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

Soil biodiversity and soil community composition determine ecosystem multifunctionality

PubMed Central

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

2014-01-01

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. PMID:24639507

Fire severity mediates climate-driven shifts in understorey community composition of black spruce stands of interior Alaska

Treesearch

Emily L. Bernhardt; Teresa N. Hollingsworth; F. Stuart Chapin

2011-01-01

Question: How do pre-fire conditions (community composition and environmental characteristics) and climate-driven disturbance characteristics (fire severity) affect post-fire community composition in black spruce stands? Location: Northern boreal forest, interior Alaska. Methods: We compared plant community composition and environmental stand characteristics in 14...

Agricultural matrices affect ground ant assemblage composition inside forest fragments

PubMed Central

Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was ‘generalist’ both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an ‘ocean of crops’. PMID:29791493

Agricultural matrices affect ground ant assemblage composition inside forest fragments.

PubMed

Assis, Diego Santana; Dos Santos, Iracenir Andrade; Ramos, Flavio Nunes; Barrios-Rojas, Katty Elena; Majer, Jonathan David; Vilela, Evaldo Ferreira

2018-01-01

The establishment of agricultural matrices generally involves deforestation, which leads to fragmentation of the remaining forest. This fragmentation can affect forest dynamics both positively and negatively. Since most animal species are affected, certain groups can be used to measure the impact of such fragmentation. This study aimed to measure the impacts of agricultural crops (matrices) on ant communities of adjacent lower montane Atlantic rainforest fragments. We sampled nine forest fragments at locations surrounded by different agricultural matrices, namely: coffee (3 replicates); sugarcane (3); and pasture (3). At each site we installed pitfall traps along a 500 m transect from the interior of the matrix to the interior of the fragment (20 pitfall traps ~25 m apart). Each transect was partitioned into four categories: interior of the matrix; edge of the matrix; edge of the fragment; and interior of the fragment. For each sample site, we measured ant species richness and ant community composition within each transect category. Ant richness and composition differed between fragments and matrices. Each sample location had a specific composition of ants, probably because of the influence of the nature and management of the agricultural matrices. Species composition in the coffee matrix had the highest similarity to its corresponding fragment. The variability in species composition within forest fragments surrounded by pasture was greatest when compared with forest fragments surrounded by sugarcane or, to a lesser extent, coffee. Functional guild composition differed between locations, but the most representative guild was 'generalist' both in the agricultural matrices and forest fragments. Our results are important for understanding how agricultural matrices act on ant communities, and also, how these isolated forest fragments could act as an island of biodiversity in an 'ocean of crops'.

Rhizosphere Microbial Community Composition Affects Cadmium and Zinc Uptake by the Metal-Hyperaccumulating Plant Arabidopsis halleri

PubMed Central

Muehe, E. Marie; Weigold, Pascal; Adaktylou, Irini J.; Planer-Friedrich, Britta; Kraemer, Ute; Kappler, Andreas

2015-01-01

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants either by directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step toward the application and optimization of phytoremediation. We compared the effects of a “native” and a strongly disturbed (gamma-irradiated) soil microbial communities on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated than on the gamma-irradiated soil. Gamma irradiation affected neither plant growth nor the 1 M HCl-extractable metal content of the soil. However, it strongly altered the soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri identified microbial taxa (Lysobacter, Streptomyces, Agromyces, Nitrospira, “Candidatus Chloracidobacterium”) of higher relative sequence abundance in the rhizospheres of A. halleri plants grown on untreated than on gamma-irradiated soil, leading to hypotheses on their potential effect on plant metal uptake. However, further experimental evidence is required, and wherefore we discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interactions between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction as an efficient and sustainable remediation strategy. PMID:25595759

Top predators affect the composition of naive protist communities, but only in their early-successional stage.

PubMed

Zander, Axel; Gravel, Dominique; Bersier, Louis-Félix; Gray, Sarah M

2016-02-01

Introduced top predators have the potential to disrupt community dynamics when prey species are naive to predation. The impact of introduced predators may also vary depending on the stage of community development. Early-succession communities are likely to have small-bodied and fast-growing species, but are not necessarily good at defending against predators. In contrast, late-succession communities are typically composed of larger-bodied species that are more predator resistant relative to small-bodied species. Yet, these aspects are greatly neglected in invasion studies. We therefore tested the effect of top predator presence on early- and late-succession communities that were either naive or non-naive to top predators. We used the aquatic community held within the leaves of Sarracenia purpurea. In North America, communities have experienced the S. purpurea top predator and are therefore non-naive. In Europe, this predator is not present and its niche has not been filled, making these communities top-predator naive. We collected early- and late-succession communities from two non-naive and two naive sites, which are climatically similar. We then conducted a common-garden experiment, with and without the presence of the top predator, in which we recorded changes in community composition, body size spectra, bacterial density, and respiration. We found that the top predator had no statistical effect on global measures of community structure and functioning. However, it significantly altered protist composition, but only in naive, early-succession communities, highlighting that the state of community development is important for understanding the impact of invasion.

Herbivore species identity and composition affect soil enzymatic activity through altered plant composition in a coastal tallgrass prairie

USDA-ARS?s Scientific Manuscript database

Although single species of herbivores are known to affect soil microbial communities, the effects of herbivore species identity and functional composition on soil microbes is unknown. We tested the effects of single species of orthopterans and multiple species combinations on soil enzymatic activity...

Plant assemblage composition and soil P concentration differentially affect communities of AM and total fungi in a semi-arid grassland.

PubMed

Klabi, Rim; Bell, Terrence H; Hamel, Chantal; Iwaasa, Alan; Schellenberg, Mike; Raies, Aly; St-Arnaud, Marc

2015-01-01

Adding inorganic P- and N-fixing legumes to semi-arid grasslands can increase forage yield, but soil nutrient concentrations and plant cover may also interact to modify soil fungal populations, impacting short- and long-term forage production. We tested the effect of plant assemblage (seven native grasses, seven native grasses + the domesticated N-fixing legume Medicago sativa, seven native grasses + the native N-fixing legume Dalea purpurea or the introduced grass Bromus biebersteinii + M. sativa) and soil P concentration (addition of 0 or 200 P2O5 kg ha(-1) at sowing) on the diversity and community structure of arbuscular mycorrhizal (AM) fungi and total fungi over two consecutive years, using 454-pyrosequencing of 18S rDNA and ITS amplicons. Treatment effects were stronger in the wet year (2008) than the dry year (2009). The presence of an N-fixing legume with native grasses generally increased AM fungal diversity, while the interaction between soil P concentration and plant assemblage modified total fungal community structure in 2008. Excluding interannual variations, which are likely driven by moisture and plant productivity, AM fungal communities in semi-arid grasslands appear to be primarily affected by plant assemblage composition, while the composition of other fungi is more closely linked to soil P. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

PubMed Central

Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C. B.; Jacobsen, Carsten S.

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha-1 to alkaline at 167 t ha-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha-1 followed by significant decrease at 167 t ha-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition.

PubMed

Bang-Andreasen, Toke; Nielsen, Jeppe T; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C B; Jacobsen, Carsten S

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha -1 . We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha -1 to alkaline at 167 t ha -1 . Bacterial numbers significantly increased up to a wood ash dose of 22 t ha -1 followed by significant decrease at 167 t ha -1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha -1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha -1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha -1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes.

PubMed

Rofner, Carina; Peter, Hannes; Catalán, Núria; Drewes, Fabian; Sommaruga, Ruben; Pérez, María Teresa

2017-06-01

Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in-lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate-change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon-specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil-derived carbon and phosphorus. Our work suggests that climate-induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Simulated nitrogen deposition affects community structure of arbuscular mycorrhizal fungi in northern hardwood forests

Treesearch

Linda T.A. Van Diepen; Erik Lilleskov; Kurt S. Pregitzer

2011-01-01

Our previous investigation found elevated nitrogen deposition caused declines in abundance of arbuscular mycorrhizal fungi (AMF) associated with forest trees, but little is known about how nitrogen affects the AMF community composition and structure within forest ecosystems. We hypothesized that N deposition would lead to significant changes in the AMF community...

Do temperate tree species diversity and identity influence soil microbial community function and composition?

PubMed

Khlifa, Rim; Paquette, Alain; Messier, Christian; Reich, Peter B; Munson, Alison D

2017-10-01

Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM), and tree identity. The site was a 4-year-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroResp ™ system, respectively. The relationship between tree species richness and glucose-induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO 2 ) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR]), with higher biomass (glucose-induced respiration [GIR]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity-leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified

Experimentally altered rainfall regimes and host root traits affect grassland arbuscular mycorrhizal fungal communities.

PubMed

Deveautour, Coline; Donn, Suzanne; Power, Sally A; Bennett, Alison E; Powell, Jeff R

2018-04-01

Future climate scenarios predict changes in rainfall regimes. These changes are expected to affect plants via effects on the expression of root traits associated with water and nutrient uptake. Associated microorganisms may also respond to these new precipitation regimes, either directly in response to changes in the soil environment or indirectly in response to altered root trait expression. We characterized arbuscular mycorrhizal (AM) fungal communities in an Australian grassland exposed to experimentally altered rainfall regimes. We used Illumina sequencing to assess the responses of AM fungal communities associated with four plant species sampled in different watering treatments and evaluated the extent to which shifts were associated with changes in root traits. We observed that altered rainfall regimes affected the composition but not the richness of the AM fungal communities, and we found distinctive communities in the increased rainfall treatment. We found no evidence of altered rainfall regime effects via changes in host physiology because none of the studied traits were affected by changes in rainfall. However, specific root length was observed to correlate with AM fungal richness, while concentrations of phosphorus and calcium in root tissue and the proportion of root length allocated to fine roots were correlated to community composition. Our study provides evidence that climate change and its effects on rainfall may influence AM fungal community assembly, as do plant traits related to plant nutrition and water uptake. We did not find evidence that host responses to altered rainfall drive AM fungal community assembly in this grassland ecosystem. © 2018 John Wiley & Sons Ltd.

Storm-scale dynamics of bacterial community composition in throughfall and stemflow

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

2017-12-01

Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization.

PubMed

Wang, Yanan; Ke, Xiubin; Wu, Liqin; Lu, Yahai

2009-02-01

Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene (amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mgNkg(-1) soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH(4)(+)-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE PAGES

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; ...

2017-03-13

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil.

PubMed

Štursová, Martina; Bárta, Jiří; Šantrůčková, Hana; Baldrian, Petr

2016-12-01

Forests are recognised as spatially heterogeneous ecosystems. However, knowledge of the small-scale spatial variation in microbial abundance, community composition and activity is limited. Here, we aimed to describe the heterogeneity of environmental properties, namely vegetation, soil chemical composition, fungal and bacterial abundance and community composition, and enzymatic activity, in the topsoil in a small area (36 m 2 ) of a highly heterogeneous regenerating temperate natural forest, and to explore the relationships among these variables. The results demonstrated a high level of spatial heterogeneity in all properties and revealed differences between litter and soil. Fungal communities had substantially higher beta-diversity than bacterial communities, which were more uniform and less spatially autocorrelated. In litter, fungal communities were affected by vegetation and appeared to be more involved in decomposition. In the soil, chemical composition affected both microbial abundance and the rates of decomposition, whereas the effect of vegetation was small. Importantly, decomposition appeared to be concentrated in hotspots with increased activity of multiple enzymes. Overall, forest topsoil should be considered a spatially heterogeneous environment in which the mean estimates of ecosystem-level processes and microbial community composition may confound the existence of highly specific microenvironments. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Urban stormwater runoff drives denitrifying community composition through changes in sediment texture and carbon content.

PubMed

Perryman, Shane E; Rees, Gavin N; Walsh, Christopher J; Grace, Michael R

2011-05-01

The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be

The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

PubMed Central

Hawlena, Hadas; Rynkiewicz, Evelyn; Toh, Evelyn; Alfred, Andrew; Durden, Lance A; Hastriter, Michael W; Nelson, David E; Rong, Ruichen; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith

2013-01-01

Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment. PMID:22739493

The Importance of Dispersal for Bacterial Community Composition and Functioning

PubMed Central

Lindström, Eva S.; Östman, Örjan

2011-01-01

We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into. PMID:21998714

Trait-specific responses of wild bee communities to landscape composition, configuration and local factors.

PubMed

Hopfenmüller, Sebastian; Steffan-Dewenter, Ingolf; Holzschuh, Andrea

2014-01-01

Land-use intensification and loss of semi-natural habitats have induced a severe decline of bee diversity in agricultural landscapes. Semi-natural habitats like calcareous grasslands are among the most important bee habitats in central Europe, but they are threatened by decreasing habitat area and quality, and by homogenization of the surrounding landscape affecting both landscape composition and configuration. In this study we tested the importance of habitat area, quality and connectivity as well as landscape composition and configuration on wild bees in calcareous grasslands. We made detailed trait-specific analyses as bees with different traits might differ in their response to the tested factors. Species richness and abundance of wild bees were surveyed on 23 calcareous grassland patches in Southern Germany with independent gradients in local and landscape factors. Total wild bee richness was positively affected by complex landscape configuration, large habitat area and high habitat quality (i.e. steep slopes). Cuckoo bee richness was positively affected by complex landscape configuration and large habitat area whereas habitat specialists were only affected by the local factors habitat area and habitat quality. Small social generalists were positively influenced by habitat area whereas large social generalists (bumblebees) were positively affected by landscape composition (high percentage of semi-natural habitats). Our results emphasize a strong dependence of habitat specialists on local habitat characteristics, whereas cuckoo bees and bumblebees are more likely affected by the surrounding landscape. We conclude that a combination of large high-quality patches and heterogeneous landscapes maintains high bee species richness and communities with diverse trait composition. Such diverse communities might stabilize pollination services provided to crops and wild plants on local and landscape scales.

Trait-Specific Responses of Wild Bee Communities to Landscape Composition, Configuration and Local Factors

PubMed Central

Hopfenmüller, Sebastian; Steffan-Dewenter, Ingolf; Holzschuh, Andrea

2014-01-01

Land-use intensification and loss of semi-natural habitats have induced a severe decline of bee diversity in agricultural landscapes. Semi-natural habitats like calcareous grasslands are among the most important bee habitats in central Europe, but they are threatened by decreasing habitat area and quality, and by homogenization of the surrounding landscape affecting both landscape composition and configuration. In this study we tested the importance of habitat area, quality and connectivity as well as landscape composition and configuration on wild bees in calcareous grasslands. We made detailed trait-specific analyses as bees with different traits might differ in their response to the tested factors. Species richness and abundance of wild bees were surveyed on 23 calcareous grassland patches in Southern Germany with independent gradients in local and landscape factors. Total wild bee richness was positively affected by complex landscape configuration, large habitat area and high habitat quality (i.e. steep slopes). Cuckoo bee richness was positively affected by complex landscape configuration and large habitat area whereas habitat specialists were only affected by the local factors habitat area and habitat quality. Small social generalists were positively influenced by habitat area whereas large social generalists (bumblebees) were positively affected by landscape composition (high percentage of semi-natural habitats). Our results emphasize a strong dependence of habitat specialists on local habitat characteristics, whereas cuckoo bees and bumblebees are more likely affected by the surrounding landscape. We conclude that a combination of large high-quality patches and heterogeneous landscapes maintains high bee species richness and communities with diverse trait composition. Such diverse communities might stabilize pollination services provided to crops and wild plants on local and landscape scales. PMID:25137311

Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

PubMed

Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

2014-01-01

Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

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.…

Eco-evolutionary processes affecting plant-herbivore interactions during early community succession.

PubMed

Howard, Mia M; Kalske, Aino; Kessler, André

2018-06-01

The quality and outcome of organismal interactions are not only a function of genotypic composition of the interacting species, but also the surrounding environment. Both the strength and direction of natural selection on interacting populations vary with the community context, which itself is changed by these interactions. Here, we test for the role of interacting evolutionary and ecological processes in plant-herbivore interactions during early community succession in the tall goldenrod, Solidago altissima. We use surveys in a large-scale field experiment with repeated plots representing 6 years of early oldfield succession and reciprocal transplant common garden experiments to test for the relative importance of rapid evolution (genetic) and environmental changes (soil quality) in affecting mean plant resistance and growth phenotypes during community succession. While plant growth varied strongly with soil quality over the first 5 years of agricultural abandonment, plant secondary metabolism, and herbivore resistance varied minimally with the soil environment. Instead, mean composition and abundance of plant secondary compound bouquets differed between S. altissima plants from populations collected in communities in the first ("early") and sixth ("intermediate") years of oldfield succession, which was reflected in the feeding preference of the specialist herbivore, Trirhabda virgata, for early succession lines. Moreover, this preference was most pronounced on poorer quality, early succession soils. Overall, our data demonstrate that plant quality varies for insect herbivores during the course of early succession and this change is a combination of altered genotypic composition of the population and phenotypic plasticity in different soil environments.

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

Agricultural factors affecting Fusarium communities in wheat kernels.

PubMed

Karlsson, Ida; Friberg, Hanna; Kolseth, Anna-Karin; Steinberg, Christian; Persson, Paula

2017-07-03

Fusarium head blight (FHB) is a devastating disease of cereals caused by Fusarium fungi. The disease is of great economic importance especially owing to reduced grain quality due to contamination by a range of mycotoxins produced by Fusarium. Disease control and prediction is difficult because of the many Fusarium species associated with FHB. Different species may respond differently to control methods and can have both competitive and synergistic interactions. Therefore, it is important to understand how agricultural practices affect Fusarium at the community level. Lower levels of Fusarium mycotoxin contamination of organically produced cereals compared with conventionally produced have been reported, but the causes of these differences are not well understood. The aim of our study was to investigate the effect of agricultural factors on Fusarium abundance and community composition in different cropping systems. Winter wheat kernels were collected from 18 organically and conventionally cultivated fields in Sweden, paired based on their geographical distance and the wheat cultivar grown. We characterised the Fusarium community in harvested wheat kernels using 454 sequencing of translation elongation factor 1-α amplicons. In addition, we quantified Fusarium spp. using real-time PCR to reveal differences in biomass between fields. We identified 12 Fusarium operational taxonomic units (OTUs) with a median of 4.5 OTUs per field. Fusarium graminearum was the most abundant species, while F. avenaceum had the highest occurrence. The abundance of Fusarium spp. ranged two orders of magnitude between fields. Two pairs of Fusarium species co-occurred between fields: F. poae with F. tricinctum and F. culmorum with F. sporotrichoides. We could not detect any difference in Fusarium communities between the organic and conventional systems. However, agricultural intensity, measured as the number of pesticide applications and the amount of nitrogen fertiliser applied, had an

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

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.

Management intensity at field and landscape levels affects the structure of generalist predator communities.

PubMed

Rusch, Adrien; Birkhofer, Klaus; Bommarco, Riccardo; Smith, Henrik G; Ekbom, Barbara

2014-07-01

Agricultural intensification is recognised as a major driver of biodiversity loss in human-modified landscapes. Several agro-environmental measures at different spatial scales have been suggested to mitigate the negative impact of intensification on biodiversity and ecosystem services. The effect of these measures on the functional structure of service-providing communities remains, however, largely unexplored. Using two distinct landscape designs, we examined how the management options of organic farming at the field scale and crop diversification at the landscape level affect the taxonomic and functional structure of generalist predator communities and how these effects vary along a landscape complexity gradient. Organic farming as well as landscapes with longer and more diversified crop rotations enhanced the activity-density of spiders and rove beetles, but not the species richness or evenness. Our results indicate that the two management options affected the functional composition of communities, as they primarily enhanced the activity-density of functionally similar species. The two management options increased the functional similarity between spider species in regards to hunting mode and habitat preference. Organic farming enhanced the functional similarity of rove beetles. Management options at field and landscape levels were generally more important predictors of community structure when compared to landscape complexity. Our study highlights the importance of considering the functional composition of generalist predators in order to understand how agro-environmental measures at various scales shape community assemblages and ecosystem functioning in agricultural landscapes.

Can anthropic fires affect epigaeic and hypogaeic Cerrado ant (Hymenoptera: Formicidae) communities in the same way?

PubMed

Canedo-Júnior, Ernesto de Oliveira; Cuissi, Rafael Gonçalves; Nelson Henrique de Almeida, Curi; Demetrio, Guilherme Ramos; Lasmar, Chaim José; Malves, Kira

2016-03-01

Fire occurrences are a common perturbation in Cerrado ecosystems, and may differently impact the local biodiversity. Arthropods are one of the taxa affected by fires, and among them, ants are known as good bioindicators. We aimed to evaluate the effect of anthropic fires on epigaeic and hypogaeic ant communities (species richness and composition) in Cerrado areas with different post-fire event recovery periods. We conducted the study in four Cerrado areas during two weeks of 2012 dry season: one unburned and three at different post-fire times (one month, one and two years). We sampled ants with pitfall traps in epigaeic and hypogaeic microhabitats. We collected 71 ant morpho-species from 25 genera. In the epigaeic microhabitat we sampled 56 morpho-species and 42 in the hypogaeic microhabitat. The area with the shortest recovery time presented lower epigaeic ant species richness (4.3 ± 2.00) in comparison to the other areas (8.1 ± 2.68 species on one year area; 10.3 ± 2.66 species on two years area; 10.4 ± 2.31 species on control area), but recovery time did not affect hypogaeic ant species richness. Regarding ant species composition, fire did not directly affect hypogaeic ant species, which remained the same even one month after fire event. However, two years were not enough to reestablish ant species composition in both microhabitats in relation to our control group samples. Our study is the first to assess anthropic fire effects upon epigaeic and hypogaeic ants communities; highlighting the importance of evaluating different microhabitats, to more accurately detect the effects of anthropic disturbances in biological communities. We concluded that ant communities are just partially affected by fire occurrences, and epigaeic assemblages are the most affected ones in comparison to hypogaeic ants. Furthermore the study provides knowledge to aid in the creation of vegetation management programs that allow Cerrado conservation.

Biodiversity increases functional and compositional resistance, but decreases resilience in phytoplankton communities.

PubMed

Baert, Jan M; De Laender, Frederik; Sabbe, Koen; Janssen, Colin R

2016-12-01

There is now ample evidence that biodiversity stabilizes aggregated ecosystem functions, such as primary production, in changing environments. In primary producer systems, this stabilizing effect is found to be driven by higher functional resistance (i.e., reduced changes in functions by environmental changes) rather than through higher functional resilience (i.e., rapid recovery following environmental changes) in more diverse systems. The stability of aggregated ecosystem functions directly depends on changes in species composition and by consequence their functional contributions to ecosystem functions. Still, it remains only theoretically explored how biodiversity can stabilize ecosystem functions by affecting compositional stability. Here, we demonstrate how biodiversity effects on compositional stability drive biodiversity effects on functional stability in diatom communities. In a microcosm experiment, we exposed 39 communities of five different levels of species richness (1, 2, 4, 6, and 8 species) to three concentrations of a chemical stressor (0, 25, and 250 μg/L atrazine) for four weeks, after which all communities were transferred to atrazine-free medium for three more weeks. Biodiversity simultaneously increased, increasing functional and compositional resistance, but decreased functional and compositional resilience. These results confirm the theoretically proposed link between biodiversity effects on functional and compositional stability in primary producer systems, and provide a mechanistic underpinning for observed biodiversity-stability relationships. Finally, we discuss how higher compositional stability can be expected to become increasingly important in stabilizing ecosystem functions under field conditions when multiple environmental stressors fluctuate simultaneously. © 2016 by the Ecological Society of America.

Predicting community composition from pairwise interactions

NASA Astrophysics Data System (ADS)

Friedman, Jonathan; Higgins, Logan; Gore, Jeff

The ability to predict the structure of complex, multispecies communities is crucial for understanding the impact of species extinction and invasion on natural communities, as well as for engineering novel, synthetic communities. Communities are often modeled using phenomenological models, such as the classical generalized Lotka-Volterra (gLV) model. While a lot of our intuition comes from such models, their predictive power has rarely been tested experimentally. To directly assess the predictive power of this approach, we constructed synthetic communities comprised of up to 8 soil bacteria. We measured the outcome of competition between all species pairs, and used these measurements to predict the composition of communities composed of more than 2 species. The pairwise competitions resulted in a diverse set of outcomes, including coexistence, exclusion, and bistability, and displayed evidence for both interference and facilitation. Most pair outcomes could be captured by the gLV framework, and the composition of multispecies communities could be predicted for communities composed solely of such pairs. Our results demonstrate the predictive ability and utility of simple phenomenology, which enables accurate predictions in the absence of mechanistic details.

Effect of ocean acidification on the structure and fatty acid composition of a natural plankton community in the Baltic Sea

NASA Astrophysics Data System (ADS)

Bermúdez, Rafael; Winder, Monika; Stuhr, Annegret; Almén, Anna-Karin; Engström-Öst, Jonna; Riebesell, Ulf

2016-12-01

Increasing atmospheric carbon dioxide (CO2) is changing seawater chemistry towards reduced pH, which affects various properties of marine organisms. Coastal and brackish water communities are expected to be less affected by ocean acidification (OA) as these communities are typically adapted to high fluctuations in CO2 and pH. Here we investigate the response of a coastal brackish water plankton community to increasing CO2 levels as projected for the coming decades and the end of this century in terms of community and biochemical fatty acid (FA) composition. A Baltic Sea plankton community was enclosed in a set of offshore mesocosms and subjected to a CO2 gradient ranging from natural concentrations ( ˜ 347 µatm fCO2) up to values projected for the year 2100 ( ˜ 1333 µatm fCO2). We show that the phytoplankton community composition was resilient to CO2 and did not diverge between the treatments. Seston FA composition was influenced by community composition, which in turn was driven by silicate and phosphate limitation in the mesocosms and showed no difference between the CO2 treatments. These results suggest that CO2 effects are dampened in coastal communities that already experience high natural fluctuations in pCO2. Although this coastal plankton community was tolerant of high pCO2 levels, hypoxia and CO2 uptake by the sea can aggravate acidification and may lead to pH changes outside the currently experienced range for coastal organisms.

[Impact of land-use type changes on soil nitrification and ammonia-oxidizing bacterial community composition].

PubMed

Yang, Li-Lin; Mao, Ren-Zhao; Liu, Jun-Jie; Liu, Xiao-Jing

2011-11-01

A comparative study was conducted to determine nitrification potentials and ammonia-oxidizing bacterial (AOB) community composition in 0-20 cm soil depth in adjacent native forest,natural grassland, and cropland soils on the Tibetan Plateau, by incubation experiment and by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, respectively. Cropland has the highest nitrification potential and nitrate concentration among the three land-use types (LUT), approximately 9 folds and more than 11 folds than that of the forests and grasslands, respectively. NO3(-) -N accounted for 70%-90% of inorganic N in cropland soil, while NH4(+) -N was the main form of inorganic N in forest and grassland soils. Nitrification potentials and nitrate concentrations showed no significant difference between native forest and grassland soils. The native forest showed the lowest nitrification potentials and the lowest AOB diversity and community composition among the three LUT. Conversions from natural grasslands to croplands remarkably decreased the AOB diversity and composition, but croplands remain high similarity in AOB community composition compared with grasslands. The minimal and the lowest diversity of AOB in native forests directly resulted to the lowest nitrification potentials compared to natural grasslands and croplands. From the fact of the highest nitrification potentials and nitrate concentrations in croplands indicated that there were the most substantial AOB with higher activity and priority. The results provide evidence that changes of land-use type can affect both soil nitrogen internal cycling process, the diversity, community and activity of AOB, which further affect soil environment quality and the long-term sustainability of ecosystems.

Landscape fragmentation affects responses of avian communities to climate change.

PubMed

Jarzyna, Marta A; Porter, William F; Maurer, Brian A; Zuckerberg, Benjamin; Finley, Andrew O

2015-08-01

Forecasting the consequences of climate change is contingent upon our understanding of the relationship between biodiversity patterns and climatic variability. While the impacts of climate change on individual species have been well-documented, there is a paucity of studies on climate-mediated changes in community dynamics. Our objectives were to investigate the relationship between temporal turnover in avian biodiversity and changes in climatic conditions and to assess the role of landscape fragmentation in affecting this relationship. We hypothesized that community turnover would be highest in regions experiencing the most pronounced changes in climate and that these patterns would be reduced in human-dominated landscapes. To test this hypothesis, we quantified temporal turnover in avian communities over a 20-year period using data from the New York State Breeding Atlases collected during 1980-1985 and 2000-2005. We applied Bayesian spatially varying intercept models to evaluate the relationship between temporal turnover and temporal trends in climatic conditions and landscape fragmentation. We found that models including interaction terms between climate change and landscape fragmentation were superior to models without the interaction terms, suggesting that the relationship between avian community turnover and changes in climatic conditions was affected by the level of landscape fragmentation. Specifically, we found weaker associations between temporal turnover and climatic change in regions with prevalent habitat fragmentation. We suggest that avian communities in fragmented landscapes are more robust to climate change than communities found in contiguous habitats because they are comprised of species with wider thermal niches and thus are less susceptible to shifts in climatic variability. We conclude that highly fragmented regions are likely to undergo less pronounced changes in composition and structure of faunal communities as a result of climate change

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

PubMed

Langer, Julia A F; Sharma, Rahul; Schmidt, Susanne I; Bahrdt, Sebastian; Horn, Henriette G; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

2017-01-01

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak

PubMed Central

Sharma, Rahul; Schmidt, Susanne I.; Bahrdt, Sebastian; Horn, Henriette G.; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P.; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

2017-01-01

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2. PMID:28445483

How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

PubMed

Munoz, François; Ramesh, B R; Couteron, Pierre

2014-08-01

Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes.

PubMed

Petermann, Jana S; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W; Gossner, Martin M

2016-01-01

Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes

PubMed Central

Petermann, Jana S.; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W.; Gossner, Martin M.

2016-01-01

Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil

PubMed Central

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil.

PubMed

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [ Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of

Long-term agricultural fertilization alters arbuscular mycorrhizal fungal community composition and barley (Hordeum vulgare) mycorrhizal carbon and phosphorus exchange.

PubMed

Williams, Alwyn; Manoharan, Lokeshwaran; Rosenstock, Nicholas P; Olsson, Pål Axel; Hedlund, Katarina

2017-01-01

Agricultural fertilization significantly affects arbuscular mycorrhizal fungal (AMF) community composition. However, the functional implications of community shifts are unknown, limiting understanding of the role of AMF in agriculture. We assessed AMF community composition at four sites managed under the same nitrogen (N) and phosphorus (P) fertilizer regimes for 55 yr. We also established a glasshouse experiment with the same soils to investigate AMF-barley (Hordeum vulgare) nutrient exchange, using carbon ( 13 C) and 33 P isotopic labelling. N fertilization affected AMF community composition, reducing diversity; P had no effect. In the glasshouse, AMF contribution to plant P declined with P fertilization, but was unaffected by N. Barley C allocation to AMF also declined with P fertilization. As N fertilization increased, C allocation to AMF per unit of P exchanged increased. This occurred with and without P fertilization, and was concomitant with reduced barley biomass. AMF community composition showed no relationship with glasshouse experiment results. The results indicate that plants can reduce C allocation to AMF in response to P fertilization. Under N fertilization, plants allocate an increasing amount of C to AMF and receive relatively less P. This suggests an alteration in the terms of P-C exchange under N fertilization regardless of soil P status. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Prolonged exposure does not increase soil microbial community compositional response to warming along geothermal gradients.

PubMed

Radujkovic, Dajana; Verbruggen, Erik; Sigurdsson, Bjarni D; Leblans, Niki I W; Janssens, Ivan A; Vicca, Sara; Weedon, James T

2018-02-01

Global change is expected to affect soil microbial communities through their responsiveness to temperature. It has been proposed that prolonged exposure to elevated temperatures may lead to progressively larger effects on soil microbial community composition. However, due to the relatively short-term nature of most warming experiments, this idea has been challenging to evaluate. The present study took the advantage of natural geothermal gradients (from +1°C to +19°C above ambient) in two subarctic grasslands to test the hypothesis that long-term exposure (>50 years) intensifies the effect of warming on microbial community composition compared to short-term exposure (5-7 years). Community profiles from amplicon sequencing of bacterial and fungal rRNA genes did not support this hypothesis: significant changes relative to ambient were observed only starting from the warming intensity of +9°C in the long term and +7°C/+3°C in the short term, for bacteria and fungi, respectively. Our results suggest that microbial communities in high-latitude grasslands will not undergo lasting shifts in community composition under the warming predicted for the coming 100 years (+2.2°C to +8.3°C). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Arbuscular mycorrhizal fungal community composition affected by original elevation rather than translocation along an altitudinal gradient on the Qinghai-Tibet Plateau

NASA Astrophysics Data System (ADS)

Yang, Wei; Zheng, Yong; Gao, Cheng; Duan, Ji-Chuang; Wang, Shi-Ping; Guo, Liang-Dong

2016-11-01

Elucidating arbuscular mycorrhizal (AM) fungal responses to elevation changes is critical to improve understanding of microbial function in ecosystems under global asymmetrical climate change scenarios. Here we examined AM fungal community in a two-year reciprocal translocation of vegetation-intact soil blocks along an altitudinal gradient (3,200 m to 3,800 m) in an alpine meadow on the Qinghai-Tibet Plateau. AM fungal spore density was significantly higher at lower elevation than at higher elevation regardless of translocation, except that this parameter was significantly increased by upward translocation from original 3,200 m to 3,400 m and 3,600 m. Seventy-three operational taxonomic units (OTUs) of AM fungi were recovered using 454-pyrosequencing of 18S rDNA sequences at a 97% sequence similarity. Original elevation, downward translocation and upward translocation did not significantly affect AM fungal OTU richness. However, with increasing altitude the OTU richness of Acaulosporaceae and Ambisporaceae increased, but the OTU richness of Gigasporaceae and Glomeraceae decreased generally. The AM fungal community composition was significantly structured by original elevation but not by downward translocation and upward translocation. Our findings highlight that compared with the short-term reciprocal translocation, original elevation is a stronger determinant in shaping AM fungal community in the Qinghai-Tibet alpine meadow.

Arbuscular mycorrhizal fungal community composition affected by original elevation rather than translocation along an altitudinal gradient on the Qinghai-Tibet Plateau.

PubMed

Yang, Wei; Zheng, Yong; Gao, Cheng; Duan, Ji-Chuang; Wang, Shi-Ping; Guo, Liang-Dong

2016-11-09

Elucidating arbuscular mycorrhizal (AM) fungal responses to elevation changes is critical to improve understanding of microbial function in ecosystems under global asymmetrical climate change scenarios. Here we examined AM fungal community in a two-year reciprocal translocation of vegetation-intact soil blocks along an altitudinal gradient (3,200 m to 3,800 m) in an alpine meadow on the Qinghai-Tibet Plateau. AM fungal spore density was significantly higher at lower elevation than at higher elevation regardless of translocation, except that this parameter was significantly increased by upward translocation from original 3,200 m to 3,400 m and 3,600 m. Seventy-three operational taxonomic units (OTUs) of AM fungi were recovered using 454-pyrosequencing of 18S rDNA sequences at a 97% sequence similarity. Original elevation, downward translocation and upward translocation did not significantly affect AM fungal OTU richness. However, with increasing altitude the OTU richness of Acaulosporaceae and Ambisporaceae increased, but the OTU richness of Gigasporaceae and Glomeraceae decreased generally. The AM fungal community composition was significantly structured by original elevation but not by downward translocation and upward translocation. Our findings highlight that compared with the short-term reciprocal translocation, original elevation is a stronger determinant in shaping AM fungal community in the Qinghai-Tibet alpine meadow.

Arbuscular mycorrhizal fungal community composition affected by original elevation rather than translocation along an altitudinal gradient on the Qinghai-Tibet Plateau

PubMed Central

Yang, Wei; Zheng, Yong; Gao, Cheng; Duan, Ji-Chuang; Wang, Shi-Ping; Guo, Liang-Dong

2016-01-01

Elucidating arbuscular mycorrhizal (AM) fungal responses to elevation changes is critical to improve understanding of microbial function in ecosystems under global asymmetrical climate change scenarios. Here we examined AM fungal community in a two-year reciprocal translocation of vegetation-intact soil blocks along an altitudinal gradient (3,200 m to 3,800 m) in an alpine meadow on the Qinghai-Tibet Plateau. AM fungal spore density was significantly higher at lower elevation than at higher elevation regardless of translocation, except that this parameter was significantly increased by upward translocation from original 3,200 m to 3,400 m and 3,600 m. Seventy-three operational taxonomic units (OTUs) of AM fungi were recovered using 454-pyrosequencing of 18S rDNA sequences at a 97% sequence similarity. Original elevation, downward translocation and upward translocation did not significantly affect AM fungal OTU richness. However, with increasing altitude the OTU richness of Acaulosporaceae and Ambisporaceae increased, but the OTU richness of Gigasporaceae and Glomeraceae decreased generally. The AM fungal community composition was significantly structured by original elevation but not by downward translocation and upward translocation. Our findings highlight that compared with the short-term reciprocal translocation, original elevation is a stronger determinant in shaping AM fungal community in the Qinghai-Tibet alpine meadow. PMID:27827400

Studies on bacterial community composition are affected by the time and storage method of the rumen content

PubMed Central

Duarte Messana, Juliana; Takeshi Kishi, Luciano; Lino Dias, Ana Veronica; Berchielli, Telma Teresinha

2017-01-01

The objective of this study was to investigate three storage methods and four storage times for rumen sampling in terms of quality and yield of extracted metagenomic DNA as well as the composition of the rumen bacterial community. One Nellore steer fitted with a ruminal silicone-type cannula was used as a donor of ruminal contents. The experiment comprised 11 experimental groups: pellet control (PC), lyophilized control (LC), P-20: pellet stored frozen at -20°C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C for a period of 3, 6, and 12 months. Metagenomic DNA concentrations were measured spectrophotometrically and fluorometrically and ion torrent sequencing was used to assess the bacterial community composition. The L-20 method could not maintain the yield of DNA during storage. In addition, the P-80 group showed a greater yield of metagenomic DNA than the other groups after 6 months of storage. Rumen samples stored as pellets (P-20 and P-80) resulted in lower richness Chao 1, ACE, and Shannon Wiener indices when compared to PC, while LC and PC were only different in richness ACE. The storage method and storage time influenced the proportions of 14 of 17 phyla identified by sequencing. In the P-20 group, the proportion of Cyanobacteria, Elusimicrobia, Fibrobacteres, Lentisphaerae, Proteobacteria, and Spirochaetes phyla identified was lower than 1%. In the P-80 group, there was an increase in the proportion of the Bacteroidetes phylum (p = 0.010); however, the proportion of Actinobacteria, Chloroflexi, SR1, Synergistetes, TM7, and WPS.2 phyla were unchanged compared to the PC group (p > 0.05). The class Clostridium was the most abundant in all stored groups and increased in its proportion, especially in the L-20 group. The rumen sample storage time significantly reduced the yield of metagenomic DNA extracted. Therefore, the storage method can

Studies on bacterial community composition are affected by the time and storage method of the rumen content.

PubMed

Granja-Salcedo, Yury Tatiana; Ramirez-Uscategui, Ricardo Andrés; Machado, Elwi Guillermo; Duarte Messana, Juliana; Takeshi Kishi, Luciano; Lino Dias, Ana Veronica; Berchielli, Telma Teresinha

2017-01-01

The objective of this study was to investigate three storage methods and four storage times for rumen sampling in terms of quality and yield of extracted metagenomic DNA as well as the composition of the rumen bacterial community. One Nellore steer fitted with a ruminal silicone-type cannula was used as a donor of ruminal contents. The experiment comprised 11 experimental groups: pellet control (PC), lyophilized control (LC), P-20: pellet stored frozen at -20°C for a period of 3, 6, and 12 months, P-80: pellet stored frozen at -80°C for a period of 3, 6, and 12 months, and L-20: lyophilized sample stored frozen at -20°C for a period of 3, 6, and 12 months. Metagenomic DNA concentrations were measured spectrophotometrically and fluorometrically and ion torrent sequencing was used to assess the bacterial community composition. The L-20 method could not maintain the yield of DNA during storage. In addition, the P-80 group showed a greater yield of metagenomic DNA than the other groups after 6 months of storage. Rumen samples stored as pellets (P-20 and P-80) resulted in lower richness Chao 1, ACE, and Shannon Wiener indices when compared to PC, while LC and PC were only different in richness ACE. The storage method and storage time influenced the proportions of 14 of 17 phyla identified by sequencing. In the P-20 group, the proportion of Cyanobacteria, Elusimicrobia, Fibrobacteres, Lentisphaerae, Proteobacteria, and Spirochaetes phyla identified was lower than 1%. In the P-80 group, there was an increase in the proportion of the Bacteroidetes phylum (p = 0.010); however, the proportion of Actinobacteria, Chloroflexi, SR1, Synergistetes, TM7, and WPS.2 phyla were unchanged compared to the PC group (p > 0.05). The class Clostridium was the most abundant in all stored groups and increased in its proportion, especially in the L-20 group. The rumen sample storage time significantly reduced the yield of metagenomic DNA extracted. Therefore, the storage method can

Transfer to forest nurseries significantly affects mycorrhizal community composition of Asteropeia mcphersonii wildings.

PubMed

Henry, Charline; Raivoarisoa, Jeanne-Françoise; Razafimamonjy, Angélo; Ramanankierana, Heriniaina; Andrianaivomahefa, Paul; Ducousso, Marc; Selosse, Marc-André

2017-05-01

Mycorrhizal symbiosis is extremely important for tree growth, survival and resistance after transplantation particularly in Madagascar where deforestation is a major concern. The importance of mycorrhizal symbiosis is further increased when soil conditions at the planting site are limiting. To identify technical itineraries capable of improving ecological restoration in Madagascar, we needed to obtain native ectomycorrhizal (ECM) saplings with a wide diversity of ECM fungi. To this end, we transplanted ECM seedlings from the wild (wildlings) to a nursery. Using molecular characterisation of internal transcribed spacer (ITS) rDNA, we tested the effect of transplanting Asteropeia mcphersonii wildlings on ECM communities after 8 months of growth in the nursery. With or without the addition of soil from the site where the seedlings were sampled to the nursery substrate, we observed a dramatic change in the composition of fungal communities with a decrease in the ECM infection rate, a tremendous increase in the abundance of an operational taxonomic unit (OTU) taxonomically close to the order Trechisporales and the disappearance of all OTUs of Boletales. Transplanting to the nursery and/or to nursery conditions was shown to be incompatible with the survival and even less with the development in the nursery of most ECM fungi naturally associated with A. mcphersonii wildings.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

USGS Publications Warehouse

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

2017-01-01

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

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.

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.

Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

USGS Publications Warehouse

Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

2015-01-01

Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study

Effects of viruses and predators on prokaryotic community composition.

PubMed

Jardillier, Ludwig; Bettarel, Yvan; Richardot, Mathilde; Bardot, Corinne; Amblard, Christian; Sime-Ngando, Télesphore; Debroas, Didier

2005-11-01

Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (<5 microm: treatment filtered on 5 microm, without ciliates and metazoans; UNF: unfiltered treatment with all planktonic communities). Enrichments of natural viruses (<1.2 microm: with a natural virus concentration; <1.2 mum V and VV: with enrichment leading to a double or triple concentration of viruses, respectively) were used to indirectly assess the control of virioplankton. Viral activity was estimated from the frequency of visibly infected cells (FVIC). PCC was determined by fluorescence in situ hybridization (FISH) and terminal restriction fragment length polymorphism (T-RFLP). In this study, PCC was affected by the eukaryote communities (especially flagellates), and viruses to a lesser extent. Cyanobacteria declined significantly during the experiment and were highly correlated with the FVIC. In addition, the 503-bp terminal restriction fragment (T-RF) disappeared in treatments with virus enrichments, suggesting possible viral-associated mortality processes, whereas the 506-bp T-RF was not affected in these treatments. On one hand, these results suggest a control of the PCC: first, by viral lysis of some dominant phylotypes and second, by interspecific competition between resistant strains for the uptake of substrates released by this lysis. The increase of Archaea may suggest that these cells benefit such resources. On the other hand, the disappearance and the stable proportion of some dominant phylotypes suggested a selection pressure due to the predatory activity on prokaryotes. In conclusion, prokaryotic abundance appears to be mainly controlled by flagellate protists, which also affected PCC, whereas viruses seemed to be essentially responsible

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

PubMed

Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

2018-07-01

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

Relationships Between Bird Communities and Forest Age, Structure, Species Composition and Fragmentation in the West Gulf Coastal Plain

Treesearch

Richard N. Conner; James G. Dickson

1997-01-01

Bird communities of the West Gulf Coastal Plain are strongly influenced by the stage of forest succession, species composition of understory and overstory vegetation, and forest structure. Alteration of plant communities through forest management and natural disturbances typically does not eliminate birds as a fauna1 group from the area affected, but will replace some...

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization.

PubMed

Enwall, Karin; Philippot, Laurent; Hallin, Sara

2005-12-01

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity

Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

USGS Publications Warehouse

Haack, S.K.; Garchow, H.; Klug, M.J.; Forney, L.J.

1995-01-01

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

Contrasting outcomes of species- and community-level analyses of the temporal consistency of functional composition.

PubMed

Katabuchi, Masatoshi; Wright, S Joseph; Swenson, Nathan G; Feeley, Kenneth J; Condit, Richard; Hubbell, Stephen P; Davies, Stuart J

2017-09-01

Multiple anthropogenic drivers affect every natural community, and there is broad interest in using functional traits to understand and predict the consequences for future biodiversity. There is, however, no consensus regarding the choice of analytical methods. We contrast species- and community-level analyses of change in the functional composition for four traits related to drought tolerance using three decades of repeat censuses of trees in the 50-ha Forest Dynamics Plot on Barro Colorado Island, Panama. Community trait distributions shifted significantly through time, which may indicate a shift toward more drought tolerant species. However, at the species level, changes in abundance were unrelated to trait values. To reconcile these seemingly contrasting results, we evaluated species-specific contributions to the directional shifts observed at the community level. Abundance changes of just one to six of 312 species were responsible for the community-level shifts observed for each trait. Our results demonstrate that directional changes in community-level functional composition can result from idiosyncratic change in a few species rather than widespread community-wide changes associated with functional traits. Future analyses of directional change in natural communities should combine community-, species-, and possibly individual-level analyses to uncover relationships with function that can improve understanding and enable prediction. © 2017 by the Ecological Society of America.

Prey dispersal rate affects prey species composition and trait diversity in response to multiple predators in metacommunities.

PubMed

Howeth, Jennifer G; Leibold, Mathew A

2010-09-01

1. Recent studies indicate that large-scale spatial processes can alter local community structuring mechanisms to determine local and regional assemblages of predators and their prey. In metacommunities, this may occur when the functional diversity represented in the regional predator species pool interacts with the rate of prey dispersal among local communities to affect prey species diversity and trait composition at multiple scales. 2. Here, we test for effects of prey dispersal rate and spatially and temporally heterogeneous predation from functionally dissimilar predators on prey structure in pond mesocosm metacommunities. An experimental metacommunity consisted of three pond mesocosm communities supporting two differentially size-selective invertebrate predators and their zooplankton prey. In each metacommunity, two communities maintained constant predation and supported either Gyrinus sp. (Coleoptera) or Notonecta ungulata (Hemiptera) predators generating a spatial prey refuge while the third community supported alternating predation from Gyrinus sp. and N. ungulata generating a temporal prey refuge. Mesocosm metacommunities were connected at either low (0.7% day(-1)) or high (10% day(-1)) planktonic prey dispersal. The diversity, composition and body size of zooplankton prey were measured at local and regional (metacommunity) scales. 3. Metacommunities experiencing the low prey dispersal rate supported the greatest regional prey species diversity (H') and evenness (J'). Neither dispersal rate nor predation regime affected local prey diversity or evenness. The spatial prey refuge at low dispersal maintained the largest difference in species composition and body size diversity between communities under Gyrinus and Notonecta predation, suggesting that species sorting was operating at the low dispersal rate. There was no effect of dispersal rate on species diversity or body size distribution in the temporal prey refuge. 4. The frequency distribution, but not

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.

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

Patterns of fish community composition along a river affected by agricultural and urban disturbance in south-central Chile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orrego, Rodrigo; Barra, Ricardo; Chiang, Gustavo

2008-03-01

Patterns of fish community composition in a south-central Chile river were investigated along the altitudinal-spatial and environmental gradient and as a function of anthropogenic factors. The spatial pattern of fish communities in different biocoenotic zones of the Chillan River is influenced by both natural factors such a hydrologic features, habitat, and feeding types, and also by water quality variables which can reduce the diversity and abundance of sensitive species. A principal component analysis incorporating both water quality parameters and biomarker responses of representative fish species was used to evaluate the status of fish communities along the spatial gradient of themore » stream. The abundance and diversity of the fish community changed from a low in the upper reaches where the low pollution-tolerant species such as salmonid dominated, to a reduced diversity in the lower reaches of the river where tolerant browser species such as cypriniformes dominated. Even though the spatial pattern of fish community structure is similar to that found for the Chilean Rivers, the structure of these communities is highly influenced by human disturbance, particularly along the lower reaches of the river.« less

Bacterial Community Composition and Extracellular Enzyme Activity in Temperate Streambed Sediment during Drying and Rewetting

PubMed Central

Pohlon, Elisabeth; Ochoa Fandino, Adriana; Marxsen, Jürgen

2013-01-01

Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany). Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow) for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes, especially after

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

PubMed

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Management type affects composition and facilitative processes in altoandine dry grassland

NASA Astrophysics Data System (ADS)

Catorci, Andrea; Cesaretti, Sabrina; Velasquez, Jose Luis; Burrascano, Sabina; Zeballos, Horacio

2013-10-01

We performed our study in the Dry Puna of the southern Peruvian Andes. Through a comparative approach we aimed to assess the effects of the two management systems, low grazing pressure by wild camelids vs. high grazing pressure by domestic livestock and periodic burning. Our general hypothesis was that the traditional high disturbance regime affects the dry Puna species diversity and composition through modifications of the magnitude of plant-plant-interactions and changes of the community structure due to shifts in species dominance. In 40 plots of 10 × 10 m, the cover value of each species was recorded and the species richness, floristic diversity, and community similarity of each treatment were compared. For each disturbance regime, differences of soil features (organic matter, carbon/nitrogen ratio, and potassium content) were tested. To evaluate plant-plant interactions, 4 linear transect divided into 500 plots of 10 × 10 cm were laid out and co-occurrence analysis was performed. We found that different disturbance regimes were associated with differences in the floristic composition, and that the high disturbance condition had lower species diversity and evenness. A decrease of tall species such as Festuca orthophylla and increase of dwarf and spiny Tetraglochin cristatum shrubs was observed as well. In addition, different disturbance intensities caused differences in the functional composition of the plant communities, since species with avoidance strategies are selected by high grazing pressure. High disturbance intensity was also associated to differences of soil features and to different clumped spatial structure of the dry Puna. Our results indicate also that: positive interactions are often species-specific mainly depending on the features of nurse and beneficiary species; the importance of positive interaction is higher at low grazing pressure than at high disturbance intensity; the magnitude and direction of the herbivory-mediated facilitation

Mesoherbivores affect grasshopper communities in a megaherbivore-dominated South African savannah.

PubMed

van der Plas, Fons; Olff, Han

2014-06-01

African savannahs are among the few places on earth where diverse communities of mega- and meso-sized ungulate grazers dominate ecosystem functioning. Less conspicuous, but even more diverse, are the communities of herbivorous insects such as grasshoppers, which share the same food. Various studies investigated the community assembly of these groups separately, but it is poorly known how ungulate communities shape grasshopper communities. Here, we investigated how ungulate species of different body size alter grasshopper communities in a South African savannah. White rhino is the most abundant vertebrate herbivore in our study site. Other common mesoherbivores include buffalo, zebra and impala. We hypothesized that white rhinos would have greater impact than mesoherbivores on grasshopper communities. Using 10-year-old exclosures, at eight sites we compared the effects of ungulates on grasshopper communities in three nested treatments: (i) unfenced plots ('control plots') with all vertebrate herbivores present, (ii) plots with a low cable fence, excluding white rhino ('megaherbivore exclosures'), and (iii) plots with tall fences, excluding all herbivores larger than rodents ('complete ungulate exclosures'). In each plot, we collected data of vegetation structure, grass and grasshopper community composition. Complete ungulate exclosures contained 30% taller vegetation than megaherbivore exclosures and they were dominated by different grass and grasshopper species. Grasshoppers in complete ungulate exclosures were on average 3.5 mm longer than grasshoppers in megaherbivore exclosures, possibly due to changes in plant communities or vegetation structure. We conclude that surprisingly, in this megaherbivore hotspot, mesoherbivores, instead of megaherbivores, most strongly affect grasshopper communities.

Receding Water Line and Interspecific Competition Determines Plant Community Composition and Diversity in Wetlands in Beijing

PubMed Central

Wang, Zhengjun; Gong, Huili; Zhang, Jing

2015-01-01

Climate and human-induced wetland degradation has accelerated in recent years, not only resulting in reduced ecosystem services but also greatly affecting the composition and diversity of wetland plant communities. To date, the knowledge of the differences in community parameters and their successional trends in degraded wetlands remains scarce. Here based on remote sensing images, geographic information system technology, and statistical methods, we produced a successional gradient map of the Yeyahu Wetland Nature Reserve in Beijing, which has experienced a steady decline in water level in recent decades. In addition, we analyzed community composition and diversity along with each identified gradient. The results showed that community diversity decreases while dominance increases with the progress of succession, with the highest diversity occurring during the early stage of succession. Moreover, the community demonstrates greater similarity among subareas during later successional stages, and the similarity coefficients calculated from the important value (IV) of each species are more accurate. Correlation analysis showed that the impact of soil factors on diversity was not significant at a subarea scale, although these nutrients showed an increasing trend with the community succession. Furthermore, the IVs of the dominant species had a particularly significant impact on diversity, showing a significantly negative correlation with diversity indices and a significantly positive correlation with dominance indices. Further analysis showed that the retreat of water level resulted from sustained drought and local human activities was a major extrinsic driving force resulting in observed differences in the community successional stages, which resulted in differences in community composition and diversity. On the other hand, interspecific competition was the main intrinsic mechanism, which significantly influenced the IVs of the dominant species and community diversity

[Changes of diversity and composition of fungal communities in rhizosphere of Panax ginseng].

PubMed

Dong, Lin-Lin; Niu, Wei-Hao; Wang, Rui; Xu, Jiang; Zhang, Lian-Juan; Zhang, Jun; Chen, Shi-Lin

2017-02-01

Continuous cropping obstacles resulted in the yield losses of Panax ginseng, and affected the development of ginseng industry. Soil fungal communities participated in the key ecological process, and their changes of diversity and composition were related to the continuous cropping obstacles. We analyzed the changes of fungal diversity and composition in the rhizosphere of ginseng using the high-throughput sequencing method, stated the effects of ginseng cultivation on the micro-ecology, and provided effective strategies for overcoming continuous cropping obstacles. Compared to those of the forest soils, the fungal diversity of ginseng rhizosphere soils was increased, and the increasing trends were declined with an increasing years of ginseng cultivation; the relative abundance of Sordariomycetes, Alatospora, Eurotiomycetes, Leotiomycetes, Saccharomycetes, Mucorales and Pezizomycetes were increased in the rhizosphere of ginseng. Pearson's correlation index indicated that soil chemical perporties affected the relative abundance of fungal communities. pH was significantly related to the relative abundance of Dothideomycetes and Alatospora; the content of available potassium was markedly associated with the relative abundance of Dothideomycetes, Alatospora and Mucorales; the content of total nitrogen was significant correlation with the relative abundance of Sordariomycetes and Mucorales. These results indicated that fertilization was one of pivotal factors affecting the rhizosphere micro-ecology of ginseng, and optimization of fertilization system was an effective method to overcome continuous cropping obstacles. Copyright© by the Chinese Pharmaceutical Association.

Microplastics alter composition of fungal communities in aquatic ecosystems.

PubMed

Kettner, Marie Therese; Rojas-Jimenez, Keilor; Oberbeckmann, Sonja; Labrenz, Matthias; Grossart, Hans-Peter

2017-11-01

Despite increasing concerns about microplastic (MP) pollution in aquatic ecosystems, there is insufficient knowledge on how MP affect fungal communities. In this study, we explored the diversity and community composition of fungi attached to polyethylene (PE) and polystyrene (PS) particles incubated in different aquatic systems in north-east Germany: the Baltic Sea, the River Warnow and a wastewater treatment plant. Based on next generation 18S rRNA gene sequencing, 347 different operational taxonomic units assigned to 81 fungal taxa were identified on PE and PS. The MP-associated communities were distinct from fungal communities in the surrounding water and on the natural substrate wood. They also differed significantly among sampling locations, pointing towards a substrate and location specific fungal colonization. Members of Chytridiomycota, Cryptomycota and Ascomycota dominated the fungal assemblages, suggesting that both parasitic and saprophytic fungi thrive in MP biofilms. Thus, considering the worldwide increasing accumulation of plastic particles as well as the substantial vector potential of MP, especially these fungal taxa might benefit from MP pollution in the aquatic environment with yet unknown impacts on their worldwide distribution, as well as biodiversity and food web dynamics at large. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing.

PubMed

Kelly, L C; Colin, Y; Turpault, M-P; Uroz, S

2016-08-01

Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hahn, Philip G.; Orrock, John L.

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.more » 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

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

DOE PAGES

Hahn, Philip G.; Orrock, John L.

2014-11-23

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.more » 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

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

PubMed

Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

2010-10-01

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon

Methyl Fluoride Affects Methanogenesis Rather than Community Composition of Methanogenic Archaea in a Rice Field Soil

PubMed Central

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 (CH3F) 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% CH3F (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 CH3F 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 CH3F 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 CH3F 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. PMID:23341965

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.

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

PubMed Central

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C.

2017-01-01

ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of Py

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment.

PubMed

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C; Xu, Jianming

2017-01-01

Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria , particularly Actinomycetales , was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem.

PubMed

David, Aaron S; Seabloom, Eric W; May, Georgiana

2016-05-01

Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes--fungi living asymptomatically within plants--to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

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

Changes in fungal community composition in response to experimental soil warming at the alpine treeline

NASA Astrophysics Data System (ADS)

Solly, Emily; Lindahl, Bjorn; Dawes, Melissa; Peter, Martina; Souza, Romulo; Rixen, Christian; Hagedorn, Frank

2017-04-01

Increased CO2 emissions and global warming may alter the composition of fungal communities through the reduction of low temperature limitation in the plant-soil system, faster nitrogen cycling and changes in the carbon allocation of host plants to the rhizosphere. Shifts in fungal community composition due to global changes are likely to affect the routes of carbon and nitrogen flows in the plant-soil system and alter the rates at which organic matter is decomposed. The main aim of our study was to estimate the effects of multiple years of free air CO2 enrichment (ambient concentration +200 ppm) and soil warming (+ 4°C) on the fungal community structure and composition. At an alpine treeline in Switzerland featuring two key high-elevation tree species, Larix decidua and Pinus uncinata, fungal communities within different organic horizons were analysed by high-throughput 454-pyrosequencing of ITS2 amplicons. In addition, we assessed the ectomycorrhizal community composition on root tips and monitored changes in sporocarp productivity of fungal species during the course of the experiment. Three years of experimental warming at the alpine treeline altered the composition of the fungal community in the organic horizons, whereas nine years of CO2 enrichment had only weak effects. Tree species influenced the composition of the fungal community and the magnitude of the responses of fungal functional groups to soil warming differed between plots with Larix and those with Pinus. The abundance of ectomycorrhizal fungi was positively correlated with nitrogen availability, and ectomycorrhizal taxa specialized for conditions of high nitrogen availability proliferated with warming, corresponding to considerable increases in extractable inorganic nitrogen in warmed soils. Changes in productivity of specific fungal fruiting bodies in response to soil warming (e.g. more Lactarius rufus sporocarps and less Hygrophorus speciousus sporocarps) were consistent with the 454-sequencing

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

PubMed

Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

2015-01-01

Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

Gasoline Composition Regulations Affecting LUST Sites

EPA Science Inventory

Passage of the Clean Air Act Amendments in 1990 imposed requirements on gasoline composition in the United States. Impacts to ground water are affected by the provisions that required oxygenated additives and limited benzene concentration. Reformulated and oxygenated gasoline w...

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

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

PubMed

Auffret, Marc D; Karhu, Kristiina; 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.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Community composition and diversity of ground beetles (Coleoptera: Carabidae) in Yaoluoping National Nature Reserve

PubMed Central

Li, Wen-Bo; Liu, Nai-Yi; Wu, Yun-He; Zhang, Yu-Cai; Xu, Qin; Chu, Jun; Wang, Shu-Yan

2017-01-01

Abstract This study used pitfall trapping to examine community composition and diversity of ground beetles in five different habitats (coniferous, deciduous, mixed coniferous, farmland, and settlements) within Anhui Yaoluoping National Nature Reserve from May to September 2014. In total, 1,352 ground beetles were collected, belonging to 16 genera and 44 species. Of these, four dominant species Dolichus halensis, Harpalus pastor, Carabus casaleianus, and Pheropsophus jessoensis were identified, respectively, comprising 370, 177, 131, and 123 individuals. The deciduous forest showed greater diversity (3.78 according to Shannon–Weiner index), equitability (0.80 according to Pielou’s index), and dominance (9.52 according to Simpson’s index) when compared with farmland, but species richness in the deciduous forest (27) was lower than that in farmland (35). One-way analysis of variance showed that ground beetle species composition and abundance among different habitats varied significantly. Cluster analysis and principal coordinate analysis showed that farmland shared low community similarity with other habitat types, and coniferous and mixed coniferous forests shared similar community types. Our results indicate that species composition, abundance, and diversity of ground beetles are affected by different habitat types, with deciduous forest types being critical in maintaining the diversity of rare species. We recommend reducing cultivated farmland area and increasing the area of carefully planned deciduous forest in order to better protect ground beetle diversity in the region.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

PubMed Central

Paz, Henry A.; Anderson, Christopher L.; Muller, Makala J.; Kononoff, Paul J.; Fernando, Samodha C.

2016-01-01

The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial

Soil Redox Conditions Are a Strong Determinant of Microbial Community Composition and the Fate of Carbon Following Permafrost Thaw.

NASA Astrophysics Data System (ADS)

Bottos, E. M.; Bramer, L.; Kim, Y. M.; Fansler, S.; Nicora, C.; Zink, E.; Chu, R. K.; Tfaily, M. M.; Metz, T. O.; Jansson, J.; Stegen, J.

2016-12-01

Permafrost-affected soils contain enormous stocks of carbon, which are becoming increasingly available to microbial transformation as permafrost regions warm; however, how this warming will influence the permafrost microbiome and the transformation of soil carbon remains unclear. We hypothesize that the redox conditions that arise following permafrost thaw will dictate the structure and function of the microbial community, and strongly influence the nature of carbon transformations. To examine this, permafrost-affected soils from Caribou Poker Creek Research Watershed, Alaska were incubated at 4 °C under aerobic and anaerobic conditions for periods of 9 and 94 days. Over the incubation period, rates of CO2 and CH4 production were measured by gas chromatography, shifts in microbial community structure were characterized by 16S rRNA gene sequencing, and changes in metabolite and organic matter composition were analyzed by GC-MS and ESI-FTICR MS, respectively. CO2 production rates were significantly higher in aerobic treatments in 9-day and 94-day incubations, by 3-times and 12-times, respectively. Rates of CH4 production were not significantly different between treatments in 9-day incubations, but were 1.6-times higher in anaerobic treatments in 94-day incubations. The community composition remained largely unchanged in the incubated samples, with the exception of the 94-day aerobic incubations, which shifted strongly to become dominated by a single OTU, Rhodoferax ferrireducens. Metabolite profiles also shifted most strongly in the 94-day aerobic incubations, with the abundance of phosphorylated carbon compounds overrepresented in these samples. This work suggests that the redox conditions that arise following permafrost thaw will be a strong determinant of community composition and will govern the ultimate fate of carbon stocks in permafrost-affected soils. Our results are currently being integrated with numerical models aimed at predicting the coupled microbiome

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. © 2015 John Wiley & Sons Ltd/CNRS.

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

PubMed Central

Porter, Teresita M.; Golding, G. Brian

2012-01-01

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys. PMID:22558215

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

PubMed

Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

2013-03-01

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

PubMed Central

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. PMID:25324836

Nitrogen Forms Influence Microcystin Concentration and Composition via Changes in Cyanobacterial Community Structure

PubMed Central

Monchamp, Marie-Eve; Pick, Frances R.; Beisner, Beatrix E.; Maranger, Roxane

2014-01-01

The eutrophication of freshwaters is a global health concern as lakes with excess nutrients are often subject to toxic cyanobacterial blooms. Although phosphorus is considered the main element regulating cyanobacterial biomass, nitrogen (N) concentration and more specifically the availability of different N forms may influence the overall toxicity of blooms. In this study of three eutrophic lakes prone to cyanobacterial blooms, we examined the effects of nitrogen species and concentrations and other environmental factors in influencing cyanobacterial community structure, microcystin (MC) concentrations and MC congener composition. The identification of specific MC congeners was of particular interest as they vary widely in toxicity. Different nitrogen forms appeared to influence cyanobacterial community structure leading to corresponding effects on MC concentrations and composition. Total MC concentrations across the lakes were largely explained by a combination of abiotic factors: dissolved organic nitrogen, water temperature and ammonium, but Microcystis spp. biomass was overall the best predictor of MC concentrations. Environmental factors did not appear to affect MC congener composition directly but there were significant associations between specific MC congeners and particular species. Based on redundancy analyses (RDA), the relative biomass of Microcystis aeruginosa was associated with MC-RR, M. wesenbergii with MC-LA and Aphanizomenon flos-aquae with MC-YR. The latter two species are not generally considered capable of MC production. Total nitrogen, water temperature, ammonium and dissolved organic nitrogen influenced the cyanobacterial community structure, which in turn resulted in differences in the dominant MC congener and the overall toxicity. PMID:24427318

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.

Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines.

PubMed

Kneitel, Jamie M; Miller, Thomas E

2003-08-01

Dispersal among local communities can have a variety of effects on species composition and diversity at local and regional scales. Local conditions (e.g., resource and predator densities) can have independent effects, as well as interact with dispersal, to alter these patterns. Based on metacommunity models, we predicted that local diversity would show a unimodal relationship with dispersal frequency. We manipulated dispersal frequencies, resource levels, and the presence of predators (mosquito larvae) among communities found in the water-filled leaves of the pitcher plant Sarracenia purpurea. Diversity and abundance of species of the middle trophic level, protozoa and rotifers, were measured. Increased dispersal frequencies significantly increased regional species richness and protozoan abundance while decreasing the variance among local communities. Dispersal frequency interacted with predation at the local community scale to produce patterns of diversity consistent with the model. When predators were absent, we found a unimodal relationship between dispersal frequency and diversity, and when predators were present, there was a flat relationship. Intermediate dispersal frequencies maintained some species in the inquiline communities by offsetting extinction rates. Local community composition and the degree of connectivity between communities are both important for understanding species diversity patterns at local and regional scales.

Bacterial diversity and community composition from seasurface to subseafloor.

PubMed

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

2016-04-01

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.

Structure and composition of oligohaline marsh plant communities exposed to salinity pulses

USGS Publications Warehouse

Howard, R.J.; Mendelssohn, I.A.

2000-01-01

The response of two oligohaline marsh macrophyte communities to pulses of increased salinity was studied over a single growing season in a greenhouse experiment. The plant communities were allowed a recovery period in freshwater following the pulse events. The experimental treatments included: (1) salinity influx rate (rate of salinity increase from 0 to 12 gl-1); (2) duration of exposure to elevated salinity; and (3) water depth. The communities both included Sagittaria lancifolia L.; the codominant species were Eleocharis palustris (L.) Roemer and J.A. Schultes in community 1 and Schoenoplectus americanus (Pers.) Volk. ex Schinz and R. Keller in community 2. Effects of the treatments on sediment chemical characteristics (salinity, pH, redox potential, and sulfide and ammonium concentrations) and plant community attributes (aboveground and belowground biomass, stem density, leaf tissue nutrients, and species richness) were examined. The treatment effects often interacted to influence sediment and plant communities characteristics following recovery in fresh water. Salinity influx rate per se, however, had little effect on the abiotic or biotic response variables; significant influx effects were found when the 0 gl-1 (zero influx) treatment was compared to the 12 gl-1 treatments, regardless of the rate salinity was raised. A salinity level of 12 gl-1 had negative effects on plant community structure and composition; these effects were usually associated with 3 months of salinity exposure. Water depth often interacted with exposure duration, but increased water depth did independently decrease the values of some community response measures. Community 1 was affected more than community 2 in the most extreme salinity treatment (3 months exposure/15-cm water depth). Although species richness in both communities was reduced, structural changes were more dramatic in community 1. Biomass and stem density were reduced in community 1 overall and in both dominant species

Effects of climate change on plant population growth rate and community composition change.

PubMed

Chang, Xiao-Yu; Chen, Bao-Ming; Liu, Gang; Zhou, Ting; Jia, Xiao-Rong; Peng, Shao-Lin

2015-01-01

The impacts of climate change on forest community composition are still not well known. Although directional trends in climate change and community composition change were reported in recent years, further quantitative analyses are urgently needed. Previous studies focused on measuring population growth rates in a single time period, neglecting the development of the populations. Here we aimed to compose a method for calculating the community composition change, and to testify the impacts of climate change on community composition change within a relatively short period (several decades) based on long-term monitoring data from two plots-Dinghushan Biosphere Reserve, China (DBR) and Barro Colorado Island, Panama (BCI)-that are located in tropical and subtropical regions. We proposed a relatively more concise index, Slnλ, which refers to an overall population growth rate based on the dominant species in a community. The results indicated that the population growth rate of a majority of populations has decreased over the past few decades. This decrease was mainly caused by population development. The increasing temperature had a positive effect on population growth rates and community change rates. Our results promote understanding and explaining variations in population growth rates and community composition rates, and are helpful to predict population dynamics and population responses to climate change.

Impact of copper on the diazotroph abundance and community composition during swine manure composting.

PubMed

Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Zhang, Kaiyu; Hu, Ting; Ma, Jiyue; Wang, Qianzhi

2018-05-01

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg -1 ) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

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

Testing the functional significance of microbial community composition.

Treesearch

Michael S. Strickland; Christian Lauber; Noah Fierer; Mark A. Bradford

2009-01-01

A critical assumption underlying terrestrial ecosystem models is that soil microbial communities, when placed in a common environment, will function in an identical manner regardless of the composition...

Experimental parasite community ecology: intraspecific variation in a large tapeworm affects community assembly.

PubMed

Benesh, Daniel P; Kalbe, Martin

2016-07-01

Non-random species associations occur in naturally sampled parasite communities. The processes resulting in predictable community structure (e.g. particular host behaviours, cross-immunity, interspecific competition) could be affected by traits that vary within a parasite species, like growth or antigenicity. We experimentally infected three-spined sticklebacks with a large tapeworm (Schistocephalus solidus) that impacts the energy needs, foraging behaviour and immune reactions of its host. The tapeworms came from two populations, characterized by high or low growth in sticklebacks. Our goal was to evaluate how this parasite, and variation in its growth, affects the acquisition of other parasites. Fish infected with S. solidus were placed into cages in a lake to expose them to the natural parasite community. We also performed a laboratory experiment in which infected fish were exposed to a fixed dose of a common trematode parasite. In the field experiment, infection with S. solidus affected the abundance of four parasite species, relative to controls. For two of the four species, changes occurred only in fish harbouring the high-growth S. solidus; one species increased in abundance and the other decreased. These changes did not appear to be directly linked to S. solidus growth though. The parasite exhibiting elevated abundance was the same trematode used in the laboratory infection. In that experiment, we found a similar infection pattern, suggesting that S. solidus affects the physiological susceptibility of fish to this trematode. Associations between S. solidus and other parasites occur and vary in direction. However, some of these associations were contingent on the S. solidus population, suggesting that intraspecific variability can affect the assembly of parasite communities. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Seasonality Affects the Diversity and Composition of Bacterioplankton Communities in Dongjiang River, a Drinking Water Source of Hong Kong.

PubMed

Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Sun, Guoping

2017-01-01

Water quality ranks the most vital criterion for rivers serving as drinking water sources, which periodically changes over seasons. Such fluctuation is believed associated with the state shifts of bacterial community within. To date, seasonality effects on bacterioplankton community patterns in large rivers serving as drinking water sources however, are still poorly understood. Here we investigated the intra-annual bacterial community structure in the Dongjiang River, a drinking water source of Hong Kong, using high-throughput pyrosequencing in concert with geochemical property measurements during dry, and wet seasons. Our results showed that Proteobacteria, Actinobacteria , and Bacteroidetes were the dominant phyla of bacterioplankton communities, which varied in composition, and distribution from dry to wet seasons, and exhibited profound seasonal changes. Actinobacteria, Bacteroidetes , and Cyanobacteria seemed to be more associated with seasonality that the relative abundances of Actinobacteria , and Bacteroidetes were significantly higher in the dry season than those in the wet season ( p < 0.01), while the relative abundance of Cyanobacteria was about 10-fold higher in the wet season than in the dry season. Temperature and [Formula: see text]-N concentration represented key contributing factors to the observed seasonal variations. These findings help understand the roles of various bacterioplankton and their interactions with the biogeochemical processes in the river ecosystem.

Response of AM fungi spore population to elevated temperature and nitrogen addition and their influence on the plant community composition and productivity

NASA Astrophysics Data System (ADS)

Zhang, Tao; Yang, Xue; Guo, Rui; Guo, Jixun

2016-04-01

To examine the influence of elevated temperature and nitrogen (N) addition on species composition and development of arbuscular mycorrhizal fungi (AMF) and the effect of AMF on plant community structure and aboveground productivity, we conducted a 5-year field experiment in a temperate meadow in northeast China and a subsequent greenhouse experiment. In the field experiment, N addition reduced spore population diversity and richness of AMF and suppressed the spore density and the hyphal length density (HLD). Elevated temperature decreased spore density and diameter and increased the HLD, but did not affect AMF spore population composition. In the greenhouse experiment, AMF altered plant community composition and increased total aboveground biomass in both elevated temperature and N addition treatments; additionally, AMF also increased the relative abundance and aboveground biomass of the grasses Leymus chinensis (Poaceae) and Setaria viridis (Gramineae) and significantly reduced the relative abundance and aboveground biomass of the Suaeda corniculata (Chenopodiaceae). Although elevated temperature and N addition can affect species composition or suppress the development of AMF, AMF are likely to play a vital role in increasing plant diversity and productivity. Notably, AMF might reduce the threat of climate change induced degradation of temperate meadow ecosystems.

Response of AM fungi spore population to elevated temperature and nitrogen addition and their influence on the plant community composition and productivity

PubMed Central

Zhang, Tao; Yang, Xue; Guo, Rui; Guo, Jixun

2016-01-01

To examine the influence of elevated temperature and nitrogen (N) addition on species composition and development of arbuscular mycorrhizal fungi (AMF) and the effect of AMF on plant community structure and aboveground productivity, we conducted a 5-year field experiment in a temperate meadow in northeast China and a subsequent greenhouse experiment. In the field experiment, N addition reduced spore population diversity and richness of AMF and suppressed the spore density and the hyphal length density (HLD). Elevated temperature decreased spore density and diameter and increased the HLD, but did not affect AMF spore population composition. In the greenhouse experiment, AMF altered plant community composition and increased total aboveground biomass in both elevated temperature and N addition treatments; additionally, AMF also increased the relative abundance and aboveground biomass of the grasses Leymus chinensis (Poaceae) and Setaria viridis (Gramineae) and significantly reduced the relative abundance and aboveground biomass of the Suaeda corniculata (Chenopodiaceae). Although elevated temperature and N addition can affect species composition or suppress the development of AMF, AMF are likely to play a vital role in increasing plant diversity and productivity. Notably, AMF might reduce the threat of climate change induced degradation of temperate meadow ecosystems. PMID:27098761

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

PubMed

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

2015-04-01

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. 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. 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. This study provides an understanding of microbial community diversity in an MDBR, which is fundamental to the optimization of reactor performance. © 2015 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

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

Land cover and rainfall interact to shape waterbird community composition.

PubMed

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

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition. PMID:24610853

Late Holocene to present climatic and anthropogenic drivers affecting wetland plant communities, Florida Everglades, USA

NASA Astrophysics Data System (ADS)

Bernhardt, C. E.; Willard, D. A.

2011-12-01

We synthesize the paleoecological results of dozens of sediment cores to evaluate the complex interactions of regional climate variability and anthropogenic modifications during the late Holocene affecting the development, stability, and resilience of the Florida Everglades wetlands. The Everglades is a mosaic of wetland types whose distributions are controlled by water depth, hydroperiod, fire, and substrate. External stressors could trigger shifts in the vegetation composition and change the community structure. Episodic severe periods of aridity during the late Holocene caused regional shifts in vegetation including the initiation and development of tree islands and sawgrass ridges, which became established during abrupt drought events. While the timing varies site to site, most droughts occurred during well-documented global climate events like the Medieval Climate Anomaly and the Little Ice Age. However, slough vegetation is more resilient to climate variability and quickly returns to its original composition after droughts. Twentieth century modification to the natural Everglades hydrology saw the distribution wetlands severely altered. The response was not homogeneous. Some communities were drowned by prolonged hydroperiods whereas other communities, such as marl prairies became drier. However, slough vegetation in the ridge and slough landscape did not respond to 20th century land use but instead has been sensitive to changes in precipitation associated with the North Atlantic Oscillation and the Atlantic Multidecadal Oscillation.

Experimental soil warming shifts the fungal community composition at the alpine treeline.

PubMed

Solly, Emily F; Lindahl, Björn D; Dawes, Melissa A; Peter, Martina; Souza, Rômulo C; Rixen, Christian; Hagedorn, Frank

2017-07-01

Increased CO 2 emissions and global warming may alter the composition of fungal communities through the removal of temperature limitation in the plant-soil system, faster nitrogen (N) cycling and changes in the carbon (C) allocation of host plants to the rhizosphere. At a Swiss treeline featuring Larix decidua and Pinus uncinata, the effects of multiple years of CO 2 enrichment and experimental soil warming on the fungal community composition in the organic horizons were analysed using 454-pyrosequencing of ITS2 amplicons. Sporocarp production and colonization of ectomycorrhizal root tips were investigated in parallel. Fungal community composition was significantly altered by soil warming, whereas CO 2 enrichment had little effect. Tree species influenced fungal community composition and the magnitude of the warming responses. The abundance of ectomycorrhizal fungal taxa was positively correlated with N availability, and ectomycorrhizal taxa specialized for conditions of high N availability proliferated with warming, corresponding to considerable increases in inorganic N in warmed soils. Traits related to N utilization are important in determining the responses of ectomycorrhizal fungi to warming in N-poor cold ecosystems. Shifts in the overall fungal community composition in response to higher temperatures may alter fungal-driven processes with potential feedbacks on ecosystem N cycling and C storage at the alpine treeline. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Arbuscular mycorrhizal communities in tropical forests are affected by host tree species and environment.

PubMed

Lovelock, Catherine E; Andersen, Kelly; Morton, Joseph B

2003-04-01

Arbuscular mycorrhizal (AM) fungi are mutualists with plant roots that are proposed to enhance plant community diversity. Models indicate that AM fungal communities could maintain plant diversity in forests if functionally different communities are spatially separated. In this study we assess the spatial and temporal distribution of the AM fungal community in a wet tropical rainforest in Costa Rica. We test whether distinct fungal communities correlate with variation in tree life history characteristics, with host tree species, and the relative importance of soil type, seasonality and rainfall. Host tree species differ in their associated AM fungal communities, but differences in the AM community between hosts could not be generalized over life history groupings of hosts. Changes in the relative abundance of a few common AM fungal species were the cause of differences in AM fungal communities for different host tree species instead of differences in the presence and absence of AM fungal species. Thus, AM fungal communities are spatially distinguishable in the forest, even though all species are widespread. Soil fertility ranging between 5 and 9 Mg/ha phosphorus did not affect composition of AM fungal communities, although sporulation was more abundant in lower fertility soils. Sampling soils over seasons revealed that some AM fungal species sporulate profusely in the dry season compared to the rainy season. On one host tree species sampled at two sites with vastly different rainfall, relative abundance of spores from Acaulospora was lower and that of Glomus was relatively higher at the site with lower and more seasonal rainfall.

Assessing Household Economic Vulnerability in HIV-Affected Communities in Five Regions of Côte d'Ivoire

PubMed Central

Burke, Holly M.; Moret, Whitney; Field, Samuel; Chen, Mario; Zeng, Yanwu; Seka, Firmin M.

2016-01-01

The objective of this study was to identify and describe levels of household economic vulnerability in HIV-affected communities in Côte d’Ivoire, defined as those with a high prevalence of HIV and large numbers of orphans and vulnerable children. We conducted a cross-sectional survey of 3,749 households in five health regions of Côte d’Ivoire. Using principal component analysis, we attempted to identify sets of correlated vulnerabilities and derive a small number of composite scores to create an index for targeting interventions to vulnerable populations. The 65 vulnerability measures examined did not cluster in ways that would allow for the creation of a small number of composite measures. Instead, we found that households face numerous unique pathways to vulnerability. PMID:27655530

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Effects of anthropogenic salinization on biological traits and community composition of stream macroinvertebrates.

PubMed

Szöcs, Eduard; Coring, Eckhard; Bäthe, Jürgen; Schäfer, Ralf B

2014-01-15

Salinization of rivers resulting from industrial discharge or road-deicing can adversely affect macroinvertebrates. Trait-based approaches are a promising tool in ecological monitoring and may perform better than taxonomy-based approaches. However only little is known how and which biological traits are affected by salinization. We investigated the effects of anthropogenic salinization on macroinvertebrate communities and biological traits in the Werra River, Germany and compared the taxonomic and trait response. We found a change in macroinvertebrate community and trait composition. Communities at saline sites were characterized by the three exotic species Gammarus tigrinus, Apocorophium lacustre and Potamopyrgus antipodarum. The frequencies of trait modalities long life cycle duration, respiration by gill, ovoviviparity, shredder and multivoltinism were statistically significantly increased at saline sites. The trait-based ordination resulted in a higher explained variance than the taxonomy-based ordination, indicating a better performance of the trait-based approach, resulting in a better discrimination between saline and non-saline sites. Our results are in general agreement with other studies from Europe, indicating a trait convergence for saline streams, being dominated by the traits ovoviviparity and multivoltinism. Three further traits (respiration by gill, life cycle duration and shredders) responded strongly to salinization, but this may primarily be attributed to the dominance of a single invasive species, G. tigrinus, at the saline sites in the Werra River. © 2013 Elsevier B.V. All rights reserved.

Night-time lighting alters the composition of marine epifaunal communities

PubMed Central

Davies, Thomas W.; Coleman, Matthew; Griffith, Katherine M.; Jenkins, Stuart R.

2015-01-01

Marine benthic communities face multiple anthropogenic pressures that compromise the future of some of the most biodiverse and functionally important ecosystems in the world. Yet one of the pressures these ecosystems face, night-time lighting, remains unstudied. Light is an important cue in guiding the settlement of invertebrate larvae, and altering natural regimes of nocturnal illumination could modify patterns of recruitment among sessile epifauna. We present the first evidence of night-time lighting changing the composition of temperate epifaunal marine invertebrate communities. Illuminating settlement surfaces with white light-emitting diode lighting at night, to levels experienced by these communities locally, both inhibited and encouraged the colonization of 39% of the taxa analysed, including three sessile and two mobile species. Our results indicate that ecological light pollution from coastal development, shipping and offshore infrastructure could be changing the composition of marine epifaunal communities. PMID:25926694

Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)

PubMed Central

Delport, Tiffany C.; Power, Michelle L.; Harcourt, Robert G.; Webster, Koa N.

2016-01-01

ABSTRACT Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of phenol on the nitrogen removal performance and microbial community structure and composition of an anammox reactor.

PubMed

Pereira, Alyne Duarte; Leal, Cíntia Dutra; Dias, Marcela França; Etchebehere, Claudia; Chernicharo, Carlos Augusto L; de Araújo, Juliana Calabria

2014-08-01

The effects of phenol on the nitrogen removal performance of a sequencing batch reactor (SBR) with anammox activity and on the microbial community within the reactor were evaluated. A phenol concentration of 300 mg L(-1) reduced the ammonium-nitrogen removal efficiency of the SBR from 96.5% to 47%. The addition of phenol changed the microbial community structure and composition considerably, as shown by denaturing gradient gel electrophoresis and 454 pyrosequencing of 16S rRNA genes. Some phyla, such as Proteobacteria, Verrucomicrobia, and Firmicutes, increased in abundance, whereas others, such as Acidobacteria, Chloroflexi, Planctomycetes, GN04, WS3, and NKB19, decreased. The diversity of the anammox bacteria was also affected by phenol: sequences related to Candidatus Brocadia fulgida were no longer detected, whereas sequences related to Ca. Brocadia sp. 40 and Ca. Jettenia asiatica persisted. These results indicate that phenol adversely affects anammox metabolism and changes the bacterial community within the anammox reactor. Copyright © 2014 Elsevier Ltd. All rights reserved.

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class

PubMed Central

Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

2015-01-01

Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10–11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class.

PubMed

Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

2015-01-01

Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10-11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities

PubMed Central

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community

The Interplay between Environmental Filtering and Spatial Processes in Structuring Communities: The Case of Neotropical Snake Communities.

PubMed

Cavalheri, Hamanda; Both, Camila; Martins, Marcio

2015-01-01

Both habitat filters and spatial processes can influence community structure. Space alone affects species immigration from the regional species pool, whereas habitat filters affect species distribution and inter-specific interactions. This study aimed to understand how the interplay between environmental and geographical processes influenced the structure of Neotropical snake communities in different habitat types. We selected six studies that sampled snakes in forests, four conducted in savannas and two in grasslands (the latter two are grouped in a non-forest category). We used the net relatedness and nearest taxon indices to assess phylogenetic structure within forest and non-forest areas. We also used the phylogenetic fuzzy-weighting algorithm to characterize phylogenetic structure across communities and the relation of phylogenetic composition patterns to habitat type, structure, and latitude. Finally, we tested for morphological trait convergence and phylogenetic niche conservatism using four forest and four non-forest areas for which morphological data were available. Community phylogenetic composition changed across forest and non-forest areas suggesting that environmental filtering influences community structure. Species traits were affected by habitat type, indicating convergence at the metacommunity level. Tail length, robustness, and number of ventral scales maximized community convergence among forest and non-forest areas. The observed patterns suggested environmental filtering, indicating that less vertically structured habitats represent a strong filter. Despite the fact that phylogenetic structure was not detected individually for each community, we observed a trend towards communities composed by more closely related species in higher latitudes and more overdispersed compositions in lower latitudes. Such pattern suggests that the limited distribution of major snake lineages constrained species distributions. Structure indices for each community

Ants impact the composition of the aquatic macroinvertebrate communities of a myrmecophytic tank bromeliad.

PubMed

Dejean, Alain; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Bonhomme, Camille; Talaga, Stanislas; Pelozuelo, Laurent; Hénaut, Yann; Corbara, Bruno

2018-03-01

In an inundated Mexican forest, 89 out of 92 myrmecophytic tank bromeliads (Aechmea bracteata) housed an associated ant colony: 13 sheltered Azteca serica, 43 Dolichoderus bispinosus, and 33 Neoponera villosa. Ant presence has a positive impact on the diversity of the aquatic macroinvertebrate communities (n=30 bromeliads studied). A Principal Component Analysis (PCA) showed that the presence and the species of ant are not correlated to bromeliad size, quantity of water, number of wells, filtered organic matter or incident radiation. The PCA and a generalized linear model showed that the presence of Azteca serica differed from the presence of the other two ant species or no ants in its effects on the aquatic invertebrate community (more predators). Therefore, both ant presence and species of ant affect the composition of the aquatic macroinvertebrate communities in the tanks of A. bracteata, likely due to ant deposition of feces and other waste in these tanks. Copyright © 2018. Published by Elsevier Masson SAS.

Rapid decay of tree-community composition in Amazonian forest fragments

PubMed Central

Laurance, William F.; Nascimento, Henrique E. M.; Laurance, Susan G.; Andrade, Ana; Ribeiro, José E. L. S.; Giraldo, Juan Pablo; Lovejoy, Thomas E.; Condit, Richard; Chave, Jerome; Harms, Kyle E.; D'Angelo, Sammya

2006-01-01

Forest fragmentation is considered a greater threat to vertebrates than to tree communities because individual trees are typically long-lived and require only small areas for survival. Here we show that forest fragmentation provokes surprisingly rapid and profound alterations in Amazonian tree-community composition. Results were derived from a 22-year study of exceptionally diverse tree communities in 40 1-ha plots in fragmented and intact forests, which were sampled repeatedly before and after fragment isolation. Within these plots, trajectories of change in abundance were assessed for 267 genera and 1,162 tree species. Abrupt shifts in floristic composition were driven by sharply accelerated tree mortality and recruitment within ≈100 m of fragment margins, causing rapid species turnover and population declines or local extinctions of many large-seeded, slow-growing, and old-growth taxa; a striking increase in a smaller set of disturbance-adapted and abiotically dispersed species; and significant shifts in tree size distributions. Even among old-growth trees, species composition in fragments is being restructured substantially, with subcanopy species that rely on animal seed-dispersers and have obligate outbreeding being the most strongly disadvantaged. These diverse changes in tree communities are likely to have wide-ranging impacts on forest architecture, canopy-gap dynamics, plant–animal interactions, and forest carbon storage. PMID:17148598

Ecological and Evolutionary Effects of Stickleback on Community Structure

PubMed Central

Des Roches, Simone; Shurin, Jonathan B.; Schluter, Dolph; Harmon, Luke J.

2013-01-01

Species’ ecology and evolution can have strong effects on communities. Both may change concurrently when species colonize a new ecosystem. We know little, however, about the combined effects of ecological and evolutionary change on community structure. We simultaneously examined the effects of top-predator ecology and evolution on freshwater community parameters using recently evolved generalist and specialist ecotypes of three-spine stickleback (Gasterosteus aculeatus). We used a mesocosm experiment to directly examine the effects of ecological (fish presence and density) and evolutionary (phenotypic diversity and specialization) factors on community structure at lower trophic levels. We evaluated zooplankton biomass and composition, periphyton and phytoplankton chlorophyll-a concentration, and net primary production among treatments containing different densities and diversities of stickleback. Our results showed that both ecological and evolutionary differences in the top-predator affect different aspects of community structure and composition. Community structure, specifically the abundance of organisms at each trophic level, was affected by stickleback presence and density, whereas composition of zooplankton was influenced by stickleback diversity and specialization. Primary productivity, in terms of chlorophyll-a concentration and net primary production was affected by ecological but not evolutionary factors. Our results stress the importance of concurrently evaluating both changes in density and phenotypic diversity on the structure and composition of communities. PMID:23573203

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

The Effect of Increased Loads of Dissolved Organic Matter on Estuarine Microbial Community Composition and Function

PubMed Central

Traving, Sachia J.; Rowe, Owen; Jakobsen, Nina M.; Sørensen, Helle; Dinasquet, Julie; Stedmon, Colin A.; Andersson, Agneta; Riemann, Lasse

2017-01-01

Increased river loads are projected as one of the major consequences of climate change in the northern hemisphere, leading to elevated inputs of riverine dissolved organic matter (DOM) and inorganic nutrients to coastal ecosystems. The objective of this study was to investigate the effects of elevated DOM on a coastal pelagic food web from the coastal northern Baltic Sea, in a 32-day mesocosm experiment. In particular, the study addresses the response of bacterioplankton to differences in character and composition of supplied DOM. The supplied DOM differed in stoichiometry and quality and had pronounced effects on the recipient bacterioplankton, driving compositional changes in response to DOM type. The shifts in bacterioplankton community composition were especially driven by the proliferation of Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Alpha- and Betaproteobacteria populations. The DOM additions stimulated protease activity and a release of inorganic nutrients, suggesting that DOM was actively processed. However, no difference between DOM types was detected in these functions despite different community compositions. Extensive release of re-mineralized carbon, nitrogen and phosphorus was associated with the bacterial processing, corresponding to 25–85% of the supplied DOM. The DOM additions had a negative effect on phytoplankton with decreased Chl a and biomass, particularly during the first half of the experiment. However, the accumulating nutrients likely stimulated phytoplankton biomass which was observed to increase towards the end of the experiment. This suggests that the nutrient access partially outweighed the negative effect of increased light attenuation by accumulating DOM. Taken together, our experimental data suggest that parts of the future elevated riverine DOM supply to the Baltic Sea will be efficiently mineralized by microbes. This will have consequences for bacterioplankton and phytoplankton community composition and function, and

How Do Learning Communities Affect First-Year Latino Students?

ERIC Educational Resources Information Center

Huerta, Juan Carlos; Bray, Jennifer J.

2013-01-01

Do learning communities with pedagogies of active learning, collaborative learning, and integration of course material affect the learning, achievement, and persistence of first-year Latino university students? The data for this project was obtained from a survey of 1,330 first-year students in the First-Year Learning Community Program at Texas…

Forest Soil Phosphorus Resources and Fertilization Affect Ectomycorrhizal Community Composition, Beech P Uptake Efficiency, and Photosynthesis

PubMed Central

Zavišić, Aljosa; Yang, Nan; Marhan, Sven; Kandeler, Ellen; Polle, Andrea

2018-01-01

Phosphorus (P) is an important nutrient, whose plant-available form phosphate is often low in natural forest ecosystems. Mycorrhizal fungi mine the soil for P and supply their host with this resource. It is unknown how ectomycorrhizal communities respond to changes in P availability. Here, we used young beech (Fagus sylvatica L.) trees in natural forest soil from a P-rich and P-poor site to investigate the impact of P amendment on soil microbes, mycorrhizas, beech P nutrition, and photosynthesis. We hypothesized that addition of P to forest soil increased P availability, thereby, leading to enhanced microbial biomass and mycorrhizal diversity in P-poor but not in P-rich soil. We expected that P amendment resulted in increased plant P uptake and enhanced photosynthesis in both soil types. Young beech trees with intact soil cores from a P-rich and a P-poor forest were kept in a common garden experiment and supplied once in fall with triple superphosphate. In the following summer, labile P in the organic layer, but not in the mineral top soil, was significantly increased in response to fertilizer treatment. P-rich soil contained higher microbial biomass than P-poor soil. P treatment had no effect on microbial biomass but influenced the mycorrhizal communities in P-poor soil and shifted their composition toward higher similarities to those in P-rich soil. Plant uptake efficiency was negatively correlated with the diversity of mycorrhizal communities and highest for trees in P-poor soil and lowest for fertilized trees. In both soil types, radioactive P tracing (H333PO4) revealed preferential aboveground allocation of new P in fertilized trees, resulting in increased bound P in xylem tissue and enhanced soluble P in bark, indicating increased storage and transport. Fertilized beeches from P-poor soil showed a strong increase in leaf P concentrations from deficient to luxurious conditions along with increased photosynthesis. Based on the divergent behavior of beech in P

Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico.

PubMed

Lüneberg, Kathia; Schneider, Dominik; Siebe, Christina; Daniel, Rolf

2018-01-23

Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic

PubMed Central

Frank-Fahle, Béatrice A.; Yergeau, Étienne; Greer, Charles W.; Lantuit, Hugues; Wagner, Dirk

2014-01-01

Permafrost-affected soils are among the most obvious ecosystems in which current microbial controls on organic matter decomposition are changing as a result of global warming. Warmer conditions in polygonal tundra will lead to a deepening of the seasonal active layer, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. To identify current microbial assemblages in carbon rich, water saturated permafrost environments, four polygonal tundra sites were investigated on Herschel Island and the Yukon Coast, Western Canadian Arctic. Ion Torrent sequencing of bacterial and archaeal 16S rRNA amplicons revealed the presence of all major microbial soil groups and indicated a local, vertical heterogeneity of the polygonal tundra soil community with increasing depth. Microbial diversity was found to be highest in the surface layers, decreasing towards the permafrost table. Quantitative PCR analysis of functional genes involved in carbon and nitrogen-cycling revealed a high functional potential in the surface layers, decreasing with increasing active layer depth. We observed that soil properties driving microbial diversity and functional potential varied in each study site. These results highlight the small-scale heterogeneity of geomorphologically comparable sites, greatly restricting generalizations about the fate of permafrost-affected environments in a warming Arctic. PMID:24416279

Termites and flooding affect microbial communities in decomposing wood

Treesearch

Michael D. Ulyshen; Susan V. Diehl; Dragica Jeremic

2016-01-01

Wood properties and microbial community characteristics were compared between loblolly pine (Pinus taeda L.) logs protected or unprotected from termites (Blattodea: Rhinotermitidae: Reticulitermes spp.) and other arthropods for two years in seasonally flooded and unflooded forests in the southeastern United States. Significant compositional differences were observed...

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Non-Random Variability in Functional Composition of Coral Reef Fish Communities along an Environmental Gradient.

PubMed

Plass-Johnson, Jeremiah G; Taylor, Marc H; Husain, Aidah A A; Teichberg, Mirta C; Ferse, Sebastian C A

2016-01-01

degradation of coral reefs is associated with increased variability in fish community functional composition resulting from selective impacts on specific traits, thereby affecting the functional response of these communities to increasing perturbations.

Non-Random Variability in Functional Composition of Coral Reef Fish Communities along an Environmental Gradient

PubMed Central

Plass-Johnson, Jeremiah G.; Taylor, Marc H.; Husain, Aidah A. A.; Teichberg, Mirta C.; Ferse, Sebastian C. A.

2016-01-01

degradation of coral reefs is associated with increased variability in fish community functional composition resulting from selective impacts on specific traits, thereby affecting the functional response of these communities to increasing perturbations. PMID:27100189

Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

PubMed

Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

2016-10-01

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

PubMed Central

Henderson, Gemma; Cox, Faith; Ganesh, Siva; Jonker, Arjan; Young, Wayne; Abecia, Leticia; Angarita, Erika; Aravena, Paula; Nora Arenas, Graciela; Ariza, Claudia; Attwood, Graeme T.; Mauricio Avila, Jose; Avila-Stagno, Jorge; Bannink, André; Barahona, Rolando; Batistotti, Mariano; Bertelsen, Mads F.; Brown-Kav, Aya; Carvajal, Andres M.; Cersosimo, Laura; Vieira Chaves, Alexandre; Church, John; Clipson, Nicholas; Cobos-Peralta, Mario A.; Cookson, Adrian L.; Cravero, Silvio; Cristobal Carballo, Omar; Crosley, Katie; Cruz, Gustavo; Cerón Cucchi, María; de la Barra, Rodrigo; De Menezes, Alexandre B.; Detmann, Edenio; Dieho, Kasper; Dijkstra, Jan; dos Reis, William L. S.; Dugan, Mike E. R.; Hadi Ebrahimi, Seyed; Eythórsdóttir, Emma; Nde Fon, Fabian; Fraga, Martín; Franco, Francisco; Friedeman, Chris; Fukuma, Naoki; Gagić, Dragana; Gangnat, Isabelle; Javier Grilli, Diego; Guan, Le Luo; Heidarian Miri, Vahideh; Hernandez-Sanabria, Emma; Gomez, Alma Ximena Ibarra; Isah, Olubukola A.; Ishaq, Suzanne; Jami, Elie; Jelincic, Juan; Kantanen, Juha; Kelly, William J.; Kim, Seon-Ho; Klieve, Athol; Kobayashi, Yasuo; Koike, Satoshi; Kopecny, Jan; Nygaard Kristensen, Torsten; Julie Krizsan, Sophie; LaChance, Hannah; Lachman, Medora; Lamberson, William R.; Lambie, Suzanne; Lassen, Jan; Leahy, Sinead C.; Lee, Sang-Suk; Leiber, Florian; Lewis, Eva; Lin, Bo; Lira, Raúl; Lund, Peter; Macipe, Edgar; Mamuad, Lovelia L.; Cuquetto Mantovani, Hilário; Marcoppido, Gisela Ariana; Márquez, Cristian; Martin, Cécile; Martinez, Gonzalo; Eugenia Martinez, Maria; Lucía Mayorga, Olga; McAllister, Tim A.; McSweeney, Chris; Mestre, Lorena; Minnee, Elena; Mitsumori, Makoto; Mizrahi, Itzhak; Molina, Isabel; Muenger, Andreas; Munoz, Camila; Murovec, Bostjan; Newbold, John; Nsereko, Victor; O’Donovan, Michael; Okunade, Sunday; O’Neill, Brendan; Ospina, Sonia; Ouwerkerk, Diane; Parra, Diana; Pereira, Luiz Gustavo Ribeiro; Pinares-Patino, Cesar; Pope, Phil B.; Poulsen, Morten; Rodehutscord, Markus; Rodriguez, Tatiana; Saito, Kunihiko; Sales, Francisco; Sauer, Catherine; Shingfield, Kevin; Shoji, Noriaki; Simunek, Jiri; Stojanović-Radić, Zorica; Stres, Blaz; Sun, Xuezhao; Swartz, Jeffery; Liang Tan, Zhi; Tapio, Ilma; Taxis, Tasia M.; Tomkins, Nigel; Ungerfeld, Emilio; Valizadeh, Reza; van Adrichem, Peter; Van Hamme, Jonathan; Van Hoven, Woulter; Waghorn, Garry; John Wallace, R.; Wang, Min; Waters, Sinéad M.; Keogh, Kate; Witzig, Maren; Wright, Andre-Denis G.; Yamano, Hidehisa; Yan, Tianhai; Yanez-Ruiz, David R.; Yeoman, Carl J.; Zambrano, Ricardo; Zeitz, Johanna; Zhou, Mi; Wei Zhou, Hua; Xia Zou, Cai; Zunino, Pablo; Janssen, Peter H.

2015-01-01

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific. PMID:26449758

Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.

PubMed

Badin, Anne Laure; Monier, Armelle; Volatier, Laurence; Geremia, Roberto A; Delolme, Cécile; Bedell, Jean-Philippe

2011-05-01

The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release

Does human pressure affect the community structure of surf zone fish in sandy beaches?

NASA Astrophysics Data System (ADS)

Costa, Leonardo Lopes; Landmann, Júlia G.; Gaelzer, Luiz R.; Zalmon, Ilana R.

2017-01-01

Intense tourism and human activities have resulted in habitat destruction in sandy beach ecosystems with negative impacts on the associated communities. To investigate whether urbanized beaches affect surf zone fish communities, fish and their benthic macrofaunal prey were collected during periods of low and high human pressure at two beaches on the Southeastern Brazilian coast. A BACI experimental design (Before-After-Control-Impact) was adapted for comparisons of tourism impact on fish community composition and structure in urbanized, intermediate and non-urbanized sectors of each beach. At the end of the summer season, we observed a significant reduction in fish richness, abundance, and diversity in the high tourist pressure areas. The negative association between visitors' abundance and the macrofaunal density suggests that urbanized beaches are avoided by surf zone fish due to higher human pressure and the reduction of food availability. Our results indicate that surf zone fish should be included in environmental impact studies in sandy beaches, including commercial species, e.g., the bluefish Pomatomus saltatrix. The comparative results from the less urbanized areas suggest that environmental zoning and visitation limits should be used as effective management and preservation strategies on beaches with high conservation potential.

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.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

PubMed Central

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-01-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil. PMID:27128990

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter.

PubMed

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-12-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared

Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

USDA-ARS?s Scientific Manuscript database

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna.

PubMed

Busse, Annika; Antiqueira, Pablo A P; Neutzling, Alexandre S; Wolf, Anna M; Romero, Gustavo Q; Petermann, Jana S

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems.

Different in the dark: The effect of habitat characteristics on community composition and beta diversity in bromeliad microfauna

PubMed Central

Antiqueira, Pablo A. P.; Neutzling, Alexandre S.; Wolf, Anna M.; Romero, Gustavo Q.; Petermann, Jana S.

2018-01-01

The mechanisms which structure communities have been the focus of a large body of research. Here, we address the question if habitat characteristics describing habitat quality may drive changes in community composition and beta diversity of bromeliad-inhabiting microfauna. In our system, changes in canopy cover along an environmental gradient may affect resource availability, disturbance in form of daily water temperature fluctuations and predation, and thus may lead to changes in community structure of bromeliad microfauna through differences in habitat quality along this gradient. Indeed, we observed distinct changes in microfauna community composition along the environmental gradient explained by changes in the extent of daily water temperature fluctuations. We found beta diversity to be higher under low habitat quality (low canopy cover) than under high habitat quality (high canopy cover), which could potentially be explained by a higher relative importance of stochastic processes under low habitat quality. We also partitioned beta diversity into turnover and nestedness components and we found a nested pattern of beta diversity along the environmental gradient, with communities from the lower-quality habitat being nested subsets of communities from the higher-quality habitat. However, this pattern resulted from an increase in microfauna alpha diversity with an increase in habitat quality. By providing insights into microfauna-environment relationships our results contribute to the mechanistic understanding of community dynamics in small freshwater bodies. Here, we highlight the importance of habitat characteristics representing habitat quality in structuring communities, and suggest that this information may help to improve conservation practices of small freshwater ecosystems. PMID:29401522

Predictability of bee community composition after floral removals differs by floral trait group.

PubMed

Urban-Mead, Katherine R

2017-11-01

Plant-bee visitor communities are complex networks. While studies show that deleting nodes alters network topology, predicting these changes in the field remains difficult. Here, a simple trait-based approach is tested for predicting bee community composition following disturbance. I selected six fields with mixed cover of flower species with shallow (open) and deep (tube) nectar access, and removed all flowers or flower heads of species of each trait in different plots paired with controls, then observed bee foraging and composition. I compared the bee community in each manipulated plot with bees on the same flower species in control plots. The bee morphospecies composition in manipulations with only tube flowers remaining was the same as that in the control plots, while the bee morphospecies on only open flowers were dissimilar from those in control plots. However, the proportion of short- and long-tongued bees on focal flowers did not differ between control and manipulated plots for either manipulation. So, bees within some functional groups are more strongly linked to their floral trait partners than others. And, it may be more fruitful to describe expected bee community compositions in terms of relative proportions of relevant ecological traits than species, particularly in species-diverse communities. © 2017 The Author(s).

Dynamics of phytoplankton community composition in the western Gulf of Maine

NASA Astrophysics Data System (ADS)

Moore, Timothy S.

This dissertation is founded on the importance of phytoplankton community composition to marine biogeochemistry and ecosystem processes and motivated by the need to understand their distributions on regional to global scales. The ultimate goal was to predict surface phytoplankton communities using satellite remote sensing by relating marine habitats--defined through a statistical description of environmental properties--to different phytoplankton communities. While phytoplankton community composition is governed by the interplay of abiotic and biotic interactions, the strategy adopted here was to focus on the physical abiotic factors. This allowed for the detection of habitats from ocean satellites based on abiotic factors that were linked to associated phytoplankton communities. The research entailed three studies that addressed different aspects of the main goal using a dataset collected in the western Gulf of Maine over a 3-year period. The first study evaluated a chemotaxonomic method that quantified phytoplankton composition from pigment data. This enabled the characterization of three phytoplankton communities, which were defined by the relative abundance of diatoms and flagellates. The second study examined the cycles of these communities along with environmental variables, and the results revealed that the three phytoplankton communities exhibited an affinity to different hydrographic regimes. The third study focused on the implementation of a classifier that predicted phytoplankton communities from environmental variables. Its ability to differentiate communities dominated by diatoms versus flagellates was shown to be high. However, the increase in data imprecision when using satellite data led to lowered performance and favored an approach that incorporated fuzzy logic. The fuzzy method is well suited to characterize the uncertainties in phytoplankton community prediction, and provides a measure of confidence on predicted communities. The final product of

Phytoplankton responses to temperature increases are constrained by abiotic conditions and community composition.

PubMed

Striebel, Maren; Schabhüttl, Stefanie; Hodapp, Dorothee; Hingsamer, Peter; Hillebrand, Helmut

2016-11-01

Effects of temperature changes on phytoplankton communities seem to be highly context-specific, but few studies have analyzed whether this context specificity depends on differences in the abiotic conditions or in species composition between studies. We present an experiment that allows disentangling the contribution of abiotic and biotic differences in shaping the response to two aspects of temperature change: permanent increase of mean temperature versus pulse disturbance in form of a heat wave. We used natural communities from six different sites of a floodplain system as well as artificially mixed communities from laboratory cultures and grew both, artificial and natural communities, in water from the six different floodplain lakes (sites). All 12 contexts (2 communities × 6 sites) were first exposed to three different temperature levels (12, 18, 24 °C, respectively) and afterward to temperature pulses (4 °C increase for 7 h day(-1)). Temperature-dependent changes in biomass and community composition depended on the initial composition of phytoplankton communities. Abiotic conditions had a major effect on biomass of phytoplankton communities exposed to different temperature conditions, however, the effect of biotic and abiotic conditions together was even more pronounced. Additionally, phytoplankton community responses to pulse temperature effects depended on the warming history. By disentangling abiotic and biotic effects, our study shows that temperature-dependent effects on phytoplankton communities depend on both, biotic and abiotic constraints.

Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

PubMed Central

Whitaker, Jeanette; Ostle, Nicholas; Nottingham, Andrew T; Ccahuana, Adan; Salinas, Norma; Bardgett, Richard D; Meir, Patrick; McNamara, Niall P; Austin, Amy

2014-01-01

1. The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil-derived CO2 released to the atmosphere. 2. We studied tropical lowland, premontane and montane forest soils taken from along a 3200-m elevation gradient located in south-east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C-cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). 3. Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. 4. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram-positive relative to gram-negative bacteria explaining much of the model variance. 5. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate

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. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Large-Scale Changes in Community Composition: Determining Land Use and Climate Change Signals

PubMed Central

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. PMID:22523579

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.

Grazing of leaf-associated Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial community composition and function.

PubMed

Flues, Sebastian; Bass, David; Bonkowski, Michael

2017-08-01

Preferential food selection in protists is well documented, but we still lack basic understanding on how protist predation modifies the taxonomic and functional composition of bacterial communities. We conducted feeding trials using leaf-associated cercomonad Cercozoa by incubating them on a standardized, diverse bacterial community washed from plant leaves. We used a shotgun metagenomics approach to investigate the taxonomic and functional changes of the bacterial community after five days protist predation on bacteria. Predation-induced shifts in bacterial community composition could be linked to phenotypic protist traits. Protist reproduction rate, morphological plasticity and cell speed were most important in determining bacterial community composition. Analyses of co-occurrence patterns showed less complex correlations between bacterial taxa in the protist-grazed treatments with a higher proportion of positive correlations than in non-grazed controls, suggesting that predation reduced the influence of strong competitors. Protist predation influenced 14 metabolic core functions including membrane transport from which type VI secretion systems were in particular upregulated. In view of the functional importance of bacterial communities in the phyllosphere and rhizosphere of plants, a more detailed understanding of predator-prey interactions, changes in microbial composition and function, and subsequent repercussions on plant performance are clearly required. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Stormwater runoff drives viral community composition changes in inland freshwaters.

PubMed

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.

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

Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

PubMed Central

Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

2014-01-01

Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt

Total electron acceptor loading and composition affect hexavalent uranium reduction and microbial community structure in a membrane biofilm reactor.

PubMed

Ontiveros-Valencia, Aura; Zhou, Chen; Ilhan, Zehra Esra; de Saint Cyr, Louis Cornette; Krajmalnik-Brown, Rosa; Rittmann, Bruce E

2017-11-15

Molecular microbiology tools (i.e., 16S rDNA gene sequencing) were employed to elucidate changes in the microbial community structure according to the total electron acceptor loading (controlled by influent flow rate and/or medium composition) in a H 2 -based membrane biofilm reactor evaluated for removal of hexavalent uranium. Once nitrate, sulfate, and dissolved oxygen were replaced by U(VI) and bicarbonate and the total acceptor loading was lowered, slow-growing bacteria capable of reducing U(VI) to U(IV) dominated in the biofilm community: Replacing denitrifying bacteria Rhodocyclales and Burkholderiales were spore-producing Clostridiales and Natranaerobiales. Though potentially competing for electrons with U(VI) reducers, homo-acetogens helped attain steady U(VI) reduction, while methanogenesis inhibited U(VI) reduction. U(VI) reduction was reinstated through suppression of methanogenesis by addition of bromoethanesulfonate or by competition from SRB when sulfate was re-introduced. Predictive metagenome analysis further points out community changes in response to alterations in the electron-acceptor loading: Sporulation and homo-acetogenesis were critical factors for strengthening stable microbial U(VI) reduction. This study documents that sporulation was important to long-term U(VI) reduction, whether or not microorganisms that carry out U(VI) reduction mediated by cytochrome c 3 , such as SRB and ferric-iron-reducers, were inhibited. Copyright © 2017 Elsevier Ltd. All rights reserved.

Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

PubMed

Hagen, Live Heldal; Vivekanand, Vivekanand; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

2015-07-01

A new biogas process is initiated by adding a microbial community, typically in the form of a sample collected from a functional biogas plant. This inoculum has considerable impact on the initial performance of a biogas reactor, affecting parameters such as stability, biogas production yields and the overall efficiency of the anaerobic digestion process. In this study, we have analyzed changes in the microbial composition and performance of an inoculum during storage using barcoded pyrosequencing of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, and determination of the biomethane potential, respectively. The inoculum was stored at room temperature, 4 and -20 °C for up to 11 months and cellulose was used as a standard substrate to test the biomethane potential. Storage up to 1 month resulted in similar final methane yields, but the rate of methane production was reduced by storage at -20 °C. Longer storage times resulted in reduced methane yields and slower production kinetics for all storage conditions, with room temperature and frozen samples consistently giving the best and worst performance, respectively. Both storage time and temperature affected the microbial community composition and methanogenic activity. In particular, fluctuations in the relative abundance of Bacteroidetes were observed. Interestingly, a shift from hydrogenotrophic methanogens to methanogens with the capacity to perform acetoclastic methanogensis was observed upon prolonged storage. In conclusion, this study suggests that biogas inocula may be stored up to 1 month with low loss of methanogenic activity, and identifies bacterial and archaeal species that are affected by the storage.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

PubMed Central

Hanschen, Franziska S.; Yim, Bunlong; Winkelmann, Traud; Smalla, Kornelia; Schreiner, Monika

2015-01-01

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products. PMID:26186695

Trophic niches, diversity and community composition of invertebrate top predators (Chilopoda) as affected by conversion of tropical lowland rainforest in Sumatra (Indonesia).

PubMed

Klarner, Bernhard; Winkelmann, Helge; Krashevska, Valentyna; Maraun, Mark; Widyastuti, Rahayu; Scheu, Stefan

2017-01-01

Conversion of tropical rainforests into plantations fundamentally alters ecological niches of animal species. Generalist predators such as centipedes (Chilopoda) may be able to persist in converted ecosystems due to their ability to adapt and switch to alternative prey populations. We investigated variations in community composition and trophic niches of soil and litter living centipedes in a range of ecosystems including rainforests, jungle rubber agroforests, and rubber and oil palm monocultures in two landscapes in Sumatra, Indonesia. Including information on environmental factors in the soil and litter habitat, we explored drivers shaping ecological niches of soil living invertebrate predators in one of the world's hotspots of rainforest conversion. Conversion of rainforests into agroforests and plantations was associated with a marked change in the composition of centipede communities. However, irrespective of major differences in habitat characteristics, changes in total abundances were small and the overall diversity and biomass of centipedes was similar in each of the systems investigated, suggesting that the number of ecological niches for this group of predators remains unchanged. By using stable isotope analysis (15N and 13C), we investigated trophic niche shifts of the centipede community; lower δ13C values of centipedes in oil palm plantations as compared to other ecosystems suggests that centipedes switch from decomposer prey to other prey, presumably understory associated herbivores, due to reduced availability of litter associated prey species. The results suggest that the ability to utilize alternative prey is a key feature enabling invertebrate predators to persist in ecosystems undergoing major structural changes due to anthropogenic land use change.

Trophic niches, diversity and community composition of invertebrate top predators (Chilopoda) as affected by conversion of tropical lowland rainforest in Sumatra (Indonesia)

PubMed Central

Winkelmann, Helge; Krashevska, Valentyna; Maraun, Mark; Widyastuti, Rahayu; Scheu, Stefan

2017-01-01

Conversion of tropical rainforests into plantations fundamentally alters ecological niches of animal species. Generalist predators such as centipedes (Chilopoda) may be able to persist in converted ecosystems due to their ability to adapt and switch to alternative prey populations. We investigated variations in community composition and trophic niches of soil and litter living centipedes in a range of ecosystems including rainforests, jungle rubber agroforests, and rubber and oil palm monocultures in two landscapes in Sumatra, Indonesia. Including information on environmental factors in the soil and litter habitat, we explored drivers shaping ecological niches of soil living invertebrate predators in one of the world’s hotspots of rainforest conversion. Conversion of rainforests into agroforests and plantations was associated with a marked change in the composition of centipede communities. However, irrespective of major differences in habitat characteristics, changes in total abundances were small and the overall diversity and biomass of centipedes was similar in each of the systems investigated, suggesting that the number of ecological niches for this group of predators remains unchanged. By using stable isotope analysis (15N and 13C), we investigated trophic niche shifts of the centipede community; lower δ13C values of centipedes in oil palm plantations as compared to other ecosystems suggests that centipedes switch from decomposer prey to other prey, presumably understory associated herbivores, due to reduced availability of litter associated prey species. The results suggest that the ability to utilize alternative prey is a key feature enabling invertebrate predators to persist in ecosystems undergoing major structural changes due to anthropogenic land use change. PMID:28763453

Endangered light-footed clapper rail affects parasite community structure in coastal wetlands

USGS Publications Warehouse

Whitney, Kathleen L.; Hechinger, Ryan F.; Kuris, Armand M.; Lafferty, Kevin D.

2007-01-01

An extinction necessarily affects community members that have obligate relationships with the extinct species. Indirect or cascading effects can lead to even broader changes at the community or ecosystem level. However, it is not clear whether generalist parasites should be affected by the extinction of one of their hosts. We tested the prediction that loss of a host species could affect the structure of a generalist parasite community by investigating the role of endangered Light-footed Clapper Rails (Rallus longirostris levipes) in structuring trematode communities in four tidal wetlands in southern California, USA (Carpinteria Salt Marsh, Mugu Lagoon) and Mexico (Estero de Punta Banda, Bahia Falsa–San Quintín). We used larval trematode parasites in first intermediate host snails (Cerithidea californica) as windows into the adult trematodes that parasitize Clapper Rails. Within and among wetlands, we found positive associations between Clapper Rails and four trematode species, particularly in the vegetated marsh habitat where Clapper Rails typically occur. This suggests that further loss of Clapper Rails is likely to affect the abundance of several competitively dominant trematode species in wetlands with California horn snails, with possible indirect effects on the trematode community and changes in the impacts of these parasites on fishes and invertebrates.

Effects of simulated acid rain on soil fauna community composition and their ecological niches.

PubMed

Wei, Hui; Liu, Wen; Zhang, Jiaen; Qin, Zhong

2017-01-01

Acid rain is one of the severest environmental issues globally. Relative to other global changes (e.g., warming, elevated atmospheric [CO 2 ], and nitrogen deposition), however, acid rain has received less attention than its due. Soil fauna play important roles in multiple ecological processes, but how soil fauna community responds to acid rain remains less studied. This microcosm experiment was conducted using latosol with simulated acid rain (SAR) manipulations to observe potential changes in soil fauna community under acid rain stress. Four pH levels, i.e., pH 2.5, 3.5, 4.5, and 5.5, and a neutral control of pH 7.0 were set according to the current pH condition and acidification trend of precipitation in southern China. As expected, we observed that the SAR treatments induced changes in soil fauna community composition and their ecological niches in the tested soil; the treatment effects tended to increase as acidity increased. This could be attributable to the environmental stresses (such as acidity, porosity and oxygen supply) induced by the SAR treatments. In addition to direct acidity effect, we propose that potential changes in permeability and movability of water and oxygen in soils induced by acid rain could also give rise to the observed shifts in soil fauna community composition. These are most likely indirect pathways of acid rain to affect belowground community. Moreover, we found that nematodes, the dominating soil fauna group in this study, moved downwards to mitigate the stress of acid rain. This is probably detrimental to soil fauna in the long term, due to the relatively severer soil conditions in the deep than surface soil layer. Our results suggest that acid rain could change soil fauna community and the vertical distribution of soil fauna groups, consequently changing the underground ecosystem functions such as organic matter decomposition and greenhouse gas emissions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Apple orchard pest control strategies affect bird communities in southeastern France.

PubMed

Bouvier, Jean-Charles; Ricci, Benoît; Agerberg, Julia; Lavigne, Claire

2011-01-01

Birds are regarded as appropriate biological indicators of how changes in agricultural practices affect the environment. They are also involved in the biocontrol of pests. In the present study, we provide an assessment of the impact of pest control strategies on bird communities in apple orchards in southeastern France. We compared the structure (abundance, species richness, and diversity) of breeding bird communities in 15 orchards under conventional or organic pest control over a three-year period (2003-2005). Pest control strategies and their evolution over time were characterized by analyzing farmers' treatment schedules. The landscape surrounding the orchards was characterized using a Geographic Information System. We observed 30 bird species overall. Bird abundance, species richness, and diversity were all affected by pest control strategies, and were highest in organic orchards and lowest in conventional orchards during the three study years. The pest control strategy affected insectivores more than granivores. We further observed a tendency for bird communities in integrated pest management orchards to change over time and become increasingly different from communities in organic orchards, which also corresponded to changes in treatment schedules. These findings indicate that within-orchard bird communities may respond quickly to changes in pesticide use and may, in turn, influence biocontrol of pests by birds. © 2010 SETAC.

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.

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

Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

Treesearch

Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

2013-01-01

Background and aims Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore...

Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zorpas, Antonis A., E-mail: antonis.zorpas@ouc.ac.cy; Lasaridi, Katia, E-mail: klasaridi@hua.gr; Voukkali, Irene

Highlights: • Waste framework directive has set clear waste prevention procedures. • Household Compositional analysis. • Waste management plans. • Zero waste approach. • Waste generation. - Abstract: Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impactmore » on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes.« less

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of

Phytoplankton community composition and primary production in the tropical tidal ecosystem, Maputo Bay (the Indian Ocean)

NASA Astrophysics Data System (ADS)

Olofsson, Malin; Karlberg, Maria; Lage, Sandra; Ploug, Helle

2017-07-01

Maputo Bay is highly affected by large tidal changes and riverine freshwater input with a phytoplankton biomass peak during March each year. Microscopy analysis was used to describe how the phytoplankton community composition was affected by tidal changes, during four in situ incubation experiments. Using stable isotope tracers, new and total primary production, based on nitrate (15NO3-)- and carbon (13C-bicarbonate)-assimilation were estimated. The highest biovolume of phytoplankton (> 2 μm) and also the highest C- and NO3--assimilation rates (nM h-1) were found at spring-high tide. The C:N (mol:mol) ratio of particulate organic matter (POM) varied between 6.0 and 8.2. The proportion of diatoms in the phytoplankton community was higher at spring-high tide as compared to neap-low tide, whereas dinoflagellates were found in a reverse pattern. New production ranged between 6.3% and 10.4% of total primary production and was thus within the range previously reported for tropical regions. The largest proportion of NO3--based new production relative to total production was estimated during calm conditions and spring-high tide. Concordantly, a large fraction of the microplanktonic community covered their N-demand by other sources of N than NO3-.

Functional homogenization of flower visitor communities with urbanization.

PubMed

Deguines, Nicolas; Julliard, Romain; de Flores, Mathieu; Fontaine, Colin

2016-04-01

Land-use intensification and resulting habitat loss are put forward as the main causes of flower visitor decline. However, the impact of urbanization, the prime driver of land-use intensification in Europe, is poorly studied. In particular, our understanding of whether and how it affects the composition and functioning of flower visitor assemblages is scant, yet required to cope with increasing urbanization worldwide. Here, we use a nation-wide dataset of plant-flower visitor (Coleoptera, Diptera, Hymenoptera, Lepidoptera) interactions sampled by citizen scientists following a standardized protocol to assess macroecological changes in richness and composition of flower visitor communities with urbanization. We measured the community composition by quantifying the relative occurrence of generalist and specialist flower visitors based on their specialisation on flowering plant families. We show that urbanization is associated with reduced flower visitor richness and a shift in community composition toward generalist insects, indicating a modification of the functional composition of communities. These results suggest that urbanization affects not only the richness of flower visitor assemblages but may also cause their large-scale functional homogenization. Future research should focus on designing measures to reconcile urban development with flower visitor conservation.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE PAGES

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; ...

2016-04-29

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE PAGES

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley; ...

2017-06-28

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community

Shifts in microbial community composition following surface application of dredged river sediments.

PubMed

Baniulyte, Dovile; Favila, Emmanuel; Kelly, John J

2009-01-01

Sediment input to the Illinois River has drastically decreased river depth and reduced habitats for aquatic organisms. Dredging is being used to remove sediment from the Illinois River, and the dredged sediment is being applied to the surface of a brownfield site in Chicago with the goal of revegetating the site. In order to determine the effects of this drastic habitat change on sediment microbial communities, we examined sediment physical, chemical, and microbial characteristics at the time of sediment application to the soil surface as well as 1 and 2 years after application. Microbial community biomass was determined by measurement of lipid phosphate. Microbial community composition was assessed using phospholipid fatty acid (PLFA) analysis, terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes, and clone library sequencing of 16S rRNA genes. Results indicated that the moisture content, organic carbon, and total nitrogen content of the sediment all decreased over time. Total microbial biomass did not change over the course of the study, but there were significant changes in the composition of the microbial communities. PLFA analysis revealed relative increases in fungi, actinomycetes, and Gram positive bacteria. T-RFLP analysis indicated a significant shift in bacterial community composition within 1 year of application, and clone library analysis revealed relative increases in Proteobacteria, Gemmatimonadetes, and Bacteriodetes and relative decreases in Acidobacteria, Spirochaetes, and Planctomycetes. These results provide insight into microbial community shifts following land application of dredged sediment.

Lichen physiological traits and growth forms affect communities of associated invertebrates.

PubMed

Bokhorst, Stef; Asplund, Johan; Kardol, Paul; Wardle, David A

2015-09-01

While there has been much interest in the relationships between traits of primary producers and composition of associated invertebrate consumer communities, our knowledge is largely based on studies from vascular plants, while other types of functionally important producers, such as lichens, have rarely been considered. To address how physiological traits of lichens drive community composition of invertebrates, we collected thalli from 27 lichen species from southern Norway and quantified the communities of associated springtails, mites, and nematodes. For each lichen species, we measured key physiological thallus traits and determined whether invertebrate communities were correlated with these traits. We also explored whether invertebrate communities differed among lichen groups, categorized according to nitrogen-fixing ability, growth form, and substratum. Lichen traits explained up to 39% of the variation in abundances of major invertebrate groups. For many invertebrate groups, abundance was positively correlated with lichen N and P concentrations, N:P ratio, and the percentage of water content on saturation (WC), but had few relationships with concentrations of carbon-based secondary compounds. Diversity and taxonomic richness of invertebrate groups were sometimes also correlated with lichen N and N:P ratios. Nitrogen-fixing lichens showed higher abundance and diversity of some invertebrate groups than did non-N-fixing lichens. However, this emerged in part because most N-fixing lichens have a foliose growth form that benefits invertebrates, through, improving the microclimate, independently of N concentration. Furthermore, invertebrate communities associated with terricolous lichens were determined more by their close proximity to the soil invertebrate pool than by lichen traits. Overall, our results reveal that differences between lichen species have a large impact on the invertebrate communities that live among the thalli. Different invertebrate groups show

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest

PubMed Central

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting. PMID:26317523

Influence of Tree Species Composition and Community Structure on Carbon Density in a Subtropical Forest.

PubMed

Hu, Yanqiu; Su, Zhiyao; Li, Wenbin; Li, Jingpeng; Ke, Xiandong

2015-01-01

We assessed the impact of species composition and stand structure on the spatial variation of forest carbon density using data collected from a 4-ha plot in a subtropical forest in southern China. We found that 1) forest biomass carbon density significantly differed among communities, reflecting a significant effect of community structure and species composition on carbon accumulation; 2) soil organic carbon density increased whereas stand biomass carbon density decreased across communities, indicating that different mechanisms might account for the accumulation of stand biomass carbon and soil organic carbon in the subtropical forest; and 3) a small number of tree individuals of the medium- and large-diameter class contributed predominantly to biomass carbon accumulation in the community, whereas a large number of seedlings and saplings were responsible for a small proportion of the total forest carbon stock. These findings demonstrate that both biomass carbon and soil carbon density in the subtropical forest are sensitive to species composition and community structure, and that heterogeneity in species composition and stand structure should be taken into account to ensure accurate forest carbon accounting.

Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans.

PubMed

Zorpas, Antonis A; Lasaridi, Katia; Voukkali, Irene; Loizia, Pantelitsa; Chroni, Christina

2015-04-01

Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impact on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

PubMed Central

Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

PubMed

Stanish, Lee F; Hull, Natalie M; Robertson, Charles E; Harris, J Kirk; Stevens, Mark J; Spear, John R; Pace, Norman R

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

PubMed

Kleindienst, Sara; Paul, John H; Joye, Samantha B

2015-06-01

Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills.

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

The assembly of ecological communities inferred from taxonomic and functional composition

Treesearch

Eric R. Sokol; E.F. Benfield; Lisa K. Belden; H. Maurice. Valett

2011-01-01

Among-site variation in metacommunities (beta diversity) is typically correlated with the distance separating the sites (spatial lag). This distance decay in similarity pattern has been linked to both niche-based and dispersal-based community assembly hypotheses. Here we show that beta diversity patterns in community composition, when supplemented with functional-trait...

Compositional stability and diversity of vascular plant communities following logging disturbance in Appalachian forests.

PubMed

Belote, R Travis; Jones, Robert H; Wieboldt, Thomas F

2012-03-01

Human-caused changes in disturbance regimes and introductions of nonnative species have the potential to result in widespread, directional changes in forest community structure. The degree that plant community composition persists or changes following disturbances depends on the balance between local extirpation and colonization by new species, including nonnatives. In this study, we examined species losses and gains, and entry of native vs. exotic species to determine how oak forests in the Appalachian Mountains might shift in species composition following a gradient of pulse disturbances (timber harvesting). We asked (1) how compositional stability of the plant community (resistance and resilience) was influenced by disturbance intensity, (2) whether community responses were driven by extirpation or colonization of species, and (3) how disturbance intensity influenced total and functional group diversity, including the nonnative proportion of the flora through time. We collected data at three spatial scales and three times, including just before, one year post-disturbance, and 10 years post-disturbance. Resistance was estimated using community distance measures between pre- and one year post-disturbance, and resilience using community distance between pre- and 10-year post-disturbance conditions. The number of colonizing and extirpated species between sampling times was analyzed for all species combined and for six functional groups. Resistance and resilience decreased with increasing timber-harvesting disturbance; compositional stability was lower in the most disturbed plots, which was driven by colonization, but not extirpation, of species. Colonization of species also led to increases in diversity after disturbance that was typically maintained after 10 years following disturbance. Most of the community-level responses were driven by post-disturbance colonization of native forbs and graminoids. The nonnative proportion of plant species tended to increase

Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

NASA Astrophysics Data System (ADS)

Wilton, E.; Flanagan, L. B.

2014-12-01

Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman-Derr, Devin; Desgarennes, Damaris; Fonseca-Garcia, Citlali

Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves,more » through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.« less

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

DOE PAGES

Coleman-Derr, Devin; Desgarennes, Damaris; Fonseca-Garcia, Citlali; ...

2015-10-15

Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves,more » through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.« less

The Role of Abiotic Environmental Conditions and Herbivory in Shaping Bacterial Community Composition in Floral Nectar

PubMed Central

Samuni-Blank, Michal; Izhaki, Ido; Laviad, Sivan; Bar-Massada, Avi; Gerchman, Yoram; Halpern, Malka

2014-01-01

Identifying the processes that drive community assembly has long been a central theme in ecology. For microorganisms, a traditional prevailing hypothesis states that “everything is everywhere, but the environment selects”. Although the bacterial community in floral nectar may be affected by both atmosphere (air-borne bacteria) and animals as dispersal vectors, the environmental and geographic factors that shape microbial communities in floral nectar are unknown. We studied culturable bacterial communities in Asphodelus aestivus floral nectar and in its typical herbivorous bug Capsodes infuscatus, along an aridity gradient. Bacteria were sampled from floral nectar and bugs at four sites, spanning a geographical range of 200 km from Mediterranean to semi-arid conditions, under open and bagged flower treatments. In agreement with the niche assembly hypothesis, the differences in bacterial community compositions were explained by differences in abiotic environmental conditions. These results suggest that microbial model systems are useful for addressing macro-ecological questions. In addition, similar bacterial communities were found in the nectar and on the surface of the bugs that were documented visiting the flowers. These similarities imply that floral nectar bacteria dispersal is shaped not only by air borne bacteria and nectar consumers as previously reported, but also by visiting vectors like the mirid bugs. PMID:24922317

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...

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.

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.

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

Associations between retail food store exterior advertisements and community demographic and socioeconomic composition.

PubMed

Isgor, Zeynep; Powell, Lisa; Rimkus, Leah; Chaloupka, Frank

2016-05-01

This paper examines the association between the prevalence of various types of outdoor food and beverage advertising found on the building exteriors and properties of retail food outlets and community racial/ethnic and socioeconomic composition in a nationwide sample of food outlets in the U.S. Our major finding from multivariable analysis is that food stores in low-income communities have higher prevalence of all food and beverage ads, including those for unhealthy products such as regular soda, controlling for community racial/ethnic composition and other covariates. This adds to growing research pointing to socioeconomic disparities in food and beverage marketing exposure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multiscale spatial and small-scale temporal variation in the composition of Riverine fish communities.

PubMed

Growns, Ivor; Astles, Karen; Gehrke, Peter

2006-03-01

We studied the multiscale (sites, river reaches and rivers) and short-term temporal (monthly) variability in a freshwater fish assemblage. We found that small-scale spatial variation and short-term temporal variability significantly influenced fish community structure in the Macquarie and Namoi Rivers. However, larger scale spatial differences between rivers were the largest source of variation in the data. The interaction between temporal change and spatial variation in fish community structure, whilst statistically significant, was smaller than the variation between rivers. This suggests that although the fish communities within each river changed between sampling occasions, the underlying differences between rivers were maintained. In contrast, the strongest interaction between temporal and spatial effects occurred at the smallest spatial scale, at the level of individual sites. This means whilst the composition of the fish assemblage at a given site may fluctuate, the magnitude of these changes is unlikely to affect larger scale differences between reaches within rivers or between rivers. These results suggest that sampling at any time within a single season will be sufficient to show spatial differences that occur over large spatial scales, such as comparisons between rivers or between biogeographical regions.

How does conversion of natural tropical rainforest ecosystems affect soil bacterial and fungal communities in the Nile river watershed of Uganda?

PubMed

Alele, Peter O; Sheil, Douglas; Surget-Groba, Yann; Lingling, Shi; Cannon, Charles H

2014-01-01

Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?

PubMed Central

Alele, Peter O.; Sheil, Douglas; Surget-Groba, Yann; Lingling, Shi; Cannon, Charles H.

2014-01-01

Uganda's forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring

Effects of long-term drainage on microbial community composition vary between peatland types

NASA Astrophysics Data System (ADS)

Urbanová, Zuzana; Barta, Jiri

2016-04-01

Peatlands represent an important reservoir of carbon, but their functioning can be threatened by water level drawdown caused by climate or land use change. Knowledge of how microbial communities respond to long-term drainage in different peatland types could help improve predictions of the effect of climate change on these ecosystems. We investigated the effect of long-term drainage on microbial community composition in bog, fen and spruce swamp forests (SSF) in the Sumava Mountains (Czech Republic), using high-throughput barcoded sequencing, in relation to peat biochemical properties. Longterm drainage had substantial effects, which depended strongly on peatland type, on peat biochemical properties and microbial community composition. The effect of drainage was most apparent on fen, followed by SSF, and lowest on bog. Long-term drainage led to lower pH, reduced peat decomposability and increased bulk density, which was reflected by reduced microbial activity. Bacterial diversity decreased and Acidobacteria became the dominant phylum on drained sites, reflecting a convergence in bacterial community composition across peatlands after long-term drainage. The archaeal communities changed very strongly and became similar across drained peatlands. Overall, the characteristic differences between distinct peatland types under natural conditions were diminished by long-term drainage. Bog represented a relatively resilient system while fen seemed to be very sensitive to environmental changes.

Factors affecting plant species composition of hedgerows: relative importance and hierarchy

NASA Astrophysics Data System (ADS)

Deckers, Bart; Hermy, Martin; Muys, Bart

2004-07-01

Although there has been a clear quantitative and qualitative decline in traditional hedgerow network landscapes during last century, hedgerows are crucial for the conservation of rural biodiversity, functioning as an important habitat, refuge and corridor for numerous species. To safeguard this conservation function, insight in the basic organizing principles of hedgerow plant communities is needed. The vegetation composition of 511 individual hedgerows situated within an ancient hedgerow network landscape in Flanders, Belgium was recorded, in combination with a wide range of explanatory variables, including a selection of spatial variables. Non-parametric statistics in combination with multivariate data analysis techniques were used to study the effect of individual explanatory variables. Next, variables were grouped in five distinct subsets and the relative importance of these variable groups was assessed by two related variation partitioning techniques, partial regression and partial canonical correspondence analysis, taking into account explicitly the existence of intercorrelations between variables of different factor groups. Most explanatory variables affected significantly hedgerow species richness and composition. Multivariate analysis showed that, besides adjacent land use, hedgerow management, soil conditions, hedgerow type and origin, the role of other factors such as hedge dimensions, intactness, etc., could certainly not be neglected. Furthermore, both methods revealed the same overall ranking of the five distinct factor groups. Besides a predominant impact of abiotic environmental conditions, it was found that management variables and structural aspects have a relatively larger influence on the distribution of plant species in hedgerows than their historical background or spatial configuration.

A hierarchical examination of methane uptake: field patterns, lab physiology, community composition and biogeography

NASA Astrophysics Data System (ADS)

von Fischer, J. C.; Koyama, A.; Johnson, N. G.; Webb, C. T.

2015-12-01

Scaling problems abound in biogeochemistry. At the finest scale, soil microbes experience habitats and environmental changes that affect the chemical transformations of interest. We collect the DNA of these organisms from sites across landscapes and note differences in who is there, and we seek to evaluate why group membership changes in space (biogeography) and why activity rates change over time (physiology). The goal of efforts at finer scales is often to better predict patterns at larger scales. We conducted such a hierarchical examination of methane uptake in the Great Plains grasslands of North America, gathering data from 22 plots at 8 field locations, scattered from South Dakota to New Mexico and Colorado to Kansas. Our work provides insight into methanotroph biogeochemistry at all of these scales. For example, we found that methane uptake rates vary mostly due to the methanotroph activity, and less so due to diffusivity. A combination of field and lab observations reveal that methanotroph communities differ in their sensitivity to soil moisture and to ammonium (an inhibitor of methanotrophy). Examination of methanotroph community composition reveals tantalizing patterns in composition, dominance and richness across sites, that appears to be structured by patterns of precipitation and soil texture. We anticipate that greater synthesis of these hierarchical findings will paint a richer picture of methanotroph life and enable improved prediction of methane uptake at regional scales.

Warming climate may negatively affect native forest understory plant richness and composition by increasing invasions of non-native plants

NASA Astrophysics Data System (ADS)

Dovciak, M.; Wason, J. W., III; Frair, J.; Lesser, M.; Hurst, J.

2016-12-01

Warming climate is often expected to cause poleward and upslope migrations of native plant species and facilitate the spread of non-native plants, and thus affect the composition and diversity of forest understory plant communities. However, changing climate can often interact with other components of global environmental change, and especially so with land use, which often varies along extant climatic gradients making it more difficult to predict species and biodiversity responses to changing climate. We used large national databases (USDA FIA, NLCD, and PRISM) within GLM and NMDS analytical frameworks to study the effects of climate (temperature and precipitation), and land management (type, fragmentation, time since disturbance) on the diversity and composition of native and non-native plant species in forest understories across large geographical (environmental) gradients of the northeastern United States. We tested how non-native and native species diversity and composition responded to existing climate gradients and land-use drivers, and we approximated how changing climate may affect both native and non-native species composition and richness under different climate change scenarios (+1.5, 2, and 4.8 degrees C). Many understory forest plant communities already contain large proportions of non-native plants, particularly so in relatively warmer and drier areas, at lower elevations, and in areas with more substantial land-use histories. On the other hand, cooler and moister areas, higher elevations, and areas used predominantly for forestry or nature conservation (i.e., large contiguous forest cover) were characterized by a low proportion of non-native plant species in terms of both species cover and richness. In contrast to native plants, non-native plant richness was related positively to mean annual temperature and negatively to precipitation. Mountain areas appeared to serve as refugia for native forest understory species under the current climate, but

Community characteristics affecting emergency department use by Medicaid enrollees.

PubMed

Lowe, Robert A; Fu, Rongwei; Ong, Emerson T; McGinnis, Paul B; Fagnan, Lyle J; Vuckovic, Nancy; Gallia, Charles

2009-01-01

In seeking to identify modifiable, system-level factors affecting emergency department (ED) use, we used a statewide Medicaid database to study community variation in ED use and ascertain community characteristics associated with higher use. This historical cohort study used administrative data from July 1, 2003 to December 31, 2004. Residence ZIP codes were used to assign all 555,219 Medicaid enrollees to 130 primary care service areas (PCSAs). PCSA characteristics studied included rural/urban status, presence of hospital(s), driving time to hospital, and several measures of primary care capacity. Statistical analyses used a 2-stage model. In the first stage (enrollee level), ED utilization rates adjusted for enrollee demographics and medical conditions were calculated for each PCSA. In the second stage (community level), a mixed effects linear model was used to determine the association between PCSA characteristics and ED use. ED utilization rates varied more than 20-fold among the PCSAs. Compared with PCSAs with primary care capacity less than need, PCSAs with capacity 1 to 2 times the need had 0.12 (95% CI: -0.044, -0.20) fewer ED visits/person/yr. Compared with PCSAs with the nearest hospital accessible within 10 minutes, PCSAs with the nearest hospital >30 minutes' drive had 0.26 (95% CI: -0.38, -0.13) fewer ED visits/person/yr. Within this Medicaid population, ED utilization was determined not only by patient characteristics but by community characteristics. Better understanding of system-level factors affecting ED use can enable communities to improve their health care delivery systems-augmenting access to care and reducing reliance on EDs.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

PubMed

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Energy composition of diet affects muscle fiber recruitment, body composition, and growth trajectory in rainbow trout (Oncorhnychus mykiss)

USDA-ARS?s Scientific Manuscript database

Energy composition of diet affects muscle fiber recruitment, body composition, and growth trajectory in rainbow trout (Oncorhnychus mykiss) The cost and scarcity of key ingredients for aquaculture feed formulation call for a wise use of resources, especially dietary proteins and energy. For years t...

Patterns of vegetation and grasshopper community composition.

PubMed

Kemp, W P; Harvey, S J; O'Neill, K M

1990-06-01

A study was conducted to evaluate differences in rangeland grasshopper communities over environmental gradients in Gallatin Valley, Montana, USA. The concept of habitat type (Daubenmire 1966) was used as a basis for discriminating between groupings of patches based on vegetation. A total of 39 patches were selected that represented five recognized grassland habitat types (Mueggler and Stewart 1980), as well as two disturbed types (replanting within a known habitat type). Repeated sampling in 1988 of both the insect and plant communities yielded a total of 40 grasshopper (19 664 individuals) and 97 plant species. Detrended Correspondence Analysis (DCA) indicated that patch classifications based on presence and percent cover of plants were appropriate and showed good between-group (habitat type) separation for patches along gradients of precipitation/elevation and plant community complexity. Results from undisturbed habitats showed that plant and grasshopper species composition changed over observed environmental gradients and suggested that habitat type influenced not only species presence, but also relative abundance. Discussion is presented that relates results with patch-use and core and satellite species paradigms.

Absence of snow cover reduces understory plant cover and alters plant community composition in boreal forests.

PubMed

Kreyling, Juergen; Haei, Mahsa; Laudon, Hjalmar

2012-02-01

Snow regimes affect biogeochemistry of boreal ecosystems and are altered by climate change. The effects on plant communities, however, are largely unexplored despite their influence on relevant processes. Here, the impact of snow cover on understory community composition and below-ground production in a boreal Picea abies forest was investigated using a long-term (8-year) snow cover manipulation experiment consisting of the treatments: snow removal, increased insulation (styrofoam pellets), and control. The snow removal treatment caused longer (118 vs. 57 days) and deeper soil frost (mean minimum temperature -5.5 vs. -2.2°C) at 10 cm soil depth in comparison to control. Understory species composition was strongly altered by the snow cover manipulations; vegetation cover declined by more than 50% in the snow removal treatment. In particular, the dominant dwarf shrub Vaccinium myrtillus (-82%) and the most abundant mosses Pleurozium schreberi (-74%) and Dicranum scoparium (-60%) declined strongly. The C:N ratio in V. myrtillus leaves and plant available N in the soil indicated no altered nitrogen nutrition. Fine-root biomass in summer, however, was negatively affected by the reduced snow cover (-50%). Observed effects are attributed to direct frost damage of roots and/ or shoots. Besides the obvious relevance of winter processes on plant ecology and distribution, we propose that shifts in the vegetation caused by frost damage may be an important driver of the reported alterations in biogeochemistry in response to altered snow cover. Understory plant performance clearly needs to be considered in the biogeochemistry of boreal systems in the face of climate change.

Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices

NASA Astrophysics Data System (ADS)

White, J. C.; Hill, M. J.; Bickerton, M. A.; Wood, P. J.

2017-09-01

The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.

Host tree phenology affects vascular epiphytes at the physiological, demographic and community level

PubMed Central

Einzmann, Helena J. R.; Beyschlag, Joachim; Hofhansl, Florian; Wanek, Wolfgang; Zotz, Gerhard

2015-01-01

The processes that govern diverse tropical plant communities have rarely been studied in life forms other than trees. Structurally dependent vascular epiphytes, a major part of tropical biodiversity, grow in a three-dimensional matrix defined by their hosts, but trees differ in their architecture, bark structure/chemistry and leaf phenology. We hypothesized that the resulting seasonal differences in microclimatic conditions in evergreen vs. deciduous trees would affect epiphytes at different levels, from organ physiology to community structure. We studied the influence of tree leaf phenology on vascular epiphytes on the Island of Barro Colorado, Panama. Five tree species were selected, which were deciduous, semi-deciduous or evergreen. The crowns of drought-deciduous trees, characterized by sunnier and drier microclimates, hosted fewer individuals and less diverse epiphyte assemblages. Differences were also observed at a functional level, e.g. epiphyte assemblages in deciduous trees had larger proportions of Crassulacean acid metabolism species and individuals. At the population level a drier microclimate was associated with lower individual growth and survival in a xerophytic fern. Some species also showed, as expected, lower specific leaf area and higher δ13C values when growing in deciduous trees compared with evergreen trees. As hypothesized, host tree leaf phenology influences vascular epiphytes at different levels. Our results suggest a cascading effect of tree composition and associated differences in tree phenology on the diversity and functioning of epiphyte communities in tropical lowland forests. PMID:25392188

Tree specie effects on soil microbial community composition and greenhouse gases emissions in a Mediterranean ecotone forest

NASA Astrophysics Data System (ADS)

Fernandez, Maria Jose; Ortiz, Carlos; Kitzler, Barbara; Curiel, Jorge; Rubio, Agustin

2016-04-01

Over recent decades in the Iberian Peninsula, altitudinal shifts from Pinus sylvestris L. to Quercus pyrenaica Willd species has been observed as a consequence of Global Change, meaning changes in temperature, precipitation, land use and forestry. The forest conversion from pine to oak can alter the litter quality and quantity provided to the soil and thereby the soil microbial community composition and functioning. Since soil microbiota plays an important role in organic matter decomposition, and this in turn is key in biogeochemical cycles and forest ecosystems productivity, the rate in which forests produce and consume greenhouse gases can be also affected by changes in forest composition. In other words, changes in litter decomposition will ultimately affect downstream carbon and nitrogen dynamics although this impact is uncertain. In order to predict changes in carbon and nitrogen stocks in Global Change scenarios, it is necessary to deepen the impact of vegetation changes on soil microbial communities, litter decomposition dynamics (priming effect) and the underlying interactions between these factors. To test this, we conducted a full-factorial transplant microcosms experiment mixing both fresh soils and litter from Pyrenean oak, Scots pine and mixed stands collected inside their transitional area in Central Spain. The microcosms consisted in soil cylinders inside Kilner jars used as chambers inside an incubator. In this experiment, we investigated how and to what extent the addition of litter with different quality (needles, oak leaves and mixed needles-leaves) to soil inoculums with contrasting soil microbiota impact on (i) soil CO2, NO, N2O and CH4 efflux rates, (ii) total organic carbon and nitrogen and (iii) dissolved organic carbon and nitrogen. Furthermore, we assessed if these responses were controlled by changes in the microbial community structure using the PLFA analyses prior and after the incubation period of 54 days.

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.

PubMed

Coleman-Derr, Devin; Desgarennes, Damaris; Fonseca-Garcia, Citlali; Gross, Stephen; Clingenpeel, Scott; Woyke, Tanja; North, Gretchen; Visel, Axel; Partida-Martinez, Laila P; Tringe, Susannah G

2016-01-01

Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions. No claim to US Government works. New Phytologist © 2015 New Phytologist Trust.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Coral Reef Community Composition in the Context of Disturbance History on the Great Barrier Reef, Australia

PubMed Central

Graham, Nicholas A. J.; Chong-Seng, Karen M.; Huchery, Cindy; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.

2014-01-01

Much research on coral reefs has documented differential declines in coral and associated organisms. In order to contextualise this general degradation, research on community composition is necessary in the context of varied disturbance histories and the biological processes and physical features thought to retard or promote recovery. We conducted a spatial assessment of coral reef communities across five reefs of the central Great Barrier Reef, Australia, with known disturbance histories, and assessed patterns of coral cover and community composition related to a range of other variables thought to be important for reef dynamics. Two of the reefs had not been extensively disturbed for at least 15 years prior to the surveys. Three of the reefs had been severely impacted by crown-of-thorns starfish outbreaks and coral bleaching approximately a decade before the surveys, from which only one of them was showing signs of recovery based on independent surveys. We incorporated wave exposure (sheltered and exposed) and reef zone (slope, crest and flat) into our design, providing a comprehensive assessment of the spatial patterns in community composition on these reefs. Categorising corals into life history groupings, we document major coral community differences in the unrecovered reefs, compared to the composition and covers found on the undisturbed reefs. The recovered reef, despite having similar coral cover, had a different community composition from the undisturbed reefs, which may indicate slow successional processes, or a different natural community dominance pattern due to hydrology and other oceanographic factors. The variables that best correlated with patterns in the coral community among sites included the density of juvenile corals, herbivore fish biomass, fish species richness and the cover of macroalgae. Given increasing impacts to the Great Barrier Reef, efforts to mitigate local stressors will be imperative to encouraging coral communities to persist into

Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil

PubMed Central

Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

2016-01-01

The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC–MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on

Logging legacies affect insect pollinator communities in southern Appalachian forests

Treesearch

Michelle M. Jackson; Monica G. Turner; Scott M. Pearson

2014-01-01

Many temperate deciduous forests are recovering from past logging, but the effects of logging legacies and environmental gradients on forest insect pollinators have not been well studied. In this study, we asked how pollinator abundance and community composition varied with distance from logging roads and elevation in old (logged >90 years ago) and young (logged 20–...

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems.

PubMed

Kokko, Marika; Epple, Stefanie; Gescher, Johannes; Kerzenmacher, Sven

2018-06-01

Over the last decade, there has been an ever-growing interest in bioelectrochemical systems (BES) as a sustainable technology enabling simultaneous wastewater treatment and biological production of, e.g. electricity, hydrogen, and further commodities. A key component of any BES degrading organic matter is the anode where electric current is biologically generated from the oxidation of organic compounds. The performance of BES depends on the interactions of the anodic microbial communities. To optimize the operational parameters and process design of BES a better comprehension of the microbial community dynamics and interactions at the anode is required. This paper reviews the abundance of different microorganisms in anodic biofilms and discusses their roles and possible side reactions with respect to their implications on the performance of BES utilizing wastewaters. The most important operational parameters affecting anodic microbial communities grown with wastewaters are highlighted and guidelines for controlling the composition of microbial communities are given. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of biochar blends on microbial community composition in two coastal plain soils

EPA Science Inventory

The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities.

PubMed

Moora, Mari; Davison, John; Öpik, Maarja; Metsis, Madis; Saks, Ülle; Jairus, Teele; Vasar, Martti; Zobel, Martin

2014-12-01

Arbuscular mycorrhizal (AM) fungi play an important role in ecosystems, but little is known about how soil AM fungal community composition varies in relation to habitat type and land-use intensity. We molecularly characterized AM fungal communities in soil samples (n = 88) from structurally open (permanent grassland, intensive and sustainable agriculture) and forested habitats (primeval forest and spruce plantation). The habitats harboured significantly different AM fungal communities, and there was a broad difference in fungal community composition between forested and open habitats, the latter being characterized by higher average AM fungal richness. Within both open and forest habitats, intensive land use significantly influenced community composition. There was a broad difference in the phylogenetic structure of AM fungal communities between mechanically disturbed and nondisturbed habitats. Taxa from Glomeraceae served as indicator species for the nondisturbed habitats, while taxa from Archaeosporaceae, Claroideoglomeraceae and Diversisporaceae were indicators for the disturbed habitats. The distribution of these indicator taxa among habitat types in the MaarjAM global database of AM fungal diversity was in accordance with their local indicator status. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

PubMed Central

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. PMID:24586863

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.

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...

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...

The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

NASA Astrophysics Data System (ADS)

Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

2016-04-01

This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

PubMed

Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

2015-06-02

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

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.

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PubMed

Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

2017-01-01

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  < 0.01), Streptococcus ( p  < 0.01), and Rothia ( p  < 0.01). Staphylococcus ( p  < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella ( p  < 0.01), Granulicatella ( p  < 0.01), Prevotella ( p  < 0.01), and Gemella ( p  = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced

Organic carbon and nitrogen availability determine bacterial community composition in paddy fields of the Indo-Gangetic plain.

PubMed

Kumar, Arvind; Rai, Lal Chand

2017-07-01

Soil quality is an important factor and maintained by inhabited microorganisms. Soil physicochemical characteristics determine indigenous microbial population and rice provides food security to major population of the world. Therefore, this study aimed to assess the impact of physicochemical variables on bacterial community composition and diversity in conventional paddy fields which could reflect a real picture of the bacterial communities operating in the paddy agro-ecosystem. To fulfill the objective; soil physicochemical characterization, bacterial community composition and diversity analysis was carried out using culture-independent PCR-DGGE method from twenty soils distributed across eight districts. Bacterial communities were grouped into three clusters based on UPGMA cluster analysis of DGGE banding pattern. The linkage of measured physicochemical variables with bacterial community composition was analyzed by canonical correspondence analysis (CCA). CCA ordination biplot results were similar to UPGMA cluster analysis. High levels of species-environment correlations (0.989 and 0.959) were observed and the largest proportion of species data variability was explained by total organic carbon (TOC), available nitrogen, total nitrogen and pH. Thus, results suggest that TOC and nitrogen are key regulators of bacterial community composition in the conventional paddy fields. Further, high diversity indices and evenness values demonstrated heterogeneity and co-abundance of the bacterial communities.

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.

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

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

USGS Publications Warehouse

Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

2013-01-01

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Nutrients affecting brain composition and behavior

NASA Technical Reports Server (NTRS)

Wurtman, R. J.

1987-01-01

This review examines the changes in brain composition and in various brain functions, including behavior, that can follow the ingestion of particular foods or nutrients. It details those that are best understood: the increases in serotonin, catecholamine, or acetylcholine synthesis that can occur subsequent to food-induced increases in brain levels of tryptophan, tyrosine, or choline; it also discusses the various processes that must intervene between the mouth and the synapse, so to speak, in order for a nutrient to affect neurotransmission, and it speculates as to additional brain chemicals that may ultimately be found to be affected by changes in the availability of their nutrient precursors. Because the brain chemicals best known to be nutrient dependent overlap with those thought to underlie the actions of most of the drugs used to treat psychiatric diseases, knowledge of this dependence may help the psychiatrist to understand some of the pathologic processes occurring in his/her patients, particularly those with appetitive symptoms. At the very least, such knowledge should provide the psychiatrist with objective criteria for judging when to take seriously assertions that particular foods or nutrients do indeed affect behavior (e.g., in hyperactive children). If the food can be shown to alter neurotransmitter release, it may be behaviorally-active; however, if it lacks a discernible neurochemical effect, the likelihood that it really alters behavior is small.

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

DOE Data Explorer

Siegrist, Julia; Norby, Richard; Sloan, Victoria; 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.

Biofilm formation affects surface properties of novel bioactive glass-containing composites.

PubMed

Hyun, Hong-Keun; Salehi, Satin; Ferracane, Jack L

2015-12-01

This study investigated the effects of bacterial biofilm on the surface properties of novel bioactive glass (BAG)-containing composites of different initial surface roughness. BAG (65 mol% Si; 4% P; 31% Ca) and BAG-F (61% Si; 31% Ca; 4% P; 3% F; 1% B) were synthesized by the sol-gel method and micronized (size ∼0.1-10 μm). Composites with 72wt% total filler load were prepared by replacing 15% of the silanized Sr glass with BAG, BAG-F, or silanized silica. Specimens (n=10/group) were light-cured and divided into 4 subgroups of different surface roughness by wet polishing with 600 and then up to 1200, 2400, or 4000 grit SiC. Surface roughness (SR), gloss, and Knoop microhardness were measured before and after incubating in media with or without a Streptococcus mutans (UA 159) biofilm for 2 weeks. Results were analyzed with ANOVA/Tukey's test (α=0.05). The SR of the BAG-containing composites with the smoothest surfaces (2400/4000 grit) increased in media or bacteria; the SR of the roughest composites (600 grit) decreased. The gloss of the smoothest BAG-containing composites decreased in bacteria and media-only, but more in media-alone. The microhardness of all of the composites decreased with exposure to media or bacteria, with BAG-containing composites affected more than the control. Exposure to bacterial biofilm and its media produced enhanced roughness and reduced gloss and surface microhardness of highly polished dental composites containing a bioactive glass additive, which could affect further biofilm formation, as well as the esthetics, of restorations made from such a material. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Interactive effects between plant functional types and soil factors on tundra species diversity and community composition.

PubMed

Iturrate-Garcia, Maitane; O'Brien, Michael J; Khitun, Olga; Abiven, Samuel; Niklaus, Pascal A; Schaepman-Strub, Gabriela

2016-11-01

Plant communities are coupled with abiotic factors, as species diversity and community composition both respond to and influence climate and soil characteristics. Interactions between vegetation and abiotic factors depend on plant functional types (PFT) as different growth forms will have differential responses to and effects on site characteristics. However, despite the importance of different PFT for community assembly and ecosystem functioning, research has mainly focused on vascular plants. Here, we established a set of observational plots in two contrasting habitats in northeastern Siberia in order to assess the relationship between species diversity and community composition with soil variables, as well as the relationship between vegetation cover and species diversity for two PFT (nonvascular and vascular). We found that nonvascular species diversity decreased with soil acidity and moisture and, to a lesser extent, with soil temperature and active layer thickness. In contrast, no such correlation was found for vascular species diversity. Differences in community composition were found mainly along soil acidity and moisture gradients. However, the proportion of variation in composition explained by the measured soil variables was much lower for nonvascular than for vascular species when considering the PFT separately. We also found different relationships between vegetation cover and species diversity according the PFT and habitat. In support of niche differentiation theory, species diversity and community composition were related to edaphic factors. The distinct relationships found for nonvascular and vascular species suggest the importance of considering multiple PFT when assessing species diversity and composition and their interaction with edaphic factors. Synthesis : Identifying vegetation responses to edaphic factors is a first step toward a better understanding of vegetation-soil feedbacks under climate change. Our results suggest that incorporating

Predator community composition is linked to soil carbon retention across a human land use gradient.

PubMed

Schmitz, Oswald J; Buchkowski, Robert W; Smith, Jeffrey R; Telthorst, Mark; Rosenblatt, Adam E

2017-05-01

Soil carbon (C) storage is a major component of the carbon cycle. Consensus holds that soil C uptake and storage is regulated by plant-microbe-soil interactions. However, the contribution of animals in aboveground food webs to this process has been overlooked. Using insights from prior long-term experimentation in an old-field ecosystem and mathematical modeling, we predicted that the amount of soil C retention within a field should increase with the proportion of active hunting predators comprising the aboveground community of active hunting and sit-and-wait predators. This comes about because predators with different hunting modes have different cascading effects on plants. Our test of the prediction revealed that the composition of the arthropod predator community and associated cascading effects on the plant community explained 41% of variation in soil C retention among 15 old fields across a human land use gradient. We also evaluated the potential for several other candidate factors to explain variation in soil C retention among fields, independent of among-field variation in the predator community. These included live plant biomass, insect herbivore community composition, soil arthropod decomposer community composition, degree of land use development around the fields, field age, and soil texture. None of these candidate variables significantly explained soil C retention among the fields. The study offers a generalizable understanding of the pathways through which arthropod predator community composition can contribute to old-field ecosystem carbon storage. This insight helps support ongoing efforts to understand and manage the effects of anthropogenic land use change on soil C storage. © 2017 by the Ecological Society of America.

[Responses of plant community structure and species composition to warming and N addition in an alpine meadow, northern Tibetan Plateau, China].

PubMed

Zong, Ning; Chai, Xi; Shi, Pei Li; Jiang, Jing; Niu, Ben; Zhang, Xian Zhou; He, Yong Tao

2016-12-01

Global climate warming and increasing nitrogen (N) deposition, as controversial global environmental issues, may distinctly affect the functions and processes of terrestrial ecosystems. It has been reported that the Qinghai-Tibet Plateau has been experiencing significant warming in recent decades, especially in winter. Previous studies have mainly focused on the effects of warming all the year round; however, few studies have tested the effects of winter warming. To investigate the effects of winter warming and N addition on plant community structure and species composition of alpine meadow, long-term N addition and simulated warming experiment was conducted in alpine meadow from 2010 in Damxung, northern Tibet. The experiment consisted of three warming patterns: Year-round warming (YW), winter warming (WW) and control (NW), crossed respectively with five N gradients: 0, 10, 20, 40, 80 kg N·hm -2 ·a -1 . From 2012 to 2014, both warming and N addition significantly affected the total coverage of plant community. Specifically, YW significantly decreased the total coverage of plant community. Without N addition, WW remarkably reduced the vegetation coverage. However, with N addition, the total vegetation coverage gradually increased with the increase of N level. Warming and N addition had different effects on plants from different functional groups. Warming significantly reduced the plant coverage of grasses and sedges, while N addition significantly enhanced the plant coverage of grasses. Regression analyses showed that the total coverage of plant community was positively related to soil water content in vigorous growth stages, indicating that the decrease in soil water content resulted from warming during dry seasons might be the main reason for the decline of total community coverage. As soil moisture in semi-arid alpine meadow is mainly regulated by rainfalls, our results indicated that changes in spatial and temporal patterns of rainfalls under the future

Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure

PubMed Central

Berg, Jeanette; Brandt, Kristian K.; Al-Soud, Waleed A.; Holm, Peter E.; Hansen, Lars H.; Sørensen, Søren J.

2012-01-01

Toxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g−1) stemming from industrial contamination with CuSO4 more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [3H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including the Proteobacteria, Bacteroidetes, Verrumicrobia, Chloroflexi, WS3, and Planctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, the Actinobacteria, showed no response and members of the Acidobacteria showed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa. PMID:22904046

Carbon and nitrogen inputs affect soil microbial community structure and function

NASA Astrophysics Data System (ADS)

Liu, X. J. A.; Mau, R. L.; Hayer, M.; Finley, B. K.; Schwartz, E.; Dijkstra, P.; Hungate, B. A.

2016-12-01

Climate change has been projected to increase energy and nutrient inputs to soils, affecting soil organic matter (SOM) decomposition (priming effect) and microbial communities. However, many important questions remain: how do labile C and/or N inputs affect priming and microbial communities? What is the relationship between them? To address these questions, we applied N (NH4NO3 ; 100 µg N g-1 wk-1), C (13C glucose; 1000 µg C g-1 wk-1), C+N to four different soils for five weeks. We found: 1) N showed no effect, whereas C induced the greatest priming, and C+N had significantly lower priming than C. 2) C and C+N additions increased the relative abundance of actinobacteria, proteobacteria, and firmicutes, but reduced relative abundance of acidobacteria, chloroflexi, verrucomicrobia, planctomycetes, and gemmatimonadetes. 3) Actinobacteria and proteobacteria increased relative abundance over time, but most others decreased over time. 4) substrate additions (N, C, C+N) significantly reduced microbial alpha diversity, which also decreased over time. 5) For beta diversity, C and C+N formed significantly different communities compare to the control and N treatments. Overtime, microbial community structure significantly altered. Four soils have drastically different community structures. These results indicate amounts of substrate C were determinant factors in modulating the rate of SOM decomposition and microbial communities. Variable responses of different microbial communities to labile C and N inputs indicate that complex relationships between priming and microbial functions. In general, we demonstrate that energy inputs can quickly accelerate SOM decomposition whereas extra N input can slow this process, though both had similar microbial community responses.

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year.

PubMed

Broissin-Vargas, L M; Snell-Castro, R; Godon, J J; González-Ríos, O; Suárez-Quiroz, M L

2018-02-01

The purpose of this study was to evaluate the effect of warehouse storage conditions on the composition of the fungal community of green coffee beans (GCB) that were stored in jute sacks for 1 year. Molecular characterization of the fungal community composition and population dynamics obtained by Q-PCR, CE-SSCP (Simpson's diversity index D) and Illumina MiSeq sequencing indicated that Saccharomycetales dominated during the first 6 months of storage period with species as Meyerozyma guilliermondii and Pichia kluyveri. However, after 6 months of storage, the filamentous genus Wallemia became dominant. Principal components analysis correlated this fungal dynamic with storage conditions and other variables as chromaticity (colour), water activity, moisture content, reducing sugars concentration, fungal infection and ochratoxin A production. This study demonstrated that GCB stored in jute sacks after 6 months of storage lead to fungal population dynamics, decreased chromaticity in GCB by bleaching and, then, affected overall quality. Storage plays an important role in the quality evolution during the handling of the GCB. In this context, the composition of the microbial community could be considered a marker to assess the trade value of the coffee beans. © 2017 The Society for Applied Microbiology.

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

Integrating community assembly and biodiversity to better understand ecosystem function: the Community Assembly and the Functioning of Ecosystems (CAFE) approach.

PubMed

Bannar-Martin, Katherine H; Kremer, Colin T; Ernest, S K Morgan; Leibold, Mathew A; Auge, Harald; Chase, Jonathan; Declerck, Steven A J; Eisenhauer, Nico; Harpole, Stanley; Hillebrand, Helmut; Isbell, Forest; Koffel, Thomas; Larsen, Stefano; Narwani, Anita; Petermann, Jana S; Roscher, Christiane; Cabral, Juliano Sarmento; Supp, Sarah R

2018-02-01

The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Temporal dynamics of bird community composition: an analysis of baseline conditions from long-term data.

PubMed

Kampichler, Christian; Angeler, David G; Holmes, Richard T; Leito, Aivar; Svensson, Sören; van der Jeugd, Henk P; Wesołowski, Tomasz

2014-08-01

Numerous anthropogenic activities threaten the biodiversity found on earth. Because all ecological communities constantly experience temporal turnover due to natural processes, it is important to distinguish between change due to anthropogenic impact and the underlying natural rate of change. In this study, we used data sets on breeding bird communities that covered at least 20 consecutive years, from a variety of terrestrial ecosystems, to address two main questions. (1) How fast does the composition of bird communities change over time, and can we identify a baseline of natural change that distinguishes primeval systems from systems experiencing varying degrees of human impact? (2) How do patterns of temporal variation in composition vary among bird communities in ecosystems with different anthropogenic impacts? Time lag analysis (TLA) showed a pattern of increasing rate of temporal compositional change from large-scale primeval systems to disturbed and protected systems to distinctly successional systems. TLA slopes of <0.04 were typical for breeding bird communities with natural turnover, while communities subjected to anthropogenic impact were characterised by TLA slopes of >0.04. Most of the temporal variability of breeding bird communities was explained by slow changes occurring over decades, regardless of the intensity of human impact. In most of the time series, medium- and short-wave periodicity was not detected, with the exception of breeding bird communities subjected to periodic pulses (e.g. caterpillar outbreaks causing food resource peaks).

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

Assessing plant community composition fails to capture impacts of white-tailed deer on native and invasive plant species.

PubMed

Nuzzo, Victoria; Dávalos, Andrea; Blossey, Bernd

2017-07-01

Excessive herbivory can have transformative effects on forest understory vegetation, converting diverse communities into depauperate ones, often with increased abundance of non-native plants. White-tailed deer are a problematic herbivore throughout much of eastern North America and alter forest understory community structure. Reducing (by culling) or eliminating (by fencing) deer herbivory is expected to return understory vegetation to a previously diverse condition. We examined this assumption from 1992 to 2006 at Fermilab (Batavia, IL) where a cull reduced white-tailed deer ( Odocoileus virginianus ) abundance in 1998/1999 by 90 % from 24.6 to 2.5/km 2 , and at West Point, NY, where we assessed interactive effects of deer, earthworms, and invasive plants using 30 × 30 m paired fenced and open plots in 12 different forests from 2009 to 2012. We recorded not only plant community responses (species presence and cover) within 1 m 2 quadrats, but also responses of select individual species (growth, reproduction). At Fermilab, introduced Alliaria petiolata abundance initially increased as deer density increased, but then declined after deer reduction. The understory community responded to the deer cull by increased cover, species richness and height, and community composition changed but was dominated by early successional native forbs. At West Point plant community composition was affected by introduced earthworm density but not deer exclusion. Native plant cover increased and non-native plant cover decreased in fenced plots, thus keeping overall plant cover similar. At both sites native forb cover increased in response to deer reduction, but the anticipated response of understory vegetation failed to materialize at the community level. Deer-favoured forbs ( Eurybia divaricata , Maianthemum racemosum , Polygonatum pubescens and Trillium recurvatum ) grew taller and flowering probability increased in the absence of deer. Plant community monitoring fails to capture

Assessing plant community composition fails to capture impacts of white-tailed deer on native and invasive plant species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nuzzo, Victoria; Davalos, Andrea; Blossey, Bernd

Excessive herbivory can have transformative effects on forest understory vegetation, converting diverse communities into depauperate ones, often with increased abundance of non-native plants. White-tailed deer are a problematic herbivore throughout much of eastern North America and alter forest understory community structure. Reducing (by culling) or eliminating (by fencing) deer herbivory is expected to return understory vegetation to a previously diverse condition. We examined this assumption from 1992 to 2006 at Fermilab (Batavia, IL) where a cull reduced white-tailed deer ( Odocoileus virginianus) abundance in 1998/1999 by 90 % from 24.6 to 2.5/km 2, and at West Point, NY, where wemore » assessed interactive effects of deer, earthworms, and invasive plants using 30 × 30 m paired fenced and open plots in 12 different forests from 2009 to 2012. We recorded not only plant community responses (species presence and cover) within 1 m 2 quadrats, but also responses of select individual species (growth, reproduction). At Fermilab, introduced Alliaria petiolata abundance initially increased as deer density increased, but then declined after deer reduction. The understory community responded to the deer cull by increased cover, species richness and height, and community composition changed but was dominated by early successional native forbs. At West Point plant community composition was affected by introduced earthworm density but not deer exclusion. Native plant cover increased and non-native plant cover decreased in fenced plots, thus keeping overall plant cover similar. At both sites native forb cover increased in response to deer reduction, but the anticipated response of understory vegetation failed to materialize at the community level. Deer-favoured forbs ( Eurybia divaricata, Maianthemum racemosum, Polygonatum pubescens and Trillium recurvatum) grew taller and flowering probability increased in the absence of deer. Plant community monitoring fails to capture

Assessing plant community composition fails to capture impacts of white-tailed deer on native and invasive plant species

DOE PAGES

Nuzzo, Victoria; Davalos, Andrea; Blossey, Bernd

2017-06-08

Excessive herbivory can have transformative effects on forest understory vegetation, converting diverse communities into depauperate ones, often with increased abundance of non-native plants. White-tailed deer are a problematic herbivore throughout much of eastern North America and alter forest understory community structure. Reducing (by culling) or eliminating (by fencing) deer herbivory is expected to return understory vegetation to a previously diverse condition. We examined this assumption from 1992 to 2006 at Fermilab (Batavia, IL) where a cull reduced white-tailed deer ( Odocoileus virginianus) abundance in 1998/1999 by 90 % from 24.6 to 2.5/km 2, and at West Point, NY, where wemore » assessed interactive effects of deer, earthworms, and invasive plants using 30 × 30 m paired fenced and open plots in 12 different forests from 2009 to 2012. We recorded not only plant community responses (species presence and cover) within 1 m 2 quadrats, but also responses of select individual species (growth, reproduction). At Fermilab, introduced Alliaria petiolata abundance initially increased as deer density increased, but then declined after deer reduction. The understory community responded to the deer cull by increased cover, species richness and height, and community composition changed but was dominated by early successional native forbs. At West Point plant community composition was affected by introduced earthworm density but not deer exclusion. Native plant cover increased and non-native plant cover decreased in fenced plots, thus keeping overall plant cover similar. At both sites native forb cover increased in response to deer reduction, but the anticipated response of understory vegetation failed to materialize at the community level. Deer-favoured forbs ( Eurybia divaricata, Maianthemum racemosum, Polygonatum pubescens and Trillium recurvatum) grew taller and flowering probability increased in the absence of deer. Plant community monitoring fails to capture

Transformative Learning, Affect, and Reciprocal Care in Community Engagement

ERIC Educational Resources Information Center

Holmes, Ashley J.

2015-01-01

Drawing on interviews with writing teachers, this article highlights some of the affective responses that may arise for students, community partners, and teachers when we situate our pedagogies in public sites beyond the classroom. I analyze a teacher-narrated moment of student distress to demonstrate how theories of transformative learning might…

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

PubMed Central

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

PubMed

Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

2018-01-01

The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Species composition, community and population dynamics of two gallery forests from the Brazilian Cerrado domain

PubMed Central

Almado, Roosevelt P; Miazaki, Angela S; Diniz, Écio S; Moreira, Luis C B; Meira-Neto, João A.A.

2016-01-01

Abstract Background To understand the impacts of global changes on future community compositions, knowledge of community dynamics is of crucial importance. To improve our knowledge of community composition, biomass stock and maintenance of gallery forests in the Brazilian Cerrado, we provide two datasets from the 0.5 ha Corrego Fazendinha Gallery Forest Dynamics Plot and the Corrego Fundo Gallery Forest Dynamics Plot situated in the Bom Despacho region, Minas Gerais, Southeastern Brazil. New information We report diameter at breast height, basal area and height measurements of 3417 trees and treelets identified during three censuses in both areas. PMID:27660529

Are cattle surrogate wildlife? Savanna plant community composition explained by total herbivory more than herbivore type.

PubMed

Veblen, Kari E; Porensky, Lauren M; Riginos, Corinna; Young, Truman P

2016-09-01

The widespread replacement of wild ungulate herbivores by domestic livestock in African savannas is composed of two interrelated phenomena: (1) loss or reduction in numbers of individual wildlife species or guilds and (2) addition of livestock to the system. Each can have important implications for plant community dynamics. Yet very few studies have experimentally addressed the individual, combined, and potentially interactive effects of wild vs. domestic herbivore species on herbaceous plant communities within a single system. Additionally, there is little information about whether, and in which contexts, livestock might functionally replace native herbivore wildlife or, alternatively, have fundamentally different effects on plant species composition. The Kenya Long-term Exclosure Experiment, which has been running since 1995, is composed of six treatment combinations of mega-herbivores, meso-herbivore ungulate wildlife, and cattle. We sampled herbaceous vegetation 25 times between 1999 and 2013. We used partial redundancy analysis and linear mixed models to assess effects of herbivore treatments on overall plant community composition and key plant species. Plant communities in the six different herbivore treatments shifted directionally over time and diverged from each other substantially by 2013. Plant community composition was strongly related (R 2  = 0.92) to residual plant biomass, a measure of herbivore utilization. Addition of any single herbivore type (cattle, wildlife, or mega-herbivores) caused a shift in plant community composition that was proportional to its removal of plant biomass. These results suggest that overall herbivory pressure, rather than herbivore type or complex interactions among different herbivore types, was the main driver of changes in plant community composition. Individual plant species, however, did respond most strongly to either wild ungulates or cattle. Although these results suggest considerable functional similarity between

Diptera community composition and succession following habitat disturbance by wildfire

Treesearch

Michael A. Patten; Jutta C. Burger; Thomas R. Prentice; John T. Rotenberry; Richard A. Redak

2005-01-01

Both biogeographic (for example, latitude) and local (for example, soil) processes determine composition and succession of biotic communities. Postfire succession of vegetation has been studied intensively in chaparral and coastal sage scrub. Fewer studies have examined postfire succession of animals, even though fires can drastically alter their abundance and...

Effects of plant diversity, community composition and environmental parameters on productivity in montane European grasslands.

PubMed

Kahmen, Ansgar; Perner, Jörg; Audorff, Volker; Weisser, Wolfgang; Buchmann, Nina

2005-02-01

In the past years, a number of studies have used experimental plant communities to test if biodiversity influences ecosystem functioning such as productivity. It has been argued, however, that the results achieved in experimental studies may have little predictive value for species loss in natural ecosystems. Studies in natural ecosystems have been equivocal, mainly because in natural ecosystems differences in diversity are often confounded with differences in land use history or abiotic parameters. In this study, we investigated the effect of plant diversity on ecosystem functioning in semi-natural grasslands. In an area of 10x20 km, we selected 78 sites and tested the effects of various measures of diversity and plant community composition on productivity. We separated the effects of plant diversity on ecosystem functioning from potentially confounding effects of community composition, management or environmental parameters, using multivariate statistical analyses. In the investigated grasslands, simple measures of biodiversity were insignificant predictors of productivity. However, plant community composition explained productivity very well (R2=0.31) and was a better predictor than environmental variables (soil and site characteristics) or management regime. Thus, complex measures such as community composition and structure are important drivers for ecosystem functions in semi-natural grasslands. Furthermore, our data show that it is difficult to extrapolate results from experimental studies to semi-natural ecosystems, although there is a need to investigate natural ecosystems to fully understand the relationship of biodiversity and ecosystem functioning.

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

Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities.

PubMed

Rea, Maria Angelica; Standish, Christopher D; Shuster, Jeremiah; Bissett, Andrew; Reith, Frank

2018-05-03

Biofilms on placer gold (Au)-particle surfaces drive Au solubilization and re-concentration thereby progressively transforming the particles. Gold solubilization induces Au-toxicity; however, Au-detoxifying community members ameliorates Au-toxicity by precipitating soluble Au to metallic Au. We hypothesize that Au-dissolution and re-concentration (precipitation) places selective pressures on associated microbial communities, leading to compositional changes and subsequent Au-particle transformation. We analyzed Au-particles from eight United Kingdom sites using next generation sequencing, electron microscopy and micro-analyses. Gold particles contained biofilms composed of prokaryotic cells and extracellular polymeric substances intermixed with (bio)minerals. Across all sites communities were dominated by Proteobacteria (689, 97% Operational Taxonomic Units, 59.3% of total reads), with β-Proteobacteria being the most abundant. A wide range of Au-morphotypes including nanoparticles, micro-crystals, sheet-like Au and secondary rims, indicated that dissolution and re-precipitation occurred, and from this transformation indices were calculated. Multivariate statistical analyses showed a significant relationship between the extent of Au-particle transformation and biofilm community composition, with putative metal-resistant Au-cycling taxa linked to progressive Au transformation. These included the genera Pseudomonas, Leptothrix and Acinetobacter. Additionally, putative exoelectrogenic genera Rhodoferax and Geobacter were highly abundant. In conclusion, biogeochemical Au-cycling and Au-particle transformation occurred at all sites and exerted a strong influence on biofilm community composition.

Modeling the effects of free-living marine bacterial community composition on heterotrophic remineralization rates and biogeochemical carbon cycling

NASA Astrophysics Data System (ADS)

Teel, E.; Liu, X.; Cram, J. A.; Sachdeva, R.; Fuhrman, J. A.; Levine, N. M.

2016-12-01

Global oceanic ecosystem models either disregard fluctuations in heterotrophic bacterial remineralization or vary remineralization as a simple function of temperature, available carbon, and nutrient limitation. Most of these models were developed before molecular techniques allowed for the description of microbial community composition and functional diversity. Here we investigate the impact of a dynamic heterotrophic community and variable remineralization rates on biogeochemical cycling. Specifically, we integrated variable microbial remineralization into an ecosystem model by utilizing molecular community composition data, association network analysis, and biogeochemical rate data from the San Pedro Ocean Time-series (SPOT) station. Fluctuations in free-living bacterial community function and composition were examined using monthly environmental and biological data collected at SPOT between 2000 and 2011. On average, the bacterial community showed predictable seasonal changes in community composition and peaked in abundance in the spring with a one-month lag from peak chlorophyll concentrations. Bacterial growth efficiency (BGE), estimated from bacterial production, was found to vary widely at the site (5% to 40%). In a multivariate analysis, 47.6% of BGE variability was predicted using primary production, bacterial community composition, and temperature. A classic Nutrient-Phytoplankton-Zooplankton-Detritus model was expanded to include a heterotroph module that captured the observed relationships at the SPOT site. Results show that the inclusion of dynamic bacterial remineralization into larger oceanic ecosystem models can significantly impact microzooplankton grazing, the duration of surface phytoplankton blooms, and picophytoplankton primary production rates.

Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

PubMed

Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

2013-07-01

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Information needs of the Chinese community affected by cancer: A systematic review.

PubMed

Lim, Bee Teng; Butow, Phyllis; Mills, Jill; Miller, Annie; Goldstein, David

2017-10-01

The information needs of patients and carers from culturally and linguistically diverse backgrounds, including from the Chinese community, are not well understood, and there has been no previous synthesis of the literature. We conducted a systematic review of the information needs of the Chinese community affected by cancer. Database, reference list, and author searches were conducted to identify studies reporting information needs of the Chinese community affected by cancer. Data synthesis was undertaken to define categories of information needs. Initial searches yielded 2558 articles. Out of the 40 full-text articles reviewed, 26 met all the eligibility criteria. Cancer-specific, treatment, and prognosis information were the most frequently reported information needs across the cancer care continuum. Similarly, this information was the most commonly reported information needs across different health systems, migration statuses, and Chinese cultural values. Though less frequent, information needs related to interpersonal/social, financial/legal, and body image/sexuality were also raised. Thirteen studies quantified the prevalence of unmet needs, and the most frequently reported unmet needs were related to health system and information, followed by psychological, patient care and support, physical daily living, and sexuality needs. Language and cultural factors were identified in all studies involving Chinese migrants living in English-speaking countries. Failing to meet the information needs of the Chinese community members affected by cancer increases the risk for poor cancer outcomes. Potential interventions such as translated resources, bilingual advocates, an online information portal, and communication aids can be helpful in addressing the unmet needs for this community. Copyright © 2016 John Wiley & Sons, Ltd.

Coastal urbanisation affects microbial communities on a dominant marine holobiont.

PubMed

Marzinelli, Ezequiel M; Qiu, Zhiguang; Dafforn, Katherine A; Johnston, Emma L; Steinberg, Peter D; Mayer-Pinto, Mariana

2018-01-01

Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia . There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.

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.

Microbial community composition along a 50 000-year lacustrine sediment sequence

PubMed Central

Ariztegui, Daniel; Horn, Fabian; Kallmeyer, Jens; Orsi, William D

2018-01-01

Abstract For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth. PMID:29471361

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

PubMed Central

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-01-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition. PMID:27256545

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition.

PubMed

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-03

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

NASA Astrophysics Data System (ADS)

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

PubMed

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescommunities' composition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

Cooperative Agreements to Support Communities Affected by the BP Oil Spill

EPA Pesticide Factsheets

The environmental justice cooperative agreements are designed to support communities in Alabama, Florida, Louisiana, Mississippi, and Texas that are directly affected by the Deepwater Horizon oil spill in the Gulf of Mexico.

Temporal changes in randomness of bird communities across Central Europe.

PubMed

Renner, Swen C; Gossner, Martin M; Kahl, Tiemo; Kalko, Elisabeth K V; Weisser, Wolfgang W; Fischer, Markus; Allan, Eric

2014-01-01

Many studies have examined whether communities are structured by random or deterministic processes, and both are likely to play a role, but relatively few studies have attempted to quantify the degree of randomness in species composition. We quantified, for the first time, the degree of randomness in forest bird communities based on an analysis of spatial autocorrelation in three regions of Germany. The compositional dissimilarity between pairs of forest patches was regressed against the distance between them. We then calculated the y-intercept of the curve, i.e. the 'nugget', which represents the compositional dissimilarity at zero spatial distance. We therefore assume, following similar work on plant communities, that this represents the degree of randomness in species composition. We then analysed how the degree of randomness in community composition varied over time and with forest management intensity, which we expected to reduce the importance of random processes by increasing the strength of environmental drivers. We found that a high portion of the bird community composition could be explained by chance (overall mean of 0.63), implying that most of the variation in local bird community composition is driven by stochastic processes. Forest management intensity did not consistently affect the mean degree of randomness in community composition, perhaps because the bird communities were relatively insensitive to management intensity. We found a high temporal variation in the degree of randomness, which may indicate temporal variation in assembly processes and in the importance of key environmental drivers. We conclude that the degree of randomness in community composition should be considered in bird community studies, and the high values we find may indicate that bird community composition is relatively hard to predict at the regional scale.

Gender and Race, Online Communities, and Composition Classrooms

ERIC Educational Resources Information Center

Morris, Jill

2011-01-01

As the culmination of a two-year long Internet ethnographic study of three separate sites, I use examples of women and minorities fighting against discrimination online to explore the power structures inherent to networks and how these might affect classroom practice. I will show how our ordinary assumptions in rhetoric and composition as well as…

A close link between bacterial community composition and environmental heterogeneity in maritime Antarctic lakes.

PubMed

Villaescusa, Juan A; Casamayor, Emilio O; Rochera, Carlos; Velázquez, David; Chicote, Alvaro; Quesada, Antonio; Camacho, Antonio

2010-06-01

Seven maritime Antarctic lakes located on Byers Peninsula (Livingston Island, South Shetland Islands) were surveyed to determine the relationship between planktonic bacterial community composition and environmental features. Specifically, the extent to which factors other than low temperature determine the composition of bacterioplankton assemblages of maritime Antarctic lakes was evaluated. Both deep and shallow lakes in the central plateau of the Peninsula, as well as a coastal lake, were studied in order to fully account for the environmental heterogeneity of the Peninsula's lakes. The results showed that shallow coastal lakes display eutrophic conditions, mainly due to the influence of marine animals, whereas plateau lakes are generally deeper and most are oligotrophic, with very limited inputs of nutrients and organic matter. Meso-eutrophic shallow lakes are also present on the Peninsula; they contain microbial mats and a higher trophic status because of the biologically mediated active nutrient release from the sediments. Diversity studies of the lakes' planktonic bacterial communities using molecular techniques showed that bacterial diversity is lower in eutrophic than in oligotrophic lakes. The former also differed in community composition with respect to dominant taxa. Multivariate statistical analyses of environmental data yielded the same clustering of lakes as obtained based on the DGGE band pattern after DNA extraction and amplification of 16S rRNA gene fragments. Thus, even in extremely cold lakes, the bacterial community composition parallels other environmental factors, such as those related to trophic status. This correspondence is not only mediated by the influence of marine fauna but also by processes including sediment and ice melting dynamics. The bacterial community can therefore be considered to be equally representative as environmental abiotic variables in demonstrating the environmental heterogeneity among maritime Antarctic lakes.

Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence.

PubMed

Albornoz, Felipe E; Teste, François P; Lambers, Hans; Bunce, Michael; Murray, Dáithí C; White, Nicole E; Laliberté, Etienne

2016-10-01

Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis-driven shifts in edaphic properties, particularly pH and resin-exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long-term ecosystem development, even within the same hosts. However, these changes could not be attributed to short-term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer-term ecosystem-level feedback between soil, vegetation and ECM fungi during pedogenesis. © 2016 John Wiley & Sons Ltd.

A fire-affected community: the case of the West Melton fire, December 2003

Treesearch

Laura Kelly; Pamela J. Jakes; E.R. Langer

2008-01-01

A study of a fire-affected community was conducted to gain an understanding of the social ramifications of a wildfire event and to analyse how one community responded to this type of disaster. The research focused on the West Melton community, located just west of Christchurch, in the Selwyn District. This is the first in a series of case studies planned by the Scion...

Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil.

PubMed

Jiang, Yuji; Jin, Chen; Sun, Bo

2014-10-01

Nitrification plays a central role in global nitrogen cycle, which is affected by interaction between soil microfauna and microorganisms. The impact of synchronized changes in nematodes and ammonia oxidizers within aggregate fractions on nitrification was investigated in an acid soil under 10-year manure application. Nematodes, ammonia oxidizers and potential nitrification activity (PNA) were examined in three soil aggregate fractions under four fertilization regimes. Pyrosequencing data revealed that the dominant bacterial amoA operational taxonomic units (OTUs) were related to Nitrosospira species, while archaeal OTUs were affiliated with Nitrososphaera and Nitrosotalea species. PNA was more strongly correlated with ammonia-oxidizing bacteria (AOB) abundance than ammonia-oxidizing archaea (AOA) abundance, although AOA were dominant in the acid soil. Plant parasites had a negative effect on AOB abundance; however, bacterivores stimulated AOB abundance and contributed more to PNA than plant parasites. Aggregate fractions exerted significant impacts on AOA abundance and AOB community composition. Total carbon content strongly affected the abundance and composition of AOA community, while soil pH primarily affected that of AOB community. Soil variables explained 62.7% and 58.1% variations, and nematode variables explained 11.7% and 19.5% variations in the AOA and AOB community composition respectively. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Relationships among plants, soils and microbial communities along a hydrological gradient in the New Jersey Pinelands, USA

PubMed Central

Yu, Shen; Ehrenfeld, Joan G.

2010-01-01

Background and Aims Understanding the role of different components of hydrology in structuring wetland communities is not well developed. A sequence of adjacent wetlands located on a catenary sequence of soils and receiving the same sources and qualities of water is used to examine specifically the role of water-table median position and variability in affecting plant and microbial community composition and soil properties. Methods Two replicates of three types of wetland found adjacent to each other along a hydrological gradient in the New Jersey Pinelands (USA) were studied. Plant-community and water-table data were obtained within a 100-m2 plot in each community (pine swamp, maple swamp and Atlantic-white-cedar swamp). Monthly soil samples from each plot were analysed for soil moisture, organic matter, extractable nitrogen fractions, N mineralization rate and microbial community composition. Multivariate ordination methods were used to compare patterns among sites within and between data sets. Key Results The maple and pine wetlands were more similar to each other in plant community composition, soil properties and microbial community composition than either was to the cedar swamps. However, maple and pine wetlands differed from each other in water-table descriptors as much as they differed from the cedar swamps. All microbial communities were dominated by Gram-positive bacteria despite hydrologic differences among the sites. Water-table variability was as important as water-table level in affecting microbial communities. Conclusions Water tables affect wetland communities through both median level and variability. Differentiation of both plant and microbial communities are not simple transforms of differences in water-table position, even when other hydrologic factors are kept constant. Rather, soil genesis, a result of both water-table position and geologic history, appears to be the main factor affecting plant and microbial community similarities. PMID

Differential response of marine flagellate communities to prokaryotic food quality

NASA Astrophysics Data System (ADS)

De Corte, D.; Paredes, G.; Sintes, E.; Herndl, G. J.

2016-02-01

Marine prokaryotes play a major role in the biogeochemical cycles. The main predators of prokaryotes are heterotrophic nanoflagellates (HNF). HNF are thus a major link connecting dissolved organic material through prokaryotic grazing to the higher trophic levels. However, little is known about the grazing specificity of HNF on specific prokaryotic taxa. Bacterial and archaeal microbes may have different nutritive values for the HNF communities, thus affecting growth rates and community composition of HNFs. In this study we investigated the influence of prey food quality on Cafeteria roenbergensis and on a natural HNF community isolated in the northern Adriatic Sea. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains and two fast growing marine Bacteria (Pseudomonas marina and Marinobacter algicola) were fed to the HNFs. The two fast growing bacterial strains resulted in high growth rates of Cafeteria roenbergensis and the mixed HNF community, while the two Nitrosococcus strains did not. Cafeteria roenbergensis fed on N. adriaticus but it did not graze N. piranensis, suggesting that the subtle metabolic and physiological differences between these two closely related thaumarchaeal strains affect the grazing pressure to which they are exposed. Our study also indicates that prokaryotic community composition influences the composition of the HNF community.

Comparison of waste composition in a continuing-care retirement community.

PubMed

Kim, T; Shanklin, C W; Su, A Y; Hackes, B L; Ferris, D

1997-04-01

To determine the composition of wastes generated in a continuing-care retirement community (CCRC) and to analyze the effects of source-reduction activities and meal delivery system change on the amount of waste generated in the facility. A waste stream analysis was conducted at the same CCRC during spring 1994 (period 1: baseline), spring 1995 (period 2: source reduction intervention), and fall 1995 (period 3: service delivery intervention). Weight, volume, and collapsed volume were determined for food and packaging wastes. Tray service and wait staff service are provided to 70 residents in a health care unit, and family-style service is an optional service available to 130 residents in the independent-living units. A mean of 229 meals are served per day. Intervention included the implementation of source-reduction activities and a change in a service-delivery system in periods 2 and 3, respectively. Descriptive statistics were used to determine the composition of waste. Analysis of variance and a multiple comparison method (least significant difference) were used to compare mean weight and volume of waste generated in period 1 with data collected during periods 2 and 3. Mean waste generated per meal by weight and volume ranged from 0.93 to 1.00 lb and 1.44 to 1.65 gal, respectively. Significantly less production waste by weight (0.18 lb/meal) and volume (0.12 gal/meal) was generated in period 2 than in period 1 (0.32 lb/meal and 0.16 gal/meal, respectively). Significantly less service waste by weight (0.31 lb/meal) and volume (0.05 gal/meal) was discarded in period 3 than in period 1 (0.37 lb/meal and 0.15 gal/meal, respectively). Significantly less total waste and plastic by weight was disposed of after the interventions. The study conclusions indicated that implementing source-reduction practices and changing the meal-delivery system affected the composition of waste generated. Knowledge of waste stream composition can help other foodservice professionals and

Methanogenic community composition in an organic waste mixture in an anaerobic bioreactor

NASA Astrophysics Data System (ADS)

Gryta, Agata; Oszust, Karolina; Brzezińska, Małgorzata; Ziemiński, Krzysztof; Bilińska-Wielgus, Nina; Frąc, Magdalena

2017-07-01

The aim of the study was to elucidate the substantial relationship between the compositions of methanogen community that assembles in the anaerobic digester mass and link it to methane production activity. The results of the metagenomic studies were used to evaluate how the methanogen structure changes during an anaerobic digestion process under various waste retention times (21, 23, 25, 29, 33, 39, 47 and 61 days). Phylogenetically coherent populations of methanogens were assessed by 16S rRNA gene next-generation sequencing and terminal restriction fragment length polymorphism fingerprinting of a specific molecular marker, the mcrA gene. The results indicated multiple phylogenetically diverse methanogen populations associated with the various steps of anaerobic digestion. The stages of the anaerobic digestion process and waste retention times determine the microbial composition. The most dominant and acclimated microbial communities in all samples belonged to the genera Methanosaeta and Methanobacterium. The methane yield was consistent with the results of the microbial community structure, which indicated that acetotrophic Methanosaeta was the most active and most important during the methanogenic stage.

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting.

PubMed

Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Tuo, Xiaxia; Zhang, Kaiyu; Zhang, Li; Guo, Aiyun; Zhang, Xin

2018-06-01

This study investigated the effects of adding copper at 3 treatment levels (0 (control: CK), 200 (low: L), and 2000 (high: H) mg·kg -1 treatments) on the bacterial communities during swine manure composting. The abundances of the bacteria were determined by quantitative PCR and their compositions were evaluated by high-throughput sequencing. The results showed that the abundance of bacteria was inhibited by the H treatment during days 7-35, and principal component analysis clearly separated the H treatment from the CK and L treatments. Actinobacteria, Firmicutes, and Proteobacteria were the dominant bacterial taxa, and a high copper concentration decreased the abundances of bacteria that degrade cellulose and lignin (e.g., class Bacilli and genus Truepera), especially in the mesophilic and thermophilic phases. Moreover, network analysis showed that copper might alter the co-occurrence patterns of bacterial communities by changing the properties of the networks and the keystone taxa, and increase the competition by increasing negative associations between bacteria during composting. Temperature, water-soluble carbohydrates, and copper significantly affected the variations in the bacterial community according to redundancy analysis. The copper content mainly contributed to the bacterial community in the thermophilic and cooling phases, where it had positive relationships with potentially pathogenic bacteria (e.g., Corynebacterium_1 and Acinetobacter).

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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Unique Bacteria Community Composition and Co-occurrence in the Milk of Different Ruminants

PubMed Central

Li, Zhipeng; Wright, André-Denis G.; Yang, Yifeng; Si, Huazhe; Li, Guangyu

2017-01-01

Lactation provides the singular source of nourishment to the offspring of mammals. This nutrition source also contains a diverse microbiota affecting the development and health of the newborn. Here, we examined the milk microbiota in water deer (Hydropotes inermis, the most primitive member of the family Cervidae), reindeer (Rangifer tarandus, the oldest semi-domesticated cervid), and the dairy goat (Capra aegagrus, member of the family Bovidae), to determine if common milk microbiota species were present across all three ruminant species. The results showed that water deer had the highest bacterial diversity, followed by reindeer, and then goat. Unifrac distance and correspondence analyses revealed that water deer harbored an increased abundance of Pseudomonas spp. and Acinetobacter spp., while milk from reindeer and goat was dominated by unclassified bacteria from the family Hyphomicrobiaceae and Bacillus spp., respectively. These data indicate significant differences in the composition of milk-based bacterial communities. The presence of Halomonas spp. in three distinct co-occurrence networks of bacterial interactions revealed both common and unique features in milk niches. These results suggest that the milk of water deer and reindeer harbor unique bacterial communities compared with the goat, which might reflect host microbial adaptation caused by evolution. PMID:28098228

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P. A.; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landescomposition turnovers. The relative importance of processes and filters was assessed by distance-based redundancy analysis. This study demonstrates significant community composition turnover rates for soil bacteria and fungi, which were dependent on the region. Bacterial and fungal community composition turnovers were mainly driven by environmental selection explaining from 10% to 20% of community composition variations, but spatial variables also explained 3% to 9% of total variance. These variables highlighted significant spatial autocorrelation of both communities unexplained by the environmental variables measured and could partly be explained by dispersal limitations. Although the identified filters and their hierarchy were dependent on the region and organism, selection was systematically based on a common group of environmental variables: pH, trophic resources, texture and land use. Spatial autocorrelation was also important at coarse (80 to

Inference methods for spatial variation in species richness and community composition when not all species are detected

USGS Publications Warehouse

Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

1998-01-01

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (an associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larer number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on the methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species

Composition Instructors' Interactions with Classroom Discourse Communities: A Qualitative Study

ERIC Educational Resources Information Center

Winterberg, Sarah Griffith

2017-01-01

This study offered insight on the intermingling of discourse communities in the learning environment by examining experiences of composition instructors from a regional Southern university and their reflections of teaching students who struggled to navigate from home discourse to academic discourse. Merriam's basic qualitative research design…

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Plant community composition and biomass in Gulf Coast Chenier Plain marshes: Responses to winter burning and structural marsh management

USGS Publications Warehouse

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

2001-01-01

Many marshes in the Gulf Coast Chenier Plain, USA, are managed through a combination of fall or winter burning and structural marsh management (i.e., levees and water control structures; hereafter SMM). The goals of winter burning and SMM include improvement of waterfowl and furbearer habitat, maintenance of historic isohaline lines, and creation and maintenance of emergent wetlands. Although management practices are intended to influence the plant community, effects of these practices on primary productivity have not been investigated. Marsh processes, such as vertical accretion and nutrient cycles, which depend on primary productivity may be affected directly or indirectly by winter burning or SMM. We compared Chenier Plain plant community characteristics (species composition and above- and belowground biomass) in experimentally burned and unburned control plots within impounded and unimpounded marshes at 7 months (1996), 19 months (1997), and 31 months (1998) after burning. Burning and SMM did not affect number of plant species or species composition in our experiment. For all three years combined, burned plots had higher live above-ground biomass than did unburned plots. Total above-ground and dead above-ground biomasses were reduced in burned plots for two and three years, respectively, compared to those in unburned control plots. During all three years, belowground biomass was lower in impounded than in unimpounded marshes but did not differ between burn treatments. Our results clearly indicate that current marsh management practices influence marsh primary productivity and may impact other marsh processes, such as vertical accretion, that are dependent on organic matter accumulation and decay.

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. Copyright © 2013

How has the economic downturn affected communities and implementation of science-based prevention in the randomized trial of communities that care?

PubMed

Kuklinski, Margaret R; Hawkins, J David; Plotnick, Robert D; Abbott, Robert D; Reid, Carolina K

2013-06-01

This study examined implications of the economic downturn that began in December 2007 for the Community Youth Development Study (CYDS), a longitudinal randomized controlled trial of the Communities That Care (CTC) prevention system. The downturn had the potential to affect the internal validity of the CYDS research design and implementation of science-based prevention in study communities. We used archival economic indicators and community key leader reports of economic conditions to assess the extent of the economic downturn in CYDS communities and potential internal validity threats. We also examined whether stronger economic downturn effects were associated with a decline in science-based prevention implementation. Economic indicators suggested the downturn affected CYDS communities to different degrees. We found no evidence of systematic differences in downturn effects in CTC compared to control communities that would threaten internal validity of the randomized trial. The Community Economic Problems scale was a reliable measure of community economic conditions, and it showed criterion validity in relation to several objective economic indicators. CTC coalitions continued to implement science-based prevention to a significantly greater degree than control coalitions 2 years after the downturn began. However, CTC implementation levels declined to some extent as unemployment, the percentage of students qualifying for free lunch, and community economic problems worsened. Control coalition implementation levels were not related to economic conditions before or after the downturn, but mean implementation levels of science-based prevention were also relatively low in both periods.

How Has the Economic Downturn Affected Communities and Implementation of Science-Based Prevention in the Randomized Trial of Communities That Care?

PubMed Central

Kuklinski, Margaret R.; Hawkins, J. David; Plotnick, Robert D.; Abbott, Robert D.; Reid, Carolina K.

2013-01-01

This study examined implications of the economic downturn that began in December 2007 for the Community Youth Development Study (CYDS), a longitudinal randomized controlled trial of the Communities That Care (CTC) prevention system. The downturn had the potential to affect the internal validity of the CYDS research design and implementation of science-based prevention in study communities. We used archival economic indicators and community key leader reports of economic conditions to assess the extent of the economic downturn in CYDS communities and potential internal validity threats. We also examined whether stronger economic downturn effects were associated with a decline in science-based prevention implementation. Economic indicators suggested the downturn affected CYDS communities to different degrees. We found no evidence of systematic differences in downturn effects in CTC compared to control communities that would threaten internal validity of the randomized trial. The Community Economic Problems scale was a reliable measure of community economic conditions, and it showed criterion validity in relation to several objective economic indicators. CTC coalitions continued to implement science-based prevention to a significantly greater degree than control coalitions 2 years after the downturn began. However, CTC implementation levels declined to some extent as unemployment, the percentage of students qualifying for free lunch, and community economic problems worsened. Control coalition implementation levels were not related to economic conditions before or after the downturn, but mean implementation levels of science-based prevention were also relatively low in both periods. PMID:23054169

Abundance, Composition and Activity of Ammonia Oxidizer and Denitrifier Communities in Metal Polluted Rice Paddies from South China

PubMed Central

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. PMID:25058658

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.

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. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling plant composition as community continua in a forest landscape with LiDAR and hyperspectral remote sensing.

PubMed

Hakkenberg, C R; Peet, R K; Urban, D L; Song, C

2018-01-01

In light of the need to operationalize the mapping of forest composition at landscape scales, this study uses multi-scale nested vegetation sampling in conjunction with LiDAR-hyperspectral remotely sensed data from the G-LiHT airborne sensor to map vascular plant compositional turnover in a compositionally and structurally complex North Carolina Piedmont forest. Reflecting a shift in emphasis from remotely sensing individual crowns to detecting aggregate optical-structural properties of forest stands, predictive maps reflect the composition of entire vascular plant communities, inclusive of those species smaller than the resolution of the remotely sensed imagery, intertwined with proximate taxa, or otherwise obscured from optical sensors by dense upper canopies. Stand-scale vascular plant composition is modeled as community continua: where discrete community-unit classes at different compositional resolutions provide interpretable context for continuous gradient maps that depict n-dimensional compositional complexity as a single, consistent RGB color combination. In total, derived remotely sensed predictors explain 71%, 54%, and 48% of the variation in the first three components of vascular plant composition, respectively. Among all remotely sensed environmental gradients, topography derived from LiDAR ground returns, forest structure estimated from LiDAR all returns, and morphological-biochemical traits determined from hyperspectral imagery each significantly correspond to the three primary axes of floristic composition in the study site. Results confirm the complementarity of LiDAR and hyperspectral sensors for modeling the environmental gradients constraining landscape turnover in vascular plant composition and hold promise for predictive mapping applications spanning local land management to global ecosystem modeling. © 2017 by the Ecological Society of America.

Riparian-associated gastropods in western Washington: community composition and the effects of forest management

Treesearch

Alex D. Foster; Joan Ziegltrum

2013-01-01

We evaluated the abundance of riparian gastropod communities along headwater streams and their response to logging in southwestern Washington State. Terrestrial mollusks near logged streams with ~15 m fixed-width buffers were compared to logged streams with no buffers and to unlogged controls. Mollusk communities varied among sites relative to vegetative composition,...

Avian community composition and habitat importance in the Rio Grande corridor of New Mexico

Treesearch

David A. Leal; Raymond A. Meyer; Bruce C. Thompson

1996-01-01

We investigated avian species richness and abundance within vegetation communities of the Rio Grande Corridor of New Mexico during spring, summer, and fall 1992 and 1993. A subset of 64 transects, for which all bird and vegetation variables were available, representing 16 composite vegetation community types were subjected to canonical correlation analysis to...

Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean

PubMed Central

Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

2013-01-01

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants.

PubMed

Weikl, Fabian; Tischer, Christina; Probst, Alexander J; Heinrich, Joachim; Markevych, Iana; Jochner, Susanne; Pritsch, Karin

2016-01-01

People spend most of their time inside buildings and the indoor microbiome is a major part of our everyday environment. It affects humans' wellbeing and therefore its composition is important for use in inferring human health impacts. It is still not well understood how environmental conditions affect indoor microbial communities. Existing studies have mostly focussed on the local (e.g., building units) or continental scale and rarely on the regional scale, e.g. a specific metropolitan area. Therefore, we wanted to identify key environmental determinants for the house dust microbiome from an existing collection of spatially (area of Munich, Germany) and temporally (301 days) distributed samples and to determine changes in the community as a function of time. To that end, dust samples that had been collected once from the living room floors of 286 individual households, were profiled for fungal and bacterial community variation and diversity using microbial fingerprinting techniques. The profiles were tested for their association with occupant behaviour, building characteristics, outdoor pollution, vegetation, and urbanization. Our results showed that more environmental and particularly outdoor factors (vegetation, urbanization, airborne particulate matter) affected the community composition of indoor fungi than of bacteria. The passage of time affected fungi and, surprisingly, also strongly affected bacteria. We inferred that fungal communities in indoor dust changed semi-annually, whereas bacterial communities paralleled outdoor plant phenological periods. These differences in temporal dynamics cannot be fully explained and should be further investigated in future studies on indoor microbiomes.

Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants

PubMed Central

Weikl, Fabian; Tischer, Christina; Probst, Alexander J.; Heinrich, Joachim; Markevych, Iana; Jochner, Susanne; Pritsch, Karin

2016-01-01

People spend most of their time inside buildings and the indoor microbiome is a major part of our everyday environment. It affects humans’ wellbeing and therefore its composition is important for use in inferring human health impacts. It is still not well understood how environmental conditions affect indoor microbial communities. Existing studies have mostly focussed on the local (e.g., building units) or continental scale and rarely on the regional scale, e.g. a specific metropolitan area. Therefore, we wanted to identify key environmental determinants for the house dust microbiome from an existing collection of spatially (area of Munich, Germany) and temporally (301 days) distributed samples and to determine changes in the community as a function of time. To that end, dust samples that had been collected once from the living room floors of 286 individual households, were profiled for fungal and bacterial community variation and diversity using microbial fingerprinting techniques. The profiles were tested for their association with occupant behaviour, building characteristics, outdoor pollution, vegetation, and urbanization. Our results showed that more environmental and particularly outdoor factors (vegetation, urbanization, airborne particulate matter) affected the community composition of indoor fungi than of bacteria. The passage of time affected fungi and, surprisingly, also strongly affected bacteria. We inferred that fungal communities in indoor dust changed semi-annually, whereas bacterial communities paralleled outdoor plant phenological periods. These differences in temporal dynamics cannot be fully explained and should be further investigated in future studies on indoor microbiomes. PMID:27100967

Looking inside and out: the impact of employee and community demographic composition on organizational diversity climate.

PubMed

Pugh, S Douglas; Dietz, Joerg; Brief, Arthur P; Wiley, Jack W

2008-11-01

An organization's diversity climate refers to employees' shared perceptions of the policies and practices that communicate the extent to which fostering diversity and eliminating discrimination is a priority in the organization. The authors propose a salient element of the organizational context, the racial composition of the community where the organization is located, serves an important signaling function that shapes the formation of climate perceptions. In a study of 142 retail bank units in the United States, evidence is found for a relationship between the racial composition of an organization's workforce and diversity climate that is moderated by the racial composition of the community where the organization is located. The results suggest that when few racial minorities live in the community in which an organization is embedded, workforce diversity has an impact on employees' diversity climate perceptions. As racial minority popular share increases, workforce diversity tends to lose this signaling value.

Long-term experimental warming alters community composition of ascomycetes in Alaskan moist and dry arctic tundra.

PubMed

Semenova, Tatiana A; Morgado, Luis N; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik; Geml, József

2015-01-01

Arctic tundra regions have been responding to global warming with visible changes in plant community composition, including expansion of shrubs and declines in lichens and bryophytes. Even though it is well known that the majority of arctic plants are associated with their symbiotic fungi, how fungal community composition will be different with climate warming remains largely unknown. In this study, we addressed the effects of long-term (18 years) experimental warming on the community composition and taxonomic richness of soil ascomycetes in dry and moist tundra types. Using deep Ion Torrent sequencing, we quantified how OTU assemblage and richness of different orders of Ascomycota changed in response to summer warming. Experimental warming significantly altered ascomycete communities with stronger responses observed in the moist tundra compared with dry tundra. The proportion of several lichenized and moss-associated fungi decreased with warming, while the proportion of several plant and insect pathogens and saprotrophic species was higher in the warming treatment. The observed alterations in both taxonomic and ecological groups of ascomycetes are discussed in relation to previously reported warming-induced shifts in arctic plant communities, including decline in lichens and bryophytes and increase in coverage and biomass of shrubs. © 2014 John Wiley & Sons Ltd.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

PubMed

Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

2017-11-01

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition.

PubMed

Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; Zhang, Li-Mei

2016-02-01

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

Bacterial Communities in Malagasy Soils with Differing Levels of Disturbance Affecting Botanical Diversity

PubMed Central

Blasiak, Leah C.; Schmidt, Alex W.; Andriamiarinoro, Honoré; Mulaw, Temesgen; Rasolomampianina, Rado; Applequist, Wendy L.; Birkinshaw, Chris; Rejo-Fienena, Félicitée; Lowry, Porter P.; Schmidt, Thomas M.; Hill, Russell T.

2014-01-01

Madagascar is well-known for the exceptional biodiversity of its macro-flora and fauna, but the biodiversity of Malagasy microbial communities remains relatively unexplored. Understanding patterns of bacterial diversity in soil and their correlations with above-ground botanical diversity could influence conservation planning as well as sampling strategies to maximize access to bacterially derived natural products. We present the first detailed description of Malagasy soil bacterial communities from a targeted 16S rRNA gene survey of greater than 290,000 sequences generated using 454 pyrosequencing. Two sampling plots in each of three forest conservation areas were established to represent different levels of disturbance resulting from human impact through agriculture and selective exploitation of trees, as well as from natural impacts of cyclones. In parallel, we performed an in-depth characterization of the total vascular plant morphospecies richness within each plot. The plots representing different levels of disturbance within each forest did not differ significantly in bacterial diversity or richness. Changes in bacterial community composition were largest between forests rather than between different levels of impact within a forest. The largest difference in bacterial community composition with disturbance was observed at the Vohibe forest conservation area, and this difference was correlated with changes in both vascular plant richness and soil pH. These results provide the first survey of Malagasy soil bacterial diversity and establish a baseline of botanical diversity within important conservation areas. PMID:24465484

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS

Quantifying Hydroperiod, Fire and Nutrient Effects on the Composition of Plant Communities in Marl Prairie of the Everglades: a Joint Probability Method Based Model

NASA Astrophysics Data System (ADS)

Zhai, L.

2017-12-01

Plant community can be simultaneously affected by human activities and climate changes, and quantifying and predicting this combined effect on plant community by appropriate model framework which is validated by field data is complex, but very useful to conservation management. Plant communities in the Everglades provide an unique set of conditions to develop and validate this model framework, because they are both experiencing intensive effects of human activities (such as changing hydroperiod by drainage and restoration projects, nutrients from upstream agriculture, prescribed fire, etc.) and climate changes (such as warming, changing precipitation patter, sea level rise, etc.). More importantly, previous research attention focuses on plant communities in slough ecosystem (including ridge, slough and their tree islands), very few studies consider the marl prairie ecosystem. Comparing with slough ecosystem featured by remaining consistently flooded almost year-round, marl prairie has relatively shorter hydroperiod (just in wet-season of one year). Therefore, plant communities of marl prairie may receive more impacts from hydroperiod change. In addition to hydroperiod, fire and nutrients also affect the plant communities in the marl prairie. Therefore, to quantify the combined effects of water level, fire, and nutrients on the composition of the plant communities, we are developing a joint probability method based vegetation dynamic model. Further, the model is being validated by field data about changes of vegetation assemblage along environmental gradients in the marl prairie. Our poster showed preliminary data from our current project.

Facility and market factors affecting transitions from nursing home to community.

PubMed

Arling, Greg; Abrahamson, Kathleen A; Cooke, Valerie; Kane, Robert L; Lewis, Teresa

2011-09-01

Research into nursing home transitions has given limited attention to the facility or community contexts. To identify facility and market factors affecting transitions of nursing home residents back to the community. Multilevel models were used to estimate effects of facility and market factors on facility-level community discharge rates after controlling for resident demographic, health, and functional conditions. Facility discharge rates were adjusted using Empirical Bayes estimation. Annual cohort of first-time admissions (N=24,648) to 378 Minnesota nursing facilities in 75 nursing home markets from July 2005 to June 2006. Community discharge within 90 days of admission; facility occupancy, payer mix, ownership, case-mix acuity, size, admissions from hospitals, nurse staffing level, and proportion of admissions preferring or having support to return to the community; and nursing market population size, average occupancy, market concentration, and availability of home and community-based services. Rates of community discharge (Empirical Bayes residual) were highest in facilities with more residents preferring community discharge, more Medicare days, higher nurse staffing levels, and higher occupancy. In addition, facilities had higher community discharge rates if they were located in markets with a greater ratio of home and community-based services recipients to nursing home residents and with larger populations. State Medicaid programs should undertake system-level interventions that encourage nursing facilities to reduce unused bed capacity, balance the mix of payers, invest in nurse staffing, and take other steps to promote community discharges. In addition, states should increase home and community-based services, particularly in markets with low community discharge rates.

Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

PubMed

Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

2010-06-01

The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

Defining microbial community composition and seasonal variation in a sewage treatment plant in India using a down-flow hanging sponge reactor.

PubMed

Nomoto, Naoki; Hatamoto, Masashi; Hirakata, Yuga; Ali, Muntjeer; Jayaswal, Komal; Iguchi, Akinori; Okubo, Tsutomu; Takahashi, Masanobu; Kubota, Kengo; Tagawa, Tadashi; Uemura, Shigeki; Yamaguchi, Takashi; Harada, Hideki

2018-05-01

The characteristics of the microbial community in a practical-scale down-flow hanging sponge (DHS) reactor, high in organic matter and sulfate ion concentration, and the seasonal variation of the microbial community composition were investigated. Microorganisms related to sulfur oxidation and reduction (2-27%), as well as Leucobacter (7.50%), were abundant in the reactor. Anaerobic bacteria (27-38% in the first layer) were also in abundance and were found to contribute to the removal of organic matter from the sewage in the reactor. By comparing the Simpson index, the abundance-based coverage estimator (ACE) index, and the species composition of the microbial community across seasons (summer/dry, summer/rainy, autumn/dry, and winter/dry), the microbial community was found to change in composition only during the winter season. In addition to the estimation of seasonal variation, the difference in the microbial community composition along the axes of the DHS reactor was investigated for the first time. Although the abundance of each bacterial species differed along both axes of the reactor, the change of the community composition in the reactor was found to be greater along the vertical axis than the horizontal axis of the DHS reactor.

Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

PubMed Central

Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth

2015-01-01

Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

PubMed Central

Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

2013-01-01

The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.

PubMed

Xie, Wei; Zhang, Chuanlun L; Wang, Jinxiang; Chen, Yufei; Zhu, Yuanqing; de la Torre, José R; Dong, Hailiang; Hartnett, Hilairy E; Hedlund, Brian P; Klotz, Martin G

2015-05-01

Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Trauma and suicidality in war affected communities.

PubMed

Jankovic, J; Bremner, S; Bogic, M; Lecic-Tosevski, D; Ajdukovic, D; Franciskovic, T; Galeazzi, G M; Kucukalic, A; Morina, N; Popovski, M; Schützwohl, M; Priebe, S

2013-10-01

The aim was to assess whether experiences of war trauma remain directly associated with suicidality in war affected communities when other risk factors are considered. In the main sample 3313 participants from former Yugoslavia who experienced war trauma were recruited using a random sampling in five Balkan countries. In the second sample 854 refugees from former Yugoslavia recruited through registers and networking in three Western European countries. Sociodemographic and data on trauma exposure, psychiatric diagnoses and level of suicidality were assessed. In the main sample 113 participants (3.4%) had high suicidality, which was associated with number of potentially traumatic war experiences (odds ratio 1.1) and war related imprisonment (odds ratio 3) once all measured risk factors were considered. These associations were confirmed in the refugee sample with a higher suicidality rate (10.2%). Number of potentially traumatic war experiences, in particular imprisonment, may be considered as a relevant risk factor for suicidality in people affected by war. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

USGS Publications Warehouse

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.

2014-01-01

Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.

Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

DOE PAGES

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; ...

2014-10-07

Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean ismore » the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.« less

Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.

Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean ismore » the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea.« less

Comparing Bacterial Community Composition of Healthy and Dark Spot-Affected Siderastrea siderea in Florida and the Caribbean

PubMed Central

Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Gray, Michael A.; Andersen, Gary L.

2014-01-01

Coral disease is one of the major causes of reef degradation. Dark Spot Syndrome (DSS) was described in the early 1990's as brown or purple amorphous areas of tissue on a coral and has since become one of the most prevalent diseases reported on Caribbean reefs. It has been identified in a number of coral species, but there is debate as to whether it is in fact the same disease in different corals. Further, it is questioned whether these macroscopic signs are in fact diagnostic of an infectious disease at all. The most commonly affected species in the Caribbean is the massive starlet coral Siderastrea siderea. We sampled this species in two locations, Dry Tortugas National Park and Virgin Islands National Park. Tissue biopsies were collected from both healthy colonies and those with dark spot lesions. Microbial-community DNA was extracted from coral samples (mucus, tissue, and skeleton), amplified using bacterial-specific primers, and applied to PhyloChip G3 microarrays to examine the bacterial diversity associated with this coral. Samples were also screened for the presence of a fungal ribotype that has recently been implicated as a causative agent of DSS in another coral species, but the amplifications were unsuccessful. S. siderea samples did not cluster consistently based on health state (i.e., normal versus dark spot). Various bacteria, including Cyanobacteria and Vibrios, were observed to have increased relative abundance in the discolored tissue, but the patterns were not consistent across all DSS samples. Overall, our findings do not support the hypothesis that DSS in S. siderea is linked to a bacterial pathogen or pathogens. This dataset provides the most comprehensive overview to date of the bacterial community associated with the scleractinian coral S. siderea. PMID:25289937

Flow regime in a restored wetland determines trophic links and species composition in the aquatic macroinvertebrate community.

PubMed

González-Ortegón, E; Walton, M E M; Moghaddam, B; Vilas, C; Prieto, A; Kennedy, H A; Pedro Cañavate, J; Le Vay, L

2015-01-15

In a restored wetland (South of Spain), where different flow regimes control water exchange with the adjacent Guadalquivir estuary, the native Palaemon varians coexists with an exotic counterpart species Palaemon macrodactylus. This controlled m\\acrocosm offers an excellent opportunity to investigate how the effects of water management, through different flow regimes, and the presence of a non-native species affect the aquatic community and the trophic niche (by gut contents and C-N isotopic composition) of the native shrimp Palaemon varians. We found that increased water exchange rate (5% day(-1) in mixed ponds vs. 0.1% day(-1) in extensive ponds) modified the aquatic community of this wetland; while extensive ponds are dominated by isopods and amphipods with low presence of P. macrodactylus, mixed ponds presented high biomass of mysids, corixids, copepods and both shrimp species. An estuarine origin of nutrients and primary production might explain seasonal and spatial differences found among ponds of this wetland. A combined analysis of gut contents and isotopic composition of the native and the exotic species showed that: (1) native P. varians is mainly omnivorous (2) while the non-native P. macrodactylus is more zooplanktivorous and (3) a dietary overlap occurred when both species coexist at mixed ponds where a higher water exchange and high abundance of mysids and copepods diversifies the native species' diet. Thus differences in the trophic ecology of both species are clearly explained by water management. This experimental study is a valuable tool for integrated management between river basin and wetlands since it allows quantification of wetland community changes in response to the flow regime. Copyright © 2014 Elsevier B.V. All rights reserved.

PERCEIVED RACISM AND NEGATIVE AFFECT: ANALYSES OF TRAIT AND STATE MEASURES OF AFFECT IN A COMMUNITY SAMPLE

PubMed Central

BRONDOLO, ELIZABETH; BRADY, NISHA; THOMPSON, SHOLA; TOBIN, JONATHAN N.; CASSELLS, ANDREA; SWEENEY, MONICA; MCFARLANE, DELANO; CONTRADA, RICHARD J.

2008-01-01

Racism is a significant psychosocial stressor that is hypothesized to have negative psychological and physical health consequences. The Reserve Capacity Model (Gallo & Matthews, 2003) suggests that low socioeconomic status may influence health through its effects on negative affect. We extend this model to study the effects of racism, examining the association of lifetime perceived racism to trait and daily negative affect. A multiethnic sample of 362 American–born Black and Latino adults completed the Perceived Ethnic Discrimination Questionnaire–Community Version (PEDQ–CV). Trait negative affect was assessed with the Positive and Negative Affect Schedule (PANAS), and state negative affect was measured using ecological momentary assessments (EMA), in the form of an electronic diary. Analyses revealed a significant relationship of lifetime perceived racism to both daily negative affect and trait negative affect, even when controlling for trait hostility and socioeconomic status. The relationship of perceived racism to negative affect was moderated by education, such that the relationships were strongest for those with less than a high school education. The findings support aspects of the Reserve Capacity Model and identify pathways through which perceived racism may affect health status. PMID:19079772

Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem.

PubMed

Guo, Xiaohong; Gong, Jun

2014-02-01

Arbuscular mycorrhizal fungi (AMF) were investigated in roots of 18 host plant species in a salinized south coastal plain of Laizhou Bay, China. From 18 clone libraries of 18S rRNA genes, all of the 22 AMF phylotypes were identified into Glomus, of which 18 and 4 were classified in group A and B in the phylogenetic tree, respectively. The phylotypes related to morphologically defined Glomus species occurred generally in soil with higher salinity. AMF phylotype richness, Shannon index, and evenness were not significantly different between root samples from halophytes vs. non-halophytes, invades vs. natives, or annuals vs. perennials. However, AMF diversity estimates frequently differed along the saline gradient or among locations, but not among pH gradients. Moreover, UniFrac tests showed that both plant traits (salt tolerance, life style or origin) and abiotic factors (salinity, pH, or location) significantly affected the community composition of AMF colonizers. Redundancy and variation partitioning analyses revealed that soil salinity and pH, which respectively explained 6.9 and 4.2 % of the variation, were the most influential abiotic variables in shaping the AMF community structure. The presented data indicate that salt tolerance, life style, and origin traits of host species may not significantly affect the AMF diversity in roots, but do influence the community composition in this salinized ecosystem. The findings also highlight the importance of soil salinity and pH in driving the distribution of AMF in plant and soil systems.

Epiphytic Macrolichen Community Composition Database—epiphytic lichen synusiae in forested areas of the US

Treesearch

Sarah. Jovan

2012-01-01

The Forest Inventory and Analysis (FIA) Program's Lichen Communities Indicator is used for tracking epiphytic macrolichen diversity and is applied for monitoring air quality and climate change effects on forest health in the United States. Started in 1994, the Epiphytic Macrolichen Community Composition Database (GIVD ID NA-US-012) now has over 8,000 surveys of...

The bacterial community composition of the surface microlayer in a high mountain lake.

PubMed

Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

2010-09-01

The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

Effects of habitat management treatments on plant community composition and biomass in a Montane wetland

USGS Publications Warehouse

Austin, J.E.; Keough, J.R.; Pyle, W.H.

2007-01-01

Grazing and burning are commonly applied practices that can impact the diversity and biomass of wetland plant communities. We evaluated the vegetative response of wetlands and adjacent upland grasslands to four treatment regimes (continuous idle, fall prescribed burning followed by idle, annual fall cattle grazing, and rotation of summer grazing and idle) commonly used by the U.S. Fish and Wildlife Service. Our study area was Grays Lake, a large, montane wetland in southeastern Idaho that is bordered by extensive wet meadows. We identified seven plant cover types, representing the transition from dry meadow to deep wetland habitats: mixed deep marsh, spikerush slough, Baltic rush (Juncus balticus), moist meadow, alkali, mesic meadow, and dry meadow. We compared changes in community composition and total aboveground biomass of each plant cover type between 1998, when all units had been idled for three years, and 1999 (1 yr post-treatment) and 2000 (2 yr post-treatment). Analysis using non-metric multidimensional scaling indicated that compositional changes varied among cover types, treatments, and years following treatment. Treatment-related changes in community composition were greatest in mixed deep marsh, Baltic rush, and mesic meadow. In mixed deep marsh and Baltic rush, grazing and associated trampling contributed to changes in the plant community toward more open water and aquatic species and lower dominance of Baltic rush; grazing and trampling also seemed to contribute to increased cover in mesic meadow. Changing hydrological conditions, from multiple years of high water to increasing drought, was an important factor influencing community composition and may have interacted with management treatments. Biomass differed among treatments and between years within cover types. In the wettest cover types, fall burning and grazing rotation treatments had greater negative impact on biomass than the idle treatment, but in drier cover types, summer grazing stimulated