooplankton abundance and species composition provide information on environmental variability in the ocean. While zooplankton time series span the west coast of North America, less data exist off north-central California. Here, we investigated a zooplankton time series, focusing specifically on copepods, collected within the Gulf of the Farallones-Cordell Bank area (37.5° to 38.5°N) from 2004 to 2009. Impacted by seasonally strong, persistent upwelling, this study area is located downstream of a major upwelling center (Point Arena). We found copepod abundance and species composition differed significantly, particularly between the first three years (2004-2006) and the latter three years (2007-2009) of the study. These changes were mainly observed as changes in abundance of boreal copepod species, Pseudocalanus mimus and Acartia longiremis. These taxa showed increasing abundances for the latter three years of the study (2007-2009). During the first three years of the time series, environmental measurements in the region showed lower alongshore wind stress, weaker upwelling, minimal surface alongshore flow, and warmer surface ocean temperatures. Temporal variations in copepod abundance and species composition correlated with several of these environmental measurements (e.g., surface cross-shore and alongshore flows, upwelling, and alongshore wind stress), indicating environmental forcing of primary consumers and ecosystem productivity in this strong, persistent upwelling zone.

  19. Land-use history alters contemporary insect herbivore community composition and decouples plant-herbivore relationships.

    PubMed

    Hahn, Philip G; Orrock, John L

    2015-05-01

    Past land use can create altered soil conditions and plant communities that persist for decades, although the effects of these altered conditions on consumers are rarely investigated. Using a large-scale field study at 36 sites in longleaf pine (Pinus palustris) woodlands, we examined whether historic agricultural land use leads to differences in the abundance and community composition of insect herbivores (grasshoppers, families Acrididae and Tettigoniidae). We measured the cover of six plant functional groups and several environmental variables to determine whether historic agricultural land use affects the relationships between plant cover or environmental conditions and grasshopper assemblages. Land-use history had taxa-specific effects and interacted with herbaceous plant cover to alter grasshopper abundances, leading to significant changes in community composition. Abundance of most grasshopper taxa increased with herbaceous cover in woodlands with no history of agriculture, but there was no relationship in post-agricultural woodlands. We also found that grasshopper abundance was negatively correlated with leaf litter cover. Soil hardness was greater in post-agricultural sites (i.e. more compacted) and was associated with grasshopper community composition. Both herbaceous cover and leaf litter cover are influenced by fire frequency, suggesting a potential indirect role of fire on grasshopper assemblages. Our results demonstrate that historic land use may create persistent differences in the composition of grasshopper assemblages, while contemporary disturbances (e.g. prescribed fire) may be important for determining the abundance of grasshoppers, largely through the effect of fire on plants and leaf litter. Therefore, our results suggest that changes in the contemporary management regimes (e.g. increasing prescribed fire) may not be sufficient to shift the structure of grasshopper communities in post-agricultural sites towards communities in non

  20. Land-use history alters contemporary insect herbivore community composition and decouples plant-herbivore relationships.

    SciTech Connect

    Hahn, Philip G.; Orrock, John L.

    2015-04-01

    1. Past land use can create altered soil conditions and plant communities that persist for decades, although the effects of these altered conditions on consumers are rarely investigated. 2. Using a large-scale field study at 36 sites in longleaf pine (Pinus palustris) woodlands, we examined whether historic agricultural land use leads to differences in the abundance and community composition of insect herbivores (grasshoppers, families Acrididae and Tettigoniidae). 3. We measured the cover of six plant functional groups and several environmental variables to determine whether historic agricultural land use affects the relationships between plant cover or environmental conditions and grasshopper assemblages. 4. Land-use history had taxa-specific effects and interacted with herbaceous plant cover to alter grasshopper abundances, leading to significant changes in community composition. Abundance of most grasshopper taxa increased with herbaceous cover in woodlands with no history of agriculture, but there was no relationship in post-agricultural woodlands. We also found that grasshopper abundance was negatively correlated with leaf litter cover. Soil hardness was greater in post-agricultural sites (i.e. more compacted) and was associated with grasshopper community composition. Both herbaceous cover and leaf litter cover are influenced by fire frequency, suggesting a potential indirect role of fire on grasshopper assemblages. 5. Our results demonstrate that historic land use may create persistent differences in the composition of grasshopper assemblages, while contemporary disturbances (e.g. prescribed fire) may be important for determining the abundance of grasshoppers, largely through the effect of fire on plants and leaf litter. Therefore, our results suggest that changes in the contemporary management regimes (e.g. increasing prescribed fire) may not be sufficient to shift the structure of grasshopper communities in post-agricultural sites towards communities in

  1. Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

    NASA Astrophysics Data System (ADS)

    Balasooriya, W. K.; Denef, K.; Peters, J.; Verhoest, N. E. C.; Boeckx, P.

    2007-10-01

    Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; textit{Caricetum gracilis} at the wet depression and textit{Arrhenatherum elatioris} at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria was significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

  2. Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

    NASA Astrophysics Data System (ADS)

    Balasooriya, W. K.; Denef, K.; Peters, J.; Verhoest, N. E. C.; Boeckx, P.

    2008-02-01

    Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

  3. Tree species composition affects the abundance of rowan (Sorbus aucuparia L.) in urban forests in Finland.

    PubMed

    Hamberg, Leena; Lehvävirta, Susanna; Kotze, D Johan; Heikkinen, Juha

    2015-03-15

    Recent studies have shown a considerable increase in the abundance of rowan (Sorbus aucuparia) saplings in urban forests in Finland, yet the reasons for this increase are not well understood. Here we investigated whether canopy cover or tree species composition, i.e., the basal areas of different tree species in Norway spruce dominated urban forests, affects the abundances of rowan seedlings, saplings and trees. Altogether 24 urban forest patches were investigated. We sampled the number of rowan and other saplings, and calculated the basal areas of trees. We showed that rowan abundance was affected by tree species composition. The basal area of rowan trees (≥ 5 cm in diameter at breast height, dbh) decreased with increasing basal area of Norway spruce, while the cover of rowan seedlings increased with an increase in Norway spruce basal area. However, a decrease in the abundance of birch (Betula pendula) and an increase in the broad-leaved tree group (Acer platanoides, Alnus glutinosa, Alnus incana, Amelanchier spicata, Prunus padus, Quercus robur, Rhamnus frangula and Salix caprea) coincided with a decreasing number of rowans. Furthermore, rowan saplings were scarce in the vicinity of mature rowan trees. Although it seems that tree species composition has an effect on rowan, the relationship between rowan saplings and mature trees is complex, and therefore we conclude that regulating tree species composition is not an easy way to keep rowan thickets under control in urban forests in Finland.

  4. 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

  5. Zooplankton Composition and Abundance as Indicators of Eutrophication in Two Small Man-made Lakes

    PubMed Central

    Ismail, Azma Hanim; Adnan, Anis Amalina Mohd

    2016-01-01

    The distribution and abundance of zooplankton species of Harapan and Aman Lakes were investigated in relation to physical parameters and chlorophyll-a content. Both lakes were characterised by the occurrence of algal bloom problem. The composition of zooplankton was collected at monthly intervals from November 2013 to February 2014. The total number of taxa in Harapan and Aman Lakes were 23 and 27, respectively. Rotifera was the highest abundance group represent 64% of the total species recorded followed by Copepoda (29%) and Cladocera (7%). Three dominant zooplankton that been recorded in both the lakes are Brachionus forficula, Brachionus nilsoni, and Trichocerca sp. High abundance of these species indicates that the lakes are eutrophic water bodies. Overall, zooplankton species distribution and abundance in the study sites are influenced by various environmental factors such as water transparency and chlorophyll-a content. PMID:27965738

  6. Tropical Aquatic Archaea Show Environment-Specific Community Composition

    PubMed Central

    Silveira, Cynthia B.; Cardoso, Alexander M.; Coutinho, Felipe H.; Lima, Joyce L.; Pinto, Leonardo H.; Albano, Rodolpho M.; Clementino, Maysa M.; Martins, Orlando B.; Vieira, Ricardo P.

    2013-01-01

    The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria. PMID:24086729

  7. Tropical aquatic Archaea show environment-specific community composition.

    PubMed

    Silveira, Cynthia B; Cardoso, Alexander M; Coutinho, Felipe H; Lima, Joyce L; Pinto, Leonardo H; Albano, Rodolpho M; Clementino, Maysa M; Martins, Orlando B; Vieira, Ricardo P

    2013-01-01

    The Archaea domain is ubiquitously distributed and extremely diverse, however, environmental factors that shape archaeal community structure are not well known. Aquatic environments, including the water column and sediments harbor many new uncultured archaeal species from which metabolic and ecological roles remain elusive. Some environments are especially neglected in terms of archaeal diversity, as is the case of pristine tropical areas. Here we investigate the archaeal composition in marine and freshwater systems from Ilha Grande, a South Atlantic tropical environment. All sampled habitats showed high archaeal diversity. No OTUs were shared between freshwater, marine and mangrove sediment samples, yet these environments are interconnected and geographically close, indicating environment-specific community structuring. Group II Euryarchaeota was the main clade in marine samples, while the new putative phylum Thaumarchaeota and LDS/RCV Euryarchaeota dominated freshwaters. Group III Euryarchaeota, a rare clade, was also retrieved in reasonable abundance in marine samples. The archaeal community from mangrove sediments was composed mainly by members of mesophilic Crenarchaeota and by a distinct clade forming a sister-group to Crenarchaeota and Thaumarchaeota. Our results show strong environment-specific community structuring in tropical aquatic Archaea, as previously seen for Bacteria.

  8. Abundance and diversity of sedimentary bacterial communities in a coastal productive setting in the Western Irish Sea

    NASA Astrophysics Data System (ADS)

    O'Reilly, S. S.; Pentlavalli, P.; Flanagan, P. V.; Allen, C. C. R.; Monteys, X.; Szpak, M. T.; Murphy, B. T.; Jordan, S. F.; Kelleher, B. P.

    2016-02-01

    The bacterial community composition and biomass abundance from a depositional mud belt in the western Irish Sea and regional sands were investigated by phospholipid ester-linked fatty acid profiling, denaturing gradient gel electrophoresis and barcoded pyrosequencing of 16S rRNA genes. The study area varied by water depth (12-111 m), organic carbon content (0.09-1.57% TOC), grain size, hydrographic regime (well-mixed vs. stratified), and water column phytodetrital input (represented by algal polyunsaturated PLFA). The relative abundance of bacterial-derived PLFA (sum of methyl-branched, cyclopropyl and odd-carbon number PLFA) was positively correlated with fine-grained sediment, and was highest in the depositional mud belt. A strong association between bacterial biomass and eukaryote primary production was suggested based on observed positive correlations with total nitrogen and algal polyunsaturated fatty acids. In addition, 16S rRNA genes affiliated to the classes Clostridia and Flavobacteria represented a major proportion of total 16S rRNA gene sequences. This suggests that benthic bacterial communities are also important degraders of phytodetrital organic matter and closely coupled to water column productivity in the western Irish Sea.

  9. Study of biological communities subject to imperfect detection: Bias and precision of community N-mixture abundance models in small-sample situations

    USGS Publications Warehouse

    Yamaura, Yuichi; Kery, Marc; Royle, Andy

    2016-01-01

    Community N-mixture abundance models for replicated counts provide a powerful and novel framework for drawing inferences related to species abundance within communities subject to imperfect detection. To assess the performance of these models, and to compare them to related community occupancy models in situations with marginal information, we used simulation to examine the effects of mean abundance (λ¯: 0.1, 0.5, 1, 5), detection probability (p¯: 0.1, 0.2, 0.5), and number of sampling sites (n site : 10, 20, 40) and visits (n visit : 2, 3, 4) on the bias and precision of species-level parameters (mean abundance and covariate effect) and a community-level parameter (species richness). Bias and imprecision of estimates decreased when any of the four variables (λ¯, p¯, n site , n visit ) increased. Detection probability p¯ was most important for the estimates of mean abundance, while λ¯ was most influential for covariate effect and species richness estimates. For all parameters, increasing n site was more beneficial than increasing n visit . Minimal conditions for obtaining adequate performance of community abundance models were n site  ≥ 20, p¯ ≥ 0.2, and λ¯ ≥ 0.5. At lower abundance, the performance of community abundance and community occupancy models as species richness estimators were comparable. We then used additive partitioning analysis to reveal that raw species counts can overestimate β diversity both of species richness and the Shannon index, while community abundance models yielded better estimates. Community N-mixture abundance models thus have great potential for use with community ecology or conservation applications provided that replicated counts are available.

  10. The distribution and abundance of Enterobius vermicularis in a South Indian fishing community.

    PubMed

    Haswell-Elkins, M R; Elkins, D B; Manjula, K; Michael, E; Anderson, R M

    1987-10-01

    The distribution and abundance of Enterobius vermicularis in a fishing community in South India, as determined by counting worms expelled following mass anthelmintic chemotherapy, was examined in samples of patients stratified by age, sex and family grouping. The results of a worm expulsion study in January 1984 are compared with those of a second expulsion programme in November 1984, following an 11-month period of reinfection. The prevalence of Enterobius infection was consistently high in all age groups of both males and females. A comparison of the overall prevalence and intensity of infection in the January and November surveys revealed significant increases in both the percent infected and the mean number of worms harboured in November relative to the initial level. No significant trends in the intensity of Enterobius according to host age or sex were detected in either survey. The frequency distribution of Enterobius was found to be highly aggregated in the population as a whole and within age groups. At both sampling dates, the most heavily infected 25% of the community harboured over 90% of the total pinworms recovered. There was a significant pattern within most age groups for individuals to re-acquire worm burdens of a similar magnitude to their initial pre-treatment burdens. Heavy infections were found to be associated with household. A selective or targetted approach to treatment of heavily infected individuals or households is likely to be an efficient means of reducing parasite abundance on a community-wide basis. It must be stressed, however, that treatment must be applied at frequent intervals in order to achieve a long-term reduction in pinworm abundance and to avoid the possibility of increasing the intensity of infection, as was observed in this community.

  11. Community structure, abundance, and activity of methanotrophs in the Zoige wetland of the Tibetan Plateau.

    PubMed

    Yun, Juanli; Zhuang, Guoqiang; Ma, Anzhou; Guo, Hongguang; Wang, Yanfen; Zhang, Hongxun

    2012-05-01

    The Zoige wetland of the Tibetan Plateau is a high-altitude tundra wetland and one of the biggest methane emission centers in China. In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detected 10(7) to 10(8) of total pmoA gene copies per gram dry weight of soil in the three marshes. Group-specific qPCR and reverse transcriptase qPCR results found that the Methylobacter genus dominates the wetland, and Methylocystis methanotrophs were less abundant, although this group of methanotrophs was estimated to be more active according to mRNA/DNA ratio. Furthermore, EV marsh demonstrated the highest methanotrophs abundance and activity among the three marshes investigated. Our study suggests that both type I and type II methanotrophs contribute to the methane oxidation in the Zoige wetland.

  12. Diversity and Composition of Bacterial Community in Soils and Lake Sediments from an Arctic Lake Area

    PubMed Central

    Wang, Neng Fei; Zhang, Tao; Yang, Xiao; Wang, Shuang; Yu, Yong; Dong, Long Long; Guo, Yu Dong; Ma, Yong Xing; Zang, Jia Ye

    2016-01-01

    This study assessed the diversity and composition of bacterial communities within soils and lake sediments from an Arctic lake area (London Island, Svalbard). A total of 2,987 operational taxonomic units were identified by high-throughput sequencing, targeting bacterial 16S rRNA gene. The samples from four sites (three samples in each site) were significantly different in geochemical properties and bacterial community composition. Proteobacteria and Acidobacteria were abundant phyla in the nine soil samples, whereas Proteobacteria and Bacteroidetes were abundant phyla in the three sediment samples. Furthermore, Actinobacteria, Chlorobi, Chloroflexi, Elusimicrobia, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria significantly varied in their abundance among the four sampling sites. Additionally, members of the dominant genera, such as Clostridium, Luteolibacter, Methylibium, Rhodococcus, and Rhodoplanes, were significantly different in their abundance among the four sampling sites. Besides, distance-based redundancy analysis revealed that pH (p < 0.001), water content (p < 0.01), ammonium nitrogen (NH4+-N, p < 0.01), silicate silicon (SiO42--Si, p < 0.01), nitrite nitrogen (NO2--N, p < 0.05), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the bacterial community composition. The results suggest soils and sediments from a lake area in the Arctic harbor a high diversity of bacterial communities, which are influenced by many geochemical factors of Arctic environments. PMID:27516761

  13. Exploration of Trends in Interspecific Abundance-Occupancy Relationships Using Empirically Derived Simulated Communities

    PubMed Central

    Martinez, Christopher M.; Duplisea, Daniel E.; Cerrato, Robert M.; Frisk, Michael G.

    2017-01-01

    The interspecific abundance-occupancy relationship (AOR) is a widely used tool that describes patterns of habitat utilization and, when evaluated over time, may be used to identify large-scale changes in community structure. Our primary goal for this research was to validate the utility of AORs as temporal indicators of community state. We used long-term survey data in four regions of the northwest Atlantic coastal shelf (NWACS) to estimate the diversity of spatial behaviors in each community, which we modeled with negative binomial (NB) distributions. NB parameters were used to generate time series data for simulated communities, from which AORs were then estimated and evaluated for temporal trends. We found that AORs from simulated communities were similar in year-to-year variation to empirical relationships. In order to further understand the role of spatial diversity in the generation of AOR trends, we did additional simulations where NB parameters were manually manipulated. In one instance, we ran simulations while holding species’ parameters constant over time. This treatment effectively removed trends, suggesting that temporal change in community relationships was the result of genuine variation in intraspecific spatial use. In another set of simulations, we conducted a case study to evaluate the impact of a select group of schooling and spatially aggregating species on an especially rapid shift in AORs in the Gulf of Maine from 1973 to 1983. Removals of these species reduced the magnitudes of most trends, demonstrating their importance to observed community changes. This research directly links variation in AORs to distribution and density-related processes and provides a potentially powerful framework to identify community-level change and to test ecological and mechanistic hypotheses. PMID:28125670

  14. 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.

  15. 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

  16. 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.

  17. Microbial community composition and denitrifying enzyme activities in salt marsh sediments.

    PubMed

    Cao, Yiping; Green, Peter G; Holden, Patricia A

    2008-12-01

    Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

  18. Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries

    PubMed Central

    Frost, Carol M.; Peralta, Guadalupe; Rand, Tatyana A.; Didham, Raphael K.; Varsani, Arvind; Tylianakis, Jason M.

    2016-01-01

    Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying of insecticide over 20 hectares. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control. PMID:27577948

  19. Mutualistic rhizobia reduce plant diversity and alter community composition.

    PubMed

    Keller, Kane R

    2014-12-01

    Mutualistic interactions can be just as important to community dynamics as antagonistic species interactions like competition and predation. Because of their large effects on both abiotic and biotic environmental variables, resource mutualisms, in particular, have the potential to influence plant communities. Moreover, the effects of resource mutualists such as nitrogen-fixing rhizobia on diversity and community composition may be more pronounced in nutrient-limited environments. I experimentally manipulated the presence of rhizobia across a nitrogen gradient in early assembling mesocosm communities with identical starting species composition to test how the classic mutualism between nitrogen-fixing rhizobia and their legume host influence diversity and community composition. After harvest, I assessed changes in α-diversity, community composition, β-diversity, and ecosystem properties such as inorganic nitrogen availability and productivity as a result of rhizobia and nitrogen availability. The presence of rhizobia decreased plant community diversity, increased community convergence (reduced β-diversity), altered plant community composition, and increased total community productivity. These community-level effects resulted from rhizobia increasing the competitive dominance of their legume host Chamaecrista fasciculata. Moreover, different non-leguminous species responded both negatively and positively to the presence of rhizobia, indicating that rhizobia are driving both inhibitory and potentially facilitative effects in communities. These findings expand our understanding of plant communities by incorporating the effects of positive symbiotic interactions on plant diversity and composition. In particular, rhizobia that specialize on dominant plants may serve as keystone mutualists in terrestrial plant communities, reducing diversity by more than 40%.

  20. Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

    PubMed

    Hubert, Nathaniel A; Gehring, Catherine A

    2008-09-01

    Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

  1. 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.

  2. Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments.

    PubMed

    Chen, Jing; Gu, Ji-Dong

    2017-01-28

    In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH4(+) but lower concentrations of both NO2(-) and NO3(-), and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH4(+) and NO2(-) were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

  3. Sulfur abundances in the solar wind measured by SWICS on Ulysses. [Solar Wind Ion Composition Spectrometer

    NASA Technical Reports Server (NTRS)

    Shafer, C. M.; Gloeckler, G.; Galvin, A. B.; Ipavich, F. M.; Geiss, J.; Von Steiger, R.; Ogilvie, K.

    1993-01-01

    One of the nine experiments on Ulysses (launched October, 1990), the Solar Wind Ion Composition Spectrometer, utilizes an energy per charge deflection system along with time of flight technology to uniquely determine the mass and mass per charge of solar wind particles. Thus the composition of various solar wind types can be analyzed. Using the SWICS data accumulated during the in-ecliptic phase of the mission, we have determined the sulfur abundance, relative to silicon, in two different types of solar wind: transient and coronal hole associated flows. Sulfur is of extreme interest because it is one of the few elements that lies in the transitional region of the FIP-dependent relative abundance enrichment function, observed for solar energetic particles and some types of solar wind flows.

  4. Effects of shorebird predation and snail abundance on an intertidal mudflat community

    NASA Astrophysics Data System (ADS)

    Cheverie, Anne V.; Hamilton, Diana J.; Coffin, Michael R. S.; Barbeau, Myriam A.

    2014-09-01

    Top-down effects of predation are well documented in a variety of ecological communities, including marine soft-sediment systems. It has been proposed that intertidal mudflats in the upper Bay of Fundy, Canada, which host a large population of foraging shorebirds each summer, may exhibit this community dynamic. Biofilm (consisting mainly of diatoms) forms the base of the mudflat community food web, which is dominated by the amphipod Corophium volutator. To assess the potential for a trophic cascade, we conducted a manipulative field experiment examining individual and combined effects of the shorebird Calidris pusilla, a primary predator of C. volutator, and the eastern mudsnail (Nassarius obsoletus), an intraguild predator, on community structure (including macrofauna and large meiofauna retained by a 250-μm screen). Snails exhibited density-dependent top-down effects, primarily from strong negative interactions with juvenile and adult C. volutator, likely due to interference, consumption and emigration. Medium and high densities of snails reduced chlorophyll a concentration (a measure of diatom abundance), likely through consumption and disturbance of the sediment. When present at higher densities, snails also increased variability in community structure. Shorebirds were less influential in determining community structure. They reduced C. volutator biomass through consumption, but there was no resulting effect on primary production. Top-down effects of snails and birds were cumulative on C. volutator, but did not generate a trophic cascade. We suggest that a combination of omnivory and intraguild predation by shorebirds and snails, coupled with relatively low grazing pressure by C. volutator, prevented transmission of top-down effects.

  5. Interactions between assembly order and temperature can alter both short- and long-term community composition

    PubMed Central

    Clements, Christopher F; Warren, Philip H; Collen, Ben; Blackburn, Tim; Worsfold, Nicholas; Petchey, Owen

    2013-01-01

    Both the order in which species arrive in a community, and environmental conditions, such as temperature, are known to affect community structure. Little is known, however, about the potential for, and occurrence of, interactions between assembly history and the environment. Of particular, interest may be the interaction between temperature and community assembly dynamics, especially in the light of predicted global climatic change and the fundamental processes that are governed, through metabolic rate, by an individual's environmental temperature. We present, to our knowledge, the first experimental exploration of how the influence of assembly history, temperature, and the interaction between the two alters the structure of communities of competitors, using small-scale protist microcosm communities where temperature and assembly order were manipulated factorially. In our experiment, the most important driver of long-term abundance was temperature but long-lasting assembly order effects influenced the relationship between temperature and abundance. Any advantage of early colonization proved to be short-lived, and there was rarely any long-term advantage to colonizing a habitat before other species. The results presented here suggest that environmental conditions shape community composition, but that occasionally temperature could interact with the stochastic nature of community assembly to significantly alter future community composition, especially where temperature change has been large. This could have important implications for the dynamics of both rare and invasive species. PMID:24455149

  6. Interactions between assembly order and temperature can alter both short- and long-term community composition.

    PubMed

    Clements, Christopher F; Warren, Philip H; Collen, Ben; Blackburn, Tim; Worsfold, Nicholas; Petchey, Owen

    2013-12-01

    Both the order in which species arrive in a community, and environmental conditions, such as temperature, are known to affect community structure. Little is known, however, about the potential for, and occurrence of, interactions between assembly history and the environment. Of particular, interest may be the interaction between temperature and community assembly dynamics, especially in the light of predicted global climatic change and the fundamental processes that are governed, through metabolic rate, by an individual's environmental temperature. We present, to our knowledge, the first experimental exploration of how the influence of assembly history, temperature, and the interaction between the two alters the structure of communities of competitors, using small-scale protist microcosm communities where temperature and assembly order were manipulated factorially. In our experiment, the most important driver of long-term abundance was temperature but long-lasting assembly order effects influenced the relationship between temperature and abundance. Any advantage of early colonization proved to be short-lived, and there was rarely any long-term advantage to colonizing a habitat before other species. The results presented here suggest that environmental conditions shape community composition, but that occasionally temperature could interact with the stochastic nature of community assembly to significantly alter future community composition, especially where temperature change has been large. This could have important implications for the dynamics of both rare and invasive species.

  7. Using underwater cameras to assess the effects of snorkeler and SCUBA diver presence on coral reef fish abundance, family richness, and species composition.

    PubMed

    Dearden, P; Theberge, M; Yasué, M

    2010-04-01

    The results of underwater visual fish censuses (UVC) could be affected by fish changing their behavior in response to the snorkeler or diver conducting the survey. We used an underwater video camera to assess how fish abundance, family richness, and community composition were affected by the presence of snorkelers (n = 12) and self-contained underwater breathing apparatus (SCUBA) divers (n = 6) on a coral reef in Thailand. The total number of families, abundance of some fish families, and overall species composition showed significant differences before and during snorkeling disturbances. We did not detect significant and consistent changes to these parameters in the presence of a SCUBA diver; however, this could be a result of lower statistical power. We suggest that the use of a stationary video camera may help cross-check data that is collected through UVC to assess the true family composition and document the presence of rare and easily disturbed species.

  8. High Ozone (O3) Affects the Fitness Associated with the Microbial Composition and Abundance of Q Biotype Bemisia tabaci

    PubMed Central

    Hong, Yanyun; Yi, Tuyong; Tan, Xiaoling; Zhao, Zihua; Ge, Feng

    2016-01-01

    Ozone (O3) affects the fitness of an insect, such as its development, reproduction and protection against fungal pathogens, but the mechanism by which it does so remains unclear. Here, we compared the fitness (i.e., the growth and development time, reproduction and protection against Beauveria bassiana (B. bassiana) of Q biotype whiteflies fumigated under hO3 (280 ± 20 ppb) and control O3 (50 ± 10 ppb) concentrations. Moreover, we determined that gene expression was related to development, reproduction and immunity to B. bassiana and examined the abundance and composition of bacteria and fungi inside of the body and on the surface of the Q biotype whitefly. We observed a significantly enhanced number of eggs that were laid by a female, shortened developmental time, prolonged adult lifespan, decreased weight of one eclosion, and reduced immunity to B. bassiana in whiteflies under hO3, but hO3 did not significantly affect the expression of genes related to development, reproduction and immunity. However, hO3 obviously changed the composition of the bacterial communities inside of the body and on the surface of the whiteflies, significantly reducing Rickettsia and enhancing Candidatus_Cardinium. Similarly, hO3 significantly enhanced Thysanophora penicillioides from the Trichocomaceae family and reduced Dothideomycetes (at the class level) inside of the body. Furthermore, positive correlations were found between the abundance of Candidatus_Cardinium and the female whitefly ratio and the fecundity of a single female, and positive correlations were found between the abundance of Rickettsia and the weight of adult whiteflies just after eclosion and immunity to B. bassiana. We conclude that hO3 enhances whitefly development and reproduction but impairs immunity to B. bassiana, and our results also suggest that the changes to the microbial environments inside of the body and on the surface could be crucial factors that alter whitefly fitness under hO3. PMID:27799921

  9. Composition of breeding bird communities in Gulf Coast Chenier Plain marshes: Effects of winter burning

    USGS Publications Warehouse

    Gabrey, S.W.; Afton, A.D.

    2004-01-01

    Marsh managers along the Gulf Coast Chenier Plain frequently use winter burns to alter marsh vegetation and improve habitat quality for wintering waterfowl. However, effects of these burns on marsh avifauna are not well documented. We recorded abundances of breeding bird species and vegetation structure in burned and unburned control marshes during one breeding season before (1996) and two breeding seasons after (1997, 1998) experimental winter burns. We used non-metric multidimensional scaling analysis to assess the extent and direction of changes in bird community compositions of burned and unburned control marshes and to investigate the influence of vegetation structure on bird community composition. Overall, we found that Seaside Sparrows (Emberizidae: Ammodramus maritimus [Wilson]) and Red-winged Blackbirds and Boat-tailed Grackles (Icteridae: Agelaius phoeniceus [L.] and Quiscalus major Vieillot, respectively) comprised > 85% of observed birds. In burned marshes during the first breeding season following experimental burns (1997), icterid abundance increased while Seaside Sparrow abundance decreased relative to pre-burn (1996) conditions. This pattern was reversed during the second breeding season post-burn. No obvious patterns of change in avian abundance were detected in unburned control marshes over the 3-year period. Qualitative changes in breeding bird community composition were related to effects of winter burning on percent cover of dead vegetation and Spartina patens (Aiton) Muhl.

  10. Long-term declines in an intertidal foundation species parallel shifts in community composition.

    PubMed

    Sorte, Cascade J B; Davidson, Victoria E; Franklin, Marcus C; Benes, Kylla M; Doellman, Meredith M; Etter, Ron J; Hannigan, Robyn E; Lubchenco, Jane; Menge, Bruce A

    2017-01-01

    The earth is in the midst of a biodiversity crisis, and projections indicate continuing and accelerating rates of global changes. Future alterations in communities and ecosystems may be precipitated by changes in the abundance of strongly interacting species, whose disappearance can lead to profound changes in abundance of other species, including an increase in extinction rate for some. Nearshore coastal communities are often dependent on the habitat and food resources provided by foundational plant (e.g., kelp) and animal (e.g., shellfish) species. We quantified changes in the abundance of the blue mussel (Mytilus edulis), a foundation species known to influence diversity and productivity of intertidal habitats, over the past 40 years in the Gulf of Maine, USA, one of the fastest warming regions in the global ocean. Using consistent survey methods, we compared contemporary population sizes to historical data from sites spanning >400 km. The results of these comparisons showed that blue mussels have declined in the Gulf of Maine by >60% (range: 29-100%) at the site level since the earliest benchmarks in the 1970s. At the same time as mussels declined, community composition shifted: at the four sites with historical community data, the sessile community became increasingly algal dominated. Contemporary (2013-2014) surveys across 20 sites showed that sessile species richness was positively correlated to mussel abundance in mid to high intertidal zones. These results suggest that declines in a critical foundation species may have already impacted the intertidal community. To inform future conservation efforts, we provide a database of historical and contemporary baselines of mussel population abundance and dynamics in the Gulf of Maine. Our results underscore the importance of anticipating not only changes in diversity but also changes in the abundance and identity of component species, as strong interactors like foundation species have the potential to drive

  11. Atmospheric Composition of Weak G Band Stars: CNO and Li Abundances

    NASA Astrophysics Data System (ADS)

    Adamczak, Jens; Lambert, David L.

    2013-03-01

    We determined the chemical composition of a large sample of weak G band stars—a rare class of G and K giants of intermediate mass with unusual abundances of C, N, and Li. We have observed 24 weak G band stars with the 2.7 m Harlan J. Smith Telescope at the McDonald Observatory and derived spectroscopic abundances for C, N, O, and Li, as well as for selected elements from Na-Eu. The results show that the atmospheres of weak G band stars are highly contaminated with CN-cycle products. The C underabundance is about a factor of 20 larger than for normal giants and the 12C/13C ratio approaches the CN-cycle equilibrium value. In addition to the striking CN-cycle signature the strong N overabundance may indicate the presence of partially ON-cycled material in the atmospheres of the weak G band stars. The exact mechanism responsible for the transport of the elements to the surface has yet to be identified but could be induced by rapid rotation of the main sequence progenitors of the stars. The unusually high Li abundances in some of the stars are an indicator for Li production by the Cameron-Fowler mechanism. A quantitative prediction of a weak G band star's Li abundance is complicated by the strong temperature sensitivity of the mechanism and its participants. In addition to the unusual abundances of CN-cycle elements and Li, we find an overabundance of Na that is in accordance with the NeNa chain running in parallel with the CN cycle. Apart from these peculiarities, the element abundances in a weak G band star's atmosphere are consistent with those of normal giants.

  12. ATMOSPHERIC COMPOSITION OF WEAK G BAND STARS: CNO AND Li ABUNDANCES

    SciTech Connect

    Adamczak, Jens; Lambert, David L.

    2013-03-10

    We determined the chemical composition of a large sample of weak G band stars-a rare class of G and K giants of intermediate mass with unusual abundances of C, N, and Li. We have observed 24 weak G band stars with the 2.7 m Harlan J. Smith Telescope at the McDonald Observatory and derived spectroscopic abundances for C, N, O, and Li, as well as for selected elements from Na-Eu. The results show that the atmospheres of weak G band stars are highly contaminated with CN-cycle products. The C underabundance is about a factor of 20 larger than for normal giants and the {sup 12}C/{sup 13}C ratio approaches the CN-cycle equilibrium value. In addition to the striking CN-cycle signature the strong N overabundance may indicate the presence of partially ON-cycled material in the atmospheres of the weak G band stars. The exact mechanism responsible for the transport of the elements to the surface has yet to be identified but could be induced by rapid rotation of the main sequence progenitors of the stars. The unusually high Li abundances in some of the stars are an indicator for Li production by the Cameron-Fowler mechanism. A quantitative prediction of a weak G band star's Li abundance is complicated by the strong temperature sensitivity of the mechanism and its participants. In addition to the unusual abundances of CN-cycle elements and Li, we find an overabundance of Na that is in accordance with the NeNa chain running in parallel with the CN cycle. Apart from these peculiarities, the element abundances in a weak G band star's atmosphere are consistent with those of normal giants.

  13. Volatile-bearing phases in carbonaceous chondrites: Compositions, modal abundance, and reaction kinetics

    NASA Technical Reports Server (NTRS)

    Ganguly, Jibamitra

    1990-01-01

    The spectral and density characteristics of Phobos and Deimos (the two small natural satellites of Mars) strongly suggest that a significant fraction of the near-earth asteroids are made of carbonaceous chondrites, which are rich in volatile components and, thus, could serve as potential resources for propellants and life supporting systems in future planetary missions. However, in order to develop energy efficient engineering designs for the extraction of volatiles, knowledge of the nature and modal abundance of the minerals in which the volatiles are structurally bound and appropriate kinetic data on the rates of the devolatilization reactions is required. Theoretical calculations to predict the modal abundances and compositions of the major volatile-bearing and other mineral phases that could develop in the bulk compositions of C1 and C2 classes (the most volatile rich classes among the carbonaceous chondrites) were performed as functions of pressure and temperature. The rates of dehydration of talc at 585, 600, 637, and 670 C at P(total) = 1 bar were determine for the reaction: Talc = 3 enstatite + quartz + water. A scanning electron microscopic study was conducted to see if the relative abundance of phases can be determined on the basis of the spectral identification and x ray mapping. The results of this study and the other studies within the project are discussed.

  14. Chlamydia caviae infection alters abundance but not composition of the guinea pig vaginal microbiota

    PubMed Central

    Neuendorf, Elizabeth; Gajer, Pawel; Bowlin, Anne K.; Marques, Patricia X.; Ma, Bing; Yang, Hongqiu; Fu, Li; Humphrys, Michael S.; Forney, Larry J.; Myers, Garry S.A.; Bavoil, Patrik M.; Rank, Roger G.; Ravel, Jacques

    2015-01-01

    In humans, the vaginal microbiota is thought to be the first line of defense again pathogens including Chlamydia trachomatis. The guinea pig has been extensively used as a model to study chlamydial infection because it shares anatomical and physiological similarities with humans, such as a squamous vaginal epithelium as well as some of the long-term outcomes caused by chlamydial infection. In this study, we aimed to evaluate the guinea pig-C. caviae model of genital infection as a surrogate for studying the role of the vaginal microbiota in the early steps of C. trachomatis infection in humans. We used culture-independent molecular methods to characterize the relative and absolute abundance of bacterial phylotypes in the guinea pig vaginal microbiota in animals non-infected, mock-infected or infected by C. caviae. We showed that the guinea pig and human vaginal microbiotas are of different bacterial composition and abundance. Chlamydia caviae infection had a profound effect on the absolute abundance of bacterial phylotypes but not on the composition of the guinea pig vaginal microbiota. Our findings compromise the validity of the guinea pig-C. caviae model to study the role of the vaginal microbiota during the early steps of sexually transmitted infection. PMID:25761873

  15. Thorium abundances on the aristarchus plateau: Insights into the composition of the aristarchus pyroclastic glass deposits

    USGS Publications Warehouse

    Hagerty, J.J.; Lawrence, D.J.; Hawke, B.R.; Gaddis, L.R.

    2009-01-01

    Thorium (Th) data from the Lunar Prospector gamma ray spectrometer (LP-GRS) are used to constrain the composition of lunar pyroclastic glass deposits on top of the Aristarchus plateau. Our goal is to use forward modeling of LP-GRS Th data to measure the Th abundances on the plateau and then to determine if the elevated Th abundances on the plateau are associated with the pyroclastic deposits or with thorium-rich ejecta from Aristarchus crater. We use a variety of remote sensing data to show that there is a large, homogenous portion of the pyroclastics on the plateau that has seen little or no contamination from the Th-rich ejecta of Aristarchus crater. Our results show that the uncontaminated pyroclastic glasses on Aristarchus plateau have an average Th content of 6.7 ppm and ???7 wt % TiO2. These Th and Ti values are consistent with Th-rich, intermediate-Ti yellow glasses from the lunar sample suite. On the basis of this information, we use petrologic equations and interelement correlations for the Moon to estimate the composition of the source region from which the Aristarchus glasses were derived. We find that the source region for the Aristarchus glasses contained high abundances of heat-producing elements, which most likely served as a thermal driver for the prolonged volcanic activity in this region of the Moon. Copyright 2009 by the American Geophysical Union.

  16. Making the Case for a Positive Approach to Improving Organizational Performance in Higher Education Institutions: The Community College Abundance Model

    ERIC Educational Resources Information Center

    Shults, Christopher

    2008-01-01

    Increasingly hostile and turbulent environments have rendered top-down, problem-focused management structures inadequate for competing in the ever-changing postsecondary knowledge industry. The community college abundance model (CCAM), a strengths-based approach to performance enhancement in community colleges, is presented as a viable…

  17. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

    PubMed

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-04-07

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought.

  18. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

    PubMed Central

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-01-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  19. Inferring community dynamics of organohalide-respiring bacteria in chemostats by covariance of rdhA gene abundance.

    PubMed

    Marshall, Ian P G; Azizian, Mohammad F; Semprini, Lewis; Spormann, Alfred M

    2014-02-01

    We have developed a novel approach to identifying and quantifying closely related organohalide-respiring bacteria. Our approach made use of the unique genomic associations of specific reductive dehalogenase subunit A encoding genes (rdhA) that exist in known strains of Dehalococcoides mccartyi and Desulfitobacterium and the distinguishing covariance pattern of observed rdhA genes to assign genes to unknown strains. To test this approach, we operated five anaerobic reductively dechlorinating chemostats for 3-4 years with tetrachloroethene and trichloroethene as terminal electron acceptors and lactate/formate as electron donors. The presence and abundance of rdhA genes were determined comprehensively at the community level using a custom-developed Reductive Dehalogenase Chip (RDH Chip) DNA microarray and used to define putative strains of Dehalococcoides mccartyi and Desulfitobacterium sp. This monitoring revealed that stable chemical performance of chemostats was reflected by a stable community of reductively dechlorinating bacteria. However, perturbations introduced by, for example, electron donor limitation or addition of the competing electron acceptor sulfate led to overall changes in the chemostat performance, including incomplete reduction in the chloroethene substrates, and in the population composition of reductively dehalogenating bacteria. Interestingly, there was a high diversity of operationally defined D. mccartyi strains between the chemostats with almost all strains unique to their specific chemostats in spite of similar selective pressure and similar inocula shared between chemostats.

  20. The sublittoral macrobenthic community composition of Lough Hyne, Ireland

    NASA Astrophysics Data System (ADS)

    Thrush, Simon F.; Townsend, Colin R.

    1986-10-01

    This paper describes a survey conducted across the floor of the South basin of Lough Hyne, a small sea-lough in south-west Ireland. To test for any pattern in macrobenthic community structure in relation to prevailing hydrographic conditions five stations at approximately 20 m depth were sampled on four occasions over a 14 month period, by SCUBA diving. Measurements of sediment pH, redox potential, sulphide potential, grain size, organic matter content and macrobenthic community structure allow two distinct habitats to be defined; coarse gravelly substratum adjacent to the inflow area and fine silty substratum over the remainder of the basin floor. A correlation of physicochemical parameters with axis loadings from an ordination of species composition at each station on each sampling occasion failed to reveal a continuum of change in relation to prevailing hydrographic conditions. Rather, sediment physicochemistry, the abundance of common macrobenthic species, number of species, number of individuals, variations in the numerical dominance hierarchy and station position in the ordination space fluctuated in a haphazard manner. Various localized disturbances, observed while conducting this survey, are considered to contribute to this pattern. The disturbing agents include smothering of areas of sediment by anoxic water, deposition of accumulations of detached seaweed and sediment excavations by Cancer pagurus.

  1. Evaluation of the ecotoxicological impact of the organochlorine chlordecone on soil microbial community structure, abundance, and function.

    PubMed

    Merlin, Chloé; Devers, Marion; Béguet, Jérémie; Boggio, Baptiste; Rouard, Nadine; Martin-Laurent, Fabrice

    2016-03-01

    The insecticide chlordecone applied for decades in banana plantations currently contaminates 20,000 ha of arable land in the French West Indies. Although the impact of various pesticides on soil microorganisms has been studied, chlordecone toxicity to the soil microbial community has never been assessed. We investigated in two different soils (sandy loam and silty loam) exposed to different concentrations of CLD (D0, control; D1 and D10, 1 and 10 times the agronomical dose) over different periods of time (3, 7, and 32 days): (i) the fate of chlordecone by measuring (14)C-chlordecone mass balance and (ii) the impact of chlordecone on microbial community structure, abundance, and function, using standardized methods (-A-RISA, taxon-specific quantitative PCR (qPCR), and (14)C-compounds mineralizing activity). Mineralization of (14)C-chlordecone was inferior below 1 % of initial (14)C-activity. Less than 2 % of (14)C-activity was retrieved from the water-soluble fraction, while most of it remained in the organic-solvent-extractable fraction (75 % of initial (14)C-activity). Only 23 % of the remaining (14)C-activity was measured in nonextractable fraction. The fate of chlordecone significantly differed between the two soils. The soluble and nonextractable fractions were significantly higher in sandy loam soil than in silty loam soil. All the measured microbiological parameters allowed discriminating statistically the two soils and showed a variation over time. The genetic structure of the bacterial community remained insensitive to chlordecone exposure in silty loam soil. In response to chlordecone exposure, the abundance of Gram-negative bacterial groups (β-, γ-Proteobacteria, Planctomycetes, and Bacteroidetes) was significantly modified only in sandy loam soil. The mineralization of (14)C-sodium acetate and (14)C-2,4-D was insensitive to chlordecone exposure in silty loam soil. However, mineralization of (14)C-sodium acetate was significantly reduced in soil

  2. [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.

  3. Invertebrate community composition differs between invasive herb alligator weed and native sedges

    NASA Astrophysics Data System (ADS)

    Bassett, Imogen E.; Paynter, Quentin; Beggs, Jacqueline R.

    2012-05-01

    Chemical and/or architectural differences between native and exotic plants may influence invertebrate community composition. According to the enemy release hypothesis, invasive weeds should host fewer and less specialised invertebrates than native vegetation. Invertebrate communities were compared on invasive Alternanthera philoxeroides (alligator weed) and native sedges (Isolepis prolifer and Schoenoplectus tabernaemontani) in a New Zealand lake. A. philoxeroides is more architecturally and chemically similar to I. prolifer than to S. tabernaemontani. Lower invertebrate abundance, richness and proportionally fewer specialists were predicted on A. philoxeroides compared to native sedges, but with greatest differences between A. philoxeroides and S. tabernaemontani. A. philoxeroides is more architecturally and chemically similar to I. prolifer than to S. tabernaemontani. Invertebrate abundance showed taxa-specific responses, rather than consistently lower abundance on A. philoxeroides. Nevertheless, as predicted, invertebrate fauna of A. philoxeroides was more similar to that of I. prolifer than to S. tabernaemontani. The prediction of a depauperate native fauna on A. philoxeroides received support from some but not all taxa. All vegetation types hosted generalist-dominated invertebrate communities with simple guild structures. The enemy release hypothesis thus had minimal ability to predict patterns in this system. Results suggest the extent of architectural and chemical differences between native and invasive vegetation may be useful in predicting the extent to which they will host different invertebrate communities. However, invertebrate ecology also affects whether invertebrate taxa respond positively or negatively to weed invasion. Thus, exotic vegetation may support distinct invertebrate communities despite similar overall invertebrate abundance to native vegetation.

  4. Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms.

    PubMed

    Lawes, Jasmin C; Neilan, Brett A; Brown, Mark V; Clark, Graeme F; Johnston, Emma L

    2016-01-01

    Biofilms are integral to many marine processes but their formation and function may be affected by anthropogenic inputs that alter environmental conditions, including fertilisers that increase nutrients. Density composition and connectivity of biofilms developed in situ (under ambient and elevated nutrients) were compared using 454-pyrosequencing of the 16S gene. Elevated nutrients shifted community composition from bacteria involved in higher processes (eg Pseudoalteromonas spp. invertebrate recruitment) towards more nutrient-tolerant bacterial species (eg Terendinibacter sp.). This may enable the persistence of biofilm communities by increasing resistance to nutrient inputs. A core biofilm microbiome was identified (predominantly Alteromonadales and Oceanospirillales) and revealed shifts in abundances of core microbes that could indicate enrichment by fertilisers. Fertiliser decreased density and connectivity within biofilms indicating that associations were disrupted perhaps via changes to energetic allocations within the core microbiome. Density composition and connectivity changes suggest nutrients can affect the stability and function of these important marine communities.

  5. Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering?

    PubMed

    Moreno-Pino, Mario; De la Iglesia, Rodrigo; Valdivia, Nelson; Henríquez-Castilo, Carlos; Galán, Alexander; Díez, Beatriz; Trefault, Nicole

    2016-07-01

    Spatial environmental heterogeneity influences diversity of organisms at different scales. Environmental filtering suggests that local environmental conditions provide habitat-specific scenarios for niche requirements, ultimately determining the composition of local communities. In this work, we analyze the spatial variation of microbial communities across environmental gradients of sea surface temperature, salinity and photosynthetically active radiation and spatial distance in Fildes Bay, King George Island, Antarctica. We hypothesize that environmental filters are the main control of the spatial variation of these communities. Thus, strong relationships between community composition and environmental variation and weak relationships between community composition and spatial distance are expected. Combining physical characterization of the water column, cell counts by flow cytometry, small ribosomal subunit genes fingerprinting and next generation sequencing, we contrast the abundance and composition of photosynthetic eukaryotes and heterotrophic bacterial local communities at a submesoscale. Our results indicate that the strength of the environmental controls differed markedly between eukaryotes and bacterial communities. Whereas eukaryotic photosynthetic assemblages responded weakly to environmental variability, bacteria respond promptly to fine-scale environmental changes in this polar marine system.

  6. Decomposition rate of carrion is dependent on composition not abundance of the assemblages of insect scavengers.

    PubMed

    Farwig, Nina; Brandl, Roland; Siemann, Stefen; Wiener, Franziska; Müller, Jörg

    2014-08-01

    Environmental factors and biodiversity affect ecosystem processes. As environmental change modifies also biodiversity it is unclear whether direct effects of environmental factors on ecosystem processes are more important than indirect effects mediated by changes in biodiversity. High-quality resources like carrion occur as heterogeneous pulses of energy and nutrients. Consequently, the distribution of scavenging insects is related to resource availability. Therefore, carrion decomposition represents a suitable process from which to unravel direct effects of environmental change from indirect biodiversity-related effects on ecosystem processes. During three field seasons in 2010 we exposed traps baited with small-mammal carrion at 21 sites along a temperature gradient to explore the insect carrion fauna and decomposition rate in the Bohemian Forest, Germany. The abundance component of beetle and fly assemblages decreased with decreasing temperature. Independently, the composition component of both taxa changed with temperature and season. The change in the composition component of beetles depicted a loss of larger species at higher temperatures. Decomposition rate did not change directly along the temperature gradient but was directly influenced by season. The composition component of beetles, and to a small extent of flies, but not their abundance component, directly affected carrion decomposition. Consequently, lower decomposition rates at lower temperatures can be explained by the absence of larger beetle species. Thus, we predict that future environmental change will modify carrion fauna composition and thereby indirectly decomposition rate. Moreover, reorganizations of the insect carrion composition will directly translate into modified decomposition rates, with potential consequences for nutrient availability and carbon storage.

  7. Synoptic patterns of meiofaunal and macrofaunal abundances and specific composition in littoral sediments

    NASA Astrophysics Data System (ADS)

    Armonies, Werner; Hellwig-Armonies, Monika

    1987-03-01

    During recent years, many investigations on small zoobenthos have been performed at the island of Sylt. As these studies were carried out sporadically over many years and as different extraction methods were used, comparisons of the results have been hampered. Therefore, in August/September 1986, 24 sites were sampled and evaluated using one quantitative method throughout. Sites range from mud to exposed sand and from the sublittoral to the supralittoral. Macrofauna and the taxa Plathelminthes, Polychaeta, and Oligochaeta are determined to species level. Macrofaunal (>0.5 mm) abundance is highest in mud and continuously decreases with increasing exposure to wave action. Meiofaunal (<0.5 mm) abundance is less variable. Nematoda dominate in mud and muddy sand, Copepoda in sheltered and exposed sand, other taxa only intermittently. Related to surface area, no correlation between macro-and meiofaunal abundance is apparent. Plathelminthes and Copepoda reach highest abundance per surface area in sand but their per volume density is higher in mud and muddy sand. Related to sediment volume instead of surface area, the meiofaunal abundance pattern is very similar to the macrofaunal pattern. The faunal composition changes gradually along the tidal gradient without general faunal boundaries. On an averange, the faunal similarity of neighbouring sites is highest in Oligochaeta and lowest in Plathelminthes. Presumably, Oligochaeta tolerate wider ranges of environmental factors. This may explain the low number of oligochaete species. On the other hand, Plathelminthes seem to adapt to relatively narrow ranges of factors and their species richness is highest. Because of macrofaunameiofauna interaction it is suggested that the meiofaunal assemblage will be least stable in mud and muddy sand, and most stable in exposed sand.

  8. Microbial community composition in sediments resists perturbation by nutrient enrichment.

    PubMed

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-09-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.

  9. Microbial community composition in sediments resists perturbation by nutrient enrichment

    PubMed Central

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-01-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. PMID:21412346

  10. The Oxygen Isotopic Composition of MIL 090001: A CR2 Chondrite with Abundant Refractory Inclusions

    NASA Technical Reports Server (NTRS)

    Keller, Lindsay P.; McKeegan, K. D.; Sharp, Z. D.

    2012-01-01

    MIL 090001 is a large (>6 kg) carbonaceous chondrite that was classified as a member of the CV reduced subgroup (CVred) that was recovered during the 2009-2010 ANSMET field season [1]. Based on the abundance of refractory inclusions and the extent of aqueous alteration, Keller [2] suggested a CV2 classification. Here we report additional mineralogical and petrographic data for MIL 090001, its whole-rock oxygen isotopic composition and ion microprobe analyses of individual phases. The whole rock oxygen isotopic analyses show that MIL 090001 should be classified as a CR chondrite.

  11. Plankton studies in San Francisco Bay; II, Phytoplankton abundance and species composition, July 1977-December 1979

    USGS Publications Warehouse

    Wong, Raymond L. J.; Cloern, James E.

    1981-01-01

    Data are presented on the phytoplankton species composition and abundance in San Francisco Bay from July 1977 through December 1979. Phytoplankton identification and enumerations were made at selected stations. Sample collections were made at selected stations in the main channel of the Bay from Rio Vista on the Sacramento River to Calaveras Point in South San Francisco Bay, and at shoal stations in the central portion of South San Francisco Bay, San Pablo Bay, and Suisun Bay. Also reported, from October 1978 through December 1979, are the calculated phytoplankton carbon and percent nondiatom carbon, and the species list. This study is one component of an ongoing interdisciplinary study of San Francisco Bay. (USGS)

  12. 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.

  13. Seasonal and Successional Influences on Bacterial Community Composition Exceed That of Protozoan Grazing in River Biofilms

    PubMed Central

    Jürgens, Klaus; Weitere, Markus

    2012-01-01

    The effects of protozoa (heterotrophic flagellates and ciliates) on the morphology and community composition of bacterial biofilms were tested under natural background conditions by applying size fractionation in a river bypass system. Confocal laser scanning microscopy (CLSM) was used to monitor the morphological structure of the biofilm, and fingerprinting methods (single-stranded conformation polymorphism [SSCP] and denaturing gradient gel electrophoresis [DGGE]) were utilized to assess changes in bacterial community composition. Season and internal population dynamics had a greater influence on the bacterial biofilm than the presence of protozoa. Within this general framework, bacterial area coverage and microcolony abundance were nevertheless enhanced by the presence of ciliates (but not by the presence of flagellates). We also found that the richness of bacterial operational taxonomic units was much higher in planktonic founder communities than in the ones establishing the biofilm. Within the first 2 h of colonization of an empty substrate by bacteria, the presence of flagellates additionally altered their biofilm community composition. As the biofilms matured, the number of bacterial operational taxonomic units increased when flagellates were present in high abundances. The additional presence of ciliates tended to at first reduce (days 2 to 7) and later increase (days 14 to 29) bacterial operational taxonomic unit richness. Altogether, the response of the bacterial community to protozoan grazing pressure was small compared to that reported in planktonic studies, but our findings contradict the assumption of a general grazing resistance of bacterial biofilms toward protozoa. PMID:22247162

  14. Diversity and composition of the bacterial community in Amphioxus feces.

    PubMed

    Pan, Minming; Yuan, Dongjuan; Chen, Shangwu; Xu, Anlong

    2015-11-01

    Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment.

  15. LogCauchy, log-sech and lognormal distributions of species abundances in forest communities

    USGS Publications Warehouse

    Yin, Z.-Y.; Peng, S.-L.; Ren, H.; Guo, Q.; Chen, Z.-H.

    2005-01-01

    Species-abundance (SA) pattern is one of the most fundamental aspects of biological community structure, providing important information regarding species richness, species-area relation and succession. To better describe the SA distribution (SAD) in a community, based on the widely used lognormal (LN) distribution model with exp(-x2) roll-off on Preston's octave scale, this study proposed two additional models, logCauchy (LC) and log-sech (LS), respectively with roll-offs of simple x-2 and e-x. The estimation of the theoretical total number of species in the whole community, S*, including very rare species not yet collected in sample, was derived from the left-truncation of each distribution. We fitted these three models by Levenberg-Marquardt nonlinear regression and measured the model fit to the data using coefficient of determination of regression, parameters' t-test and distribution's Kolmogorov-Smirnov (KS) test. Examining the SA data from six forest communities (five in lower subtropics and one in tropics), we found that: (1) on a log scale, all three models that are bell-shaped and left-truncated statistically adequately fitted the observed SADs, and the LC and LS did better than the LN; (2) from each model and for each community the S* values estimated by the integral and summation methods were almost equal, allowing us to estimate S* using a simple integral formula and to estimate its asymptotic confidence internals by regression of a transformed model containing it; (3) following the order of LC, LS, and LN, the fitted distributions became lower in the peak, less concave in the side, and shorter in the tail, and overall the LC tended to overestimate, the LN tended to underestimate, while the LS was intermediate but slightly tended to underestimate, the observed SADs (particularly the number of common species in the right tail); (4) the six communities had some similar structural properties such as following similar distribution models, having a common

  16. Carbon, hydrogen and nitrogen in carbonaceous chondrites Abundances and isotopic compositions in bulk samples

    NASA Technical Reports Server (NTRS)

    Kerridge, J. F.

    1985-01-01

    Whole-rock samples of 25 carbonaceous chondrites were analyzed for contents of C, H and N and delta C-13, delta D and delta N-15. Inhomogeneous distribution of these isotopes within individual meteorites is pronounced in several cases. Few systematic intermeteorite trends were observed; N data are suggestive of isotopic inhomogeneity in the early solar system. Several chondrites revealed unusual compositions which would repay further, more detailed study. The data are also useful for classification of carbonaceous chondrites; N abundance and isotopic compositions can differentiate existing taxonomic groups with close to 100 percent reliability; Al Rais and Renazzo clearly constitute a discrete 'grouplet', and there are hints that both CI and CM groups may each be divisible into two subgroups.

  17. Composition and abundance of epibenthic-sledge catches in the South Polar Front of the Atlantic

    NASA Astrophysics Data System (ADS)

    Brandt, A.; Havermans, C.; Janussen, D.; Jörger, K. M.; Meyer-Löbbecke, A.; Schnurr, S.; Schüller, M.; Schwabe, E.; Brandão, S. N.; Würzberg, L.

    2014-10-01

    An epibenthic sledge (EBS) was deployed at seven different deep-sea stations along the South Polar Front of the Atlantic in order to explore the composition and abundance of macrofaunal organisms and to identify the most abundant taxa in this transition zone to the Southern Ocean. In total 3,130 specimens were sampled by means of the EBS on board of RV Polarstern during the expedition ANT-XXVIII/3 in the austral summer of 2012. Benthic and suprabenthic Crustacea occurred to be most frequent in the samples. Among those, copepods were by far most numerous, with 1,585 specimens followed by the peracarid taxa Isopoda (236 ind.), Amphipoda (103 ind.), Tanaidacea (78 ind.) and Cumacea (50 ind.). Annelida were represented by a high number of specimens belonging to different polychaete taxa (404 ind.). The molluscan fauna was clearly dominated by Bivalvia (255 ind.), followed in numbers of specimens by Gastropoda (47 ind.). The deep-sea benthos sampled along the Southern Polar Front occurred in surprisingly low abundances, contrasting the largely high surface productivity of the area. Numbers of specimens across different macrofaunal taxa and especially of peracarid crustaceans underscored by far those from South Ocean sites at higher latitudes in the Weddell Sea.

  18. [Environmental heterogeneity and its relationship with diversity and abundance of the fish community in a coastal system of Gulf of Mexico].

    PubMed

    Aguirre-León, Arturo; Pérez-Ponce, Hilda Elín; Díaz-Ruiz, Silvia

    2014-03-01

    The coastal lagoons of Veracruz, Gulf of Mexico, include a great variety of biological resources. These resources, especially fish communities, have been barely described and that require more ecological studies. With this aim, this investigation analyzed the spatial and temporal variation of diversity, abundance and assemblages of the fish community and its relationship with physical-chemical parameters of the Chica-Grande coastal system. For this, eight defined sites were monthly sampled for water characteristics and fish community composition (10min hauls of 1 500m2 a shrimp trawl net), between September 2005 and November 2006. The spatial-temporal variation of physical-chemical parameters, allowed the definition of two contrasting environments according to salinity, temperature, transparency, dissolved oxygen and depth gradients. A total of 1 947 fishes were collected for a total weight of 57.88kg. From these, 22 species, 20 genera and 14 families were identified; and four species were new records for the system. As it was detected for the physical-chemical conditions, the diversity of the fish community also showed a spatial gradient, with high values (H'=2.37, D=3.35, J'=0.82) in the brackish habitat, and low ones in freshwater environments. Fish abundance did not show such a marked gradient response, however, it was higher in the freshwater habitat. The highest diversity (H'=2.05) and species richness (D=2.99) was recorded during the North winds ("nortes") months (November-February), while density and biomass were higher (0.034 ind./m2, 1.42g/m2) during the rainy months (July-October). The Importance Value Index (IVI) defined six dominant species accounting for 77.8% of the fish abundance and 87.9% of total catch by weight. The Canonical Correspondence Analysis (CCA) showed that the fish-habitat relationship was explained by 68% of total variance for the two first axes, where salinity, transparency and temperature changes were the most important

  19. Size-abundance relationships in an Amazonian bird community: implications for the energetic equivalence rule.

    PubMed

    Russo, Sabrina E; Robinson, Scott K; Terborgh, John

    2003-02-01

    We studied size-abundance relationships in a species-rich Amazonian bird community and found that the slope of the logarithmic relationship between population density and bodymass (b = -0.22) is significantly shallower than expected under Damuth's energetic equivalence rule (EER), which states that population energy use (PEU) is independent of species body mass. We used estimates of avian field metabolic rates to examine the logarithmic relationship between PEU and body mass and its variation among ecological guilds. The relationship for all species had a significantly positive slope (b = 0.46), indicating that PEU of larger species was greater than that of smaller species. Analyses of guilds revealed significant variation. The slopes of the frugivore-omnivore, insectivore, and granivore guilds were all significantly positive, with that of the frugivore-omnivore guild being the steepest. In contrast, PEU did not vary significantly with species body mass among raptors. These results were confirmed, in analyses using both species values and phylogenetically independent contrasts, and the results do not support the EER in this community. The spatial distribution of resources and mechanisms of interference competition within guilds may explain why most patterns differed from the predictions of the EER. Other sources of variation, including the effects of scale, are also discussed.

  20. Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils.

    PubMed

    Koyama, Akihiro; Wallenstein, Matthew D; Simpson, Rodney T; Moore, John C

    2014-01-01

    The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-Proteobacteria and β-Proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming.

  1. Intraspecific variation in herbivore community composition and transcriptional profiles in field-grown Brassica oleracea cultivars

    PubMed Central

    Broekgaarden, Colette; Poelman, Erik H.; Voorrips, Roeland E.; Dicke, Marcel; Vosman, Ben

    2010-01-01

    Intraspecific differences in plant defence traits are often correlated with variation in transcriptional profiles and can affect the composition of herbivore communities on field-grown plants. However, most studies on transcriptional profiling of plant–herbivore interactions have been carried out under controlled conditions in the laboratory or greenhouse and only a few examine intraspecific transcriptional variation. Here, intraspecific variation in herbivore community composition and transcriptional profiles between two Brassica oleracea cultivars grown in the field is addressed. Early in the season, no differences in community composition were found for naturally occurring herbivores, whereas cultivars differed greatly in abundance, species richness, and herbivore community later in the season. Genome-wide transcriptomic analysis using an Arabidopsis thaliana oligonucleotide microarray showed clear differences for the expression levels of 26 genes between the two cultivars later in the season. Several defence-related genes showed higher levels of expression in the cultivar that harboured the lowest numbers of herbivores. Our study shows that herbivore community composition develops differentially throughout the season on the two B. oleracea cultivars grown in the field. The correlation between the differences in herbivore communities and differential expression of particular defence-related genes is discussed. PMID:19934173

  2. Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu

    PubMed Central

    Li, Junfeng; Zhang, Junyi; Liu, Liyang; Fan, Yucai; Li, Lianshuo; Yang, Yunfeng; Lu, Zuhong; Zhang, Xuegong

    2015-01-01

    Bacterioplankton plays a key role in nutrient cycling and is closely related to water eutrophication and algal bloom. We used high-throughput 16S rRNA gene sequencing to profile archaeal and bacterial community compositions in the surface water of Lake Taihu. It is one of the largest lakes in China and has suffered from recurring cyanobacterial bloom. A total of 81 water samples were collected from 9 different sites in 9 different months of 2012. We found that temporal variation of the microbial community was significantly greater than spatial variation (adonis, n = 9999, P < 1e−4). The composition of bacterial community in December was similar to that in January, and so was the archaeal community, suggesting potential annual periodicity. Unsupervised K-means clustering was used to identify the synchrony of abundance variations between different taxa. We found that the cluster consisting mostly of ACK-M1, C111 (members of acIV), Pelagibacteraceae (alfV-A) and Synechococcaceae showed relatively higher abundance in autumn. On the contrary, the cluster of Comamonadaceae and Methylophilaceae (members of lineage betI and betIV) had higher abundance in spring. The co-occurrence relationships between taxa were greatly altered during the cyanobacterial bloom according to our further network module analysis. PMID:26503553

  3. Drying effects on archaeal community composition and methanogenesis in bromeliad tanks.

    PubMed

    Brandt, Franziska B; Martinson, Guntars O; Pommerenke, Bianca; Pump, Judith; Conrad, Ralf

    2015-02-01

    Tank bromeliads are highly abundant epiphytes in neotropical forests and form a unique canopy wetland ecosystem which is involved in the global methane cycle. Although the tropical climate is characterized by high annual precipitation, the plants can face periods of restricted water. Thus, we hypothesized that water is an important controller of the archaeal community composition and the pathway of methane formation in tank bromeliads. Greenhouse experiments were established to investigate the resident and active archaeal community targeting the 16S rDNA and 16S rRNA in the tank slurry of bromeliads at three different moisture levels. Archaeal community composition and abundance were determined using terminal restriction fragment length polymorphism and quantitative PCR. Release of methane and its stable carbon isotopic signature were determined in a further incubation experiment under two moisture levels. The relative abundance of aceticlastic Methanosaetaceae increased up to 34% and that of hydrogenotrophic Methanobacteriales decreased by more than half with decreasing moisture. Furthermore, at low moisture levels, methane production was up to 100-fold lower (≤0.1-1.1 nmol gdw(-1) d(-1)) than under high moisture levels (10-15 nmol gdw(-1) d(-1)). The rapid response of the archaeal community indicates that the pathway of methane formation in bromeliad tanks may indeed be strongly susceptible to periods of drought in neotropical forest canopies.

  4. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    PubMed

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

  5. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    PubMed Central

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  6. Recurrence and Frequency of Disturbance have Cumulative Effect on Methanotrophic Activity, Abundance, and Community Structure

    PubMed Central

    Ho, Adrian; van den Brink, Erik; Reim, Andreas; Krause, Sascha M. B.; Bodelier, Paul L. E.

    2016-01-01

    Alternate prolonged drought and heavy rainfall is predicted to intensify with global warming. Desiccation-rewetting events alter the soil quality and nutrient concentrations which drive microbial-mediated processes, including methane oxidation, a key biogeochemical process catalyzed by methanotrophic bacteria. Although aerobic methanotrophs showed remarkable resilience to a suite of physical disturbances induced as a single event, their resilience to recurring disturbances is less known. Here, using a rice field soil in a microcosm study, we determined whether recurrence and frequency of desiccation-rewetting impose an accumulating effect on the methanotrophic activity. The response of key aerobic methanotroph subgroups (type Ia, Ib, and II) were monitored using qPCR assays, and was supported by a t-RFLP analysis. The methanotrophic activity was resilient to recurring desiccation-rewetting, but increasing the frequency of the disturbance by twofold significantly decreased methane uptake rate. Both the qPCR and t-RFLP analyses were congruent, showing the dominance of type Ia/Ib methanotrophs prior to disturbance, and after disturbance, the recovering community was predominantly comprised of type Ia (Methylobacter) methanotrophs. Both type Ib and type II (Methylosinus/Methylocystis) methanotrophs were adversely affected by the disturbance, but type II methanotrophs showed recovery over time, indicating relatively higher resilience to the disturbance. This revealed distinct, yet unrecognized traits among the methanotroph community members. Our results show that recurring desiccation-rewetting before a recovery in community abundance had an accumulated effect, compromising methanotrophic activity. While methanotrophs may recover well following sporadic disturbances, their resilience may reach a ‘tipping point’ where activity no longer recovered if disturbance persists and increase in frequency. PMID:26779148

  7. Predicting effects of climate change on the composition and function of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

    2008-12-01

    Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences

  8. Determinants of the abundance of invasive annual weeds: community structure and non-equilibrium dynamics.

    PubMed

    Freckleton, R P; Watkinson, A R; Dowling, P M; Ley, A R

    2000-06-07

    The dynamics of an annual pasture community are described from a five-year experimental and monitoring study. The community was dominated by two grasses (Lolium rigidum and Vulpia bromoides) and a legume (Trifolium subterraneum). Fits of population dynamic models to per capita rates of population change indicate that interactions between the grasses were generally strong, while interactions between the grasses and legumes were weaker. Most, but not all, of the net effects of competition on population growth could be attributed to interactions occurring during plant growth. Phase-plane analysis indicated that, for a constant environment, a joint equilibrium of the two grasses is unstable since interspecific competition between Lolium and Vulpia is stronger than intraspecific competition. Consequently, the community will tend to a mixture of only one or other of the grass species and T. subterraneum, depending on the founding composition of the pasture. Analysis of data taken from a year in which a drought occurred (1993-1994) demonstrated profound effects on all three species. Modelling of the long-term impacts of the effects of repeated droughts showed that disturbance of this form overrides the founder effect observed under constant conditions. Consequently, Vulpia is ultimately able to invade any mixture of the other species in environments where stochastic disturbances occur.

  9. Changes in Bacterial Denitrifier Community Abundance over Time in an Agricultural Field and Their Relationship with Denitrification Activity▿

    PubMed Central

    Dandie, Catherine E.; Burton, David L.; Zebarth, Bernie J.; Henderson, Sherri L.; Trevors, Jack T.; Goyer, Claudia

    2008-01-01

    This study measured total bacterial and denitrifier community abundances over time in an agricultural soil cropped to potatoes (Solanum tuberosum L.) by using quantitative PCR. Samples were collected on 10 dates from spring to autumn and from three spatial locations: in the potato “hill” between plants (H), close to the plant (Hp), and in the “furrow” (F). The denitrification rates, N2O emissions, and environmental parameters were also measured. Changes in denitrifier abundance over time and spatial location were small (1.7- to 2.7-fold for the nirK, nosZ, and cnorBB guilds), whereas the cnorBP community (Pseudomonas mandelii and closely related spp.) showed an ∼4.6-fold change. The seasonal patterns of denitrifier gene numbers varied with the specific community: lower nosZ gene numbers in April and May than in June and July, higher cnorBP gene numbers in May and June than in March and April and September and November, higher nirK gene numbers in early spring than in late autumn, and no change in cnorBB gene numbers. Gene numbers were higher for the Hp than the H location for the nosZ and nirK communities and for the cnorBP community on individual dates, presumably indicating an effect of the plant on denitrifier abundance. Higher cnorBP gene numbers for the H location than the F location and for nosZ and cnorBB on individual dates reflect the effect of spatial location on abundance. Denitrifier abundance changes were not related to any environmental parameter, although a weak relationship exists between cnorBP gene numbers, extractable organic carbon values, and temperature. Denitrification and N2O emissions were mostly regulated by inorganic nitrogen availability and water-filled pore space but were uncoupled from denitrifier community abundances measured in this system. PMID:18689522

  10. Mercury Abundances and Isotopic Compositions in the Murchison (CM) and Allende (CV)Carbonaceous Chondrites

    NASA Technical Reports Server (NTRS)

    Lauretta, D. S.; Klaue, B.; Blum, J. D.; Buseck, P. R.

    2001-01-01

    The abundance and isotopic composition of Hg was determined in bulk samples of both the Murchison (CM) and Allende (CV) carbonaceous chondrites using single- and multi-collector inductively coupled plasma mass spectrometry (ICP-MS). The bulk abundances of Hg are 294 6 15 ng/g in Murchison and 30.0 6 1.5 ng/g in Allende. These values are within the range of previous measurements of bulk Hg abundances by neutron activation analysis (NAA). Prior studies suggested that both meteorites contain isotopically anomalous Hg, with d l 96/202Hg values for the anomalous, thermal-release components from bulk samples ranging from 2260 %o to 1440 9/00 in Murchison and from 2620 9/00 to 1540 9/00 in Allende (Jovanovic and Reed, 1976a; 1976b; Kumar and Goel, 1992). Our multi-collector ICP-MS measurements suggest that the relative abundances of all seven stable Hg isotopes in both meteorites are identical to terrestrial values within 0.2 to 0.5 9/00m. On-line thermal-release experiments were performed by coupling a programmable oven with the singlecollector ICP-MS. Powdered aliquots of each meteorite were linearly heated from room temperature to 900 C over twenty-five minutes under an Ar atmosphere to measure the isotopic composition of Hg released fiom the meteorites as a h c t i o n of temperature. In separate experiments, the release profiles of S and Se were determined simultaneously with Hg to constrain the Hg distribution within the meteorites and to evaluate the possibility of Se interferences in previous NAA studies. The Hg-release patterns differ between Allende and Murchison. The Hg-release profile for Allende contains two distinct peaks, at 225" and 343"C, whereas the profile for Murchison has only one peak, at 344 C. No isotopically anomalous Hg was detected in the thermal-release experiments at a precision level of 5 to 30 9/00, depending on the isotope ratio. In both meteorites the Hg peak at ;340"C correlates with a peak in the S-release profile. This correlation

  11. Endolithic community composition of Orbicella faveolata (Scleractinia) underneath the interface between coral tissue and turf algae

    NASA Astrophysics Data System (ADS)

    Gutiérrez-Isaza, N.; Espinoza-Avalos, J.; León-Tejera, H. P.; González-Solís, D.

    2015-06-01

    We evaluated the species composition, richness, and total abundance of the endolithic community in the skeleton of Orbicella faveolata under coral tissue and under turf algae using cores that were extracted at different distances (0.5, 2.5, and 7.0 cm) from both sides of the external coral tissue-turf algae competitive boundary. We found high endolith richness as never before reported for Orbicella species. Nineteen endolith taxa were found within the O. faveolata skeleton, seven below the coral tissue zone, and twelve exclusively below the turf algae zone. Significant differences existed in the community composition, species richness, and the total abundance of endoliths in the cores that were extracted from the turf algae zone compared with those of the coral tissue zone. The endolithic community composition and species richness changed abruptly across the coral-turf algae interface, forming a clear boundary between different endolithic communities just underneath the interface between the coral tissue and turf algae zones.

  12. Invertebrate composition and abundance associated with Didymosphenia geminata in a montane stream

    USGS Publications Warehouse

    James, Daniel A.; Ranney, Steven H.; Chipps, Steven R.; Spindler, Bryan D.

    2010-01-01

    Didymosphenia geminata, a relatively new aquatic nuisance species that can form extensive, mucilaginous mats on stream substrates, was reported from Rapid Creek, South Dakota in 2002. To examine the association between D. geminata and the invertebrate community in Rapid Creek, macroinvertebrates were quantified using three gear types in the fall of 2006. D. geminata was present at two of four sites sampled (range = 5.53 to 809.68 g m−2 dry mass). At each site, invertebrates were collected using dip nets, Surber samplers, and drift nets. The combined percentage of Ephemeroptera, Plecoptera, and Trichoptera in areas with D. geminata was lower (41%) than in areas without D. geminata (76%). Diptera abundance was higher at sites with D. geminata than in sites where D. geminata was absent.

  13. Composition and structure of bird communities in vegetational gradients of Bodoquena Mountains, western Brazil.

    PubMed

    Godoi, Mauricio N; Souza, Franco L; Laps, Rudi R; Ribeiro, Danilo B

    2016-03-01

    The informations of bird species distribution in different habitats and the structure of their communities are crucial for bird conservation. We tested the differences in composition, richness and abundance of birds in different phytophysiognomies at Bodoquena Mountains, western Brazil, and we demonstrated the variations in richness and abundance of birds between different trophic groups. Sampling was conducted between July 2011 and June 2012 in 200 point counts arranged in the study area. A total of 3350 contacts were obtained belonging to 156 bird species. Woodland savannas, seasonal forests and arboreal savannas had higher bird abundance and richness, while riparian forests, clean pastures and dirty pastures had smaller values of these parameters. The bird community was organized according to local vegetational gradient, with communities of forests, open areas and savannas, although many species occurred in more than one vegetation type. The insectivorous, omnivorous, frugivorous and gramnivorous birds composed most of the community. These data showed how important environmental heterogeneity is to bird communities. Furthermore, the presence of extensive patches of natural habitats, the small distance between these patches and the permeability of pastures, with high arboreal and shrubby cover, are indicated as important factors to maintain the bird diversity.

  14. Impact of biological soil crusts and desert plants on soil microfaunal community composition

    USGS Publications Warehouse

    Darby, B.J.; Neher, D.A.; Belnap, J.

    2010-01-01

    Carbon and nitrogen are supplied by a variety of sources in the desert food web; both vascular and non-vascular plants and cyanobacteria supply carbon, and cyanobacteria and plant-associated rhizosphere bacteria are sources of biological nitrogen fixation. The objective of this study was to compare the relative influence of vascular plants and biological soil crusts on desert soil nematode and protozoan abundance and community composition. In the first experiment, biological soil crusts were removed by physical trampling. Treatments with crust removed had fewer nematodes and a greater relative ratio of bacterivores to microphytophages than treatments with intact crust. However, protozoa composition was similar with or without the presence of crusts. In a second experiment, nematode community composition was characterized along a spatial gradient away from stems of grasses or shrubs. Although nematodes generally occurred in increasing abundance nearer to plant stems, some genera (such as the enrichment-type Panagrolaimus) increased disproportionately more than others (such as the stress-tolerant Acromoldavicus). We propose that the impact of biological soil crusts and desert plants on soil microfauna, as reflected in the community composition of microbivorous nematodes, is a combination of carbon input, microclimate amelioration, and altered soil hydrology. ?? Springer Science + Business Media B.V. 2009.

  15. 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.

  16. Sensitivity of grassland plant community composition to spatial vs. temporal variation in precipitation.

    PubMed

    Cleland, Elsa E; Collins, Scott L; Dickson, Timothy L; Farrer, Emily C; Gross, Katherine L; Gherardi, Laureano A; Hallett, Lauren M; Hobbs, Richard J; Hsu, Joanna S; Turnbull, Laura; Suding, Katharine N

    2013-08-01

    Climate gradients shape spatial variation in the richness and composition of plant communities. Given future predicted changes in climate means and variability, and likely regional variation in the magnitudes of these changes, it is important to determine how temporal variation in climate influences temporal variation in plant community structure. Here, we evaluated how species richness, turnover, and composition of grassland plant communities responded to interannual variation in precipitation by synthesizing long-term data from grasslands across the United States. We found that mean annual precipitation,(MAP) was a positive predictor of species richness across sites, but a positive temporal relationship between annual precipitation and richness was only evident within two sites with low MAP. We also found higher average rates of species turnover in dry sites that in turn had a high proportion of annual species, although interannual rates of species turnover were surprisingly high across all locations. Annual species were less abundant than perennial species at nearly all sites, and our analysis showed that the probability of a species being lost or gained from one year to the next increased with decreasing species abundance. Bray-Curtis dissimilarity from one year to the next, a measure of species composition change that is influenced mainly by abundant species, was insensitive to precipitation at all sites. These results suggest that the richness and turnover patterns we observed were driven primarily by rare species, which comprise the majority of the local species pools at these grassland sites. These findings are consistent with the idea that short-lived and less abundant species are more sensitive to interannual climate variability than longer-lived and more abundant species. We conclude that, among grassland ecosystems, xeric grasslands are likely to exhibit the greatest responsiveness of community composition (richness and turnover) to predicted future

  17. Effects of habitat-forming species richness, evenness, identity, and abundance on benthic intertidal community establishment and productivity.

    PubMed

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS.

  18. Effects of Habitat-Forming Species Richness, Evenness, Identity, and Abundance on Benthic Intertidal Community Establishment and Productivity

    PubMed Central

    Lemieux, Julie; Cusson, Mathieu

    2014-01-01

    In a context of reduced global biodiversity, the potential impacts from the loss of habitat-forming species (HFS) on ecosystem structure and functioning must be established. These species are often the main community primary producers and have a major role in the establishment of organisms through facilitation processes. This study focuses on macroalgae and mussels as HFS within an intertidal zone along the St. Lawrence estuary (Quebec, Canada). Over a 16-week period, we manipulated the in situ diversity profile (richness, evenness, identity, and abundance) of the dominant HFS (Fucus distichus edentatus, F. vesiculosus, and Mytilus spp.) in order to define their role in both the establishment of associated species and community primary production. Contrary to expectation, no general change in HFS richness, evenness, abundance, or identity on associated species community establishment was observed. However, over the study period, the HFS diversity profile modified the structure within the trophic guilds, which may potentially affect further community functions. Also, our results showed that the low abundance of HFS had a negative impact on the primary productivity of the community. Our results suggest that HFS diversity profiles have a limited short-term role in our study habitat and may indicate that biological forcing in these intertidal communities is less important than environmental conditions. As such, there was an opportunistic establishment of species that ensured rapid colonization regardless of the absence, or the diversity profile, of facilitators such as HFS. PMID:25313459

  19. Abundance, species composition of microzooplankton from the coastal waters of Port Blair, South Andaman Island

    PubMed Central

    2012-01-01

    Background Microzooplankton consisting of protists and metazoa <200 μm. It displays unique feeding mechanisms and behaviours that allow them to graze cells up to five times their own volume. They can grow at rates which equal or exceed prey growth and can serve as a viable food source for metazoans. Moreover, they are individually inconspicuous, their recognition as significant consumers of oceanic primary production. The microzooplankton can be the dominant consumers of phytoplankton production in both oligo- and eutrophic regions of the ocean and are capable of consuming >100% of primary production. Results The microzooplankton of the South Andaman Sea were investigated during September 2011 to January 2012. A total of 44 species belong to 19 genera were recorded in this study. Tintinnids made larger contribution to the total abundance (34%) followed in order by dinoflagellates (24%), ciliates (20%) and copepod nauplii (18%). Foraminifera were numerically less (4%). Tintinnids were represented by 20 species belong to 13 genera, Heterotrophic dinoflagellates were represented by 17 species belong to 3 genera and Ciliates comprised 5 species belong to 3 genera. Eutintinus tineus, Tintinnopsis cylindrical, T. incertum, Protoperidinium divergens, Lomaniella oviformes, Strombidium minimum were the most prevalent microzooplankton. Standing stock of tintinnids ranged from 30–80 cells.L-1 and showed a reverse distribution with the distribution of chlorophyll a relatively higher species diversity and equitability was found in polluted harbour areas. Conclusions The change of environmental variability affects the species composition and abundance of microzooplankton varied spatially and temporarily. The observations clearly demonstrated that the harbor area differed considerably from other area in terms of species present and phytoplankton biomass. Further, the phytoplankton abundance is showed to be strongly influenced by tintinnid with respect to the relationship of

  20. Abundance, Composition, and Sinking Rates of Fish Fecal Pellets in the Santa Barbara Channel

    PubMed Central

    Saba, Grace K.; Steinberg, Deborah K.

    2012-01-01

    Rapidly sinking fecal pellets are an important component of the vertical flux of particulate organic matter (POM) from the surface to the ocean's interior; however, few studies have examined the role fish play in this export. We determined abundance, size, prey composition, particulate organic carbon/nitrogen (POC/PON), and sinking rates of fecal pellets produced by a forage fish, likely the northern anchovy, in the Santa Barbara Channel. Pellet abundance ranged from 0.1–5.9 pellets m−3. POC and PON contents averaged 21.7 µg C pellet−1 and 2.7 µg N pellet−1. The sinking rate averaged 787 m d−1; thus pellets produced at the surface would reach the benthos (~500 m) in <1 day. Estimated downward flux of fish fecal POC reached a maximum of 251 mg C m−2 d−1. This is equal to or exceeds previous measurements of sediment trap POM flux, and thus may transport significant amounts of repackaged surface material to depth. PMID:23056908

  1. Importance of the H2 abundance in protoplanetary disk ices for the molecular layer chemical composition

    NASA Astrophysics Data System (ADS)

    Wakelam, V.; Ruaud, M.; Hersant, F.; Dutrey, A.; Semenov, D.; Majumdar, L.; Guilloteau, S.

    2016-10-01

    Context. Protoplanetary disks are the target of many chemical studies (both observational and theoretical) as they contain the building material for planets. Their large vertical and radial gradients in density and temperature make them challenging objects for chemical models. In the outer part of these disks, the large densities and low temperatures provide a particular environment where the binding of species onto the dust grains can be very efficient and can affect the gas-phase chemical composition. Aims: We attempt to quantify to what extent the vertical abundance profiles and the integrated column densities of molecules predicted by a detailed gas-grain code are affected by the treatment of the molecular hydrogen physisorption at the surface of the grains. Methods: We performed three different models using the Nautilus gas-grain code. One model uses a H2 binding energy on the surface of water (440 K) and produces strong sticking of H2. Another model uses a small binding energy of 23 K (as if there were already a monolayer of H2), and the sticking of H2 is almost negligible. Finally, the remaining model is an intermediate solution known as the encounter desorption mechanism. Results: We show that the efficiency of molecular hydrogen binding (and thus its abundance at the surface of the grains) can have a quantitative effect on the predicted column densities in the gas phase of major species such as CO, CS, CN, and HCN.

  2. 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.

  3. A database of marine phytoplankton abundance, biomass and species composition in Australian waters

    NASA Astrophysics Data System (ADS)

    Davies, Claire H.; Coughlan, Alex; Hallegraeff, Gustaaf; Ajani, Penelope; Armbrecht, Linda; Atkins, Natalia; Bonham, Prudence; Brett, Steve; Brinkman, Richard; Burford, Michele; Clementson, Lesley; Coad, Peter; Coman, Frank; Davies, Diana; Dela-Cruz, Jocelyn; Devlin, Michelle; Edgar, Steven; Eriksen, Ruth; Furnas, Miles; Hassler, Christel; Hill, David; Holmes, Michael; Ingleton, Tim; Jameson, Ian; Leterme, Sophie C.; Lønborg, Christian; McLaughlin, James; McEnnulty, Felicity; McKinnon, A. David; Miller, Margaret; Murray, Shauna; Nayar, Sasi; Patten, Renee; Pritchard, Tim; Proctor, Roger; Purcell-Meyerink, Diane; Raes, Eric; Rissik, David; Ruszczyk, Jason; Slotwinski, Anita; Swadling, Kerrie M.; Tattersall, Katherine; Thompson, Peter; Thomson, Paul; Tonks, Mark; Trull, Thomas W.; Uribe-Palomino, Julian; Waite, Anya M.; Yauwenas, Rouna; Zammit, Anthony; Richardson, Anthony J.

    2016-06-01

    There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels.

  4. A database of marine phytoplankton abundance, biomass and species composition in Australian waters

    PubMed Central

    Davies, Claire H.; Coughlan, Alex; Hallegraeff, Gustaaf; Ajani, Penelope; Armbrecht, Linda; Atkins, Natalia; Bonham, Prudence; Brett, Steve; Brinkman, Richard; Burford, Michele; Clementson, Lesley; Coad, Peter; Coman, Frank; Davies, Diana; Dela-Cruz, Jocelyn; Devlin, Michelle; Edgar, Steven; Eriksen, Ruth; Furnas, Miles; Hassler, Christel; Hill, David; Holmes, Michael; Ingleton, Tim; Jameson, Ian; Leterme, Sophie C.; Lønborg, Christian; McLaughlin, James; McEnnulty, Felicity; McKinnon, A. David; Miller, Margaret; Murray, Shauna; Nayar, Sasi; Patten, Renee; Pritchard, Tim; Proctor, Roger; Purcell-Meyerink, Diane; Raes, Eric; Rissik, David; Ruszczyk, Jason; Slotwinski, Anita; Swadling, Kerrie M.; Tattersall, Katherine; Thompson, Peter; Thomson, Paul; Tonks, Mark; Trull, Thomas W.; Uribe-Palomino, Julian; Waite, Anya M.; Yauwenas, Rouna; Zammit, Anthony; Richardson, Anthony J.

    2016-01-01

    There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels. PMID:27328409

  5. Microbial community composition controls the effects of climate change on methane emission from rice paddies.

    PubMed

    Liu, Guang Cheng; Tokida, Takesi; Matsunami, Toshinori; Nakamura, Hirofumi; Okada, Masumi; Sameshima, Ryoji; Hasegawa, Toshihiro; Sugiyama, Shu-Ichi

    2012-12-01

    Rice paddies are one of the most important sources of CH4 emission from the terrestrial ecosystem. A Free-air CO2 Enrichment (FACE) experiment, which included a soil warming treatment, was conducted in a rice paddy at Shizukuishi, Japan. In this study, the changes in CH4 emission from a rice paddy, caused by global climate change, were explored in relation to the structural changes that have occurred in the methanogenic archaeal communities found in the soil and roots. The composition of the archaeal community was examined by terminal restriction fragment length polymorphism (T-RFLP) using the 16S rRNA gene, while its abundance was measured by real-time PCR using the methyl coenzyme M reductase (mcrA) gene. The archaeal community in the roots showed considerable change, characterized by the dominance of hydrogenotrophic methanogens and a corresponding decrease in acetoclastic methanogens. Seasonal changes in CH4 flux were closely related to the changes in methanogen abundance in the roots. Elevated CO2 caused an increase in root mass, which increased the abundance of methanogens leading to a rise in CH4 emissions. However, soil warming stimulated CH4 emissions by increasing CH4 production per individual methanogen. These results demonstrated that climate warming stimulates CH4 emission in a rice paddy by altering the abundance and activity of methanogenic archaea in the roots.

  6. Response of compost maturity and microbial community composition to pentachlorophenol (PCP)-contaminated soil during composting.

    PubMed

    Zeng, Guangming; Yu, Zhen; Chen, Yaoning; Zhang, Jiachao; Li, Hui; Yu, Man; Zhao, Mingjie

    2011-05-01

    Two composting piles were prepared by adding to a mixture of rice straw, vegetables and bran: (i) raw soil free from pentachlorophenol (PCP) contamination (pile A) and (ii) PCP-contaminated soil (pile B). It was shown by the results that compost maturity characterized by water soluble carbon (WSC), TOC/TN ratio, germination index (GI) and dehydrogenase activity (DA) was significantly affected by PCP exposure, which resulted in an inferior degree of maturity for pile B. DGGE analysis revealed an inhibited effect of PCP on compost microbial abundance. The bacteria community shifts were mainly consistent with composting factors such as temperature, pH, moisture content and substrates. By contrast, the fungal communities were more sensitive to PCP contamination due to the significant correlation between fungal community shifts and PCP removal. Therefore, the different microbial community compositions for properly evaluating the degree of maturity and PCP contamination were suggested.

  7. The effect of seasonality in phytoplankton community composition on CO2 uptake on the Scotian Shelf

    NASA Astrophysics Data System (ADS)

    Craig, Susanne E.; Thomas, Helmuth; Jones, Chris T.; Li, William K. W.; Greenan, Blair J. W.; Shadwick, Elizabeth H.; Burt, William J.

    2015-07-01

    We characterise seasonal patterns in phytoplankton community composition on the Scotian Shelf, northwest Atlantic Ocean, through a study of the numerical abundance of different cell sizes - pico-, nano- and microphytoplankton. Cell abundances of each size class were converted to cellular carbon and their seasonal patterns compared with the partial pressure of carbon dioxide (pCO2) also measured at the study site. We observed a persistent drawdown of CO2 throughout the summer months, despite nutrient depleted conditions and apparent low biomass suggested by the chlorophyll record. This drawdown was associated with a summertime phytoplankton assemblage numerically dominated by small phytoplankton that reach their peak abundance during this period. It was found that phytoplankton carbon during this period accounted for approximately 10% of spring bloom phytoplankton carbon and pointed to the importance role that small cells play in annual CO2 uptake.

  8. Community composition has greater impact on the functioning of marine phytoplankton communities than ocean acidification.

    PubMed

    Eggers, Sarah L; Lewandowska, Aleksandra M; Barcelos E Ramos, Joana; Blanco-Ameijeiras, Sonia; Gallo, Francesca; Matthiessen, Birte

    2014-03-01

    Ecosystem functioning is simultaneously affected by changes in community composition and environmental change such as increasing atmospheric carbon dioxide (CO2 ) and subsequent ocean acidification. However, it largely remains uncertain how the effects of these factors compare to each other. Addressing this question, we experimentally tested the hypothesis that initial community composition and elevated CO2 are equally important to the regulation of phytoplankton biomass. We full-factorially exposed three compositionally different marine phytoplankton communities to two different CO2 levels and examined the effects and relative importance (ω(2) ) of the two factors and their interaction on phytoplankton biomass at bloom peak. The results showed that initial community composition had a significantly greater impact than elevated CO2 on phytoplankton biomass, which varied largely among communities. We suggest that the different initial ratios between cyanobacteria, diatoms, and dinoflagellates might be the key for the varying competitive and thus functional outcome among communities. Furthermore, the results showed that depending on initial community composition elevated CO2 selected for larger sized diatoms, which led to increased total phytoplankton biomass. This study highlights the relevance of initial community composition, which strongly drives the functional outcome, when assessing impacts of climate change on ecosystem functioning. In particular, the increase in phytoplankton biomass driven by the gain of larger sized diatoms in response to elevated CO2 potentially has strong implications for nutrient cycling and carbon export in future oceans.

  9. The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

    PubMed

    He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

    2012-02-01

    One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

  10. Arbuscular mycorrhizal fungal community composition associated with Juniperus brevifolia in native Azorean forest

    NASA Astrophysics Data System (ADS)

    Melo, Catarina Drumonde; Luna, Sara; Krüger, Claudia; Walker, Christopher; Mendonça, Duarte; Fonseca, Henrique M. A. C.; Jaizme-Vega, Maria; da Câmara Machado, Artur

    2017-02-01

    The communities of glomeromycotan fungi (arbuscular mycorrhizal fungi, AMF) under native Juniperus brevifolia forest from two Azorean islands, Terceira and São Miguel, were compared, mainly by spore morphology, and when possible, by molecular analysis. Thirty-nine morphotypes were detected from 12 genera. Glomeromycotan fungal richness was similar in Terceira and São Miguel, but significantly different among the four fragments of native forest. Spore diversity and community composition differed significantly between the two islands. The less degraded island, Terceira, showed 10 exclusive morphotypes including more rare types, whereas the more disturbed forest on São Miguel showed 13 morphs, mostly of common types. Forests from Terceira were dominated by Acaulosporaceae and Glomeraceae. Whereas members of Acaulosporaceae, Glomeraceae and Ambisporaceae were most frequent and abundant in those from São Miguel. Spore abundance was greatest on Terceira, and correlated with soil chemical properties (pH), average monthly temperature and relative humidity.

  11. Spatial and temporal variation in enterococcal abundance and its relationship to the microbial community in Hawaii beach sand and water.

    PubMed

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn; Yan, Tao

    2013-06-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.

  12. The relationship between deer density, tick abundance, and human cases of Lyme disease in a residential community.

    PubMed

    Kilpatrick, Howard J; LaBonte, Andrew M; Stafford, Kirby C

    2014-07-01

    White-tailed deer (Odocoileus virginianus Zimmerman), serve as the primary host for the adult blacklegged tick (Ixodes scapularis Say), the vector for Lyme disease, human babesiosis, and human granulocytic anaplasmosis. Our objective was to evaluate the degree of association between deer density, tick abundance, and human cases of Lyme disease in one Connecticut community over a 13-yr period. We surveyed 90-98% of all permanent residents in the community six times from 1995 to 2008 to document resident's exposure to tick-related disease and frequency and abundance of deer observations. After hunts were initiated, number and frequency of deer observations in the community were greatly reduced as were resident-reported cases of Lyme disease. Number of resident-reported cases of Lyme disease per 100 households was strongly correlated to deer density in the community. Reducing deer density to 5.1 deer per square kilometer resulted in a 76% reduction in tick abundance, 70% reduction in the entomological risk index, and 80% reduction in resident-reported cases of Lyme disease in the community from before to after a hunt was initiated.

  13. Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

    PubMed Central

    Cui, Henglin; Yang, Kun; Pagaling, Eulyn

    2013-01-01

    Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

  14. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

    PubMed

    Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

    2017-05-01

    The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures.

  15. Mesoscale and sub-mesoscale variability in phytoplankton community composition in the Sargasso Sea

    NASA Astrophysics Data System (ADS)

    Cotti-Rausch, Bridget E.; Lomas, Michael W.; Lachenmyer, Eric M.; Goldman, Emily A.; Bell, Douglas W.; Goldberg, Stacey R.; Richardson, Tammi L.

    2016-04-01

    The Sargasso Sea is a dynamic physical environment in which strong seasonal variability combines with forcing by mesoscale (~100 km) eddies. These drivers determine nutrient, light, and temperature regimes and, ultimately, the composition and productivity of the phytoplankton community. On four cruises (2011 and 2012; one eddy per cruise), we investigated links between water column structure and phytoplankton community composition in the Sargasso at a range of time and space scales. On all cruises, cyanobacteria (Prochlorococcus and Synechococcus) dominated the phytoplankton numerically, while haptophytes were the dominant eukaryotes (up to 60% of total chl-a). There were substantial effects of mesoscale and sub-mesoscale forcing on phytoplankton community composition in both spring and summer. Downwelling (in anticyclones) resulted in Prochlorococcus abundances that were 22-66% higher than at 'outside' stations. Upwelling (in cyclones) was associated with significantly higher abundances and POC biomass of nanoeukaryotes. In general, however, each eddy had its own unique characteristics. The center of anticyclone AC1 (spring 2011) had the lowest phytoplankton biomass (chl-a) of any eddy we studied and had lower nitrate+nitrite (N+N <5 mmol m-2) and eukaryote chl-a biomass as compared to its edge and to the Bermuda Atlantic Time-Series station (BATS). At the center of cyclone C1 (summer 2011), we observed uplift of the 26.5 kg m-3 isopycnal and high nutrient inventories (N+N=74±46 mmol m-2). We also observed significantly higher haptophyte chl-a (non-coccolithophores) and lower cyanobacterial chl-a at the center and edge of C1 as compared to outside the eddy at BATS. Cyclone C2 (spring 2012) exhibited a deep mixed layer, yet had relatively low nutrient concentrations. We observed a shift in the taxonomic composition of haptophytes between a coccolithophore-dominated community in C2 (98% of total haptophyte chl-a) and a non-coccolithophore community at BATS. In

  16. Links between plant community composition, soil organic matter quality and microbial communities in contrasting tundra habitats.

    PubMed

    Eskelinen, Anu; Stark, Sari; Männistö, Minna

    2009-08-01

    Plant communities, soil organic matter and microbial communities are predicted to be interlinked and to exhibit concordant patterns along major environmental gradients. We investigated the relationships between plant functional type composition, soil organic matter quality and decomposer community composition, and how these are related to major environmental variation in non-acid and acid soils derived from calcareous versus siliceous bedrocks, respectively. We analysed vegetation, organic matter and microbial community compositions from five non-acidic and five acidic heath sites in alpine tundra in northern Europe. Sequential organic matter fractionation was used to characterize organic matter quality and phospholipid fatty acid analysis to detect major variation in decomposer communities. Non-acidic and acidic heaths differed substantially in vegetation composition, and these disparities were associated with congruent shifts in soil organic matter and microbial communities. A high proportion of forbs in the vegetation was positively associated with low C:N and high soluble N:phenolics ratios in soil organic matter, and a high proportion of bacteria in the microbial community. On the contrary, dwarf shrub-rich vegetation was associated with high C:N and low soluble N:phenolics ratios, and a high proportion of fungi in the microbial community. Our study demonstrates a strong link between the plant community composition, soil organic matter quality, and microbial community composition, and that differences in one compartment are paralleled by changes in others. Variation in the forb-shrub gradient of vegetation may largely dictate variations in the chemical quality of organic matter and decomposer communities in tundra ecosystems. Soil pH, through its direct and indirect effects on plant and microbial communities, seems to function as an ultimate environmental driver that gives rise to and amplifies the interactions between above- and belowground systems.

  17. Marine litter in the upper São Vicente submarine canyon (SW Portugal): Abundance, distribution, composition and fauna interactions.

    PubMed

    Oliveira, Frederico; Monteiro, Pedro; Bentes, Luis; Henriques, Nuno Sales; Aguilar, Ricardo; Gonçalves, Jorge M S

    2015-08-15

    Marine litter has become a worldwide environmental problem, tainting all ocean habitats. The abundance, distribution and composition of litter and its interactions with fauna were evaluated in the upper S. Vicente canyon using video images from 3 remote operated vehicle exploratory dives. Litter was present in all dives and the abundance was as high as 3.31 items100m(-1). Mean abundance of litter over rock bottom was higher than on soft substrate. Mean litter abundance was slightly higher than reported for other canyons on the Portuguese margin, but lower in comparison to more urbanized coastal areas of the world. Lost fishing gear was the prevalent type of litter, indicating that the majority of litter originates from maritime sources, mainly fishing activity. Physical contact with sessile fauna and entanglement of specimens were the major impacts of lost fishing gear. Based on the importance of this region for the local fishermen, litter abundance is expected to increase.

  18. Characterisation of the soil bacterial community structure and composition of natural and constructed wetlands.

    PubMed

    Ansola, Gemma; Arroyo, Paula; Sáenz de Miera, Luis E

    2014-03-01

    In the present study, the pyrosequencing of 16S ribosomal DNA was used to characterise the soil bacterial community composition of a constructed wetland receiving municipal wastewater and a nearby natural wetland. Soil samples were taken from different locations in each wetland (lagoon, zone with T. latifolia, zone with S. atrocinerea). Moreover, the water quality parameters were evaluated (pH, Tª, conductivity, dissolved oxygen, redox potential, nutrients and suspended solids), revealing that the organic matter and nutrient contents were significantly higher in the constructed wetland than in the natural one. In general, the bacterial communities of the natural wetland were more diverse than those of the constructed wetland. The major phylogenic groups of all soils included Proteobacteria, Verrucomicrobia and Chloroflexi, with Proteobacteria being the majority of the community composition. The Verrucomicrobia and Chloroflexi phyla were more abundant in the natural wetland than the constructed wetland; in contrast, the Proteobacteria phylum was more abundant in the constructed wetland than the natural wetland. Beta diversity analyses reveal that the soil bacterial communities in the natural wetland were less dissimilar to each other than to those of the constructed wetland.

  19. Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu.

    PubMed

    Fan, Xianfang; Xing, Peng

    2016-01-01

    In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats.

  20. Effects of Functionalized and Raw Multi-Walled Carbon Nanotubes on Soil Bacterial Community Composition

    PubMed Central

    Kerfahi, Dorsaf; Tripathi, Binu M.; Singh, Dharmesh; Kim, Hyoki; Lee, Sujin; Lee, Junghoon; Adams, Jonathan M.

    2015-01-01

    Carbon nanotubes (CNTs) are widely used in industry, but their environmental impacts on soil microbial communities are poorly known. In this paper, we compare the effect of both raw and acid treated or functionalized (fCNTs) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Soil DNA was extracted at 0, 2 and 8 weeks and the V3 region of the 16S rRNA gene was PCR-amplified and sequenced using paired-end Illumina bar-coded sequencing. The results show that bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition, as illustrated by NMDS, was affected only by fMWCNT at high concentrations. This effect, detectable at 2 weeks, remained equally strong by 8 weeks. In the case of fMWCNTs, overall changes in relative abundance of the dominant phyla were also found. The stronger effect of fMWCNTs could be explained by their intrinsically acidic nature, as the soil pH was lower at higher concentrations of fMWCNTs. Overall, this study suggests that fMWCNTs may at least temporarily alter microbial community composition on the timescale of at least weeks to months. It appears, by contrast, that raw MWCNTs do not affect soil microbial community composition. PMID:25825905

  1. Effects of functionalized and raw multi-walled carbon nanotubes on soil bacterial community composition.

    PubMed

    Kerfahi, Dorsaf; Tripathi, Binu M; Singh, Dharmesh; Kim, Hyoki; Lee, Sujin; Lee, Junghoon; Adams, Jonathan M

    2015-01-01

    Carbon nanotubes (CNTs) are widely used in industry, but their environmental impacts on soil microbial communities are poorly known. In this paper, we compare the effect of both raw and acid treated or functionalized (fCNTs) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Soil DNA was extracted at 0, 2 and 8 weeks and the V3 region of the 16S rRNA gene was PCR-amplified and sequenced using paired-end Illumina bar-coded sequencing. The results show that bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition, as illustrated by NMDS, was affected only by fMWCNT at high concentrations. This effect, detectable at 2 weeks, remained equally strong by 8 weeks. In the case of fMWCNTs, overall changes in relative abundance of the dominant phyla were also found. The stronger effect of fMWCNTs could be explained by their intrinsically acidic nature, as the soil pH was lower at higher concentrations of fMWCNTs. Overall, this study suggests that fMWCNTs may at least temporarily alter microbial community composition on the timescale of at least weeks to months. It appears, by contrast, that raw MWCNTs do not affect soil microbial community composition.

  2. Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine

    PubMed Central

    Wu, Shangong; Wang, Guitang; Angert, Esther R.; Wang, Weiwei; Li, Wenxiang; Zou, Hong

    2012-01-01

    Gut microbiota has become an integral component of the host, and received increasing attention. However, for many domestic animals, information on the microbiota is insufficient and more effort should be exerted to manage the gastrointestinal bacterial community. Understanding the factors that influence the composition of microbial community in the host alimentary canal is essential to manage or improve the microbial community composition. In the present study, 16S rRNA gene sequence-based comparisons of the bacterial communities in the grass carp (Ctenopharyngodon idellus) intestinal contents and fish culture-associated environments are performed. The results show that the fish intestinal microbiota harbors many cellulose-decomposing bacteria, including sequences related to Anoxybacillus, Leuconostoc, Clostridium, Actinomyces, and Citrobacter. The most abundant bacterial operational taxonomic units (OTUs) in the grass carp intestinal content are those related to feed digestion. In addition, the potential pathogens and probiotics are important members of the intestinal microbiota. Further analyses show that grass carp intestine holds a core microbiota composed of Proteobacteria, Firmicutes, and Actinobacteria. The comparison analyses reveal that the bacterial community in the intestinal contents is most similar to those from the culture water and sediment. However, feed also plays significant influence on the composition of gut microbiota. PMID:22363439

  3. Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalga Fucus vesiculosus.

    PubMed

    Stratil, Stephanie B; Neulinger, Sven C; Knecht, Henrik; Friedrichs, Anette K; Wahl, Martin

    2013-04-01

    The thallus surface of the brown macroalga Fucus vesiculosus is covered by a specific biofilm community. This biofilm supposedly plays an important role in the interaction between host and environment. So far, we know little about compositional or functional shifts of this epibiotic bacterial community under changing environmental conditions. In this study, the response of the microbiota to different temperatures with respect to cell density and community composition was analyzed by nonculture-based methods (denaturing gradient gel electrophoresis and 454 pyrosequencing of the 16S rRNA gene). Redundancy analysis showed that despite high variability among host individuals temperature accounted for 20% of the variation in the bacterial community composition, whereas cell density did not differ between groups. Across all samples, 4341 bacterial operational taxonomic units (OTUs) at a 97% similarity level were identified. Eight percent of OTUs were significantly correlated with low, medium, and high temperatures. Notably, the family Rhodobacteraceae increased in relative abundance from 20% to 50% with increasing temperature. OTU diversity (evenness and richness) was higher at 15 °C than at the lower and higher temperatures. Considering their known and presumed ecological functions for the host, change in the epibacterial community may entail shifts in the performance of the host alga.

  4. Seasonal trends in abundance and composition of marine debris in selected public beaches in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Mobilik, Julyus-Melvin; Ling, Teck-Yee; Husain, Mohd-Lokman Bin; Hassan, Ruhana

    2015-09-01

    The abundance and composition of marine debris were investigated at Saujana (in the state of Negeri Sembilan) and Batu Rakit (in the state of Terengganu) beaches during surveys conducted in December 2012 (northeast monsoon), May 2013 (intermediate monsoon) and July 2013 (southwest monsoon). A total of 4,682 items of debris weighing 231.4 kg were collected and sorted. Batu Rakit received substantially greater quantities of debris (815±717 items/km or 40.4±13.0 kg/km) compared to Saujana (745±444 items/km or 36.7±18.0 kg/km). Total debris item was more abundant during the southwest monsoon (SWM) (1,122±737 items/km) compared to the northeast monsoon (NEM) (825±593 items/ km) and the intermediate monsoon (IM) (394±4 items/km) seasons. Plastic category (88%) was the most numerous items collected and object items contributed 44.18% includes packaging, plastic fragments, cups, plastic shopping bags, plastic food wrapper, clear plastic bottles from the total debris items collected. Object items associated with common source (47%) were the highest debris accumulated, followed by terrestrial (30%) and marine (23%) sources. The high percentage of common and terrestrial sources during SWM season requires immediate action by marine environment stakeholders to develop and introduce strategies to reduce if not totally eliminates the marine debris in the marine environment. Awareness should be continued and focused on beach users and vessels' crew to alert them on the alarming accumulation rate of marine debris and its pathways into the marine environment.

  5. Distinctive lipid composition of the copepod Limnocalanus macrurus with a high abundance of polyunsaturated fatty acids.

    PubMed

    Hiltunen, Minna; Strandberg, Ursula; Keinänen, Markku; Taipale, Sami; Kankaala, Paula

    2014-09-01

    We studied the copepod Limnocalanus macrurus for seasonal variation in the composition of fatty acids, wax esters and sterols in large boreal lakes, where it occurs as a glacial-relict. Vast wax ester reserves of Limnocalanus were accumulated in a period of only two months, and comprised mono- and polyunsaturated fatty acids (PUFA) and saturated fatty alcohols. In winter, the mobilization of wax esters was selective, and the proportion of long-chain polyunsaturated wax esters declined first. PUFA accounted for >50% of all fatty acids throughout the year reaching up to ca. 65% during late summer and fall. Long-chain PUFA 20:5n-3 and 22:6n-3 together comprised 17-40% of all fatty acids. The rarely reported C24 and C26 very-long-chain PUFA (VLC-PUFA) comprised 6.2 ± 3.4 % of all fatty acids in August and 2.1 ± 1.7% in September. The VLC-PUFA are presumably synthesized by Limnocalanus from shorter chain-length precursors because they were not found in the potential food sources. We hypothesize that these VLC-PUFA help Limnocalanus to maximize lipid reserves when food is abundant. Sterol content of Limnocalanus, consisting ca. 90% of cholesterol, did not show great seasonal variation. As a lipid-rich copepod with high abundance of PUFA, Limnocalanus is excellent quality food for fish. The VLC-PUFA were also detected in planktivorous fish, suggesting that these compounds can be used as a trophic marker indicating feeding on Limnocalanus.

  6. [Influences of long-term application of organic and inorganic fertilizers on the composition and abundance of nirS-type denitrifiers in black soil].

    PubMed

    Yin, Chang; Fan, Fen-Liang; Li, Zhao-Jun; Song, A-Lin; Zhu, Ping; Peng, Chang; Liang, Yong-Chao

    2012-11-01

    The objectives of this study were to explore the effects of long-term organic and inorganic fertilizations on the composition and abundance of nirS-type denitrifiers in black soil. Soil samples were collected from 4 treatments (i. e. no fertilizer treatment, CK; organic manure treatment, OM; chemical fertilizer treatment (NPK) and combination of organic and chemical fertilizers treatment (MNPK)) in Gongzhuling Long-term Fertilization Experiment Station. Composition and abundance of nirS-type denitrifiers were analyzed with terminal restriction fragment length polymorphism (T-RFLP) and real-time quantitative PCR (Q-PCR), respectively. Denitrification enzyme activity (DEA) and soil properties were also measured. Application of organic fertilizers (OM and MNPK) significantly increased the DEAs of black soil, with the DEAs in OM and MNPK being 5.92 and 6.03 times higher than that in CK treatment, respectively, whereas there was no significant difference between NPK and CK. OM and MNPK treatments increased the abundances of nirS-type denitrifiers by 2.73 and 3.83 times relative to that of CK treatment, respectively. The abundance of nirS-type denitrifiers in NPK treatment was not significantly different from that of CK. The T-RFLP analysis of nirS genes showed significant differences in community composition between organic and inorganic treatments, with the emergence of a 79 bp T-RF, a significant decrease in relative abundance of the 84 bp T-RF and a loss of the 99 bp T-RF in all organic treatments. Phylogenetic analysis indicated that the airS-type denitrifiers in the black soil were mainly composed of alpha, beta and gamma-Proteobacteria. The 79 bp-type denitrifiers inhabiting exclusively in organic treatments (OM and MNPK) were affiliated to Pseudomonadaceae in gamma-Proteobacteria and Burkholderiales in beta-Proteobacteria. The 84 bp-types were related to Burkholderiales and Rhodocyclales. Correlation analysis indicated that pH, concentrations of total nitrogen

  7. Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

    PubMed Central

    Lindh, Markus V.; Figueroa, Daniela; Sjöstedt, Johanna; Baltar, Federico; Lundin, Daniel; Andersson, Agneta; Legrand, Catherine; Pinhassi, Jarone

    2015-01-01

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates. PMID

  8. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera

    NASA Astrophysics Data System (ADS)

    Ulrich, Werner

    2005-09-01

    Recent investigations about the relationship between the number of species of taxonomic lineages and regional patterns of species abundances gave indecisive results. Here, it is shown that mean densities of species of a species-rich community of forest Hymenoptera (673 species out of 25 families) were positively related to the number of European species per family. The fraction of abundant species per family declined and the fraction of rare species increased with species richness. Species rich families contained relatively more species, which were present in only one study year (occasional species), and relatively fewer species present during the whole study period (frequent species).

  9. Drivers of cyanobacterial diversity and community composition in mangrove soils in south-east Brazil.

    PubMed

    Rigonato, Janaina; Kent, Angela D; Alvarenga, Danillo O; Andreote, Fernando D; Beirigo, Raphael M; Vidal-Torrado, Pablo; Fiore, Marli F

    2013-04-01

    Cyanobacteria act as primary producers of carbon and nitrogen in nutrient-poor ecosystems such as mangroves. This important group of microorganisms plays a critical role in sustaining the productivity of mangrove ecosystems, but the structure and function of cyanobacteria assemblages can be perturbed by anthropogenic influences. The aim of this work was to assess the community structure and ecological drivers that influence the cyanobacterial community harboured in two Brazilian mangrove soils, and examine the long-term effects of oil contamination on these keystone species. Community fingerprinting results showed that, although cyanobacterial communities are distinct between the two mangroves, the structure and diversity of the assemblages exhibit similar responses to environmental gradients. In each ecosystem, cyanobacteria occupying near-shore areas were similar in composition, indicating importance of marine influences for structuring the community. Analysis of 16S rRNA sequences revealed the presence of diverse cyanobacterial communities in mangrove sediments, with clear differences among mangrove habitats along a transect from shore to forest. While near-shore sites in both mangroves were mainly occupied by Prochlorococcus and Synechococcus genera, sequences retrieved from other mangrove niches were mainly affiliated with uncultured cyanobacterial 16S rRNA. The most intriguing finding was the large number of potentially novel cyanobacteria 16S rRNA sequences obtained from a previously oil-contaminated site. The abundance of cyanobacterial 16S rRNA sequences observed in sites with a history of oil contamination was significantly lower than in the unimpacted areas. This study emphasized the role of environmental drivers in determining the structure of cyanobacterial communities in mangrove soils, and suggests that anthropogenic impacts may also act as ecological filters that select cyanobacterial taxa. These results are an important contribution to our

  10. Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice.

    PubMed

    Hatam, Ido; Lange, Benjamin; Beckers, Justin; Haas, Christian; Lanoil, Brian

    2016-10-01

    Arctic sea ice can be classified into two types: seasonal ice (first-year ice, FYI) and multi-year ice (MYI). Despite striking differences in the physical and chemical characteristics of FYI and MYI, and the key role sea ice bacteria play in biogeochemical cycles of the Arctic Ocean, there are a limited number of studies comparing the bacterial communities from these two ice types. Here, we compare the membership and composition of bacterial communities from FYI and MYI sampled north of Ellesmere Island, Canada. Our results show that communities from both ice types were dominated by similar class-level phylogenetic groups. However, at the operational taxonomic unit (OTU) level, communities from MYI and FYI differed in both membership and composition. Communities from MYI sites had consistent structure, with similar membership (presence/absence) and composition (OTU abundance) independent of location and year of sample. By contrast, communities from FYI were more variable. Although FYI bacterial communities from different locations and different years shared similar membership, they varied significantly in composition. Should these findings apply to sea ice across the Arctic, we predict increased compositional variability in sea ice bacterial communities resulting from the ongoing transition from predominantly MYI to FYI, which may impact nutrient dynamics in the Arctic Ocean.

  11. Sediment composition influences spatial variation in the abundance of human pathogen indicator bacteria within an estuarine environment.

    PubMed

    Perkins, Tracy L; Clements, Katie; Baas, Jaco H; Jago, Colin F; Jones, Davey L; Malham, Shelagh K; McDonald, James E

    2014-01-01

    Faecal contamination of estuarine and coastal waters can pose a risk to human health, particularly in areas used for shellfish production or recreation. Routine microbiological water quality testing highlights areas of faecal indicator bacteria (FIB) contamination within the water column, but fails to consider the abundance of FIB in sediments, which under certain hydrodynamic conditions can become resuspended. Sediments can enhance the survival of FIB in estuarine environments, but the influence of sediment composition on the ecology and abundance of FIB is poorly understood. To determine the relationship between sediment composition (grain size and organic matter) and the abundance of pathogen indicator bacteria (PIB), sediments were collected from four transverse transects of the Conwy estuary, UK. The abundance of culturable Escherichia coli, total coliforms, enterococci, Campylobacter, Salmonella and Vibrio spp. in sediments was determined in relation to sediment grain size, organic matter content, salinity, depth and temperature. Sediments that contained higher proportions of silt and/or clay and associated organic matter content showed significant positive correlations with the abundance of PIB. Furthermore, the abundance of each bacterial group was positively correlated with the presence of all other groups enumerated. Campylobacter spp. were not isolated from estuarine sediments. Comparisons of the number of culturable E. coli, total coliforms and Vibrio spp. in sediments and the water column revealed that their abundance was 281, 433 and 58-fold greater in sediments (colony forming units (CFU)/100g) when compared with the water column (CFU/100ml), respectively. These data provide important insights into sediment compositions that promote the abundance of PIB in estuarine environments, with important implications for the modelling and prediction of public health risk based on sediment resuspension and transport.

  12. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

    PubMed Central

    Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

    2016-01-01

    Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

  13. Seasonal composition, abundance and biomass of the subestuarine fish assemblage in Solís Chico (Río de la Plata estuary, Uruguay).

    PubMed

    Plavan, A Acuña; Gurdek, R; Muñoz, N; Gutierrez, J M; Spósito, M; Correa, P; Caride, A

    2016-10-24

    The large estuaries can present long narrow branches called subestuaries or tidal creeks. These types of subsystems are distributed along the Uruguayan coast of the Río de la Plata estuary and are very important as nursery and refuge areas for fish. For the first time, the seasonal composition and abundance of the fish community of the Solís Chico subestuary was studied by using beach and gill nets. Fourteen species, mainly euryhaline (86%) presented a significant representation of juvenile stages. The fish community was dominated by Odontesthes argentinensis, Platanichthys platana, Mugil liza, Brevoortia aurea, Micropogonias furnieri and Paralichthys orbignyanus, similar to adjacent subestuaries. While Micropogonias furnieri and B. aurea were the most abundant species, some other species were rarely caught. A seasonal variation of the fish assemblage abundance was detected, with higher values in autumn showing a positive correlation with temperature. Species that complete their life cycle in the Río de la Plata estuary, some of which are relevant to fisheries (64% of the analyzed species) were captured in the Solís Chico subestuary. The importance of this environment as a transitional system for some estuarine fish species is advised.

  14. Effects of Triclosan and biosolids on microbial community composition in an agricultural soil

    PubMed Central

    Ogunyoku, Temitope A.; Young, Thomas M.; Scow, Kate M.

    2014-01-01

    Triclosan (TCS) is a widely used antimicrobial agent found at high concentrations in biosolids produced during municipal wastewater treatment. The effect of adding TCS, in the presence or absence of biosolids, on the composition of an agricultural soil microbial community was measured using phospholipid fatty acid analysis (PLFA). Most changes observed in microbial community composition were attributable to addition of biosolids or passage of time, with smaller changes due to TCS exposure, regardless of the biosolids presence. TCS slightly reduced the relative abundance of Gram positive and negative bacteria and fungi, both with or without biosolids. Bacteria were more sensitive than eukaryotes, consistent with the mode of action of TCS, which selectively targets fatty acid synthesis and disrupts cell membranes of bacteria. TCS slightly increased biomarkers of microbial stress, but stress biomarkers were lower in all biosolid treated soils, presumably due to increased availability of nutrients mitigating potential TCS toxicity. PMID:24597039

  15. Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

    NASA Astrophysics Data System (ADS)

    Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

    2013-12-01

    The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order

  16. Soil biodiversity and soil community composition determine ecosystem multifunctionality.

    PubMed

    Wagg, Cameron; Bender, S Franz; Widmer, Franco; van der Heijden, Marcel G A

    2014-04-08

    Biodiversity loss has become a global concern as evidence accumulates that it will negatively affect ecosystem services on which society depends. So far, most studies have focused on the ecological consequences of above-ground biodiversity loss; yet a large part of Earth's biodiversity is literally hidden below ground. Whether reductions of biodiversity in soil communities below ground have consequences for the overall performance of an ecosystem remains unresolved. It is important to investigate this in view of recent observations that soil biodiversity is declining and that soil communities are changing upon land use intensification. We established soil communities differing in composition and diversity and tested their impact on eight ecosystem functions in model grassland communities. We show that soil biodiversity loss and simplification of soil community composition impair multiple ecosystem functions, including plant diversity, decomposition, nutrient retention, and nutrient cycling. The average response of all measured ecosystem functions (ecosystem multifunctionality) exhibited a strong positive linear relationship to indicators of soil biodiversity, suggesting that soil community composition is a key factor in regulating ecosystem functioning. Our results indicate that changes in soil communities and the loss of soil biodiversity threaten ecosystem multifunctionality and sustainability.

  17. Community Composition of Photosynthetic Picoeukaryotes in a Subtropical Coastal Ecosystem, with Particular Emphasis on Micromonas.

    PubMed

    Lin, Yun-Chi; Chung, Chih-Ching; Chen, Liang-Yin; Gong, Gwo-Ching; Huang, Chin-Yi; Chiang, Kuo-Ping

    2016-09-16

    Photosynthetic picoeukaryotes (PPEs) are important constituents in picoplankton communities in many marine ecosystems. However, little is known about their community composition in the subtropical coastal waters of the Northwestern Pacific Ocean. In order to study their taxonomic composition, this study constructed 18S rRNA gene libraries using flow cytometric sorting during the warm season. The results show that, after diatoms, prasinophyte clones are numerically dominant. Within prasinophytes, Micromonas produced the most common sequences, and included clades II, III, IV, and VI. We are establishing the new Micromonas clade VI based on our phylogenetic analysis. Sequences of this clade have previously been retrieved from the South China Sea and Red Sea, indicating a worldwide distribution, but this is the first study to detect clade VI in the coastal waters of Taiwan. The TSA-FISH results indicated that Micromonas clade VI peaked in the summer (~4 × 10(2)  cells/ml), accounting for one-fifth of Micromonas abundance on average. Overall, Micromonas contributed half of Mamiellophyceae abundance, while Mamiellophyceae contributed 40% of PPE abundance. This study demonstrates the importance of Micromonas within the Mamiellophyceae in a subtropical coastal ecosystem.

  18. Species composition and seasonal abundance of sandflies (Diptera: Psychodidae: Phlebotominae) in coffee agroecosystems.

    PubMed

    Pérez, Jeanneth; Virgen, Armando; Rojas, Julio Cesar; Rebollar-Téllez, Eduardo Alfonso; Alfredo, Castillo; Infante, Francisco; Mikery, Oscar; Marina, Carlos Felix; Ibáñez-Bernal, Sergio

    2014-02-01

    The composition and seasonal occurrence of sandflies were investigated in coffee agroecosystems in the Soconusco region of Chiapas, Mexico. Insect sampling was performed on three plantations located at different altitudes: Finca Guadalupe Zajú [1,000 m above sea level (a.s.l.)], Finca Argovia (613 m a.s.l.) and Teotihuacán del Valle (429 m a.s.l.). Sandflies were sampled monthly from August 2007-July 2008 using three sampling methods: Shannon traps, CDC miniature light traps and Disney traps. Sampling was conducted for 3 h during three consecutive nights, beginning at sunset. A total of 4,387 sandflies were collected during the course of the study: 2,718 individuals in Finca Guadalupe Zajú, 605 in Finca Argovia and 1,064 in Teotihuacán del Valle. The Shannon traps captured 94.3% of the total sandflies, while the CDC light traps and Disney traps captured 4.9% and 0.8%, respectively. More females than males were collected at all sites. While the number of sandflies captured was positively correlated with temperature and relative humidity, a negative correlation was observed between sandfly numbers and rainfall. Five species of sandflies were captured: Lutzomyia cruciata , Lutzomyia texana , Lutzomyia ovallesi , Lutzomyia cratifer / undulata and Brumptomyia sp. Lu. cruciata , constituting 98.8% of the total, was the most abundant species. None of the captured sandflies was infected with Leishmania spp.

  19. Determination of the abundance and carbon isotope composition of elemental carbon in sediments

    NASA Astrophysics Data System (ADS)

    Bird, Michael I.; Gröcke, Darren R.

    1997-08-01

    We report measurements of the susceptibility of a variety of elemental and organic carbon samples to oxidative degradation using both acid dichromate and basic peroxide reagents. Organic carbon is rapidly oxidized using either reagent, or both reagents sequentially. Elemental carbon exhibits a wide range of susceptibilities to oxidation related both to the degree to which the precursor plant material was carbonized during pyrolysis and to the surface area available for oxidation. Despite a range of susceptibilities, a component of oxidation-resistant elemental carbon has been identified which can be reproducibly separated from organic contaminants. The carbon isotope composition (δ 13C value) of the precursor plant materials underwent a 0-1.6‰ decrease during the production of the elemental carbon by pyrolysis, while the subsequent oxidative degradation of the samples resulted in only small (generally < 0.5%o) changes in the δ 13C value of the remaining elemental carbon. The results suggest that the technique can be used to obtain records of elemental carbon abundance in marine sediment cores, and thus a record of the intensity of biomass burning on adjacent continental land masses in the geologic past. In addition, the δ 13C value of the elemental carbon can provide an indication of the type of vegetation being burnt.

  20. Species composition and seasonal abundance of sandflies (Diptera: Psychodidae: Phlebotominae) in coffee agroecosystems

    PubMed Central

    Pérez, Jeanneth; Virgen, Armando; Rojas, Julio Cesar; Rebollar-Téllez, Eduardo Alfonso; Alfredo, Castillo; Infante, Francisco; Mikery, Oscar; Marina, Carlos Felix; Ibáñez-Bernal, Sergio

    2013-01-01

    The composition and seasonal occurrence of sandflies were investigated in coffee agroecosystems in the Soconusco region of Chiapas, Mexico. Insect sampling was performed on three plantations located at different altitudes: Finca Guadalupe Zajú [1,000 m above sea level (a.s.l.)], Finca Argovia (613 m a.s.l.) and Teotihuacán del Valle (429 m a.s.l.). Sandflies were sampled monthly from August 2007-July 2008 using three sampling methods: Shannon traps, CDC miniature light traps and Disney traps. Sampling was conducted for 3 h during three consecutive nights, beginning at sunset. A total of 4,387 sandflies were collected during the course of the study: 2,718 individuals in Finca Guadalupe Zajú, 605 in Finca Argovia and 1,064 in Teotihuacán del Valle. The Shannon traps captured 94.3% of the total sandflies, while the CDC light traps and Disney traps captured 4.9% and 0.8%, respectively. More females than males were collected at all sites. While the number of sandflies captured was positively correlated with temperature and relative humidity, a negative correlation was observed between sandfly numbers and rainfall. Five species of sandflies were captured: Lutzomyia cruciata , Lutzomyia texana , Lutzomyia ovallesi , Lutzomyia cratifer / undulata and Brumptomyia sp. Lu. cruciata , constituting 98.8% of the total, was the most abundant species. None of the captured sandflies was infected with Leishmania spp. PMID:24271002

  1. Plankton communities and summertime declines in algal abundance associated with low dissolved oxygen in the Tualatin River, Oregon

    USGS Publications Warehouse

    Carpenter, Kurt D.; Rounds, Stewart A.

    2013-01-01

    and water-quality sample data from 2006 to 2008 were combined with parts of a larger discrete-sample and continuous water-quality monitoring dataset and examined to identify patterns in water-quality and algal conditions since 1991, with a particular emphasis on 2003–08. Longitudinal plankton surveys were conducted in 2006–08 at six sites between river miles (RM) 24.5 and 3.4 at 2- to 3-week intervals, or 5–6 per season, and in-situ bioassay experiments were conducted in 2008 to examine the potential effects of wastewater treatment facility (WWTF) effluent and phosphorus additions on phytoplankton biomass and algal photosynthesis. Phytoplankton and zooplankton community composition, streamflow, and water-quality data were analyzed using multivariate statistical techniques to gain insights into plankton dynamics to determine what factors might be most tied to the abundance and characteristics of the phytoplankton assemblages, and identify possible causes of their declines. The connection between low-DO events and algal declines was clearly evident, as bloom crashes were nearly always followed by periods of low DO. Algal blooms occurred each year during 2006–08, producing maximum chlorophyll-a (Chl-a) values in June or July generally in the range of 50–80 micrograms per liter (µg/L). Bloom crashes and absence of sufficient algal photosynthesis in mid- to late-summer contributed to minimum DO concentrations that were less than the State standard of 6.5 milligrams per liter (mg/L) based on the 30-day mean daily concentration, for 62–74 days each year. At times, the absolute minimum State standard (4 mg/L DO) also was not met. To learn more about why low-DO events occurred, specific algal declines during 2003–08 were scrutinized to determine their likely causal factors. From this information, a series of hypotheses were formulated and evaluated in terms of their ability to explain recent declines in algal populations in the river in late summer

  2. Street lighting changes the composition of invertebrate communities.

    PubMed

    Davies, Thomas W; Bennie, Jonathan; Gaston, Kevin J

    2012-10-23

    Artificial lighting has been used to illuminate the nocturnal environment for centuries and continues to expand with urbanization and economic development. Yet, the potential ecological impact of the resultant light pollution has only recently emerged as a major cause for concern. While investigations have demonstrated that artificial lighting can influence organism behaviour, reproductive success and survivorship, none have addressed whether it is altering the composition of communities. We show, for the first time, that invertebrate community composition is affected by proximity to street lighting independently of the time of day. Five major invertebrate groups contributed to compositional differences, resulting in an increase in the number of predatory and scavenging individuals in brightly lit communities. Our results indicate that street lighting changes the environment at higher levels of biological organization than previously recognized, raising the potential that it can alter the structure and function of ecosystems.

  3. The effects of weather on fungal abundance and richness among 25 communities in the Intermountain West

    PubMed Central

    Talley, Sharon M; Coley, Phyllis D; Kursar, Thomas A

    2002-01-01

    Background Because moisture and temperature influence the growth of fungi, characterizing weather conditions favorable for fungi may be used to predict the abundance and richness of fungi in habitats with different climate conditions. To estimate habitat favorability to fungi, we examined the relationship of fungal abundance and species richness to various weather and environmental parameters in the Intermountain West. We cultured fungi from air and leaf surfaces, and collected continuous temperature and relative humidity measures over the growing season at 25 sites. Results Fungal richness was positively correlated with fungal abundance (r = 0.75). Measures of moisture availability, such as relative humidity and vapor pressure deficit, explained more of the variance in fungal abundance and richness than did temperature. Climate measurements from nearby weather stations were good predictors of fungal abundance and richness but not as good as weather measurements obtained in the field. Weather variables that took into account the proportion of time habitats experienced favorable or unfavorable relative humidity and temperatures were the best predictors, explaining up to 56% of the variation in fungal abundance and 72% for fungal richness. Conclusion Our results suggest that the abundance and richness of fungi in a habitat is limited by the duration of unfavorable weather conditions. Because fungal pathogens likely have similar abiotic requirements for growth as other fungi, characterizing weather conditions favorable for fungi also may be used to predict the selective pressures imposed by pathogenic fungi on plants in different habitats. PMID:12079496

  4. Asexual endophytes and associated alkaloids alter arthropod community structure and increase herbivore abundances on a native grass.

    PubMed

    Jani, Andrea J; Faeth, Stanley H; Gardner, Dale

    2010-01-01

    Despite their minute biomass, microbial symbionts of plants potentially alter herbivory, diversity and community structure. Infection of grasses by asexual endophytic fungi often decreases herbivore loads and alters arthropod diversity. However, most studies to date have involved agronomic grasses and often consider only infection status (infected vs. uninfected), without explicitly measuring endophyte-produced alkaloids, which vary among endophyte isolates and may impact consumers. We combined field experiments and population surveys to investigate how endophyte infection and associated alkaloids influence abundances, species richness, evenness and guild structure of arthropod communities on a native grass, Achnatherum robustum (sleepygrass). Surprisingly, we found that endophyte-produced alkaloids were associated with increased herbivore abundances and species richness. Our results suggest that, unlike what has been found in agronomic grass systems, high alkaloid levels in native grasses may not protect host grasses from arthropod herbivores, and may instead more negatively affect natural enemies of herbivores.

  5. Effects of oxytetracycline on the abundance and community structure of nitrogen-fixing bacteria during cattle manure composting.

    PubMed

    Sun, Jiajun; Qian, Xun; Gu, Jie; Wang, Xiaojuan; Gao, Hua

    2016-09-01

    The effects of oxytetracycline (OTC) on nitrogen-fixing bacterial communities were investigated during cattle manure composting. The abundance and community structure of nitrogen-fixing bacteria were determined by qPCR and denaturing gradient gel electrophoresis (DGGE), respectively. The matrix was spiked with OTC at four levels: no OTC, 10mg/kg dry weight (DW) OTC (L), 60mg/kg DW OTC (M), and 200mg/kg DW OTC (H). The high temperature period of composting was shorter with M and H, and the decline in temperature during the cooling stage was accelerated by OTC. OTC had a concentration-dependent inhibitory effect on the nitrogenase activity during early composting, and the nifH gene abundance declined significantly during the later composting stage. The DGGE profile and statistical analysis showed that OTC changed the nitrogen-fixing bacterial community succession and reduced the community richness and dominance. The nitrogen-fixing bacterial community structure was affected greatly by the high level of OTC.

  6. Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance.

    PubMed

    Lee, Jessica A; Francis, Christopher A

    2017-02-01

    Denitrifying bacteria play a critical role in the estuarine nitrogen cycle. Through the transformation of nitrate into nitrogen gas, these organisms contribute to the loss of bioavailable (i.e., fixed) nitrogen from low-oxygen environments such as estuary sediments. Denitrifiers have been shown to vary in abundance and diversity across the spatial environmental gradients that characterize estuaries, such as salinity and nitrogen availability; however, little is known about how their communities change in response to temporal changes in those environmental properties. Here, we present a 1-year survey of sediment denitrifier communities along the estuarine salinity gradient of San Francisco Bay. We used quantitative PCR and sequencing of functional genes coding for a key denitrifying enzyme, dissimilatory nitrite reductase, to compare two groups of denitrifiers: those with nirK (encoding copper-dependent nitrite reductase) and those with nirS (encoding the cytochrome-cd 1-dependent variant). We found that nirS was consistently more abundant and more diverse than nirK in all parts of the estuary. The abundances of the two genes were tightly linked across space but differed temporally, with nirK peaking when temperature was low and nirS peaking when nitrate was high. Likewise, the diversity and composition of nirK- versus nirS-type communities differed in their responses to seasonal variations, though both were strongly determined by site. Furthermore, our sequence libraries detected deeply branching clades with no cultured isolates, evidence of enormous diversity within the denitrifiers that remains to be explored.

  7. Using counts to simultaneously estimate abundance and detection probabilities in a salamander community

    USGS Publications Warehouse

    Dodd, C.K.; Dorazio, R.M.

    2004-01-01

    A critical variable in both ecological and conservation field studies is determining how many individuals of a species are present within a defined sampling area. Labor intensive techniques such as capture-mark-recapture and removal sampling may provide estimates of abundance, but there are many logistical constraints to their widespread application. Many studies on terrestrial and aquatic salamanders use counts as an index of abundance, assuming that detection remains constant while sampling. If this constancy is violated, determination of detection probabilities is critical to the accurate estimation of abundance. Recently, a model was developed that provides a statistical approach that allows abundance and detection to be estimated simultaneously from spatially and temporally replicated counts. We adapted this model to estimate these parameters for salamanders sampled over a six vear period in area-constrained plots in Great Smoky Mountains National Park. Estimates of salamander abundance varied among years, but annual changes in abundance did not vary uniformly among species. Except for one species, abundance estimates were not correlated with site covariates (elevation/soil and water pH, conductivity, air and water temperature). The uncertainty in the estimates was so large as to make correlations ineffectual in predicting which covariates might influence abundance. Detection probabilities also varied among species and sometimes among years for the six species examined. We found such a high degree of variation in our counts and in estimates of detection among species, sites, and years as to cast doubt upon the appropriateness of using count data to monitor population trends using a small number of area-constrained survey plots. Still, the model provided reasonable estimates of abundance that could make it useful in estimating population size from count surveys.

  8. Abundance, composition, and distribution of crustacean zooplankton in relation to hypolimnetic oxygen depletion in west-central Lake Erie

    USGS Publications Warehouse

    Heberger, Roy F.; Reynolds, James B.

    1977-01-01

    Samples of crustacean zooplankton were collected monthly in west-central Lake Erie in April and June to October 1968, and in July and August 1970, before and during periods of hypolimnetic dissolved oxygen (DO) depletion. The water column at offshore stations was thermally stratified from June through September 1968, and the hypolimnion contained no DO in mid-August of 1968 or 1970. Composition, abundance, and vertical distribution of crustacean zooplankton changed coincidentally with oxygen depletion. From July to early August, zooplankton abundance dropped 79% in 1968 and 50% in 1970. The declines were attributed largely to a sharp decrease in abundance of planktonic Cyclops bicuspidatus thomasi. Zooplankton composition shifted from mainly cyclopoid copepods in July to mainly cladocerans and copepod nauplii in middle to late August. We believe that mortality of adults and dormancy of copepodites in response to anoxia was the probable reason for the late summer decline in planktonic C. b. thomasi.

  9. Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants.

    PubMed

    Meerbergen, Ken; Van Geel, Maarten; Waud, Michael; Willems, Kris A; Dewil, Raf; Van Impe, Jan; Appels, Lise; Lievens, Bart

    2017-02-01

    It is assumed that microbial communities involved in the biological treatment of different wastewaters having a different chemical composition harbor different microbial populations which are specifically adapted to the environmental stresses encountered in these systems. Yet, little is known about the composition of these microbial communities. Therefore, the aim of this study was to assess the microbial community composition over two seasons (winter and summer) in activated sludge from well-operating textile wastewater treatment plants (WWTPs) in comparison with municipal WWTPs, and to explain observed differences by environmental variables. 454-pyrosequencing generated 160 archaeal and 1645 bacterial species-level Operational Taxonomic Units (OTUs), with lower observed richness in activated sludge from textile WWTPs compared to municipal WWTPs. The bacterial phyla Planctomycetes, Chloroflexi, Chlorobi, and Acidobacteria were more abundant in activated sludge samples from textile WWTPs, together with archaeal members of Thaumarchaeota. Nonmetric multidimensional scaling analysis of the microbial communities showed that microbial communities from textile and municipal WWTPs were significantly different, with a seasonal effect on archaea. Nitrifying and denitrifying bacteria as well as phosphate-accumulation bacteria were more abundant in municipal WWTPs, while sulfate-reducing bacteria were almost only detected in textile WWTPs. Additionally, microbial communities from textile WWTPs were more dissimilar than those of municipal WWTPs, possibly due to a wider diversity in environmental stresses to which microbial communities in textile WWTPs are subjected to. High salinity, high organic loads, and a higher water temperature were important potential variables driving the microbial community composition in textile WWTPs. This study provides a general view on the composition of microbial communities in activated sludge of textile WWTPs, and may provide novel insights

  10. Full-scale mesophilic biogas plants using manure as C-source: bacterial community shifts along the process cause changes in the abundance of resistance genes and mobile genetic elements.

    PubMed

    Wolters, Birgit; Ding, Guo-Chun; Kreuzig, Robert; Smalla, Kornelia

    2016-02-01

    The application of manure, typically harboring bacteria carrying resistance genes (RGs) and mobile genetic elements (MGEs), as co-substrate in biogas plants (BGPs) might be critical when digestates are used as fertilizers. In the present study, the relative abundance of RGs and MGEs in total community (TC-) DNA from manure, fermenters and digestate samples taken at eight full-scale BGPs co-fermenting manure were determined by real-time PCR. In addition, the bacterial community composition of all digestates as well as manure and fermenter material from one BGP (BGP3) was characterized by 454-pyrosequencing of 16S rRNA amplicons from TC-DNA. Compared to respective input manures, relative abundances determined for sul1, sul2, tet(M), tet(Q), intI1, qacEΔ1, korB and traN were significantly lower in fermenters, whereas relative abundances of tet(W) were often higher in fermenters. The bacterial communities in all digestates were dominated by Firmicutes and Bacteroidetes while Proteobacteria were low in abundance and no Enterobacteriaceae were detected. High-throughput sequencing revealed shifts in bacterial communities during treatment for BGP3. Although in comparison to manure, digestate bacteria had lower relative abundances of RGs and MGEs except for tet(W), mesophilic BGPs seem not to be effective for prevention of the spread of RGs and MGEs via digestates into arable soils.

  11. Soil microbial community composition changes according to the tillage practice and plant development stage

    NASA Astrophysics Data System (ADS)

    Degrune, Florine; Dufrêne, Marc; Colinet, Gilles; Taminiau, Bernard; Hiel, Marie-Pierre; Daube, Georges; Vandenbol, Micheline

    2015-04-01

    Soil microorganisms are abundant and diverse and can have both beneficial and adverse effects on crop growth. Some, such as plant-growth-promoting rhizobacteria and mycorrhizae, are well known to favor crop productivity and plant health. They are notably involved in key processes such as improving plant nutrient acquisition, and they also play major roles in stimulating plant growth and protecting plants against pathogens by producing bioactive substances. Conversely, both agricultural practices and the plant development stage are known to influence the physical and chemical properties of the soil and hence the abundance and diversity of soil microorganisms. Here we investigated the impact of both tillage practice (conventional versus reduced tillage) and plant development stage (germination versus flowering) on the microbial community composition of an agricultural soil supporting a faba bean crop. Samples were taken at a depth of 15-20 cm from a silty soil in Belgium. For bacteria, we observed significant shifts in community composition according to both factors. Some changes were strongly related to the plant development stage and others to the tillage practice. Some taxa, including Gemmatimonas, Xanthomonadaceae, and Sinobacteraceae, showed a higher relative abundance at the flowering stage than at the germination stage, but no effect of tillage practice. Other taxa, including Flovobacterium, Chitinophaga, and Luteolibacter, showed a higher relative abundance under conventional tillage than under reduced tillage, but no change according to the stage of plant development. For fungi, significant shifts in community composition were observed according to the plant development stage. No effect of tillage practice was observed. The relative abundances of certain taxa, including Chaetomium and Clavicipitaceae, were higher during germination than during flowering, whereas other taxa, including Minimedusa and Teberdinia, showed a higher relative abundance during

  12. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.

    PubMed

    Newton, Ryan J; Huse, Susan M; Morrison, Hilary G; Peake, Colin S; Sogin, Mitchell L; McLellan, Sandra L

    2013-01-01

    Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand

  13. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

    PubMed Central

    Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

    2015-01-01

    Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio

  14. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia).

    PubMed

    Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D; Scheu, Stefan; Daniel, Rolf

    2015-01-01

    Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio

  15. Shifts in the Microbial Community Composition of Gulf Coast Beaches Following Beach Oiling

    PubMed Central

    Newton, Ryan J.; Huse, Susan M.; Morrison, Hilary G.; Peake, Colin S.; Sogin, Mitchell L.; McLellan, Sandra L.

    2013-01-01

    Microorganisms associated with coastal sands serve as a natural biofilter, providing essential nutrient recycling in nearshore environments and acting to maintain coastal ecosystem health. Anthropogenic stressors often impact these ecosystems, but little is known about whether these disturbances can be identified through microbial community change. The blowout of the Macondo Prospect reservoir on April 20, 2010, which released oil hydrocarbons into the Gulf of Mexico, presented an opportunity to examine whether microbial community composition might provide a sensitive measure of ecosystem disturbance. Samples were collected on four occasions, beginning in mid-June, during initial beach oiling, until mid-November from surface sand and surf zone waters at seven beaches stretching from Bay St. Louis, MS to St. George Island, FL USA. Oil hydrocarbon measurements and NOAA shoreline assessments indicated little to no impact on the two most eastern beaches (controls). Sequence comparisons of bacterial ribosomal RNA gene hypervariable regions isolated from beach sands located to the east and west of Mobile Bay in Alabama demonstrated that regional drivers account for markedly different bacterial communities. Individual beaches had unique community signatures that persisted over time and exhibited spatial relationships, where community similarity decreased as horizontal distance between samples increased from one to hundreds of meters. In contrast, sequence analyses detected larger temporal and less spatial variation among the water samples. Superimposed upon these beach community distance and time relationships, was increased variability in bacterial community composition from oil hydrocarbon contaminated sands. The increased variability was observed among the core, resident, and transient community members, indicating the occurrence of community-wide impacts rather than solely an overprinting of oil hydrocarbon-degrading bacteria onto otherwise relatively stable sand

  16. The effect of positive interactions on temporal turnover of community composition along an environmental gradient.

    PubMed

    Wang, Youshi; Yang, Zhiyong; Zhou, Shurong; Soininen, Janne; Ai, Dexiecuo; Li, Yali; Chu, Chengjin

    2013-01-01

    It has been demonstrated that the interplay between negative and positive interactions simultaneously shapes community structure and composition. However, few studies have attempted to examine the effect of facilitation on compositional changes in communities through time. Additionally, due to the difficulties in collecting the long-term data, it would be useful to indicate the rate of temporal turnover using a readily obtainable metric. Using an individual-based model incorporating plant strategies, we examined the role of facilitation on the temporal turnover of communities located at different positions along an environmental gradient for three model scenarios: CM without facilitation; CFM-U, a unimodal relationship between facilitation and environmental severity; and CFM-L, a positively linear relationship between facilitation and environmental severity. Our results demonstrated that facilitation could increase, decrease or have no remarkable effect on temporal turnover. The specific outcome depended on the location of the focal community across the environmental gradient and the model employed. Compared with CM, the inclusion of positive interactions (i.e. CFM-U and CFM-L), at intermediate environmental stress levels (such as S = 0.7 and 0.8) resulted in lower Bray-Curtis similarity values; at other severity levels, facilitation slowed down (such as S = 0.3 and 0.4 at low to medium stress levels, and S = 0.9 at high stress levels) or had only a subtle effect (such as at S = 0.1) on temporal turnover. We also found that the coefficient of variation (CV) in species abundances and the rate of temporal variability showed a significant quadratic relationship. Our theoretical analysis contributes to the understanding of factors driving temporal turnover in biotic communities, and presents a potential metric (i.e. CV in species abundances) assessing the consequences of ongoing environmental change on community structure.

  17. 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.

  18. [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.

  19. Large-scale changes in community composition: determining land use and climate change signals.

    PubMed

    Kampichler, Christian; van Turnhout, Chris A M; Devictor, Vincent; van der Jeugd, Henk P

    2012-01-01

    Human land use and climate change are regarded as the main driving forces of present-day and future species extinction. They may potentially lead to a profound reorganisation of the composition and structure of natural communities throughout the world. However, studies that explicitly investigate both forms of impact--land use and climate change--are uncommon. Here, we quantify community change of Dutch breeding bird communities over the past 25 years using time lag analysis. We evaluate the chronological sequence of the community temperature index (CTI) which reflects community response to temperature increase (increasing CTI indicates an increase in relative abundance of more southerly species), and the temporal trend of the community specialisation index (CSI) which reflects community response to land use change (declining CSI indicates an increase of generalist species). We show that the breeding bird fauna underwent distinct directional change accompanied by significant changes both in CTI and CSI which suggests a causal connection between climate and land use change and bird community change. The assemblages of particular breeding habitats neither changed at the same speed and nor were they equally affected by climate versus land use changes. In the rapidly changing farmland community, CTI and CSI both declined slightly. In contrast, CTI increased in the more slowly changing forest and heath communities, while CSI remained stable. Coastal assemblages experienced both an increase in CTI and a decline in CSI. Wetland birds experienced the fastest community change of all breeding habitat assemblages but neither CTI nor CSI showed a significant trend. Overall, our results suggest that the interaction between climate and land use changes differs between habitats, and that comparing trends in CSI and CTI may be useful in tracking the impact of each determinant.

  20. Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee.

    PubMed

    McFrederick, Quinn S; Rehan, Sandra M

    2016-05-01

    Many insects obtain gut microbes from their diet, but how a mother's foraging patterns influence the microbes found in her offspring's food remains an open question. To address this gap, we studied a bee that forages for pollen from multiple species of plants and may therefore acquire diverse bacteria from different plants. We tested the hypothesis that pollen diversity correlates with bacterial diversity by simultaneously characterizing these two communities in bee brood provisions for the first time. We used deep sequencing of the plant RBCL gene and the bacterial 16S rRNA gene to characterize pollen and bacterial diversity. We then tested for associations between pollen and bacterial species richness and community composition, as well as co-occurrence of specific bacteria and pollen types. We found that both pollen and bacterial communities were extremely diverse, indicating that mother bees visit a wide variety of flowers for pollen and nectar and subsequently bring a diversity of microbes back into their nests. Pollen and bacterial species richness and community composition, however, were not correlated. Certain pollen types significantly co-occurred with the most proportionally abundant bacteria, indicating that the plants these pollen types came from may serve as reservoirs for these bacteria. Even so, the overall diversity of these communities appears to mask these associations at a broader scale. Further study of these pollen and bacteria associations will be important for understanding the complicated relationship between bacteria and wild bees.

  1. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    PubMed

    Dupont, Chris L; Larsson, John; Yooseph, Shibu; Ininbergs, Karolina; Goll, Johannes; Asplund-Samuelsson, Johannes; McCrow, John P; Celepli, Narin; Allen, Lisa Zeigler; Ekman, Martin; Lucas, Andrew J; Hagström, Åke; Thiagarajan, Mathangi; Brindefalk, Björn; Richter, Alexander R; Andersson, Anders F; Tenney, Aaron; Lundin, Daniel; Tovchigrechko, Andrey; Nylander, Johan A A; Brami, Daniel; Badger, Jonathan H; Allen, Andrew E; Rusch, Douglas B; Hoffman, Jeff; Norrby, Erling; Friedman, Robert; Pinhassi, Jarone; Venter, J Craig; Bergman, Birgitta

    2014-01-01

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  2. Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

    PubMed Central

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T.; Halpern, Malka

    2015-01-01

    Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness. PMID:26122961

  3. Arctic root-associated fungal community composition reflects environmental filtering.

    PubMed

    Blaalid, Rakel; Davey, Marie L; Kauserud, Håvard; Carlsen, Tor; Halvorsen, Rune; Høiland, Klaus; Eidesen, Pernille B

    2014-02-01

    There is growing evidence that root-associated fungi have important roles in Arctic ecosystems. Here, we assess the diversity of fungal communities associated with roots of the ectomycorrhizal perennial herb Bistorta vivipara on the Arctic archipelago of Svalbard and investigate whether spatial separation and bioclimatic variation are important structuring factors of fungal community composition. We sampled 160 plants of B. vivipara from 32 localities across Svalbard. DNA was extracted from entire root systems, and 454 pyrosequencing of ITS1 amplicons was used to profile the fungal communities. The fungal communities were predominantly composed of Basidiomycota (55% of reads) and Ascomycota (35%), with the orders Thelephorales (24%), Agaricales (13.8%), Pezizales (12.6%) and Sebacinales (11.3%) accounting for most of the reads. Plants from the same site or region had more similar fungal communities to one another than plants from other sites or regions, and sites clustered together along a weak latitudinal gradient. Furthermore, a decrease in per-plant OTU richness with increasing latitude was observed. However, no statistically significant spatial autocorrelation between sites was detected, suggesting that environmental filtering, not dispersal limitation, causes the observed patterns. Our analyses suggest that while latitudinal patterns in community composition and richness might reflect bioclimatic influences at global spatial scales, at the smaller spatial scale of the Svalbard archipelago, these changes more likely reflect varied bedrock composition and associated edaphic factors. The need for further studies focusing on identifying those specific bioclimatic and edaphic factors structuring root-associated fungal community composition at both global and local scales is emphasized.

  4. Benson Beach Demonstration Project: Composition and Abundance of Biota at Three Alternative Sump Sites

    SciTech Connect

    Williams, Greg D.; Pearson, Walter H.; Evans, Nathan R.; Anderson, Michael G.

    2004-01-15

    The Portland District of the U.S. Army Corps of Engineers is investigating plans to provide sediment to nourish beaches north of the Mouth of the Columbia River (MCR). Under the currently designed proposal, sediment dredged from the MCR will be temporarily stored at one of three proposed areas south of the North Jetty before being redredged and moved by a cutterhead pipeline dredge over the jetty to nourish Benson Beach. Resulting potential impacts to resident Dungeness crab (Cancer magister) and fishes represent one of the criteria for evaluating each of the alternative locations. To establish the species composition and relative abundance of crabs and fishes associated with each of the three proposed sump areas, researchers from the Pacific Northwest National Laboratory Marine Sciences Division completed nine field sampling trips from July 8, 2003, to November 1, 2003, for a total of 113 successful trawls comprising an area of over 7.4 ha (74,156 m2). This report documents the results of that effort. To understand the relative risk of losses to crab populations associated with dredging impacts at the sump alternative areas, it is recommended that a modified dredge impact model be developed using the data collected in this study. This model should estimate crab adult equivalent loss and associated error rates to gain a population-level perspective on the potential entrainment impacts at each of the three alternative sump areas. As well, a sustained survey of Dungeness crab distribution and movement within the Columbia River estuary would clarify the relative value of the sump areas as a migratory corridor for crab populations, and support management decisions relative to issues associated with dredged material handling and disposal.

  5. The origin of aubrites: Evidence from lithophile trace element abundances and oxygen isotope compositions

    NASA Astrophysics Data System (ADS)

    Barrat, J. A.; Greenwood, R. C.; Keil, K.; Rouget, M. L.; Boesenberg, J. S.; Zanda, B.; Franchi, I. A.

    2016-11-01

    We report the abundances of a selected set of ;lithophile; trace elements (including lanthanides, actinides and high field strength elements) and high-precision oxygen isotope analyses of a comprehensive suite of aubrites. Two distinct groups of aubrites can be distinguished: (a) the main-group aubrites display flat or light-REE depleted REE patterns with variable Eu and Y anomalies; their pyroxenes are light-REE depleted and show marked negative Eu anomalies; (b) the Mount Egerton enstatites and the silicate fraction from Larned display distinctive light-REE enrichments, and high Th/Sm ratios; Mount Egerton pyroxenes have much less pronounced negative Eu anomalies than pyroxenes from the main-group aubrites. Leaching experiments were undertaken to investigate the contribution of sulfides to the whole rock budget of the main-group aubrites. Sulfides contain in most cases at least 50% of the REEs and of the actinides. Among the elements we have analyzed, those displaying the strongest lithophile behaviors are Rb, Ba, Sr and Sc. The homogeneity of the Δ17O values obtained for main-group aubrite falls [Δ17O = +0.009 ± 0.010‰ (2σ)] suggests that they originated from a single parent body whose differentiation involved an early phase of large-scale melting that may have led to the development of a magma ocean. This interpretation is at first glance in agreement with the limited variability of the shapes of the REE patterns of these aubrites. However, the trace element concentrations of their phases cannot be used to discuss this hypothesis, because their igneous trace-element signatures have been modified by subsolidus exchange. Finally, despite similar O isotopic compositions, the marked light-REE enrichments displayed by Mount Egerton and Larned suggest that they are unrelated to the main-group aubrites and probably originated from a distinct parent body.

  6. Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat.

    PubMed

    Hamonts, Kelly; Clough, Tim J; Stewart, Alison; Clinton, Peter W; Richardson, Alan E; Wakelin, Steven A; O'Callaghan, Maureen; Condron, Leo M

    2013-03-01

    Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role.

  7. The Effects of Nutrient Stoichiometry on Bacterial Community Composition in Streams

    NASA Astrophysics Data System (ADS)

    Rubin, M. A.; Leff, L. G.

    2005-05-01

    Bacterial biofilm community composition in streams may be affected by the nutrient stoichiometry of the surrounding water. Specifically, varying nitrogen to phosphorus (N:P) molar ratios potentially can select for or against different taxa, such as various subclasses of Proteobacteria, and thus alter community structure. In this study, bacterial communities at three sites along the Mahoning River (Ohio) with different inorganic nutrient concentrations were compared. Bacteria in biofilms on cobbles were enumerated using fluorescent in situ hybridization (FISH) to determine the abundance of alpha-, beta-, and gamma-Proteobacteria, and the Cytophaga-Flavobacterium-cluster. Nitrate, ammonia, and soluble reactive phosphate (SRP) concentrations in the water ranged from undetectable to 0.05 g/L of SRP and 0.3 g/L of ammonia. Beta-Proteobacteria appeared to be the most affected by N:P (ranging from 11 to 150) showing a positive correlation between their abundance and the N:P ratio. The Cytophaga-Flavobacterium showed effects that were nearly opposite of the beta-Proteobacteria. These findings provide evidence that limitation by single nutrients may not be as good a predictor of bacterial community structure as the molar ratios of these nutrients. Also, the nutrient stoichiometry could have a bottom up effect on stream ecosystems because of the central role that microbes play in stream food webs.

  8. Spatial variation of bacterial community composition at the expiry of spring phytoplankton bloom in Sendai Bay, Japan.

    PubMed

    Sakami, Tomoko; Watanabe, Tsuyoshi; Kakehi, Shigeho; Taniuchi, Yukiko; Kuwata, Akira

    2016-02-01

    In order to characterize how bacterial communities are propagated over spatial scales in a coastal area, the bacterial community composition was examined along with a transect line set in a bay at an expiry of spring phytoplankton bloom. Four distinctive bacterial communities were found within the bay by a fingerprinting method of 16S rRNA gene amplicons. The most widely distributed one was distributed in the surface and middle layers at whole area of the bay. The water was characterized by low inorganic nutrients concentration and high bacterial abundance, suggesting that the bacterial community had been developed in the bloom. Pyrosequencing analyses of the gene amplicons indicated that Rhodobacteriaceae and Flavobacteriaceae were abundant in the bacterial community, though the most abundant bacterial taxon was SAR11. The second group was distributed in the bottom water at the coastal side of the bay where considerably high Chl. a concentration was observed, probably because of the sedimentation of phytoplankton bloom. The community diversity was high and Alteromonadaceae, Saprospiraceae, and some families of Actinobacter existed more in this community than the others. The third group was distributed in the deep water near the border with the outside of the bay. The ratio of SAR11 was the highest in this community; besides, Burkholderianceae and Rhodospilliraceae existed in relatively high abundances. Another bacterial community having intermediate characters was observed in the middle to bottom layers around a central part of the bay where vertical water mixing was observed. These findings suggest that spatially different bacterial communities were formed under the influences of phytoplankton bloom and/or hydrographic events such as oceanic seawater intrusion of the bay.

  9. Evaluating abundance and trends in a Hawaiian avian community using state-space analysis

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P.M.; Paxton, Eben

    2015-01-01

    Estimating population abundances and patterns of change over time are important in both ecology and conservation. Trend assessment typically entails fitting a regression to a time series of abundances to estimate population trajectory. However, changes in abundance estimates from year-to-year across time are due to both true variation in population size (process variation) and variation due to imperfect sampling and model fit. State-space models are a relatively new method that can be used to partition the error components and quantify trends based only on process variation. We compare a state-space modelling approach with a more traditional linear regression approach to assess trends in uncorrected raw counts and detection-corrected abundance estimates of forest birds at Hakalau Forest National Wildlife Refuge, Hawai‘i. Most species demonstrated similar trends using either method. In general, evidence for trends using state-space models was less strong than for linear regression, as measured by estimates of precision. However, while the state-space models may sacrifice precision, the expectation is that these estimates provide a better representation of the real world biological processes of interest because they are partitioning process variation (environmental and demographic variation) and observation variation (sampling and model variation). The state-space approach also provides annual estimates of abundance which can be used by managers to set conservation strategies, and can be linked to factors that vary by year, such as climate, to better understand processes that drive population trends.

  10. The rainy season increases the abundance and richness of the aquatic insect community in a Neotropical reservoir.

    PubMed

    Santana, H S; Silva, L C F; Pereira, C L; Simião-Ferreira, J; Angelini, R

    2015-01-01

    Alterations in aquatic systems and changes in water levels, whether due to rains or dam-mediated control can cause changes in community structure, forcing the community to readjust to the new environment. This study tested the hypothesis that there is an increase in the richness and abundance of aquatic insects during the rainy season in the Serra da Mesa Reservoir, with the premise that increasing the reservoir level provides greater external material input and habitat diversity, and, therefore, conditions that promote colonization by more species. We used the paired t test to test the differences in richness, beta diversity, and abundance, and a Non-metric Multidimensional Scaling (NMDS) was performed to identify patterns in the community under study. Additionally, Pearson correlations were analyzed between the richness, abundance, and beta diversity and the level of the reservoir. We collected 35,028 aquatic insect larvae (9,513 in dry period and 25,515 in the rainy season), predominantly of the Chironomidae family, followed by orders Ephemeroptera, Trichoptera, and Odonata. Among the 33 families collected, only 12 occurred in the dry season, while all occurred in the rainy season. These families are common in lentic environments, and the dominance of Chironomidae was associated with its fast colonization, their behavior of living at high densities and the great tolerance to low levels of oxygen in the environment. The hypothesis was confirmed, as the richness, beta diversity, and abundance were positively affected by the increase in water levels due to the rainy season, which most likely led to greater external material input, greater heterogeneity of habitat, and better conditions for colonization by several families.

  11. Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia.

    PubMed

    Cleary, Daniel F R; de Voogd, Nicole J; Polónia, Ana R M; Freitas, Rossana; Gomes, Newton C M

    2015-11-01

    In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus

  12. Spatial patterns of microbial community composition within Lake Erie sediments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones w...

  13. Plankton studies in San Francisco Bay; V, Zooplankton species composition and abundance in the South Bay, 1980-1981

    USGS Publications Warehouse

    Hutchinson, Anne

    1982-01-01

    Data are presented that summarize zooplankton species composition and abundance in South San Francisco Bay during 1980 and 1981. Sampling was conducted at least twice monthly at thirteen stations, from the southern extremity of the South Bay to the Golden Gate Bridge between January 1980 and May 1981. Samples were collected by pump at three depths in the shipping channel and one depth over the shoals. Subsamples were enumerated while alive. Total zooplankton biomass as carbon was calculated from estimated carbon quotas and abundances of each organism enumerated.

  14. The Abundance of Iron-Peak Elements and the Dust Composition in eta Carinae: Manganese

    NASA Technical Reports Server (NTRS)

    Bautista, M. A.; Melendez, M.; Hartman, H.; Gull, T. R.; Lodders, K.

    2010-01-01

    We study the chemical abundances of the Strontium Filament found in the ejecta of (eta) Carinae. In particular, we derive the abundances of iron-peak elements front spectra of their singly ionized ions present in the optical/IR spectra. In this paper we analyze the spectrum of Mn II using a new non-LTE model for this system. In constructing this models we carried out theoretical calculations of radiative transition rates and electron impact excitation rate coefficients. We find that relative to Ni the gas phase abundance ratio of Mn is roughly solar, similar to the Cr abundance but in contrast to the large enhancements in the abundances of Sc and Ti. NVe interpret this result as an indication of non-equilibrium condensation in the ejecta of (eta) Carinae.

  15. Microbial community composition of transiently wetted Antarctic Dry Valley soils

    PubMed Central

    Niederberger, Thomas D.; Sohm, Jill A.; Gunderson, Troy E.; Parker, Alexander E.; Tirindelli, Joëlle; Capone, Douglas G.; Carpenter, Edward J.; Cary, Stephen C.

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas. PMID:25674080

  16. Microbial community composition of transiently wetted Antarctic Dry Valley soils.

    PubMed

    Niederberger, Thomas D; Sohm, Jill A; Gunderson, Troy E; Parker, Alexander E; Tirindelli, Joëlle; Capone, Douglas G; Carpenter, Edward J; Cary, Stephen C

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

  17. Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

    PubMed Central

    Highton, Matthew P.; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E.

    2016-01-01

    Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI, and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns. PMID:27826296

  18. Floral diversity increases beneficial arthropod richness and decreases variability in arthropod community composition.

    PubMed

    Bennett, Ashley B; Gratton, Claudio

    2013-01-01

    Declines in species diversity resulting from anthropogenic alterations of the environment heighten the need to develop management strategies that conserve species and ecosystem services. This study examined how native plant species and their diversity influence the abundance and richness of beneficial arthropods, a functionally important group that provides ecosystem services such as pollination and natural pest suppression. Beneficial arthropods were sampled in replicated study plots containing native perennials planted in one-, two-, and seven-species mixtures. We found plant diversity had a positive impact on arthropod richness but not on arthropod abundance. An analysis of arthropod community composition revealed that each flower species attracted a different assemblage of beneficial arthropods. In addition, the full seven-species mixture also attracted a distinct arthropod community compared to single-species monocultures. Using a multivariate approach, we determined whether arthropod assemblages in two- and seven-species plots were additive and could be predicted based on assemblages from their component single-species plots. On average, assemblages in diverse plots were nonadditive when compared to assemblages predicted using single-species plots. Arthropod assemblages in two-species plots most closely resembled those of only one of the flower species in the mixture. However, the arthropod assemblages in seven-species plots, although statistically deviating from the expectation of an additive model, more closely resembled predicted communities compared to the assemblages found in two-species plots, suggesting that variability in arthropod community composition decreased as planting diversity increased. Our study demonstrates that careful selection of plants in managed landscapes can augment beneficial arthropod richness and support a more predictable arthropod community, suggesting that planning and design efforts could shape arthropod assemblages in natural

  19. Stable microbial community composition on the Greenland Ice Sheet

    PubMed Central

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A.; Wadham, Jemma; Anesio, Alexandre M.

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered ‘hot spots’ for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ13C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers. PMID:25852658

  20. Stable microbial community composition on the Greenland Ice Sheet.

    PubMed

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A; Wadham, Jemma; Anesio, Alexandre M

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered 'hot spots' for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ(13)C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers.

  1. Land Cover and Rainfall Interact to Shape Waterbird Community Composition

    PubMed Central

    Studds, Colin E.; DeLuca, William V.; Baker, Matthew E.; King, Ryan S.; Marra, Peter P.

    2012-01-01

    Human land cover can degrade estuaries directly through habitat loss and fragmentation or indirectly through nutrient inputs that reduce water quality. Strong precipitation events are occurring more frequently, causing greater hydrological connectivity between watersheds and estuaries. Nutrient enrichment and dissolved oxygen depletion that occur following these events are known to limit populations of benthic macroinvertebrates and commercially harvested species, but the consequences for top consumers such as birds remain largely unknown. We used non-metric multidimensional scaling (MDS) and structural equation modeling (SEM) to understand how land cover and annual variation in rainfall interact to shape waterbird community composition in Chesapeake Bay, USA. The MDS ordination indicated that urban subestuaries shifted from a mixed generalist-specialist community in 2002, a year of severe drought, to generalist-dominated community in 2003, of year of high rainfall. The SEM revealed that this change was concurrent with a sixfold increase in nitrate-N concentration in subestuaries. In the drought year of 2002, waterbird community composition depended only on the direct effect of urban development in watersheds. In the wet year of 2003, community composition depended both on this direct effect and on indirect effects associated with high nitrate-N inputs to northern parts of the Bay, particularly in urban subestuaries. Our findings suggest that increased runoff during periods of high rainfall can depress water quality enough to alter the composition of estuarine waterbird communities, and that this effect is compounded in subestuaries dominated by urban development. Estuarine restoration programs often chart progress by monitoring stressors and indicators, but rarely assess multivariate relationships among them. Estuarine management planning could be improved by tracking the structure of relationships among land cover, water quality, and waterbirds. Unraveling these

  2. Plant community responses to long-term fertilization: changes in functional group abundance drive changes in species richness.

    PubMed

    Dickson, Timothy L; Gross, Katherine L

    2013-12-01

    Declines in species richness due to fertilization are typically rapid and associated with increases in aboveground production. However, in a long-term experiment examining the impacts of fertilization in an early successional community, we found it took 14 years for plant species richness to significantly decline in fertilized plots, despite fertilization causing a rapid increase in aboveground production. To determine what accounted for this lag in the species richness response, we examined several potential mechanisms. We found evidence suggesting the abundance of one functional group-tall species with long-distance (runner) clonality-drove changes in species richness, and we found little support for other mechanisms. Tall runner species initially increased in abundance due to fertilization, then declined dramatically and were not abundant again until later in the experiment, when species richness and the combined biomass of all other functional groups (non-tall runner) declined. Over 86 % of the species found throughout the course of our study are non-tall runner, and there is a strong negative relationship between non-tall runner and tall runner biomass. We therefore suggest that declines in species richness in the fertilized treatment are due to high tall runner abundance that decreases the abundance and richness of non-tall runner species. By identifying the functional group that drives declines in richness due to fertilization, our results help to elucidate how fertilization decreases plant richness and also suggest that declines in richness due to fertilization can be lessened by controlling the abundance of species with a tall runner growth form.

  3. Distribution and abundance of sea urchins in Singapore reefs and their potential ecological impacts on macroalgae and coral communities

    NASA Astrophysics Data System (ADS)

    Goh, Beverly P. L.; Lim, Dawn Y. F.

    2015-06-01

    The sea urchin Diadema setosum is often encountered in the coral reefs in the Southern Islands of Singapore. While sea urchins have been known to play a role in regulating algal communities and influencing coral recruitment in other parts of the world, their role in Singapore reefs has not been determined. This study was conducted to determine the distribution and abundance of sea urchins in Singapore reefs, to examine algal cover, algal biomass, algal species and live coral cover, and to determine any interactions between urchin density and algal communities that may impact coral cover. Several reefs in Singapore were surveyed using belt transects measuring 20 m by 2 m, laid down on the reef crest. Abundance of urchins, algal species, biomass, and live coral cover were determined by the use of quadrats within each belt transect. This study revealed an increasing abundance of the sea urchin Diadema setosum in reefs progressing southwards away from mainland Singapore with low density of urchins occurring in Sisters' Island, St John's Island, Pulau Tekukor, and Kusu Island, and the highest density observed at Raffles Lighthouse. A significant negative linear relationship between algal cover and live coral cover (P < 0.05) was established. The results of this study indicate that sea urchins may not be an important component of the herbivore guild in Singapore.

  4. Microbial response to a mesoscale iron enrichment in the NE Subarctic Pacific: Bacterial community composition

    NASA Astrophysics Data System (ADS)

    Agawin, Nona S. R.; Hale, Michelle S.; Rivkin, Richard B.; Matthews, Paul; Li, William K. W.

    2006-10-01

    Changes in microbial community composition were determined during the subarctic ecosystem response to iron enrichment study (SERIES), a mesoscale Fe enrichment conducted in a high-nutrient low-chlorophyll (HNLC) region of the Northeast Subarctic Pacific, in July 2002. Phylogenetic composition using fluorescence in situ hybridization (FISH), relative DNA content using flow cytometry (FCM), and cellular morphometrics (shape and volume) of heterotrophic bacteria were used to characterize community composition from samples collected within and below the mixed layer, inside and outside the Fe-patch. The proportion of total cells detected as members of the Cytophaga-Flavobacterium cluster increased in a log-linear manner from 16 (±1.0)% to 47 (±1.9)% in samples within the mixed layer, inside the Fe-enriched patch, while outside the patch, the proportion remained ⩽21 (±2.2)%. Temporal changes in the proportion of cells in the mixed layer with high DNA content (% HDNA) were significantly different inside and outside the Fe-enriched patch, where inside the patch % HDNA increased 2-fold after a week, reaching 93% towards the end of the observation period. Coupling in situ observations with the results of manipulation experiments allowed us to determine the relative contributions of bottom-up (nutrient limitation) and top-down (grazing) processes on heterotrophic bacterial abundance and community composition. Shifts in heterotrophic bacterial community composition inside the Fe-enriched patch were mainly controlled by top-down processes and moderately controlled by bottom-up controls (organic substrate limitation).

  5. Seed bank and big sagebrush plant community composition in a range margin for big sagebrush

    USGS Publications Warehouse

    Martyn, Trace E.; Bradford, John B.; Schlaepfer, Daniel R.; Burke, Ingrid C.; Laurenroth, William K.

    2016-01-01

    The potential influence of seed bank composition on range shifts of species due to climate change is unclear. Seed banks can provide a means of both species persistence in an area and local range expansion in the case of increasing habitat suitability, as may occur under future climate change. However, a mismatch between the seed bank and the established plant community may represent an obstacle to persistence and expansion. In big sagebrush (Artemisia tridentata) plant communities in Montana, USA, we compared the seed bank to the established plant community. There was less than a 20% similarity in the relative abundance of species between the established plant community and the seed bank. This difference was primarily driven by an overrepresentation of native annual forbs and an underrepresentation of big sagebrush in the seed bank compared to the established plant community. Even though we expect an increase in habitat suitability for big sagebrush under future climate conditions at our sites, the current mismatch between the plant community and the seed bank could impede big sagebrush range expansion into increasingly suitable habitat in the future.

  6. From source to filter: changes in bacterial community composition during potable water treatment.

    PubMed

    Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

    2017-03-06

    Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of two rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of sections through a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although the abundance of Mycobacterium was high, and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

  7. Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil.

    PubMed

    Frenk, Sammy; Dag, Arnon; Yermiyahu, Uri; Zipori, Isaac; Hadar, Yitzhak; Minz, Dror

    2015-09-01

    Several anthropogenic interventions, common in agriculture, may influence active bacterial communities in soil without affecting their total composition. Therefore, the composition of an active bacterial community in soil may reflect its relation to biogeochemical processes. This issue was addressed during two consecutive years in olive-orchard soil, irrigated with treated wastewater (TWW) in a Mediterranean climate, by following the active (rRNA) and total (rRNA gene) bacterial community in the soil. Although TWW irrigation did not affect the composition of the total soil bacterial community, it had an effect on the active fraction of the community. These results, based on 16S rRNA data, indicate that the organic matter and minerals in TWW were not directly utilized for the rapid proliferation of specific taxonomic groups. Activity levels, manifested by variance in the relative abundance of the active and total communities of selected operational taxonomic units, revealed annual and seasonal fluctuations and fluctuations dependent on the type of irrigation. The potential activity (nitrification rates) and community composition of ammonia-oxidizing bacteria were affected by TWW irrigation, and this group of bacteria was therefore further explored. It was concluded that irrigation with TWW had little effect on "who is there", i.e. which bacteria were present, but influenced "who is active", with a distinct effect on bacteria associated with the biochemical cycling of nitrogen.

  8. Controls of picophytoplankton abundance and composition in a highly dynamic marine system, the Northern Alboran Sea (Western Mediterranean)

    NASA Astrophysics Data System (ADS)

    Amorim, Ana L.; León, Pablo; Mercado, Jesús M.; Cortés, Dolores; Gómez, Francisco; Putzeys, Sebastien; Salles, Soluna; Yebra, Lidia

    2016-06-01

    The Alboran Sea is a highly dynamic basin which exhibits a high spatio-temporal variability of hydrographic structures (e.g. fronts, gyres, coastal upwellings). This work compares the abundance and composition of picophytoplankton observed across the northern Alboran Sea among eleven cruises between 2008 and 2012 using flow cytometry. We evaluate the seasonal and longitudinal variability of picophytoplankton on the basis of the circulation regimes at a regional scale and explore the presence of cyanobacteria ecotypes in the basin. The maximal abundances obtained for Prochlorococcus, Synechococcus and picoeukaryotes (12.7 × 104, 13.9 × 104 and 8.6 × 104 cells mL- 1 respectively) were consistent with those reported for other adjacent marine areas. Seasonal changes in the abundance of the three picophytoplankton groups were highly significant although they did not match the patterns described for other coastal waters. Higher abundances of Prochlorococcus were obtained in autumn-winter while Synechococcus and picoeukaryotes exhibited a different seasonal abundance pattern depending on the sector (e.g. Synechococcus showed higher abundance in summer in the west sector and during winter in the eastern study area). Additionally, conspicuous longitudinal gradients were observed for Prochlorococcus and Synechococcus, with Prochlorococcus decreasing from west to east and Synechococcus following the opposite pattern. The analysis of environmental variables (i.e. temperature, salinity and inorganic nutrients) and cell abundances indicates that Prochlorococcus preferred high salinity and nitrate to phosphate ratio. On the contrary, temperature did not seem to play a role in Prochlorococcus distribution as it was numerically important during the whole seasonal cycle. Variability in Synechococcus abundance could not be explained by changes in any environmental variable suggesting that different ecotypes were sampled during the surveys. In particular, our data would indicate

  9. Effects of a Nonnative, Invasive Lovegrass on Agave palmeri Distribution, Abundance, and Insect Pollinator Communities

    DTIC Science & Technology

    2010-05-01

    could alter A. palmeri germination , growth, abundance, and resource availability and foraging behavior of pollinators (Geiger 2006; Gucker 2006...fied per site, and size class was calculated by measuring the average diameter of each living A. palmeri using a standard measuring tape . Diameter

  10. Influence of environmental variables on the structure and composition of soil bacterial communities in natural and constructed wetlands.

    PubMed

    Arroyo, Paula; Sáenz de Miera, Luis E; Ansola, Gemma

    2015-02-15

    Bacteria are key players in wetland ecosystems, however many essential aspects regarding the ecology of wetland bacterial communities remain unknown. The present study characterizes soil bacterial communities from natural and constructed wetlands through the pyrosequencing of 16S rDNA genes in order to evaluate the influence of wetland variables on bacterial community composition and structure. The results show that the composition of soil bacterial communities was significantly associated with the wetland type (natural or constructed wetland), the type of environment (lagoon, Typha or Salix) and three continuous parameters (SOM, COD and TKN). However, no clear associations were observed with soil pH. Bacterial diversity values were significantly lower in the constructed wetland with the highest inlet nutrient concentrations. The abundances of particular metabolic groups were also related to wetland characteristics.

  11. Prokaryotic community composition revealed by denaturing gradient gel electrophoresis in the East Sea

    NASA Astrophysics Data System (ADS)

    Jang, Gwang Il; Choi, Dong Han

    2015-12-01

    To understand the temporal and spatial variation of the prokaryotic community in the East Sea, their composition was determined by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE)-sequencing techniques. The investigations were conducted twice annually in 2007 and 2009 in coastal and offshore stations. Prokaryotic abundance (PA), leucine incorporation rate, and other environmental parameters were also measured. By using the DGGE approach, we obtained 283 bacterial sequences and 160 archaeal sequences. The most frequently detected bacterial phylotypes during the investigations belonged to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. However, their relative compositions differed in time and space. Although Alphaproteobacteria and Bacteroidetes were the dominant groups in the surface water in May 2007 and in May and October 2007, Gammaproteobacteria was dominant in mesopelagic samples. However, Gammaproteobacteria was overwhelmingly dominant in most samples in August 2009. Although Deltaproteobacteria was rarely found as a dominant bacterial group, it occupied the highest fraction in a mesopelagic sample in October 2007. Epsilonproteobacteria also showed a similar trend, although its maximal dominance was found in a mesopelagic sample in August 2009. The archaeal community was dominated overwhelmingly by members of the Euryarchaeota in most of the investigations. However, Nitrosopumilales was dominant in aphotic samples in August 2009. Further, their spatiotemporal composition at the family level changed more dynamically in the East Sea. These temporal and spatial distributions of the prokaryotic community were influenced mainly by seawater temperature and depth in the East Sea.

  12. Seasonal variation in species composition and abundance of demersal fish and invertebrates in a Seagrass Natural Reserve on the eastern coast of the Shandong Peninsula, China

    NASA Astrophysics Data System (ADS)

    Xu, Qiang; Guo, Dong; Zhang, Peidong; Zhang, Xiumei; Li, Wentao; Wu, Zhongxin

    2016-03-01

    Seagrass habitats are structurally complex ecosystems, which support high productivity and biodiversity. In temperate systems the density of seagrass may change seasonally, and this may influence the associated fish and invertebrate community. Little is known about the role of seagrass beds as possible nursery areas for fish and invertebrates in China. To study the functioning of a seagrass habitat in northern China, demersal fish and invertebrates were collected monthly using traps, from February 2009 to January 2010. The density, leaf length and biomass of the dominant seagrass Zostera marina and water temperature were also measured. The study was conducted in a Seagrass Natural Reserve (SNR) on the eastern coast of the Shandong Peninsula, China. A total of 22 fish species and five invertebrate species were recorded over the year. The dominant fish species were Synechogobius ommaturus, Sebastes schlegelii, Pholis fangi, Pagrus major and Hexagrammos otakii and these species accounted for 87% of the total number of fish. The dominant invertebrate species were Charybdis japonica and Octopus variabilis and these accounted for 98% of the total abundance of invertebrates. There was high temporal variation in species composition and abundance. The peak number of fish species occurred in August-October 2009, while the number of individual fish and biomass was highest during November 2009. Invertebrate numbers and biomass was highest in March, April, July and September 2009. Temporal changes in species abundance of fishes and invertebrates corresponded with changes in the shoot density and leaf length of the seagrass, Zostera marina.

  13. Absolute isotopic composition of molybdenum and the solar abundances of the p-process nuclides Mo92,94

    NASA Astrophysics Data System (ADS)

    Wieser, M. E.; de Laeter, J. R.

    2007-05-01

    The isotopic composition of molybdenum has been measured with high precision using a thermal ionization mass spectrometer, the linearity of which has been verified by measuring the isotopically-certified reference material for strontium (NIST 987). The abundance sensitivity of the mass spectrometer in the vicinity of the molybdenum ion beams has been carefully examined to ensure the absence of tailing effects. Particular care was given to ensuring that potential isobaric interferences from zirconium and ruthenium did not affect the measurement of the isotopic composition of molybdenum. Gravimetric mixtures of two isotopically enriched isotopes, Mo92 and Mo98, were analyzed mass spectrometrically to calibrate the mass spectrometer, in order to establish the isotope fractionation of the spectrometer for the molybdenum isotopes. This enabled the “absolute” isotopic composition of molybdenum to be determined. An accurate determination of the isotopic composition is required in order to calculate the atomic weight of molybdenum, which is one of the least accurately known values of all the elements. The absolute isotope abundances (in atom %) of molybdenum measured in this experiment are as follows: Mo92=14.5246±0.0015; Mo94=9.1514±0.0074; Mo95=15.8375±0.0098; Mo96=16.672±0.019; Mo97=9.5991±0.0073; Mo98=24.391±0.018; and Mo100=9.824±0.050, with uncertainties at the 1s level. These values enable an atomic weight Ar(Mo) of 95.9602±0.0023 (1s) to be calculated, which is slightly higher than the current Standard Atomic Weight Ar(Mo) =95.94±0.02 and with a much improved uncertainty interval. These “absolute” isotope abundances also enable the Solar System abundances of molybdenum to be calculated for astrophysical purposes. Of particular interest are the Solar System abundances of the two p-process nuclides—Mo92 and Mo94, which are present in far greater abundance than p-process theory suggests. The Solar System abundances for Mo92 and Mo94 of 0.364±0

  14. Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

    PubMed

    Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

    2013-07-01

    Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks.

  15. Vertical changes in abundance, biomass and community structure of copepods down to 3000 m in the southern Bering Sea

    NASA Astrophysics Data System (ADS)

    Homma, Tomoe; Yamaguchi, Atsushi

    2010-08-01

    Vertical changes in abundance, biomass and community structure of copepods down to 3000 m depth were studied at a single station of the Aleutian Basin of the Bering Sea (53°28'N, 177°00'W, depth 3779 m) on the 14th June 2006. Both abundance and biomass of copepods were greatest near the surface layer and decreased with increase in depth. Abundance and biomass of copepods integrated over 0-3000 m were 1,390,000 inds. m -2 and 5056 mg C m -2, respectively. Copepod carcasses occurred throughout the layer, and the carcass:living specimen ratio was the greatest in the oxygen minimum layer (750-100 m, the ratio was 2.3). A total of 72 calanoid copepod species belonging to 34 genera and 15 families occurred in the 0-3000 m water column (Cyclopoida, Harpacticoida and Poecilostomatoida were not identified to species level). Cluster analysis separated calanoid copepod communities into 5 groups (A-E). Each group was separated by depth, and the depth range of each group was at 0-75 m (A), 75-500 m (B), 500-750 m (C), 750-1500 m (D) and 1500-3000 m (E). Copepods were divided into four types based on the feeding pattern: suspension feeders, suspension feeders in diapause, detritivores and carnivores. In terms of abundance the most dominant group was suspension feeders (mainly Cyclopoida) in the epipelagic zone, and detritivores (mainly Poecilostomatoida) were dominant in the meso- and bathypelagic zones. In terms of biomass, suspension feeders in diapause (calanoid copepods Neocalanus spp. and Eucalanus bungii) were the major component (ca. 10-45%), especially in the 250-3000 m depth. These results are compared with the previous studies in the same region and that down to greater depths in the worldwide oceans.

  16. Abundance and community of snow bacteria from three glaciers in the Tibetan Plateau.

    PubMed

    Zhang, Shuhong; Yang, Guangli; Wang, Yetang; Hou, Shugui

    2010-01-01

    Bacterial abundance and diversity in snow of East Rongbuk, Laohugou and Hailuogou glaciers on the Tibetan Plateau were investigated through epifluorescence microscope and denaturing gradient gel electrophoresis. Cell abundance ranged from 4.0 x 10(3) to 290.2 x 10(3) cells/mL. The phylogenetic trees placed the 16S rRNA sequences in four major groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Brevundimonas, Flavobacterium, Hymenobacter, Bacillus, Polaromonas, Rhodoferax and Streptomyces were widely distributed bacteria in glaciers from different cold regions. The remaining five genera of Hylemonella, Delftia, Zoogloea, Blastococcus and Rhodococcus were endemism, only recovered from our investigated glaciers. It is proposed that the three glaciers on the Tibetan Plateau provide a specific ecological niche for prolonging survival of diverse microbial lineages.

  17. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments

    PubMed Central

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L−1 (200 NH4+-N) and 400 mg NH4+-N L−1 (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater. PMID:26444015

  18. The Significance of Myriophyllum elatinoides for Swine Wastewater Treatment: Abundance and Community Structure of Ammonia-Oxidizing Microorganisms in Sediments.

    PubMed

    Li, Xi; Zhang, Miaomiao; Liu, Feng; Li, Yong; He, Yang; Zhang, Shunan; Wu, Jinshui

    2015-01-01

    Myriophyllum elatinoides was reported to effectively treat wastewater by removing nitrogen (N) and phosphorus (P). However, little is known about the abundance and community structure of ammonia-oxidizing microorganisms associated with M. elatinoides purification systems. The objective of this research was to characterize the abundance and community structure of ammonia-oxidizing microorganisms in swine wastewater and determine the main nitrogen removal pathways. In this study, five different waters were treated by M. elatinoides in microcosms for one month. The five waters included tap water (Control), swine wastewater (SW), 50% diluted swine wastewater (50% SW), and two synthetic wastewaters: 200 mg NH4+-N L(-1) (200 NH4+-N) and 400 mg NH4+-N L(-1) (400 NH4+-N). The most dramatic changes were in NH4+-N and total N (TN) concentrations, with average removal rates of 84% and 90%, respectively, in the treatments containing swine wastewater. On days 7, 14, and 28, the dissolved oxygen (DO) increased by 81.8%, 210.4% and 136.5%, respectively, compared with on day 0, in the swine wastewater. The results also showed that the bacterial amoA (AOB) copy numbers in the sediments of the treatments were significantly higher than those of archaeal amoA (AOA) copy numbers (p = 0.015). In addition, the high DO concentrations in swine wastewater responded well to the high abundance of AOB. The AOA and AOB community distributions were positively related with NO3-N and were negatively related with DO in swine wastewater treatments. In summary, our experimental results suggested that the M. elatinoides purification system could improve the activity of ammonia-oxidizing microorganisms and consequently might contribute to the significant N removal from the swine wastewater.

  19. Deoxygenation alters bacterial diversity and community composition in the ocean’s largest oxygen minimum zone

    NASA Astrophysics Data System (ADS)

    Beman, J. Michael; Carolan, Molly T.

    2013-10-01

    Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans’ largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

  20. Deoxygenation alters bacterial diversity and community composition in the ocean's largest oxygen minimum zone.

    PubMed

    Beman, J Michael; Carolan, Molly T

    2013-01-01

    Oceanic oxygen minimum zones (OMZs) have a central role in biogeochemical cycles and are expanding as a consequence of climate change, yet how deoxygenation will affect the microbial communities that control these cycles is unclear. Here we sample across dissolved oxygen gradients in the oceans' largest OMZ and show that bacterial richness displays a unimodal pattern with decreasing dissolved oxygen, reaching maximum values on the edge of the OMZ and decreasing within it. Rare groups on the OMZ margin are abundant at lower dissolved oxygen concentrations, including sulphur-cycling Chromatiales, for which 16S rRNA was amplified from extracted RNA. Microbial species distribution models accurately replicate community patterns based on multivariate environmental data, demonstrate likely changes in distributions and diversity in the eastern tropical North Pacific Ocean, and highlight the sensitivity of key bacterial groups to deoxygenation. Through these mechanisms, OMZ expansion may alter microbial composition, competition, diversity and function, all of which have implications for biogeochemical cycling in OMZs.

  1. Ant community composition across a gradient of disturbed military landscapes at Fort Benning, Georgia

    USGS Publications Warehouse

    Graham, J.H.; Krzysik, A.J.; Kovacic, D.A.; Duda, J.J.; Freeman, D.C.; Emlen, J.M.; Zak, J.C.; Long, W.R.; Wallace, M.P.; Chamberlin-Graham, C.; Nutter, J.P.; Balbach, H.E.

    2008-01-01

    Military training, soil texture, and ground cover influence ant communities at Fort Benning, a military installation in west-central Georgia. We sampled 81,237 ground-dwelling ants (47 species in 20 genera) with pitfall traps at 40 sites on a continuum from nearly pristine forest to highly disturbed training areas. We also measured 15 environmental variables related to vegetation and soil. Sites disturbed by military training had fewer trees, less canopy cover, more bare ground, and more compact soils with shallower A-horizons than comparable undisturbed sites. Pheidole bicarinata, Dorymyrmex smithi, and Pogonomyrmex badius dominated the most highly disturbed sites. Competitively submissive myrmicines, such as Aphaenogaster and Crematogaster, and formicines, such as Camponotus and Formica, were abundant in the undisturbed sites. Solenopsis invicta occurred in all but the least disturbed sites. Ant community composition was a useful indicator of disturbance at Fort Benning.

  2. Comparison of zooplankton abundance and community in seagrass and non-seagrass areas of Merambong shoal

    NASA Astrophysics Data System (ADS)

    Azmi, Afiq Auji; Yoshida, Teruaki; Toda, Tatsuki; Ross, Othman bin Haji; Cob, Zaidi Che

    2016-11-01

    A zooplankton comparison study of Merambong shoal's seagrass and non-seagrass area was conducted from April 2013 to October 2014. Sampling was conducted monthly at fixed stations by horizontal tows of a 140 µm plankton net. Mean temperature was significantly higher during the south-west (SW) monsoon at both stations. Salinity and Chlorophyll a concentrations were not significantly different between the monsoons for both stations. However, Chlorophyll a concentrations were significantly higher in the seagrass compared to non-seagrass station. Mean zooplankton abundance was 1.32-fold higher in the non-seagrass area (4006.5±1990.5 ind/mł) than the seagrass area (3030.1± 855.6 ind/mł), despite overall higher Chlorophyll a levels in the seagrass station. At the seagrass station, the dominant copepods Paracalanus and Parvocalanus abundances were significantly higher (p<0.01, Mann-Whitney) during the SW monsoon, while Euterpina was significantly lower (p<0.04, Mann-Whitney). The non-seagrass station also showed a similar trend where the dominant copepods Paracalanus and Parvocalanus abundances were significantly higher in the SW monsoon (p<0.02, Mann-Whitney). Higher percentage of meroplankton was recorded during the study period in seagrass area with 11.6 %, 1.5 fold of non-seagrass area.

  3. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture.

    PubMed Central

    González, J M; Whitman, W B; Hodson, R E; Moran, M A

    1996-01-01

    Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the alpha-subclass of Proteobacteria, and the other two were in the gamma-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented. PMID:8953714

  4. Plant community composition promotes multiple ecosystem functions in grassland at low and high soil fertility

    NASA Astrophysics Data System (ADS)

    de Deyn, Gerlinde; Ostle, Nick; Bardgett, Richard

    2010-05-01

    It is well known that plant species richness can enhance primary productivity through complementarity in resource use by component plant species. Fewer studies have explored the role of plant species diversity and composition for the delivery of other ecosystem services than primary production and its dependency on resource availability. In this study we investigated how carbon (C) and nitrogen (N) stocks in vegetation, soil and soil microbes, the loss of C and N from soil through leaching and ecosystem exchange rates of CO2 are affected by the composition and richness of grassland plant communities and soil fertility. We used two soils of contrasting fertility in which we planted plant communities using a pool of six plant species from one of three functional groups (legumes, forbs and C3 grasses). The levels of plant species richness were one, two, three or six species and were composed of one, two or three functional groups. Soil fertility stimulated pools of C and N in shoots and roots, and the soil microbial biomass, but also increased significantly with increased plant functional group and plant species richness. Moreover, plant diversity suppressed N and water loss via soil leaching. We also found changes in the C and N content in soil, but these were not related to the richness of plant species or functional groups. The changes in soil were rather specifically due to the abundance of the legumes. The leaching of water and N was related negative to plant species richness but also specifically to the abundance of the forb species. Our findings show that the relation between plant community composition and storage of C and N in vegetation is not directly reflected in the changes in C and N storage in soil. These soil based storage functions, and the leaching of N from soil, appeared to be most strongly related to different key plant species. Together these results indicate that the maintenance of plant diversity is important to sustain the multiple functions

  5. Plant community composition and vegetation height, Barrow, Alaska, Ver. 1

    DOE Data Explorer

    Sloan, Victoria; Norby, Richard; Siegrist, Julia; Iversen, Colleen; Brooks, Jonathan; Liebig, Jennifer; Wood, Sarah

    2014-04-25

    This dataset contains i) the results of field surveys of plant community composition and vegetation height made between 17th and 29th July 2012 in 48, 1 x 1 m plots located in areas A-D of Intensive Site 1 at the Next-Generation Ecosystem Experiments (NGEE) Arctic site near Barrow, Alaska and ii) results of a mapping exercise undertaken in August 2013 using two perpendicular transects across each polygon containing vegetation plots to determine the boundaries of vegetation communities described in 2012.

  6. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community.

    PubMed

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  7. Dynamic relationships between body size, species richness, abundance, and energy use in a shallow marine epibenthic faunal community

    PubMed Central

    Labra, Fabio A; Hernández-Miranda, Eduardo; Quiñones, Renato A

    2015-01-01

    We study the temporal variation in the empirical relationships among body size (S), species richness (R), and abundance (A) in a shallow marine epibenthic faunal community in Coliumo Bay, Chile. We also extend previous analyses by calculating individual energy use (E) and test whether its bivariate and trivariate relationships with S and R are in agreement with expectations derived from the energetic equivalence rule. Carnivorous and scavenger species representing over 95% of sample abundance and biomass were studied. For each individual, body size (g) was measured and E was estimated following published allometric relationships. Data for each sample were tabulated into exponential body size bins, comparing species-averaged values with individual-based estimates which allow species to potentially occupy multiple size classes. For individual-based data, both the number of individuals and species across body size classes are fit by a Weibull function rather than by a power law scaling. Species richness is also a power law of the number of individuals. Energy use shows a piecewise scaling relationship with body size, with energetic equivalence holding true only for size classes above the modal abundance class. Species-based data showed either weak linear or no significant patterns, likely due to the decrease in the number of data points across body size classes. Hence, for individual-based size spectra, the SRA relationship seems to be general despite seasonal forcing and strong disturbances in Coliumo Bay. The unimodal abundance distribution results in a piecewise energy scaling relationship, with small individuals showing a positive scaling and large individuals showing energetic equivalence. Hence, strict energetic equivalence should not be expected for unimodal abundance distributions. On the other hand, while species-based data do not show unimodal SRA relationships, energy use across body size classes did not show significant trends, supporting energetic

  8. Impacts of poultry house environment on poultry litter bacterial community composition.

    PubMed

    Dumas, Michael D; Polson, Shawn W; Ritter, Don; Ravel, Jacques; Gelb, Jack; Morgan, Robin; Wommack, K Eric

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.

  9. Impacts of Poultry House Environment on Poultry Litter Bacterial Community Composition

    PubMed Central

    Dumas, Michael D.; Polson, Shawn W.; Ritter, Don; Ravel, Jacques; Gelb, Jack; Morgan, Robin; Wommack, K. Eric

    2011-01-01

    Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly Gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens. PMID:21949751

  10. Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

    PubMed Central

    Fan, Xianfang; Xing, Peng

    2016-01-01

    In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats. PMID:27708641

  11. Cyanobacteria drive community composition and functionality in rock-soil interface communities.

    PubMed

    Valverde, Angel; Makhalanyane, Thulani P; Seely, Mary; Cowan, Don A

    2015-02-01

    Most ecological research on hypoliths, significant primary producers in hyperarid deserts, has focused on the diversity of individual groups of microbes (i.e. bacteria). However, microbial communities are inherently complex, and the interactions between cyanobacteria, heterotrophic bacteria, protista and metazoa are likely to be very important for ecosystem functioning. Cyanobacterial and heterotrophic bacterial communities were analysed by pyrosequencing, while metazoan and protistan communities were assessed by T-RFLP analysis. Microbial functionality was estimated using carbon substrate utilization. Cyanobacterial community composition was significant in shaping community structure and function in hypoliths. Ecological network analysis showed that most significant co-occurrences were positive, representing potential synergistic interactions. There were several highly interconnected associations (modules), and specific cyanobacteria were important in driving the modular structure of hypolithic networks. Together, our results suggest that hypolithic cyanobacteria have strong effects on higher trophic levels and ecosystem functioning.

  12. Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils

    PubMed Central

    Herzog, Sarah; Wemheuer, Franziska; Wemheuer, Bernd; Daniel, Rolf

    2015-01-01

    Soil bacteria are major players in driving and regulating ecosystem processes. Thus, the identification of factors shaping the diversity and structure of these communities is crucial for understanding bacterial-mediated processes such as nutrient transformation and cycling. As most studies only target the entire soil bacterial community, the response of active community members to environmental changes is still poorly understood. The objective of this study was to investigate the effect of fertilizer application and sampling time on structure and diversity of potentially active (RNA-based) and the entire (DNA-based) bacterial communities in German grassland soils. Analysis of more than 2.3 million 16S rRNA transcripts and gene sequences derived from amplicon-based sequencing of 16S rRNA genes revealed that fertilizer application and sampling time significantly altered the diversity and composition of entire and active bacterial communities. Although the composition of both the entire and the active bacterial community was correlated with environmental factors such as pH or C/N ratio, the active community showed a higher sensitivity to environmental changes than the entire community. In addition, functional analyses were performed based on predictions derived from 16S rRNA data. Genes encoding the uptake of nitrate/nitrite, nitrification, and denitrification were significantly more abundant in fertilized plots compared to non-fertilized plots. Hence, this study provided novel insights into changes in dynamics and functions of soil bacterial communities as response to season and fertilizer application. PMID:26694644

  13. Richness and Composition of Niche-Assembled Viral Pathogen Communities

    PubMed Central

    Seabloom, Eric W.; Borer, Elizabeth T.; Lacroix, Christelle; Mitchell, Charles E.; Power, Alison G.

    2013-01-01

    The pathogen and parasite community that inhabits every free-living organism can control host vital rates including lifespan and reproductive output. To date, however, there have been few experiments examining pathogen community assembly replicated at large-enough spatial scales to inform our understanding of pathogen dynamics in natural systems. Pathogen community assembly may be driven by neutral stochastic colonization and extinction events or by niche differentiation that constrains pathogen distributions to particular environmental conditions, hosts, or vectors. Here, we present results from a regionally-replicated experiment investigating the community of barley and cereal yellow dwarf viruses (B/CYDV's) in over 5000 experimentally planted individuals of six grass species along a 700 km latitudinal gradient along the Pacific coast of North America (USA) in response to experimentally manipulated nitrogen and phosphorus supplies. The composition of the virus community varied predictably among hosts and across nutrient-addition treatments, indicating niche differentiation among virus species. There were some concordant responses among the viral species. For example, the prevalence of most viral species increased consistently with perennial grass cover, leading to a 60% increase in the richness of the viral community within individual hosts (i.e., coinfection) in perennial-dominated plots. Furthermore, infection rates of the six host species in the field were highly correlated with vector preferences assessed in laboratory trials. Our results reveal the importance of niche differentiation in structuring virus assemblages. Virus species distributions reflected a combination of local host community composition, host species-specific vector preferences, and virus responses to host nutrition. In addition, our results suggest that heterogeneity among host species in their capacity to attract vectors or support pathogens between growing seasons can lead to positive

  14. Spatio-temporal variability of airborne bacterial communities and their correlation with particulate matter chemical composition across two urban areas.

    PubMed

    Gandolfi, I; Bertolini, V; Bestetti, G; Ambrosini, R; Innocente, E; Rampazzo, G; Papacchini, M; Franzetti, A

    2015-06-01

    The study of spatio-temporal variability of airborne bacterial communities has recently gained importance due to the evidence that airborne bacteria are involved in atmospheric processes and can affect human health. In this work, we described the structure of airborne microbial communities in two urban areas (Milan and Venice, Northern Italy) through the sequencing, by the Illumina platform, of libraries containing the V5-V6 hypervariable regions of the 16S rRNA gene and estimated the abundance of airborne bacteria with quantitative PCR (qPCR). Airborne microbial communities were dominated by few taxa, particularly Burkholderiales and Actinomycetales, more abundant in colder seasons, and Chloroplasts, more abundant in warmer seasons. By partitioning the variation in bacterial community structure, we could assess that environmental and meteorological conditions, including variability between cities and seasons, were the major determinants of the observed variation in bacterial community structure, while chemical composition of atmospheric particulate matter (PM) had a minor contribution. Particularly, Ba, SO4 (2-) and Mg(2+) concentrations were significantly correlated with microbial community structure, but it was not possible to assess whether they simply co-varied with seasonal shifts of bacterial inputs to the atmosphere, or their variation favoured specific taxa. Both local sources of bacteria and atmospheric dispersal were involved in the assembling of airborne microbial communities, as suggested, to the one side by the large abundance of bacteria typical of lagoon environments (Rhodobacterales) observed in spring air samples from Venice and to the other by the significant effect of wind speed in shaping airborne bacterial communities at all sites.

  15. Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea

    PubMed Central

    Herlemann, Daniel P. R.; Lundin, Daniel; Andersson, Anders F.; Labrenz, Matthias; Jürgens, Klaus

    2016-01-01

    Understanding the key processes that control bacterial community composition has enabled predictions of bacterial distribution and function within ecosystems. In this study, we used the Baltic Sea as a model system to quantify the phylogenetic signal of salinity and season with respect to bacterioplankton community composition. The abundances of 16S rRNA gene amplicon sequencing reads were analyzed from samples obtained from similar geographic locations in July and February along a brackish to marine salinity gradient in the Baltic Sea. While there was no distinct pattern of bacterial richness at different salinities, the number of bacterial phylotypes in winter was significantly higher than in summer. Bacterial community composition in brackish vs. marine conditions, and in July vs. February was significantly different. Non-metric multidimensional scaling showed that bacterial community composition was primarily separated according to salinity and secondly according to seasonal differences at all taxonomic ranks tested. Similarly, quantitative phylogenetic clustering implicated a phylogenetic signal for both salinity and seasonality. Our results suggest that global patterns of bacterial community composition with respect to salinity and season are the result of phylogenetically clustered ecological preferences with stronger imprints from salinity. PMID:27933046

  16. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

    PubMed

    Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

    2015-01-01

    Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy.

  17. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-12-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

  18. Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

    PubMed Central

    Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

    2016-01-01

    Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing. PMID:27934957

  19. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments.

    PubMed

    Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

    2017-01-01

    Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios.

  20. Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

    PubMed Central

    Hoffmann, Katy; Hassenrück, Christiane; Salman-Carvalho, Verena; Holtappels, Moritz; Bienhold, Christina

    2017-01-01

    Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor, an important feedback mechanism to be considered in future climate change scenarios. PMID:28286496

  1. Heavy metal immobilization and microbial community abundance by vegetable waste and pine cone biochar of agricultural soils.

    PubMed

    Igalavithana, Avanthi Deshani; Lee, Sung-Eun; Lee, Young Han; Tsang, Daniel C W; Rinklebe, Jörg; Kwon, Eilhann E; Ok, Yong Sik

    2017-05-01

    In order to determine the efficacy of vegetable waste and pine cone biochar for immobilization of metal/metalloid (lead and arsenic) and abundance of microbial community in different agricultural soils, we applied the biochar produced at two different temperatures to two contaminated soils. Biochar was produced by vegetable waste, pine cone, and their mixture (1:1 ww(-1)) at 200 °C (torrefied biomass) and 500 °C (biochar). Contaminated soils were incubated with 5% (ww(-1)) torrefied biomass or biochar. Sequential extraction, thermodynamic modeling, and scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy were used to evaluate the metal immobilization. Microbial communities were characterized by microbial fatty acid profiles and microbial activity was assessed by dehydrogenase activity. Vegetable waste and the mixture of vegetable waste and pine cone biochar exhibited greater ability for Pb immobilization than pine cone biochar and three torrefied biomass, and vegetable waste biochar was found to be most effective. However, torrefied biomass was most effective in increasing both microbial community and dehydrogenase activity. This study confirms that vegetable waste could be a vital biomass to produce biochar to immobilize Pb, and increase the microbial communities and enzyme activity in soils. Biomass and pyrolytic temperature were not found to be effective in the immobilization of As in this study.

  2. Interplay between Senecio jacobaea and plant, soil, and aboveground insect community composition.

    PubMed

    Bezemer, T Martijn; Harvey, Jeffrey A; Kowalchuk, George A; Korpershoek, Hanna; van der Putten, Wim H

    2006-08-01

    To elucidate the factors that affect the performance of plants in their natural environment, it is essential to study interactions with other neighboring plants, as well as with above- and belowground higher trophic organisms. We used a long-term field experiment to study how local plant community diversity influenced colonization by the biennial composite Senecio jacobaea in its native range in The Netherlands in Europe. We tested the effect of sowing later-succession plant species (0, 4, or 15 species) on plant succession and S. jacobaea performance. Over a period of eight years, the percent cover of S. jacobaea was relatively low in communities sown with 15 or 4 later-succession plant species compared to plots that were not sown, but that were colonized naturally. However, after four years of high abundance, the density of S. jacobaea in unsown plots started to decline, and the size of the individual plants was smaller than in the plots sown with 15 or 4 plant species. In the unsown plots, densities of aboveground leaf-mining, flower-feeding, and stem-boring insects on S. jacobaea plants were lower than on plants in sown plots, and there was a strong positive relationship between plant size and levels of herbivory. In a greenhouse experiment, we grew S. jacobaea in sterilized soil inoculated with soil from the different sowing treatments of the field experiment. Biomass production was lower when S. jacobaea test plants were grown in soil from the unsown plots than in soil from the sown plots (4 or 15 species). Molecular analysis of the fungal and bacterial communities revealed that the composition of fungal communities in unsown plots differed significantly from those in sown plots, suggesting that soil fungi could have been involved in the relative growth reduction of S. jacobaea in the greenhouse bioassay. Our results show that, in its native habitat, the abundance of S. jacobaea depends on the initial composition of the plant community and that, on a scale of

  3. Phytoplankton Composition and Abundance in Restored Maltański Reservoir under the Influence of Physico-Chemical Variables and Zooplankton Grazing Pressure.

    PubMed

    Kozak, Anna; Gołdyn, Ryszard; Dondajewska, Renata

    2015-01-01

    In this paper we present the effects of environmental factors and zooplankton food pressure on phytoplankton in the restored man-made Maltański Reservoir (MR). Two methods of restoration: biomanipulation and phosphorus inactivation have been applied in the reservoir. Nine taxonomical groups of phytoplankton represented in total by 183 taxa were stated there. The richest groups in respect of taxa number were green algae, cyanobacteria and diatoms. The diatoms, cryptophytes, chrysophytes, cyanobacteria, green algae and euglenophytes dominated in terms of abundance and/or biomass. There were significant changes among environmental parameters resulting from restoration measures which influenced the phytoplankton populations in the reservoir. These measures led to a decrease of phosphorus concentration due to its chemical inactivation and enhanced zooplankton grazing as a result of planktivorous fish stocking. The aim of the study is to analyse the reaction of phytoplankton to the restoration measures and, most importantly, to determine the extent to which the qualitative and quantitative composition of phytoplankton depends on variables changing under the influence of restoration in comparison with other environmental variables. We stated that application of restoration methods did cause significant changes in phytoplankton community structure. The abundance of most phytoplankton taxa was negatively correlated with large zooplankton filter feeders, and positively with zooplankton predators and concentrations of ammonium nitrogen and partly of phosphates. However, restoration was insufficient in the case of decreasing phytoplankton abundance. The effects of restoration treatments were of less importance for the abundance of phytoplankton than parameters that were independent of the restoration. This was due to the continuous inflow of large loads of nutrients from the area of the river catchment.

  4. Phytoplankton Composition and Abundance in Restored Maltański Reservoir under the Influence of Physico-Chemical Variables and Zooplankton Grazing Pressure

    PubMed Central

    Kozak, Anna; Gołdyn, Ryszard; Dondajewska, Renata

    2015-01-01

    In this paper we present the effects of environmental factors and zooplankton food pressure on phytoplankton in the restored man-made Maltański Reservoir (MR). Two methods of restoration: biomanipulation and phosphorus inactivation have been applied in the reservoir. Nine taxonomical groups of phytoplankton represented in total by 183 taxa were stated there. The richest groups in respect of taxa number were green algae, cyanobacteria and diatoms. The diatoms, cryptophytes, chrysophytes, cyanobacteria, green algae and euglenophytes dominated in terms of abundance and/or biomass. There were significant changes among environmental parameters resulting from restoration measures which influenced the phytoplankton populations in the reservoir. These measures led to a decrease of phosphorus concentration due to its chemical inactivation and enhanced zooplankton grazing as a result of planktivorous fish stocking. The aim of the study is to analyse the reaction of phytoplankton to the restoration measures and, most importantly, to determine the extent to which the qualitative and quantitative composition of phytoplankton depends on variables changing under the influence of restoration in comparison with other environmental variables. We stated that application of restoration methods did cause significant changes in phytoplankton community structure. The abundance of most phytoplankton taxa was negatively correlated with large zooplankton filter feeders, and positively with zooplankton predators and concentrations of ammonium nitrogen and partly of phosphates. However, restoration was insufficient in the case of decreasing phytoplankton abundance. The effects of restoration treatments were of less importance for the abundance of phytoplankton than parameters that were independent of the restoration. This was due to the continuous inflow of large loads of nutrients from the area of the river catchment. PMID:25906352

  5. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    PubMed Central

    Reis, Mariana P.; Ávila, Marcelo P.; Keijzer, Rosalinde M.; Barbosa, Francisco A. R.; Chartone-Souza, Edmar; Nascimento, Andréa M. A.; Laanbroek, Hendrikus J.

    2015-01-01

    Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms. PMID:26379659

  6. Microbial biomass, activity and community composition in constructed wetlands.

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

    The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters.

  7. Species composition and abundance of Brevipalpus spp. on different citrus species in Mexican orchards.

    PubMed

    Salinas-Vargas, D; Santillán-Galicia, M T; Valdez-Carrasco, J; Mora-Aguilera, G; Atanacio-Serrano, Y; Romero-Pescador, P

    2013-08-01

    We studied the abundance of Brevipalpus spp. in citrus orchards in the Mexican states of Yucatan, Quintana Roo and Campeche. Mites were collected from 100 trees containing a mixture of citrus species where sweet orange was always the main species. Eight collections were made at each location from February 2010 to February 2011. Mites from the genus Brevipalpus were separated from other mites surveyed and their abundance and relationships with the different citrus species were quantified throughout the collection period. A subsample of 25% of the total Brevipalpus mites collected were identified to species level and the interaction of mite species and citrus species were described. Brevipalpus spp. were present on all collection dates and their relative abundance was similar on all citrus species studies. The smallest number of mites collected was during the rainy season. Brevipalpus phoenicis (Geijskes) and Brevipalpus californicus (Banks) were the only two species present and they were found in all locations except Campeche, where only B. phoenicis was present. Yucatan and Campeche are at greater risk of leprosis virus transmission than Quintana Roo because the main vector, B. phoenicis, was more abundant than B. californicus. The implications of our results for the design of more accurate sampling and control methods for Brevipalpus spp. are discussed.

  8. The Abundance and Isotopic Composition of Water in Howardite-Eucrite-Diogenite Meteorites

    NASA Astrophysics Data System (ADS)

    Barrett, T. J.; Tartèse, R.; Anand, M.; Franchi, I. A.; Grady, M. M.; Greenwood, R. C.; Charlier, B. L. A.

    2014-09-01

    Using SIMs techniques we measure OH abundances and D/H ratios in apatite grains from two Eucrites (DaG 945, DaG 844).The average δD values of these two samples are also similar to carbonaceous chondrites, the Earth and the Moon.

  9. Abundance and composition of juvenile corals reveals divergent trajectories for coral assemblages across the United Arab Emirates.

    PubMed

    Pratchett, Morgan S; Baird, Andrew H; Bauman, Andrew G; Burt, John A

    2017-01-30

    Marked shifts in the composition of coral assemblages are occurring at many locations, but it is unknown whether these are permanent shifts reinforced by patterns of population replenishment. This study examined the composition of juvenile coral assemblages across the United Arab Emirates (UAE). Densities of juvenile corals varied significantly among locations, but were highest where coral cover was highest. Juvenile coral assemblages within the Persian Gulf were dominated by Porites, while no Acropora were recorded. We expect therefore, continued declines in Acropora abundance, while observed dominance of Porites is likely to persist. In the Oman Sea, Pocillopora was the dominant juvenile coral, with Acropora and Stylophora also recorded. This study shows that taxonomic differences in replenishment are reinforcing temporal shifts in coral composition within the southern Persian Gulf, but not in the Oman Sea. Differences in environmental conditions and disturbance regimes likely explain the divergent responses between regions.

  10. Mnemiopsis leidyi (Ctenophora) in Narragansett Bay, 1975-1979: Abundance, size composition and estimation of grazing

    NASA Astrophysics Data System (ADS)

    Deason, Ellen E.

    1982-08-01

    Surveys of the distribution, abundance and size of the ctenophore Mnemiopsis leidyi were carried out in Narragansett Bay, R.I. over a 5-year period, 1975-1979. Yearly variations were observed in time of initiation of the ctenophore increase and maximum abundance. Biomass maxima ranged from 0·2 to 3 g dry weight m -3 at Station 2 in lower Narragansett Bay while maximum abundance varied from 20 to 100 animals m -3. Ctenophores less than 1 cm in length generally composed up to 50% of the biomass and 95% of the numerical abundance during the peak of the M. leidyi pulse. During the 1978 maxima and the declining stages of the pulse each year, 100% of the population was composed of small animals. M. leidyi populations increased earlier, reached greater maximum abundances, and were more highly dominated by small animals in the upper bay than toward the mouth of the bay. The averageclearance rate of M. leidyi larvae feeding on A. tonsa at 22°C was 0·36 l mg -1 dry weight day -1, with apparent selection for nauplii relative to copepodites. Predation and excretion rates applied to ctenophore biomass estimated for Narragansett Bay indicated that M. leidyi excretion is minor but predation removed a bay-wide mean of 20% of the zooplankton standing stock daily during August of 1975 and 1976. Variation in M. leidyi predation at Station 2 was inversely related to mean zooplankton biomass during August and September, which increased 4-fold during the 5-year period.

  11. Forecasting climate change impacts to plant community composition in the Sonoran Desert region

    USGS Publications Warehouse

    Munson, Seth M.; Webb, Robert H.; Belnap, Jayne; Hubbard, J. Andrew; Swann, Don E.; Rutman, Sue

    2012-01-01

    Hotter and drier conditions projected for the southwestern United States can have a large impact on the abundance and composition of long-lived desert plant species. We used long-term vegetation monitoring results from 39 large plots across four protected sites in the Sonoran Desert region to determine how plant species have responded to past climate variability. This cross-site analysis identified the plant species and functional types susceptible to climate change, the magnitude of their responses, and potential climate thresholds. In the relatively mesic mesquite savanna communities, perennial grasses declined with a decrease in annual precipitation, cacti increased, and there was a reversal of the Prosopis velutina expansion experienced in the 20th century in response to increasing mean annual temperature (MAT). In the more xeric Arizona Upland communities, the dominant leguminous tree, Cercidium microphyllum, declined on hillslopes, and the shrub Fouquieria splendens decreased, especially on south- and west-facing slopes in response to increasing MAT. In the most xeric shrublands, the codominant species Larrea tridentata and its hemiparasite Krameria grayi decreased with a decrease in cool season precipitation and increased aridity, respectively. This regional-scale assessment of plant species response to recent climate variability is critical for forecasting future shifts in plant community composition, structure, and productivity.

  12. No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

    PubMed

    Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

    2016-04-01

    Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

  13. Long-term regional shifts in plant community composition are largely explained by local deer impact experiments.

    PubMed

    Frerker, Katie; Sabo, Autumn; Waller, Donald

    2014-01-01

    The fact that herbivores and predators exert top-down effects to alter community composition and dynamics at lower trophic levels is no longer controversial, yet we still lack evidence of the full nature, extent, and longer-term effects of these impacts. Here, we use results from a set of replicated experiments on the local impacts of white-tailed deer to evaluate the extent to which such impacts could account for half-century shifts in forest plant communities across the upper Midwest, USA. We measured species' responses to deer at four sites using 10-20 year-old deer exclosures. Among common species, eight were more abundant outside the exclosures, seven were commoner inside, and 16 had similar abundances in- and outside. Deer herbivory greatly increased the abundance of ferns and graminoids and doubled the abundance of exotic plants. In contrast, deer greatly reduced tree regeneration, shrub cover (100-200 fold in two species), plant height, plant reproduction, and the abundance of forbs. None of 36 focal species increased in reproduction or grew taller in the presence of deer, contrary to expectations. We compared these results to data on 50-year regional shifts in species abundances across 62 sites. The effects of herbivory by white-tailed deer accurately account for many of the long-term regional shifts observed in species' abundances (R2 = 0.41). These results support the conjecture that deer impacts have driven many of the regional shifts in forest understory cover and composition observed in recent decades. Our ability to link results from shorter-term, local experiments to regional long-term studies of ecological change strengthens the inferences we can draw from both approaches.

  14. Slow pyrolyzed biochars from crop residues for soil metal(loid) immobilization and microbial community abundance in contaminated agricultural soils.

    PubMed

    Igalavithana, Avanthi Deshani; Park, Jinje; Ryu, Changkook; Lee, Young Han; Hashimoto, Yohey; Huang, Longbin; Kwon, Eilhann E; Ok, Yong Sik; Lee, Sang Soo

    2017-06-01

    This study evaluated the feasibility of using biochars produced from three types of crop residues for immobilizing Pb and As and their effects on the abundance of microbial community in contaminated lowland paddy (P-soil) and upland (U-soil) agricultural soils. Biochars were produced from umbrella tree [Maesopsis eminii] wood bark [WB], cocopeat [CP], and palm kernel shell [PKS] at 500 °C by slow pyrolysis at a heating rate of 10 °C min(-1). Soils were incubated with 5% (w w(-1)) biochars at 25 °C and 70% water holding capacity for 45 d. The biochar effects on metal immobilization were evaluated by sequential extraction of the treated soil, and the microbial community was determined by microbial fatty acid profiles and dehydrogenase activity. The addition of WB caused the largest decrease in Pb in the exchangeable fraction (P-soil: 77.7%, U-soil: 91.5%), followed by CP (P-soil: 67.1%, U-soil: 81.1%) and PKS (P-soil: 9.1%, U-soil: 20.0%) compared to that by the control. In contrast, the additions of WB and CP increased the exchangeable As in U-soil by 84.6% and 14.8%, respectively. Alkalinity and high phosphorous content of biochars might be attributed to the Pb immobilization and As mobilization, respectively. The silicon content in biochars is also an influencing factor in increasing the As mobility. However, no considerable effects of biochars on the microbial community abundance and dehydrogenase activity were found in both soils.

  15. The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem.

    PubMed

    Wymore, Adam S; Liu, Cindy M; Hungate, Bruce A; Schwartz, Egbert; Price, Lance B; Whitham, Thomas G; Marks, Jane C

    2016-05-01

    Foliar chemistry influences leaf decomposition, but little is known about how litter chemistry affects the assemblage of bacterial communities during decomposition. Here we examined relationships between initial litter chemistry and the composition of the bacterial community in a stream ecosystem. We incubated replicated genotypes of Populus fremontii and P. angustifolia leaf litter that differ in percent tannin and lignin, then followed changes in bacterial community composition during 28 days of decomposition using 16S rRNA gene-based pyrosequencing. Using a nested experimental design, the majority of variation in bacterial community composition was explained by time (i.e., harvest day) (R(2) = 0.50). Plant species, nested within harvest date, explained a significant but smaller proportion of the variation (R(2) = 0.03). Significant differences in community composition between leaf species were apparent at day 14, but no significant differences existed among genotypes. Foliar chemistry correlated significantly with community composition at day 14 (r = 0.46) indicating that leaf litter with more similar phytochemistry harbor bacterial communities that are alike. Bacteroidetes and β-proteobacteria dominated the bacterial assemblage on decomposing leaves, and Verrucomicrobia and α- and δ-proteobacteria became more abundant over time. After 14 days, bacterial diversity diverged significantly between leaf litter types with fast-decomposing P. fremontii hosting greater richness than slowly decomposing P. angustifolia; however, differences were no longer present after 28 days in the stream. Leaf litter tannin, lignin, and lignin: N ratios all correlated negatively with diversity. This work shows that the bacterial community on decomposing leaves in streams changes rapidly over time, influenced by leaf species via differences in genotype-level foliar chemistry.

  16. Do honeybees shape the bacterial community composition in floral nectar?

    PubMed

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

  17. Canada's Composite Learning Index: A path towards learning communities

    NASA Astrophysics Data System (ADS)

    Cappon, Paul; Laughlin, Jarrett

    2013-09-01

    In the development of learning cities/communities, benchmarking progress is a key element. Not only does it permit cities/communities to assess their current strengths and weaknesses, it also engenders a dialogue within and between cities/communities on the means of enhancing learning conditions. Benchmarking thereby is a potentially motivational tool, energising further progress. In Canada, the Canadian Council on Learning created the world's first Composite Learning Index (CLI), the purpose of which is to measure the conditions of learning nationally, regionally and locally. Cities/communities in Canada have utilised the CLI Simulator, an online tool provided by the Canadian Council on Learning, to gauge the change in overall learning conditions which may be expected depending on which particular indicator is emphasised. In this way, the CLI has proved to be both a dynamic and a locally relevant tool for improvement, moreover a strong motivational factor in the development of learning cities/communities. After presenting the main features of the CLI, the authors of this paper sum up the lessons learned during its first 5 years (2006-2010) of existence, also with a view to its transferability to other regions. Indeed, the CLI model was already adopted in Europe by the German Bertelsmann foundation in 2010 and has the potential to be useful in many other countries as well.

  18. Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

    PubMed Central

    Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

    2013-01-01

    Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

  19. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

    PubMed Central

    van Agtmaal, Maaike; van Os, Gera J.; Hol, W.H. Gera; Hundscheid, Maria P.J.; Runia, Willemien T.; Hordijk, Cornelis A.; de Boer, Wietse

    2015-01-01

    There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the

  20. The cosmic ray composition as viewed from the chemical abundances of the solar system

    NASA Technical Reports Server (NTRS)

    Sakurai, K.

    1985-01-01

    It is shown that the chemical composition of cosmic rays at their sources for the elements up to the atomic number as 80 is quite similar to that of the carbonaceous chondrites, which have been keeping the properties of the protosolar nebula. In particular, the similarity between these two compositions is significant to the elements classified as refractory and siderphile, in addition to the elements, Ca and Al. These results as cited above suggest that cosmic rays, being currently observed near the Earth, may have been accelerated from the matter with the composition similar to that which is found of these chondrites as Allende.

  1. Assessment of beetle diversity, community composition and potential threats to forestry using kairomone-baited traps.

    PubMed

    Olivier-Espejel, S; Hurley, B P; Garnas, J

    2017-02-01

    Traps designed to capture insects during normal movement/dispersal, or via attraction to non-specific (plant) volatile lures, yield by-catch that carries valuable information about patterns of community diversity and composition. In order to identify potential native/introduced pests and detect predictors of colonization of non-native pines, we examined beetle assemblages captured in intercept panel traps baited with kairomone lures used during a national monitoring of the woodwasp, Sirex noctilio, in Southern Africa. We identified 50 families and 436 morphospecies of beetles from nine sites sampled in both 2008 and 2009 and six areas in 2007 (trap catch pooled by region) across a latitudinal and elevational gradient. The most diverse groups were mainly those strongly associated with trees, known to include damaging pests. While native species dominated the samples in terms of richness, the dominant species was the introduced bark beetle Orthotomicus erosus (Curculionidae: Scolytinae) (22 ± 34 individuals/site). Four Scolytinae species without previous records in South Africa, namely Coccotrypes niger, Hypocryphalus robustus (formerly Hypocryphalus mangiferae), Hypothenemus birmanus and Xyleborus perforans, were captured in low abundances. Communities showed temporal stability within sites and strong biogeographic patterns across the landscape. The strongest single predictors of community composition were potential evaporation, latitude and maximum relative humidity, while the strongest multifactor model contained elevation, potential evaporation and maximum relative humidity. Temperature, land use variables and distance to natural areas did not significantly correlate with community composition. Non-phytophagous beetles were also captured and were highly diverse (32 families) perhaps representing important beneficial insects.

  2. Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

    USGS Publications Warehouse

    Harris, Theodore D.; Graham, Jennifer

    2015-01-01

    The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

  3. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions

    PubMed Central

    Shchegolkova, Nataliya M.; Krasnov, George S.; Belova, Anastasia A.; Dmitriev, Alexey A.; Kharitonov, Sergey L.; Klimina, Kseniya M.; Melnikova, Nataliya V.; Kudryavtseva, Anna V.

    2016-01-01

    Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs) responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc.), which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater. Additional load of bioreactors with influent rich in petroleum products and organic matter was associated with the increase of bacteria responsible for AS bulking and foaming. Here, we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS bulking and foaming (most abundant in AS of slaughterhouse wastewater) played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect) represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will

  4. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.

    PubMed

    Shchegolkova, Nataliya M; Krasnov, George S; Belova, Anastasia A; Dmitriev, Alexey A; Kharitonov, Sergey L; Klimina, Kseniya M; Melnikova, Nataliya V; Kudryavtseva, Anna V

    2016-01-01

    Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs) responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc.), which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater. Additional load of bioreactors with influent rich in petroleum products and organic matter was associated with the increase of bacteria responsible for AS bulking and foaming. Here, we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS bulking and foaming (most abundant in AS of slaughterhouse wastewater) played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect) represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will

  5. 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.

  6. The effect of native and introduced biofuel crops on the composition of soil biota communities

    NASA Astrophysics Data System (ADS)

    Heděnec, Petr; Ustak, Sergej; Novotný, David; Frouz, Jan

    2015-04-01

    Biofuel crops are an accepted alternative to fossil fuels, but little is known about the ecological impact of their production. The aim of this contribution is to study the effect of native (Salix viminalis and Phalaris arundinacea) and introduced (Helianthus tuberosus, Reynoutria sachalinensis and Silphium perfoliatum) biofuel crop plantations on the soil biota in comparison with cultural meadow vegetation used as control. The study was performed as part of a split plot field experiment of the Crop Research Institute in the city of Chomutov (Czech Republic). The composition of the soil meso- and macrofauna community, composition of the cultivable fraction of the soil fungal community, cellulose decomposition (using litter bags), microbial biomass, basal soil respiration and PLFA composition (incl. F/B ratio) were studied in each site. The C:N ratio and content of polyphenols differed among plant species, but these results could not be considered significant between introduced and native plant species. Abundance of the soil meso- and macrofauna was higher in field sites planted with S. viminalis and P. arundinacea than those planted with S. perfoliatum, H. tuberosus and R. sachalinensis. RDA and Monte Carlo Permutation Test showed that the composition of the faunal community differed significantly between various native and introduced plants. Significantly different basal soil respiration was found in sites planted with various energy crops; however, this difference was not significant between native and introduced species. Microbial biomass carbon and cellulose decomposition did not exhibit any statistical differences among the biofuel crops. The largest statistically significant difference we found was in the content of actinobacterial and bacterial (bacteria, G+ bacteria and G- bacteria) PLFA in sites overgrown by P. arundinacea compared to introduced as well as native biofuel crops. In conclusion, certain parameters significantly differ between various native

  7. The effect of native and introduced biofuel crops on the composition of soil biota communities

    NASA Astrophysics Data System (ADS)

    Frouz, Jan; Hedenec, Petr

    2016-04-01

    Biofuel crops are an accepted alternative to fossil fuels, but little is known about the ecological impact of their production. The aim of this contribution is to study the effect of native (Salix viminalis and Phalaris arundinacea) and introduced (Helianthus tuberosus, Reynoutria sachalinensis and Silphium perfoliatum) biofuel crop plantations on the soil biota in comparison with cultural meadow vegetation used as control. The study was performed as part of a split plot field experiment of the Crop Research Institute in the city of Chomutov (Czech Republic). The composition of the soil meso- and macrofauna community, composition of the cultivable fraction of the soil fungal community, cellulose decomposition (using litter bags), microbial biomass, basal soil respiration and PLFA composition (incl. F/B ratio) were studied in each site. The C:N ratio and content of polyphenols differed among plant species, but these results could not be considered significant between introduced and native plant species. Abundance of the soil meso- and macrofauna was higher in field sites planted with S. viminalis and P. arundinacea than those planted with S. perfoliatum, H. tuberosus and R. sachalinensis. RDA and Monte Carlo Permutation Test showed that the composition of the faunal community differed significantly between various native and introduced plants. Significantly different basal soil respiration was found in sites planted with various energy crops; however, this difference was not significant between native and introduced species. Microbial biomass carbon and cellulose decomposition did not exhibit any statistical differences among the biofuel crops. The largest statistically significant difference we found was in the content of actinobacterial and bacterial (bacteria, G+ bacteria and G- bacteria) PLFA in sites overgrown by P. arundinacea compared to introduced as well as native biofuel crops. In conclusion, certain parameters significantly differ between various native

  8. Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

    NASA Astrophysics Data System (ADS)

    Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

    2015-12-01

    Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of

  9. Phytoplankton community succession shaping bacterioplankton community composition in Lake Taihu, China.

    PubMed

    Niu, Yuan; Shen, Hong; Chen, Jun; Xie, Ping; Yang, Xi; Tao, Min; Ma, Zhimei; Qi, Min

    2011-08-01

    PCR-denaturing gradient gel electrophoresis (DGGE) and canonical correspondence analysis (CCA) were used to explore the relationship between succession of phytoplankton community and temporal variation of bacterioplankton community composition (BCC) in the eutrophic Lake Taihu. Serious Microcystis bloom was observed in July-December 2008 and Bacillariophyta and Cryptophyta dominated in January-June 2009. BCC was characterized by DGGE of 16S rRNA gene with subsequent sequencing. The DGGE banding patterns revealed a remarkable seasonality which was closely related to phytoplankton community succession. Variation trend of Shannon-Wiener diversity index in bacterioplankton community was similar to that of phytoplankton community. CCA revealed that temperature and phytoplankton played key roles in structuring BCC. Sequencing of DGGE bands suggested that the majority of the sequences were affiliated with common phylogenetic groups in freshwater: Alphaproteobacteria, Betaproteobacteria, Bacteroidetes and Actinobacteria. The cluster STA2-30 (affiliated with Actinobacteria) was found almost across the sampling time at the two study sites. We observed that the family Flavobacteriaceae (affiliated with Bacteroidetes) tightly coupled to diatom bloom and the cluster ML-5-51.2 (affiliated with Actinobacteria) dominated the bacterioplankton communities during Microcystis bloom. These results were quite similar at the two sampling sites, indicating that BCC changes were not random but with fixed pattern. Our study showed insights into relationships between phytoplankton and bacterioplankton communities at species level, facilitating a better understanding of microbial loop and ecosystem functioning in the lake.

  10. Impact of physicochemical parameters on phytoplankton compositions and abundances in Selameko Manmade Reservoir, Debre Tabor, South Gondar, Ethiopia

    NASA Astrophysics Data System (ADS)

    Wassie, Tilahun Adugna; Melese, Ayalew Wondie

    2015-12-01

    Impact of physicochemical parameters on 2 compositions and abundances in Selameko Reservoir, Debre Tabor, South Gondar from August 2009 to May 2010 was assessed. Water quality parameters, such as temperature, water transparency, water depth, dissolved oxygen, pH, total dissolved solids, phosphate, nitrate, and silicate were measured in situ from two sites (littoral and open water zone) of the reservoir. Phytoplankton compositions and abundances were analyzed in Tana fisheries and other aquatic organisms' research center. ANOVA result of the physicochemical parameters included chlorophyll-a showed the presence of significance difference among seasons and between sites (P < 0.05). A total of seven families, 36 genera from three groups (Diatom, Blue green algae and Green algae) of phytoplankton were identified during the study period. From all groups, diatoms were the most abundant at both sites and Blue green algae were the least abundant. ANOVA of all phytoplankton showed highly significant difference among seasons and between sites (P < 0.05). ANOVA of all phytoplankton showed highly significant difference among seasons and between sites (P < 0.05). Based on the stepwise regression, a total number of phytoplanktons had positive correlation with some of the physicochemical parameters (R2 = 0.99, P < 0.001, N = 16). The study concluded that some of physicochemical parameters (NO3-N and PO4-P) indicated the presence of reservoir water pollution. This is supported by the presence of pollution-resistant phytoplankton species such as Melosira and Microcystis. The reservoir water was eutrophic (productive) throughout the year. To avoid such pollution, basin and reservoir management are recommended.

  11. Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season.

    PubMed

    Yamaguchi, Nobuyasu; Baba, Takashi; Ichijo, Tomoaki; Himezawa, Yuka; Enoki, Kanami; Saraya, Makoto; Li, Pin-Fang; Nasu, Masao

    2016-01-01

    Approximately 180 t/km(2) of Asian dust particles are estimated to fall annually on Beijing, China, and there is significant concern about the influence of microbes transported by Asian dust events on human health and downwind ecosystems. In this study, we collected Asian dust particles in Beijing, and analyzed the bacterial communities on these particles by culture-independent methods. Bacterial cells on Asian dust particles were visualized first by laser scanning microscopy, which demonstrated that Asian dust particles carry bacterial cells to Beijing. Bacterial abundance, as determined by quantitative polymerase chain reaction (PCR), was 10(8) to 10(9) cells/g, a value about 10 times higher than that in Asian dust source soils. Inter-seasonal variability of bacterial community structures among Asian dust samples, as compared by terminal restriction fragment length polymorphism (T-RFLP), was low during the Asian dust season. Several viable bacteria, including intestinal bacteria, were found in Asian dust samples by denaturing gradient gel electrophoresis (DGGE). Clone library analysis targeting 16S ribosomal RNA (rRNA) gene sequences demonstrated that bacterial phylogenetic diversity was high in the dust samples, and most of these were environmental bacteria distributed in soil and air. The dominant species in the clone library was Segetibacter aerophilus (Bacteroidetes), which was first isolated from an Asian dust sample collected in Korea. Our results also indicate the possibility of a change in the bacterial community structure during transportation and increases in desiccation-tolerant bacteria such as Firmicutes.

  12. The chemical composition of red giants in 47 Tucanae. I. Fundamental parameters and chemical abundance patterns

    NASA Astrophysics Data System (ADS)

    Thygesen, A. O.; Sbordone, L.; Andrievsky, S.; Korotin, S.; Yong, D.; Zaggia, S.; Ludwig, H.-G.; Collet, R.; Asplund, M.; Ventura, P.; D'Antona, F.; Meléndez, J.; D'Ercole, A.

    2014-12-01

    Context. The study of chemical abundance patterns in globular clusters is key importance to constraining the different candidates for intracluster pollution of light elements. Aims: We aim at deriving accurate abundances for a wide range of elements in the globular cluster 47 Tucanae (NGC 104) to add new constraints to the pollution scenarios for this particular cluster, expanding the range of previously derived element abundances. Methods: Using tailored 1D local thermodynamic equilibrium (LTE) atmospheric models, together with a combination of equivalent width measurements, LTE, and NLTE synthesis, we derive stellar parameters and element abundances from high-resolution, high signal-to-noise spectra of 13 red giant stars near the tip of the RGB. Results: We derive abundances of a total 27 elements (O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ru, Ba, La, Ce, Pr, Nd, Eu, Dy). Departures from LTE were taken into account for Na, Al, and Ba. We find a mean [Fe/H] = -0.78 ± 0.07 and [ α/ Fe ] = 0.34 ± 0.03 in good agreement with previous studies. The remaining elements show good agreement with the literature, but including NLTE for Al has a significant impact on the behavior of this key element. Conclusions: We confirm the presence of an Na-O anti-correlation in 47 Tucanae found by several other works. Our NLTE analysis of Al shifts the [Al/Fe] to lower values, indicating that this may be overestimated in earlier works. No evidence of an intrinsic variation is found in any of the remaining elements. Based on observations made with the ESO Very Large Telescope at Paranal Observatory, Chile (Programmes 084.B-0810 and 086.B-0237).Full Tables 2, 5, and 9 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/572/A108Appendix A is available in electronic form at http://www.aanda.org

  13. Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil.

    PubMed

    Daebeler, Anne; Gansen, Martina; Frenzel, Peter

    2013-01-01

    The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH(3)F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH(3)F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH(3)F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH(3)F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH(3)F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens.

  14. Mineral composition and charcoal determine the bacterial community structure in artificial soils.

    PubMed

    Ding, Guo-Chun; Pronk, Geertje Johanna; Babin, Doreen; Heuer, Holger; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

    2013-10-01

    To study the influence of the clay minerals montmorillonite (M) and illite (I), the metal oxides ferrihydrite (F) and aluminum hydroxide (A), and charcoal (C) on soil bacterial communities, seven artificial soils with identical texture provided by quartz (Q) were mixed with sterilized manure as organic carbon source before adding a microbial inoculant derived from a Cambisol. Bacterial communities established in artificial soils after 90 days of incubation were compared by DGGE analysis of bacterial and taxon-specific 16S rRNA gene amplicons. The bacterial community structure of charcoal-containing soils highly differed from the other soils at all taxonomic levels studied. Effects of montmorillonite and illite were observed for Bacteria and Betaproteobacteria, but not for Actinobacteria or Alphaproteobacteria. A weak influence of metal oxides on Betaproteobacteria was found. Barcoded pyrosequencing of 16S rRNA gene amplicons done for QM, QI, QIF, and QMC revealed a high bacterial diversity in the artificial soils. The composition of the artificial soils was different from the inoculant, and the structure of the bacterial communities established in QMC soil was most different from the other soils, suggesting that charcoal provided distinct microenvironments and biogeochemical interfaces formed. Several populations with discriminative relative abundance between artificial soils were identified.

  15. Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils

    PubMed Central

    Latz, Ellen; Eisenhauer, Nico; Rall, Björn Christian; Scheu, Stefan; Jousset, Alexandre

    2016-01-01

    Plant diseases cause dramatic yield losses worldwide. Current disease control practices can be deleterious for the environment and human health, calling for alternative and sustainable management regimes. Soils harbour microorganisms that can efficiently suppress pathogens. Uncovering mediators driving their functioning in the field still remains challenging, but represents an essential step in order to develop strategies for increased soil health. We set up plant communities of varying richness to experimentally test the potential of soils differing in plant community history to suppress the pathogen Rhizoctonia solani. The results indicate that plant communities shape soil-disease suppression via changes in abiotic soil properties and the abundance of bacterial groups including species of the genera Actinomyces, Bacillus and Pseudomonas. Further, the results suggest that pairwise interactions between specific plant species strongly affect soil suppressiveness. Using structural equation modelling, we provide a pathway orientated framework showing how the complex interactions between plants, soil and microorganisms jointly shape soil suppressiveness. Our results stress the importance of plant community composition as a determinant of soil functioning, such as the disease suppressive potential of soils. PMID:27021053

  16. 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

  17. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield

    PubMed Central

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-01-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions. PMID:21124490

  18. 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.

  19. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

    PubMed Central

    Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B.

    2013-01-01

    Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition. PMID:23847601

  20. Biofouling of reverse-osmosis membranes during tertiary wastewater desalination: microbial community composition.

    PubMed

    Al Ashhab, Ashraf; Herzberg, Moshe; Gillor, Osnat

    2014-03-01

    Reverse-osmosis (RO) desalination is frequently used for the production of high-quality water from tertiary treated wastewater (TTWW). However, the RO desalination process is often hampered by biofouling, including membrane conditioning, microbial adhesion, and biofilm growth. The vast majority of biofilm exploration concentrated on the role of bacteria in biofouling neglecting additional microbial contributors, i.e., fungi and archaea. To better understand the RO biofouling process, bacterial, archaeal and fungal diversity was characterized in a laboratory-scale RO desalination plant exploring the TTWW (RO feed), the RO membrane and the RO feed tube biofilms. We sequenced 77,400 fragments of the ribosome small subunit-encoding gene (16S and 18S rRNA) to identify the microbial community members in these matrices. Our results suggest that the bacterial, archaeal but not fungal community significantly differ from the RO membrane biofouling layer to the feedwater and tube biofilm (P < 0.01). Moreover, the RO membrane supported a more diverse community compared to the communities monitored in the feedwater and the biofilm attached to the RO feedwater tube. The tube biofilm was dominated by Actinobacteria (91.2 ± 4.6%), while the Proteobacteria phylum dominated the feedwater and RO membrane (at relative abundance of 92.3 ± 4.4% and 71.5 ± 8.3%, respectively), albeit comprising different members. The archaea communities were dominated by Crenarchaeota (53.0 ± 6.9%, 32.5 ± 7.2% and 69%, respectively) and Euryarchaeota (43.3 ± 6.3%, 23.2 ± 4.8% and 24%, respectively) in all three matrices, though the communities' composition differed. But the fungal communities composition was similar in all matrices, dominated by Ascomycota (97.6 ± 2.7%). Our results suggest that the RO membrane is a selective surface, supporting unique bacterial, and to a lesser extent archaeal communities, yet it does not select for a fungal community.

  1. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions

    SciTech Connect

    He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.; Anderson, Frank E.; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P.; Windham-Myers, Lisamarie; Tringe, Susannah G.

    2015-05-19

    Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

  2. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions

    DOE PAGES

    He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.; ...

    2015-05-19

    Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhousemore » gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial

  3. Influence of a large herbivore reintroduction on plant invasions and community composition in a California grassland.

    PubMed

    Johnson, Brent E; Cushman, J Hall

    2007-04-01

    Despite many successful reintroductions of large mammalian herbivores throughout the world, remarkably little attention has focused on how these actions affect native and exotic vegetation at reintroduction sites. One such herbivore is tule elk (Cervus elaphus nannodes), which was on the brink of extinction in the mid 1800s, but now has numerous stable populations due to intensive reintroduction efforts. Here, we summarize results from a 5-year exclosure experiment that explored the effects of tule elk on a coastal grassland in northern California. Elk significantly altered the species composition of this community; the response of annual species (dominated heavily by exotic taxa) was dramatically different from perennial species. Elk herbivory increased the abundance and aboveground biomass of native and exotic annuals, whereas it either had no effect on or caused significant decreases in perennials. Elk also decreased the cover of native shrubs, suggesting that these herbivores play an important role in maintaining open grasslands. In addition, elk significantly reduced the abundance and biomass of a highly invasive exotic grass, Holcus lanatus, which is a major problem in mesic perennial grasslands. Our results demonstrate that the successful reintroduction of a charismatic and long-extirpated mammal had extremely complex effects on the plant community, giving rise to both desirable and undesirable outcomes from a management perspective. We suspect that these kinds of opposing effects are not unique to tule elk and that land managers will frequently encounter them when dealing with reintroduced mammals.

  4. Abundances and isotopic compositions of rhenium and osmium in pyrite samples from the Huaibei coalfield, Anhui, China

    USGS Publications Warehouse

    Liu, Gaisheng; Chou, C.-L.; Peng, Z.; Yang, G.

    2008-01-01

    Two pyrite samples from the Shihezi Formation (Lower Permian), Huaibei coalfield, Anhui, China, have been analyzed for abundances and isotopic compositions of rhenium and osmium using negative thermal ion mass spectrometry. The Re-Os ages of the pyrites are 64.4 and 226 Ma, which are younger than the formation age of the coal seam. The pyrite samples may consist of pyrite formed at various stages during the history of coal formation. The ??Osvalues of the two pyrite samples are +17 and +18, respectively. Such high ??Osvalues are reported for the first time for recycles crustal materials from a sedimentary basin. ?? Springer-Verlag 2007.

  5. Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

    PubMed

    Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

    2016-10-01

    The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river.

  6. Fermentable non-starch polysaccharides increases the abundance of Bacteroides-Prevotella-Porphyromonas in ileal microbial community of growing pigs.

    PubMed

    Ivarsson, E; Roos, S; Liu, H Y; Lindberg, J E

    2014-11-01

    Most plant-origin fiber sources used in pig production contains a mixture of soluble and insoluble non-starch polysaccharides (NSP). The knowledge about effects of these sources of NSP on the gut microbiota and its fermentation products is still scarce. The aim of this study was to investigate effects of feeding diets with native sources of NSP on the ileal and fecal microbial composition and the dietary impact on the concentration of short-chain fatty acids (SCFA) and lactic acid. The experiment comprised four diets and four periods in a change-over design with seven post valve t-cecum cannulated growing pigs. The four diets were balanced to be similar in NSP content and included one of four fiber sources, two diets were rich in pectins, through inclusion of chicory forage (CFO) and sugar beet pulp, and two were rich in arabinoxylan, through inclusion of wheat bran (WB) and grass meal. The gut microbial composition was assessed with terminal restriction fragment (TRF) length polymorphism and the abundance of Lactobacillus spp., Enterobacteriaceae, Bacteroides-Prevotella-Porphyromonas and the β-xylosidase gene, xynB, were assessed with quantitative PCR. The gut microbiota did not cluster based on NSP structure (arabinoxylan or pectin) rather, the effect was to a high degree ingredient specific. In pigs fed diet CFO, three TRFs related to Prevotellaceae together consisted of more than 25% of the fecal microbiota, which is about 3 to 23 times higher (P<0.05) than in pigs fed the other diets. Whereas pigs fed diet WB had about 2 to 22 times higher abundance (P<0.05) of Megasphaera elsdenii in feces and about six times higher abundance (P<0.05) of Lactobacillus reuteri in ileal digesta than pigs fed the other diets. The total amount of digested NSP (r=0.57; P=0.002), xylose (r=0.53; P=0.004) and dietary fiber (r=0.60; P=0.001) in ileal digesta were positively correlated with an increased abundance of Bacteroides-Prevotella-Porphyromonas. The effect on SCFA was

  7. Tempo-spatial patterns of bacterial community composition in the western North Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Kataoka, Takafumi; Hodoki, Yoshikuni; Suzuki, Koji; Saito, Hiroaki; Higashi, Seigo

    2009-04-01

    In the western North Pacific, where subarctic Oyashio waters encounter subtropical Kuroshio waters, phylotype composition of heterotrophic bacteria was estimated by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified bacterial 16S ribosomal DNA. Total bacterial abundance was also measured by flow cytometry. The study area was divided into four water masses: coastal, Oyashio, Kuroshio, and the Kuroshio-Oyashio transition. Abundances of heterotrophic bacteria in the Oyashio, Kuroshio, and Kuroshio-Oyashio transition regions ranged from 0.2 × 10 5 cells mL - 1 to 1.4 × 10 5 cells mL - 1 and were not significantly different, except in the Oyashio region during September. Bacterial compositions were distinct in each water mass. Furthermore, phylotype distributions differed between surface and subsurface waters in the Kuroshio-Oyashio transition region. Out of 61 DGGE bands obtained, 41 were successfully identified as 31 phylotypes: 22 Gammaproteobacteria, 4 Alphaproteobacteria, 2 unknown bacteria, 2 cyanobacteria, and 1 plastid. Although the Gammaproteobacteria OM60 clade was eurytopic in the study area, Psychrobacter glacincola and the uncultured Gammaproteobacteria SAR92 clade were often observed in the Oyashio region. Overall, our results indicated that Gammaproteobacteria were predominant in the bacterial community, which was influenced by the hydrographic properties of each water mass in the study area.

  8. Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.

    PubMed

    Zhang, Jinping; Zhou, Xiaohong; Chen, Lei; Chen, Zhigang; Chu, Jinyu; Li, Yimin

    2016-05-01

    The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil.

  9. A Comparison of Anammox Bacterial Abundance and Community Structures in Three Different Emerged Plants-Related Sediments.

    PubMed

    Chu, Jinyu; Zhang, Jinping; Zhou, Xiaohong; Liu, Biao; Li, Yimin

    2015-09-01

    Quantitative polymerase chain reaction (qPCR) assays and 16S rRNA gene clone libraries were used to document the abundance, diversity and community structure of anaerobic ammonia-oxidising (anammox) bacteria in the rhizosphere and non-rhizosphere sediments of three emergent macrophyte species (Iris pseudacorus, Thalia dealbata and Typha orientalis). The qPCR results confirmed the existence of anammox bacteria (AMX) with observed log number of gene copies per dry gram sediment ranging from 5.00 to 6.78. AMX was more abundant in T. orientalis-associated sediments than in the other two plant species. The I. pseudacorus- and T. orientalis-associated sediments had higher Shannon diversity values, indicating higher AMX diversity in these sediments. Based on the 16S rRNA gene, Candidatus 'Brocadia', Candidatus 'Kuenenia', Candidatus 'Jettenia' and new clusters were observed with the predominant Candidatus 'Kuenenia' cluster. The I. pseudacorus-associated sediments contained all the sequences of the C. 'Jettenia' cluster. Sequences obtained from T. orientalis-associated sediments contributed more than 90 % sequences in the new cluster, whereas none was found from I. pseudacorus. The new cluster was distantly related to known sequences; thus, this cluster was grouped outside the known clusters, indicating that the new cluster may be a new Planctomycetales genus. Further studies should be undertaken to confirm this finding.

  10. A study of Culicoides in Rondônia, in the Brazilian Amazon: species composition, relative abundance and potential vectors.

    PubMed

    Carvalho, L P C; Pereira Júnior, A M; Farias, E S; Almeida, J F; Rodrigues, M S; Resadore, F; Pessoa, F A C; Medeiros, J F

    2017-03-01

    There is very little information available about Culicoides species (Diptera: Ceratopogonidae) in the western Brazilian Amazon. However, studies of the fauna of this region are essential to knowledge of the species and potential vectors within it. Thus, the present study aims to evaluate the abundance, richness and composition of Culicoides species in rural areas in the state of Rondônia, Brazil. Culicoides specimens were collected in forest and pasture environments in the municipality of Porto Velho, using light traps. A total of 1708 individuals (1136 females and 572 males) belonging to 33 species were collected; 28 of these samples represent new records for the state of Rondônia and include the first record of Culicoides contubernalis in Brazil. Culicoides insignis was the most abundant species (86.1%). Species richness was greater in forest areas (32 species, 96.96%), whereas pastures presented the greatest number of Culicoides captured (n = 1540, 90.1%). This study shows that Culicoides populations differ between forest and pasture environments and indicates that the abundance of C. insignis is an important factor in epidemiological vigilance studies in the region.

  11. 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.

  12. Abundance and composition of ammonia-oxidizing bacteria and archaea in different types of soil in the Yangtze River estuary*

    PubMed Central

    Li, Xiao-ran; Xiao, Yi-ping; Ren, Wen-wei; Liu, Zeng-fu; Shi, Jin-huan; Quan, Zhe-xue

    2012-01-01

    Tidal flats are soil resources of great significance. Nitrification plays a central role in the nitrogen cycle and is often a critical first step in nitrogen removal from estuarine and coastal environments. We determined the abundance as well as composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in different soils during land reclamation process. The abundance of AOA was higher than that of AOB in farm land and wild land while AOA was not detected in tidal flats using real-time polymerase chain reaction (PCR). The different abundances of AOB and AOA were negatively correlated with the salinity. The diversities of AOB and AOA were also investigated using clone libraries by amplification of amoA gene. Among AOB, nearly all sequences belonged to the Nitrosomonas lineage in the initial land reclamation process, i.e., tidal flats, while both Nitrosomonas and Nitrosospira lineages were detected in later and transition phases of land reclamation process, farm land and wild land. The ratio of the numbers of sequences of Nitrosomonas and Nitrosospira lineages was positively correlated with the salinity and the net nitrification rate. As for AOA, there was no obvious correlation with the changes in the physicochemical properties of the soil. This study suggests that AOB may be more import than AOA with respect to influencing the different land reclamation process stages. PMID:23024044

  13. Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

    PubMed

    Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid; Höfle, Manfred G

    2012-05-01

    The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

  14. Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

    PubMed Central

    Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

    2012-01-01

    The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

  15. Late-summer zooplankton community structure, abundance, and distribution in the Hudson Bay system (Canada) and their relationships with environmental conditions, 2003-2006

    NASA Astrophysics Data System (ADS)

    Estrada, Rafael; Harvey, Michel; Gosselin, Michel; Starr, Michel; Galbraith, Peter S.; Straneo, Fiammetta

    2012-08-01

    Zooplankton communities were examined for the first time in three different hydrographic regions of the Hudson Bay system (HBS) in early August to early September from 2003 to 2006. Sampling was conducted at 50 stations distributed along different transects located in Hudson Bay (HB), Hudson Strait (HS), and Foxe Basin (FB). Variations in zooplankton biomass, abundance, taxonomic composition, and diversity in relation to environmental variables were studied using multivariate techniques. During all sampling years, the total zooplankton biomass was on average four times lower in HB than in HS and FB. Clustering samples by their relative species compositions revealed no interannual variation in zooplankton community but showed a marked interregional variability between the three regions. Water column stratification explained the greatest proportion (25%) of this spatial variability. According to redundancy analysis (RDA), the zooplankton taxa that contribute most to the separation of the three regions are Microcalanus spp., Oithona similis, Oncaea borealis, Aeginopsis laurentii, Sagitta elegans, Fritillaria sp., and larvae of cnidaria, chaetognatha, and pteropoda in HB; hyperiid amphipods in FB; and Pseudocalanus spp. CI-CV, Calanus glacialis CI-CVI, Calanus finmarchicus CI-CVI, Calanus hyperboreus CV-CVI, Acartia longiremis CI-CV, Metridia longa N3-N6 CI-CIII CVIf, Eukrohnia hamata, larvae of echinodermata, mollusca, cirripedia, appendicularia, and polychaeta in the northwestern and southeastern HS transects. For the HB transect, the RDA analyzed allowed us to distinguish three regions (HB west, central, and east) with different environmental gradients and zooplankton assemblages, in particular higher concentration of Pseudocalanus spp. nauplii and CI-CVI, as well as benthic macrozooplankton and meroplankton larvae in western HB. In HS, Calanoid species (mainly C. finmarchicus and C. glacialis) were mostly observed at the north shore stations associated with the

  16. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  17. Relative abundance of biotic communities of plankton and zoobenthos in three ox-bow lakes of Eastern India

    NASA Astrophysics Data System (ADS)

    Chakrabarty, Debajyoti; Biswas, Probir; Das, Sanjib Kumar

    2010-07-01

    We made comparative studies of three tropical ox-bow lakes in India with different trophic states. The species number of zooplanktons was negatively correlated with the degree of water eutrophication, and lakes of similar trophic status had higher similarity of species. The most significant differences of species composition were observed with rotifers and zoobenthos. The density and biomass of phytoplankton, rotifers, oligochaetes and chironomids tended to increase with increasing nutrients. We observed a significant difference of dominant species in different waters, especially the eutrophic lake, which was dominated by a few species of oligochaetes. The abundance of Tanypus bilobatus showed a highly significant correlation with the degree of eutrophication. Rotifers and zoobenthos showed considerably lower biodiversity in the eutrophic lake.

  18. [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

  19. Soil microbial community composition and its role in carbon mineralization in long-term fertilization paddy soils.

    PubMed

    Dai, Xiaoqin; Wang, Huimin; Fu, Xiaoli

    2017-02-15

    Microbial communities are critical in mediating soil biological processes, including C mineralization; yet, the mechanism of microbial mediation for soil C mineralization remains poorly understood under the long-term fertilization. To identify the relative roles of microbes in C mineralization in the soil of rice paddies, we investigated the long-term (11years) effects of repeated N, P, and K fertilization on crop yield, soil properties and microbial communities and their relationships with C mineralization. The treatments included: no fertilization (control); normal fertilization (NPK); doubling the amount of N, P or K fertilizer (2NPK, N2PK, or NP2K); and doubling the amount of all three (2(NPK)). Long-term fertilization significantly increased rice yields by 3.4 to 4.8 times, and yield significantly improved by 23-32% with higher N fertilization. Increasing N fertilization significantly decreased total N and total P concentrations, while increasing P fertilization significantly increased soil pH, Olsen-P and total P concentrations. Increasing N and P fertilization changed soil microbial community compositions; pH and ratio of SOC and TN (C:N) were the most important contributors to the variance in microbial community composition. Increasing P fertilization decreased the abundance of Gram-positive and actinomycetes phospholipid fatty acid (PLFA) and significantly increased the ratio of fungal to bacterial PLFA. However, the alterations in soil microbial abundance and community composition did not significantly influence the C mineralization, while it significantly was determined by C:N ratio and marginally by crop yield. The results suggest that substrate quality (C:N ratio) and availability (crop yield), having a closer relationship with C mineralization compared to soil microbial communities, should be preferentially considered to predicting C mineralization under long-term fertilization.

  20. Differences found in the macroinvertebrate community composition in the presence or absence of the invasive alien crayfish, Orconectes hylas

    USGS Publications Warehouse

    Freeland-Riggert, Brandye T.; Cairns, Stefan H.; Poulton, Barry C.; Riggert, Chris M.

    2016-01-01

    Introductions of alien species into aquatic ecosystems have been well documented, including invasions of crayfish species; however, little is known about the effects of these introductions on macroinvertebrate communities. The woodland crayfish (Orconectes hylas (Faxon)) has been introduced into the St. Francis River watershed in southeast Missouri and has displaced populations of native crayfish. The effects of O. hylas on macroinvertebrate community composition were investigated in a fourth-order Ozark stream at two locations, one with the presence of O. hylas and one without. Significant differences between sites and across four sampling periods and two habitats were found in five categories of benthic macroinvertebrate metrics: species richness, percent/composition, dominance/diversity, functional feeding groups, and biotic indices. In most seasons and habitat combinations, the invaded site had significantly higher relative abundance of riffle beetles (Coleoptera: Elmidae), and significantly lower Missouri biotic index values, total taxa richness, and both richness and relative abundance of midges (Diptera: Chironomidae). Overall study results indicate that some macroinvertebrate community differences due to the O. hylas invasion were not consistent between seasons and habitats, suggesting that further research on spatial and temporal habitat use and feeding ecology of Ozark crayfish species is needed to improve our understanding of the effects of these invasions on aquatic communities.

  1. Differences Found in the Macroinvertebrate Community Composition in the Presence or Absence of the Invasive Alien Crayfish, Orconectes hylas

    PubMed Central

    Freeland-Riggert, Brandye T.

    2016-01-01

    Introductions of alien species into aquatic ecosystems have been well documented, including invasions of crayfish species; however, little is known about the effects of these introductions on macroinvertebrate communities. The woodland crayfish (Orconectes hylas (Faxon)) has been introduced into the St. Francis River watershed in southeast Missouri and has displaced populations of native crayfish. The effects of O. hylas on macroinvertebrate community composition were investigated in a fourth-order Ozark stream at two locations, one with the presence of O. hylas and one without. Significant differences between sites and across four sampling periods and two habitats were found in five categories of benthic macroinvertebrate metrics: species richness, percent/composition, dominance/diversity, functional feeding groups, and biotic indices. In most seasons and habitat combinations, the invaded site had significantly higher relative abundance of riffle beetles (Coleoptera: Elmidae), and significantly lower Missouri biotic index values, total taxa richness, and both richness and relative abundance of midges (Diptera: Chironomidae). Overall study results indicate that some macroinvertebrate community differences due to the O. hylas invasion were not consistent between seasons and habitats, suggesting that further research on spatial and temporal habitat use and feeding ecology of Ozark crayfish species is needed to improve our understanding of the effects of these invasions on aquatic communities. PMID:26986207

  2. Differences Found in the Macroinvertebrate Community Composition in the Presence or Absence of the Invasive Alien Crayfish, Orconectes hylas.

    PubMed

    Freeland-Riggert, Brandye T; Cairns, Stefan H; Poulton, Barry C; Riggert, Christopher M

    2016-01-01

    Introductions of alien species into aquatic ecosystems have been well documented, including invasions of crayfish species; however, little is known about the effects of these introductions on macroinvertebrate communities