Abiotic and biotic controls over biogeochemical cycles in drylands: Insights from climate change and nitrogen deposition experiments on the Colorado Plateau

NASA Astrophysics Data System (ADS)

Reed, S.; Ferrenberg, S.; Tucker, C.; Rutherford, W. A.; Wertin, T. M.; McHugh, T. A.; Morrissey, E.; Kuske, C.; Mueller, R.; Belnap, J.

2016-12-01

As for all ecosystems, biogeochemical cycling in drylands represents numerous intricate connections between biotic and abiotic controls. However, patterns of many fundamental ecosystem processes that generally hold across global gradients fall apart at the arid and semiarid end of the spectrum, and data point to an exceptionally strong role for abiotic controls in explaining these patterns. Further, there are multiple dryland characteristics - such as extreme aridity and high UV radiation, as well as specialized biological communities - which can point to a conclusion that "drylands are different". Indeed, drylands are often characterized by their harsh environment, by the diverse classes of biota representing a range of traits aimed at surviving such harsh conditions, and, more recently, by the suggestion of dramatic biotic responses to seemingly subtle changes in abiotic factors. In this talk, we will explore a range of biotic and abiotic controls over fundamental biogeochemical cycling in drylands using data from a suite of manipulation experiments on the Colorado Plateau, USA. We will present results from field treatments that speak to the effects of increasing temperature, altered precipitation regimes, increased nitrogen availability via deposition, and the effects of altered litterfall inputs. Biogeochemical processes we explore will include plant photosynthesis, soil photosynthesis and respiration (with a focus on biological soil crusts), litter decomposition, and nutrient cycling. In addition, we will assess how treatments alter dryland community composition, as well as the resultant feedbacks of community shifts to environmental change. Taken together we will use these diverse datasets to ask questions about what makes drylands different or, instead, if a holistic joining of biotic and abiotic perspectives suggests they are not so different after all. These data will not only lend insight into the partitioning of and balance between biotic and abiotic controls, but will also provide perspective on how a changing world may shift this balance.

Assessment of fish assemblages and minimum sampling effort required to determine botic integrity of large rivers in southern Idaho, 2002

USGS Publications Warehouse

Maret, Terry R.; Ott, D.S.

2004-01-01

width was determined to be sufficient for collecting an adequate number of fish to estimate species richness and evaluate biotic integrity. At most sites, about 250 fish were needed to effectively represent 95 percent of the species present. Fifty-three percent of the sites assessed, using an IBI developed specifically for large Idaho rivers, received scores of less than 50, indicating poor biotic integrity.

Electrofishing effort required to estimate biotic condition in southern Idaho Rivers

USGS Publications Warehouse

Maret, Terry R.; Ott, Douglas S.; Herlihy, Alan T.

2007-01-01

An important issue surrounding biomonitoring in large rivers is the minimum sampling effort required to collect an adequate number of fish for accurate and precise determinations of biotic condition. During the summer of 2002, we sampled 15 randomly selected large-river sites in southern Idaho to evaluate the effects of sampling effort on an index of biotic integrity (IBI). Boat electrofishing was used to collect sample populations of fish in river reaches representing 40 and 100 times the mean channel width (MCW; wetted channel) at base flow. Minimum sampling effort was assessed by comparing the relation between reach length sampled and change in IBI score. Thirty-two species of fish in the families Catostomidae, Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, and Salmonidae were collected. Of these, 12 alien species were collected at 80% (12 of 15) of the sample sites; alien species represented about 38% of all species (N = 32) collected during the study. A total of 60% (9 of 15) of the sample sites had poor IBI scores. A minimum reach length of about 36 times MCW was determined to be sufficient for collecting an adequate number of fish for estimating biotic condition based on an IBI score. For most sites, this equates to collecting 275 fish at a site. Results may be applicable to other semiarid, fifth-order through seventh-order rivers sampled during summer low-flow conditions.

The H2/CH4 ratio during serpentinization cannot reliably identify biological signatures

NASA Astrophysics Data System (ADS)

Huang, Ruifang; Sun, Weidong; Liu, Jinzhong; Ding, Xing; Peng, Shaobang; Zhan, Wenhuan

2016-09-01

Serpentinization potentially contributes to the origin and evolution of life during early history of the Earth. Serpentinization produces molecular hydrogen (H2) that can be utilized by microorganisms to gain metabolic energy. Methane can be formed through reactions between molecular hydrogen and oxidized carbon (e.g., carbon dioxide) or through biotic processes. A simple criterion, the H2/CH4 ratio, has been proposed to differentiate abiotic from biotic methane, with values approximately larger than 40 for abiotic methane and values of <40 for biotic methane. The definition of the criterion was based on two serpentinization experiments at 200 °C and 0.3 kbar. However, it is not clear whether the criterion is applicable at a wider range of temperatures. In this study, we performed sixteen experiments at 311-500 °C and 3.0 kbar using natural ground peridotite. Our results demonstrate that the H2/CH4 ratios strongly depend on temperature. At 311 °C and 3.0 kbar, the H2/CH4 ratios ranged from 58 to 2,120, much greater than the critical value of 40. By contrast, at 400-500 °C, the H2/CH4 ratios were much lower, ranging from 0.1 to 8.2. The results of this study suggest that the H2/CH4 ratios cannot reliably discriminate abiotic from biotic methane.

The H2/CH4 ratio during serpentinization cannot reliably identify biological signatures.

PubMed

Huang, Ruifang; Sun, Weidong; Liu, Jinzhong; Ding, Xing; Peng, Shaobang; Zhan, Wenhuan

2016-09-26

Serpentinization potentially contributes to the origin and evolution of life during early history of the Earth. Serpentinization produces molecular hydrogen (H 2 ) that can be utilized by microorganisms to gain metabolic energy. Methane can be formed through reactions between molecular hydrogen and oxidized carbon (e.g., carbon dioxide) or through biotic processes. A simple criterion, the H 2 /CH 4 ratio, has been proposed to differentiate abiotic from biotic methane, with values approximately larger than 40 for abiotic methane and values of <40 for biotic methane. The definition of the criterion was based on two serpentinization experiments at 200 °C and 0.3 kbar. However, it is not clear whether the criterion is applicable at a wider range of temperatures. In this study, we performed sixteen experiments at 311-500 °C and 3.0 kbar using natural ground peridotite. Our results demonstrate that the H 2 /CH 4 ratios strongly depend on temperature. At 311 °C and 3.0 kbar, the H 2 /CH 4 ratios ranged from 58 to 2,120, much greater than the critical value of 40. By contrast, at 400-500 °C, the H 2 /CH 4 ratios were much lower, ranging from 0.1 to 8.2. The results of this study suggest that the H 2 /CH 4 ratios cannot reliably discriminate abiotic from biotic methane.

The H2/CH4 ratio during serpentinization cannot reliably identify biological signatures

PubMed Central

Huang, Ruifang; Sun, Weidong; Liu, Jinzhong; Ding, Xing; Peng, Shaobang; Zhan, Wenhuan

2016-01-01

Serpentinization potentially contributes to the origin and evolution of life during early history of the Earth. Serpentinization produces molecular hydrogen (H2) that can be utilized by microorganisms to gain metabolic energy. Methane can be formed through reactions between molecular hydrogen and oxidized carbon (e.g., carbon dioxide) or through biotic processes. A simple criterion, the H2/CH4 ratio, has been proposed to differentiate abiotic from biotic methane, with values approximately larger than 40 for abiotic methane and values of <40 for biotic methane. The definition of the criterion was based on two serpentinization experiments at 200 °C and 0.3 kbar. However, it is not clear whether the criterion is applicable at a wider range of temperatures. In this study, we performed sixteen experiments at 311–500 °C and 3.0 kbar using natural ground peridotite. Our results demonstrate that the H2/CH4 ratios strongly depend on temperature. At 311 °C and 3.0 kbar, the H2/CH4 ratios ranged from 58 to 2,120, much greater than the critical value of 40. By contrast, at 400–500 °C, the H2/CH4 ratios were much lower, ranging from 0.1 to 8.2. The results of this study suggest that the H2/CH4 ratios cannot reliably discriminate abiotic from biotic methane. PMID:27666288

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.

PubMed

Pawlowski, Jan; Kelly-Quinn, Mary; Altermatt, Florian; Apothéloz-Perret-Gentil, Laure; Beja, Pedro; Boggero, Angela; Borja, Angel; Bouchez, Agnès; Cordier, Tristan; Domaizon, Isabelle; Feio, Maria Joao; Filipe, Ana Filipa; Fornaroli, Riccardo; Graf, Wolfram; Herder, Jelger; van der Hoorn, Berry; Iwan Jones, J; Sagova-Mareckova, Marketa; Moritz, Christian; Barquín, Jose; Piggott, Jeremy J; Pinna, Maurizio; Rimet, Frederic; Rinkevich, Buki; Sousa-Santos, Carla; Specchia, Valeria; Trobajo, Rosa; Vasselon, Valentin; Vitecek, Simon; Zimmerman, Jonas; Weigand, Alexander; Leese, Florian; Kahlert, Maria

2018-05-15

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Biotic ligand modeling approach: Synthesis of the effect of major cations on the toxicity of metals to soil and aquatic organisms.

PubMed

Ardestani, Masoud M; van Straalen, Nico M; van Gestel, Cornelis A M

2015-10-01

The biotic ligand model (BLM) approach is used to assess metal toxicity, taking into account the competition of other cations with the free metal ions for binding to the biotic ligand sites of aquatic and soil organisms. The bioavailable fraction of metals, represented by the free metal ion, is a better measure than the total concentration for assessing their potential risk to the environment. Because BLMs are relating toxicity to the fraction of biotic ligands occupied by the metal, they can be useful for investigating factors affecting metal bioaccumulation and toxicity. In the present review, the effects of major cations on the toxicity of metals to soil and aquatic organisms were comprehensively studied by performing a meta-analysis of BLM literature data. Interactions at the binding sites were shown to be species- and metal-specific. The main factors affecting the relationships between toxicity and conditional binding constants for metal binding at the biotic ligand appeared to be Ca(2+) , Mg(2+) , and protons. Other important characteristics of the exposure medium, such as levels of dissolved organic carbon and concentrations of other cations, should also be considered to obtain a proper assessment of metal toxicity to soil and aquatic organisms. © 2015 SETAC.

Division within the North American boreal forest: Ecological niche divergence between the Bicknell's Thrush (Catharus bicknelli) and Gray-cheeked Thrush (C. minimus).

PubMed

FitzGerald, Alyssa M

2017-07-01

Sister species that diverged in allopatry in similar environments are expected to exhibit niche conservatism. Using ecological niche modeling and a multivariate analysis of climate and habitat data, I test the hypothesis that the Bicknell's Thrush ( Catharus bicknelli ) and Gray-cheeked Thrush ( C. mimimus ), sister species that breed in the North American boreal forest, show niche conservatism. Three tree species that are important components of breeding territories of both thrush species were combined with climatic variables to create niche models consisting of abiotic and biotic components. Abiotic-only, abiotic+biotic, and biotic-only models were evaluated using the area under the curve (AUC) criterion. Abiotic+biotic models had higher AUC scores and did not over-project thrush distributions compared to abiotic-only or biotic-only models. From the abiotic+biotic models, I tested for niche conservatism or divergence by accounting for the differences in the availability of niche components by calculating (1) niche overlap from ecological niche models and (2) mean niche differences of environmental values at occurrence points. Niche background similarity tests revealed significant niche divergence in 10 of 12 comparisons, and multivariate tests revealed niche divergence along 2 of 3 niche axes. The Bicknell's Thrush breeds in warmer and wetter regions with a high abundance of balsam fir ( Abies balsamea ), whereas Gray-cheeked Thrush often co-occurs with black spruce ( Picea mariana ). Niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in the speciation of the Bicknell's Thrush and Gray-cheeked Thrush. Furthermore, because niche models were improved by the incorporation of biotic variables, this study validates the inclusion of relevant biotic factors in ecological niche modeling to increase model accuracy.

Nitrogen cycling in an extreme hyperarid environment inferred from δ(15)N analyses of plants, soils and herbivore diet.

PubMed

Díaz, Francisca P; Frugone, Matías; Gutiérrez, Rodrigo A; Latorre, Claudio

2016-03-09

Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ(15)N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ(15)N and δ(13)C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ(15)N values span the entire gradient, soil δ(15)N values show a positive correlation with aridity as expected. In contrast, foliar δ(15)N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ(15)N values.

Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

NASA Astrophysics Data System (ADS)

Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

2016-03-01

Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values.

Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

PubMed Central

Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

2016-01-01

Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values. PMID:26956399

A meta-analysis of soil microbial biomass responses to forest disturbances

PubMed Central

Holden, Sandra R.; Treseder, Kathleen K.

2013-01-01

Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

The relationship between metal toxicity and biotic ligand binding affinities in aquatic and soil organisms: a review.

PubMed

Ardestani, Masoud M; van Straalen, Nico M; van Gestel, Cornelis A M

2014-12-01

The biotic ligand model (BLM) is a theoretical, potentially mechanistic approach to assess metal bioavailability in soil and aquatic systems. In a BLM, toxicity is linked to the fraction of biotic ligand occupied, which in turn, depends on the various components of the solution, including activity of the metal. Bioavailability is a key factor in determining toxicity and uptake of metals in organisms. In this study, the present status of BLM development for soil and aquatic organisms is summarized. For all species and all metals, toxicity was correlated with the conditional biotic ligand binding constants. For almost all organisms, values for Ag, Cu, and Cd were higher than those for Zn and Ni. The constants derived for aquatic systems seem to be equally valid for soil organisms, but in the case of soils, bioavailability from the soil solution is greatly influenced by the presence of the soil solid phase. Copyright © 2014 Elsevier Ltd. All rights reserved.

ALien Biotic IndEX (ALEX) - a new index for assessing impacts of alien species on benthic communities.

PubMed

Çinar, Melih Ertan; Bakir, Kerem

2014-10-15

Biotic indices are mainly aimed at assessing levels of deterioration caused by chemical or organic pollution. However, no biotic index to date has been developed to detect impacts of alien species on benthic communities. In this paper, a new biotic index, namely ALEX, is proposed to address the objectives of the Water Framework Directive and was tested in Mersin Bay (Levantine Sea, Turkey). Species were divided into four biogeographic groups, namely native species, casual species, established species and invasive species, and the metric considers the relative importance of these groups in samples. The index classified the ecological status of some stations which are shallow, and close to harbor and river mouths as bad or poor in February and October. The ALEX values were positively and significantly correlated with total nitrogen, silicate and silt percentage in sediment, and negatively correlated with depth and the distance from the harbor. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nutrient Concentrations and Their Relations to the Biotic Integrity of Nonwadeable Rivers in Wisconsin

USGS Publications Warehouse

Robertson, Dale M.; Weigel, Brian M.; Graczyk, David J.

2008-01-01

Excessive nutrient [phosphorus (P) and nitrogen (N)] input from point and nonpoint sources is frequently associated with degraded water quality in streams and rivers. Point-source discharges of nutrients are fairly constant and are controlled by the U.S. Environmental Protection Agency's (USEPA) National Pollutant Discharge Elimination System. To reduce inputs from nonpoint sources, agricultural performance standards and regulations for croplands and livestock operations are being proposed by various States. In addition, the USEPA is establishing regionally based nutrient criteria that can be refined by each State to determine whether actions are needed to improve water quality. More confidence in the environmental benefits of the proposed performance standards and nutrient criteria would be possible with improved understanding of the biotic responses to a range of nutrient concentrations in different environmental settings. To achieve this general goal, the U.S. Geological Survey and the Wisconsin Department of Natural Resources collected data from 282 streams and rivers throughout Wisconsin during 2001 through 2003 to: (1) describe how nutrient concentrations and biotic-community structure differ throughout the State, (2) determine which environmental characteristics are most strongly related to the distribution of nutrient concentrations and biotic-community structure, (3) determine reference conditions for water quality and biotic indices for streams and rivers in the State, (4) determine how the biotic communities in streams and rivers in different areas of the State respond to differences in nutrient concentrations, (5) determine the best regionalization scheme to describe the patterns in reference conditions and the corresponding responses in water quality and the biotic communities (primarily for smaller streams), and (6) develop algorithms to estimate nutrient concentrations in streams and rivers from a combination of biotic indices. The ultimate goal of this study is to provide the information needed to guide the development of regionally based nutrient criteria for Wisconsin streams and rivers. In this report, data collected, primarily in 2003, from 42 nonwadeable rivers are used to describe nutrient concentrations and their relations to the biotic integrity of rivers in Wisconsin. In a separate report by Robertson and others (2006a), the data collected from 240 wadeable streams are used to describe these relations in streams in Wisconsin. Reference water-quality conditions for nonwadeable rivers were found to be similar throughout Wisconsin (approximately 0.035 milligrams per liter (mg/L) for total P (TP), 0.500 mg/L for total N (TN), 4 micrograms per liter for suspended chlorophyll a (SCHL), and greater than 110 centimeters for Secchi-tube depth (SD)). For each category of the biotic community (SCHL, macroinvertebrates, and fish), a few indices were more strongly related to differences in nutrient concentrations than were others. For the indices most strongly related to nutrient concentrations, reference conditions were obtained with a regression approach, from values corresponding to the worst 75th-percentile value from a subset of minimally impacted streams (streams having reference nutrient concentrations), and from the best 25th-percentile value of all the data. Concentrations of TP and TN in nonwadeable rivers increased as the percentage of agricultural land in the basin increased; these increases resulted in increased SCHL concentrations and decreased SDs. The responses in SDs and SCHL concentrations to changes in nutrient concentrations were similar throughout most of the State except in rivers in the southeastern part, where SCHL concentrations were lower than would be expected given their nutrient concentrations. Rivers in the southeastern part of the State had high concentrations of total suspended sediment compared to the SCHL concentrations. Many biotic indices responded to increases in nu

Four Reasons to Question the Accuracy of a Biotic Index; the Risk of Metric Bias and the Scope to Improve Accuracy

PubMed Central

Monaghan, Kieran A.

2016-01-01

Natural ecological variability and analytical design can bias the derived value of a biotic index through the variable influence of indicator body-size, abundance, richness, and ascribed tolerance scores. Descriptive statistics highlight this risk for 26 aquatic indicator systems; detailed analysis is provided for contrasting weighted-average indices applying the example of the BMWP, which has the best supporting data. Differences in body size between taxa from respective tolerance classes is a common feature of indicator systems; in some it represents a trend ranging from comparatively small pollution tolerant to larger intolerant organisms. Under this scenario, the propensity to collect a greater proportion of smaller organisms is associated with negative bias however, positive bias may occur when equipment (e.g. mesh-size) selectively samples larger organisms. Biotic indices are often derived from systems where indicator taxa are unevenly distributed along the gradient of tolerance classes. Such skews in indicator richness can distort index values in the direction of taxonomically rich indicator classes with the subsequent degree of bias related to the treatment of abundance data. The misclassification of indicator taxa causes bias that varies with the magnitude of the misclassification, the relative abundance of misclassified taxa and the treatment of abundance data. These artifacts of assessment design can compromise the ability to monitor biological quality. The statistical treatment of abundance data and the manipulation of indicator assignment and class richness can be used to improve index accuracy. While advances in methods of data collection (i.e. DNA barcoding) may facilitate improvement, the scope to reduce systematic bias is ultimately limited to a strategy of optimal compromise. The shortfall in accuracy must be addressed by statistical pragmatism. At any particular site, the net bias is a probabilistic function of the sample data, resulting in an error variance around an average deviation. Following standardized protocols and assigning precise reference conditions, the error variance of their comparative ratio (test-site:reference) can be measured and used to estimate the accuracy of the resultant assessment. PMID:27392036

[Continuity and discontinuity of the geomerida: the bionomic and biotic aspects].

PubMed

Kafanov, A I

2005-01-01

The view of the spatial structure of the geomerida (Earth's life cover) as a continuum that prevails in modern phytocoenology is mostly determined by a physiognomic (landscape-bionomic) discrimination of vegetation components. In this connection, geography of life forms appears as subject of the landscapebionomic biogeography. In zoocoenology there is a tendency of synthesis of alternative concepts based on the assumption that there are no absolute continuum and absolute discontinuum in the organic nature. The problem of continuum and discontinuum of living cover being problem of scale aries from fractal structure of geomerida. This problem arises from fractal nature of the spatial structure of geomerida. The continuum mainly belongs to regularities of topological order. At regional and subregional scale the continuum of biochores is rather rare. The objective evidences of relative discontinuity of the living cover are determined by significant alterations of species diversity at the regional, subregional and even topological scale Alternatively to conventionally discriminated units in physionomically continuous vegetation, the same biotic complexes, represented as operational units of biogeographical and biocenological zoning, are distinguished repeatedly and independently by different researchers. An area occupied by certain flora (fauna, biota) could be considered as elementary unit of biotic diversity (elementary biotic complex).

The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

PubMed

Roux, F; Bergelson, J

2016-01-01

In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. © 2016 Elsevier Inc. All rights reserved.

Comparison of U.S. Geological Survey and Ohio Environmental Protection Agency fish-collection methods using the index of biotic integrity and modified index of well-being, 1996-97

USGS Publications Warehouse

Covert, S. Alex

2001-01-01

The U.S. Geological Survey (USGS) and Ohio Environmental Protection Agency (OEPA) collected data on fish from 10 stream sites in 1996 and 3 stream sites in 1997 as part of a comparative study of fish community assessment methods. The sites sampled represent a wide range of basin sizes (ranging from 132?6,330 square kilometers) and surrounding land-use types (urban, agricultural, and mixed). Each agency used its own fish-sampling protocol. Using the Index of Biotic Integrity and Modified Index of Well-Being, differences between data sets were tested for significance by means of the Wilcoxon signed-ranks test (a = 0.05). Results showed that the median of Index of Biotic Integrity differences between data sets was not significantly different from zero (p = 0.2521); however, the same statistical test showed the median differences in the Modified Index of Well-Being scores to be significantly different from zero (p = 0.0158). The differences observed in the Index of Biotic Integrity scores are likely due to natural variability, increased variability at sites with degraded water quality, differences in sampling methods, and low-end adjustments in the Index of Biotic Integrity calculation when fewer than 50 fish were collected. The Modified Index of Well-Being scores calculated by OEPA were significantly higher than those calculated by the USGS. This finding was attributed to the comparatively large numbers and biomass of fish collected by the OEPA. By combining the two indices and viewing them in terms of the percentage attainment of Ohio Warmwater Habitat criteria, the two agencies? data seemed comparable, although the Index of Biotic Integrity scores were more similar than the Modified Index of Well-Being scores.

Invasion by nonnative brook trout in Panther Creek, Idaho: Roles of local habitat quality, biotic resistance, and connectivity to source habitats

USGS Publications Warehouse

Benjamin, Joseph R.; Dunham, Jason B.; Dare, M.R.

2007-01-01

Theoretical models and empirical evidence suggest that the invasion of nonnative species in freshwaters is facilitated through the interaction of three factors: habitat quality, biotic resistance, and connectivity. We measured variables that represented each factor to determine which were associated with the occurrence of nonnative brook trout Salvelinus fontinalis in Panther Creek, a tributary to the Salmon River, Idaho. Habitat variables included measures of summer and winter temperature, instream cover, and channel size. The abundance of native rainbow trout Oncorhynchus mykiss within sampled sites was used as a measure of biotic resistance. We also considered the connectivity of sample sites to unconfined valley bottoms, which were considered habitats that may serve as sources for the spread of established populations of brook trout. We analyzed the occurrence of small (<150‐mm [fork length]) and large (≥150‐mm) brook trout separately, assuming that the former represents an established invasion while accounting for the higher potential mobility of the latter. The occurrence of small brook trout was strongly associated with the proximity of sites to large, unconstrained valley bottoms, providing evidence that such habitats may serve as sources for the spread of brook trout invasion. Within sites, winter degree‐days and maximum summer temperature were positively associated with the occurrence of small brook trout. The occurrence of large brook trout was not related to any of the variables considered, perhaps due to the difficulty of linking site‐specific habitat factors to larger and more mobile individuals. The abundance of rainbow trout was not conclusively associated with the occurrence of either small or large brook trout, providing little support for the role of biotic resistance. Overall, our results suggest that source connectivity and local habitat characteristics, but not biotic resistance, influence the establishment and spread of nonnative brook trout populations. Further work is needed to confirm that the patterns observed here are relevant to other localities where brook trout have invaded and to understand the mechanisms contributing to the invasion process.

Towards Establishment of a Rice Stress Response Interactome

PubMed Central

Seo, Young-Su; Chern, Mawsheng; Bartley, Laura E.; Han, Muho; Jung, Ki-Hong; Lee, Insuk; Walia, Harkamal; Richter, Todd; Xu, Xia; Cao, Peijian; Bai, Wei; Ramanan, Rajeshwari; Amonpant, Fawn; Arul, Loganathan; Canlas, Patrick E.; Ruan, Randy; Park, Chang-Jin; Chen, Xuewei; Hwang, Sohyun; Jeon, Jong-Seong; Ronald, Pamela C.

2011-01-01

Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance. PMID:21533176

ELECTROFISHING EFFORT REQUIREMENTS FOR ASSESSING SPECIES RICHNESS AND BIOTIC INTEGRITY IN WESTERN OREGON STREAMS

EPA Science Inventory

We empirically examined the sampling effort required to adequately represent species richness and proportionate abundance when backpack electrofishing western Oregon streams. When sampling, we separately recorded data for each habitat unit. In data analyses, we repositioned each...

Subsequent biotic crises delayed marine recovery following the late Permian mass extinction event in northern Italy

PubMed Central

Danise, Silvia; Price, Gregory D.; Twitchett, Richard J.

2017-01-01

The late Permian mass extinction event was the largest biotic crisis of the Phanerozoic and has the longest recovery interval of any extinction event. It has been hypothesised that subsequent carbon isotope perturbations during the Early Triassic are associated with biotic crises that impeded benthic recovery. We test this hypothesis by undertaking the highest-resolution study yet made of the rock and fossil records of the entire Werfen Formation, Italy. Here, we show that elevated extinction rates were recorded not only in the Dienerian, as previously recognised, but also around the Smithian/Spathian boundary. Functional richness increases across the Smithian/Spathian boundary associated with elevated origination rates in the lower Spathian. The taxonomic and functional composition of benthic faunas only recorded two significant changes: (1) reduced heterogeneity in the Dienerian, and (2) and a faunal turnover across the Smithian/Spathian boundary. The elevated extinctions and compositional shifts in the Dienerian and across the Smithian/Spathian boundary are associated with a negative and positive isotope excursion, respectively, which supports the hypothesis that subsequent biotic crises are associated with carbon isotope shifts. The Spathian fauna represents a more advanced ecological state, not recognised in the previous members of the Werfen Formation, with increased habitat differentiation, a shift in the dominant modes of life, appearance of stenohaline taxa and the occupation of the erect and infaunal tiers. In addition to subsequent biotic crises delaying the recovery, therefore, persistent environmental stress limited the ecological complexity of benthic recovery prior to the Spathian. PMID:28296886

THE USE OF PERIPHYTON ASSEMBLAGE DATA AS AN INDEX OF BIOTIC INTEGRITY. (R824783)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

TRANSFERABILITY OF AN INDEX OF ESTUARINE BIOTIC INTEGRITY BASED ON FISH COMMUNITIES. (R825757)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Biotic and abiotic pathways of phosphorus cycling in minerals and sediments: insights from oxygen isotopes in phosphate

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

Jaisi, Deb P.; Kukkadapu, Ravi K.; Stout, Lisa M.

2011-07-06

A key question to address in the development of oxygen isotope ratios in phosphate (18Op) as a tracer of biogeochemical cycling of phosphorus in ancient and modern environments is the nature of isotopic signatures associated with uptake and cycling of mineral-bound phosphate by microorganisms. Here we present experimental results aimed at understanding the biotic and abiotic pathway of P cycling during biological uptake of phosphate sorbed to ferrihydrite and the selective uptake of specific sedimentary phosphate phases by Escherichia coli, Vibrio fischeri and Marinobacter aquaeolei. Results indicate that a significant fraction of ferrihydrite-bound phosphate is biologically available. The fraction ofmore » phosphate taken up by E. coli attained an equilibrium isotopic composition in a short time (<50 hrs) due to efficient O-isotope exchange between phosphate and water (biotic pathway). The difference in isotopic composition between newly equilibrated aqueous and residual sorbed phosphate promoted the exchange of intact phosphate radicals (abiotic pathway) so that this difference gradually became negligible. In sediment containing different P phases, E. coli and V. fischeri ‘extracted’ loosely sorbed phosphate first while M. aquaeolei preferred iron-oxide bound phosphate. Each bacterium imprinted a biotic isotopic signature on each P phase that it took up and cycled. For example, the 18Op value of the sorbed phosphate phase shifted gradually towards equilibrium isotopic composition and the value of Fe oxide-bound phosphate showed slight changes at first, but when new iron oxides were formed, co-precipitated/occluded phosphate retained 18O values of aqueous phosphate at that time. Concentrations and isotopic compositions of authigenic and detrital phosphates did not change, suggesting that these phosphate phases were not utilized by bacteria. These findings support burgeoning applications of 18Op as a tracer of phosphorus cycling in sediments, soils and aquatic environments and as an indicator of paleo- environmental conditions.« less

Biotic and Climatic Velocity Identify Contrasting Areas of Vulnerability to Climate Change.

PubMed

Carroll, Carlos; Lawler, Joshua J; Roberts, David R; Hamann, Andreas

2015-01-01

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth's surface to maintain constant climatic conditions. However, "analog-based" velocities, which represent the actual distance to where analogous climates will be found in the future, may provide contrasting results to the more common form of velocity based on local climate gradients. Additionally, whereas climatic velocity reflects the exposure of organisms to climate change, resultant biotic effects are dependent on the sensitivity of individual species as reflected in part by their climatic niche width. This has motivated development of biotic velocity, a metric which uses data on projected species range shifts to estimate the velocity at which species must move to track their climatic niche. We calculated climatic and biotic velocity for the Western Hemisphere for 1961-2100, and applied the results to example ecological and conservation planning questions, to demonstrate the potential of such analog-based metrics to provide information on broad-scale patterns of exposure and sensitivity. Geographic patterns of biotic velocity for 2954 species of birds, mammals, and amphibians differed from climatic velocity in north temperate and boreal regions. However, both biotic and climatic velocities were greatest at low latitudes, implying that threats to equatorial species arise from both the future magnitude of climatic velocities and the narrow climatic tolerances of species in these regions, which currently experience low seasonal and interannual climatic variability. Biotic and climatic velocity, by approximating lower and upper bounds on migration rates, can inform conservation of species and locally-adapted populations, respectively, and in combination with backward velocity, a function of distance to a source of colonizers adapted to a site's future climate, can facilitate conservation of diversity at multiple scales in the face of climate change.

Biotic and Climatic Velocity Identify Contrasting Areas of Vulnerability to Climate Change

PubMed Central

Carroll, Carlos; Lawler, Joshua J.; Roberts, David R.; Hamann, Andreas

2015-01-01

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth’s surface to maintain constant climatic conditions. However, “analog-based” velocities, which represent the actual distance to where analogous climates will be found in the future, may provide contrasting results to the more common form of velocity based on local climate gradients. Additionally, whereas climatic velocity reflects the exposure of organisms to climate change, resultant biotic effects are dependent on the sensitivity of individual species as reflected in part by their climatic niche width. This has motivated development of biotic velocity, a metric which uses data on projected species range shifts to estimate the velocity at which species must move to track their climatic niche. We calculated climatic and biotic velocity for the Western Hemisphere for 1961–2100, and applied the results to example ecological and conservation planning questions, to demonstrate the potential of such analog-based metrics to provide information on broad-scale patterns of exposure and sensitivity. Geographic patterns of biotic velocity for 2954 species of birds, mammals, and amphibians differed from climatic velocity in north temperate and boreal regions. However, both biotic and climatic velocities were greatest at low latitudes, implying that threats to equatorial species arise from both the future magnitude of climatic velocities and the narrow climatic tolerances of species in these regions, which currently experience low seasonal and interannual climatic variability. Biotic and climatic velocity, by approximating lower and upper bounds on migration rates, can inform conservation of species and locally-adapted populations, respectively, and in combination with backward velocity, a function of distance to a source of colonizers adapted to a site’s future climate, can facilitate conservation of diversity at multiple scales in the face of climate change. PMID:26466364

REGIONAL APPLICATION OF AN INDEX OF ESTUARINE BIOTIC INTEGRITY BASED ON FISH COMMUNITIES. (R825757)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Sebkhet Karkura: an example of a semi-arid Mediterranean wetland rich in biotic sediments

NASA Astrophysics Data System (ADS)

Abdulsamad, Esam O.; Elbabour, Mansour M.

2014-05-01

Habitat wetlands in Libya may be grouped into several distinct varieties, according to climate, water supply, soils, and biotic diversity. They include coastal Sebkhas (salt marshes), karst lakes, Wadi estuaries, below sea-level desert lakes, and balat flats (playas) where the soil is saturated part of some rainy seasons forming a kind of ephemeral, shallow lakes in pre-desert areas. The most prominent, however, are the extensive coastal salt marshes. These have either organic or inorganic soils, or both, depending on their location and climate conditions. Soils common to most coastal wetlands are composed largely of inorganic material in the form of sand, silt, or clay; in addition to organic material formed by decayed plants and various biotic sediments. For the purpose of the present poster, however, Sebkhet Karkura, an extensive stretch of about 50 km square (20 km long by an average width of 2.5 km) of Sebkha/wetland formation, located about 80 km southwest of Benghazi, will serve as an example of coastal Sebkhas. Here, the sediments are consisting mostly of dark earth brown sandy silt with salt and gypsum. Pure-salt deposits are normally extracted for salt processing in the area. Loams, silt, gravel, and calcareous sand are also present. At the surface of the wetland, calcarenites are fairly common but sand-beach and sand-dunes are representing the major sediments along the coastal wetland area. The recent biotal components of these sediments are described and a number of recent small-sized benthic seashells, belonging to phylum mollusca, have been investigated along the seaside of Sabkhet Karkura and several species have been identified. It is worth noting that Sebkhet Karkura, as well as other similar coastal wetlands, currently face serious threats due to human action, especially over exploitation of their resources, urban encroachments, dredging, and solid waste dumping. Increased awareness on the part of the general public of wetland ecological values and functions is essential as a preventive measure against such threats.

Maximum sustainable yield and species extinction in a prey-predator system: some new results.

PubMed

Ghosh, Bapan; Kar, T K

2013-06-01

Though the maximum sustainable yield (MSY) approach has been legally adopted for the management of world fisheries, it does not provide any guarantee against from species extinction in multispecies communities. In the present article, we describe the appropriateness of the MSY policy in a Holling-Tanner prey-predator system with different types of functional responses. It is observed that for both type I and type II functional responses, harvesting of either prey or predator species at the MSY level is a sustainable fishing policy. In the case of combined harvesting, both the species coexist at the maximum sustainable total yield (MSTY) level if the biotic potential of the prey species is greater than a threshold value. Further, increase of the biotic potential beyond the threshold value affects the persistence of the system.

Are large-scale manipulations of streamflow for ecological outcomes effective either as experiments or management actions? (Invited)

NASA Astrophysics Data System (ADS)

Konrad, C. P.; Olden, J.

2013-12-01

Dams impose a host of impacts on freshwater and estuary ecosystems. In recent decades, dam releases for ecological outcomes have been increasingly implemented to mitigate for these impacts and are gaining global scope. Many are designed and conducted using an experimental framework. A recent review of large-scale flow experiments (FE) evaluates their effectiveness and identifies ways to enhance their scientific and management value. At least 113 large-scale flow experiments affecting 98 river systems globally have been documented over the last 50 years. These experiments span a range of flow manipulations from single pulse events to comprehensive changes in flow regime across all seasons and different water year types. Clear articulation of experimental objectives, while not universally practiced, was crucial for achieving management outcomes and changing dam operating policies. We found a strong disparity between the recognized ecological importance of a multi faceted flow regimes and discrete flow events that characterized 80% of FEs. Over three quarters of FEs documented both abiotic and biotic outcomes, but only one third examined multiple trophic groups, thus limiting how this information informs future dam management. Large-scale flow experiments represent a unique opportunity for integrated biophysical investigations for advancing ecosystem science. Nonetheless, they must remain responsive to site-specific issues regarding water management, evolving societal values and changing environmental conditions and, in particular, can characterize the incremental benefits from and necessary conditions for changing dam operations to improve ecological outcomes. This type of information is essential for understanding the full context of value based trade-offs in benefits and costs from different dam operations that can serve as an empirical basis for societal decisions regarding water and ecosystem management. FE may be the best approach available to managers for resolving critical uncertainties that impede decision making in adaptive settings, for example, when we lack sufficient understanding to model biophysical responses to alternative operations. Integrated long term monitoring of biotic abiotic responses and defining clear management based objectives highlight ways for improving the efficiency and value of FEs.

Strangelove ocean at era boundaries, terrestrial or extraterrestrial cause

NASA Astrophysics Data System (ADS)

Hsue, Kenneth J.

Negative perturbations in carbon-isotope value of calcite in pelagic sediments were found at times of biotic crisis, marking horizons which are, or were proposed as era boundaries: Cretaceous/Tertiary (K/T), Permian/Triassic (P/T), and Precambrian/Cambrian (PreC/C). The anomaly was also found at several other mass-extinction horizons, such as terminal Ordovician, Frasnian-Famenian, etc. Studies of K/T boundary indicate that only the planktic fraction of the sediments has the negative isotope anomaly, whereas the benthic fraction has the same value across the boundary. This geochemical signal is thus considered a record of strangelove ocean, or an ocean where isotope fractionation of dissolved carbonate ions in surface waters (by biotic function of planktic organisms) has been significantly reduced because of the drastic reduction of the biomass in the oceans. The reduction of marine biomass at each of the era boundaries was related to chemical pollution of the oceans as a consequence of a catastrophic event; a pH decrease of 0.5 could inhibit the fertility of planktons. Studies of earthquakes, volcanic eruptions, and meteorite-impact occurrences have indicated a linearly inverse log/log relationship between the magnitude and frequency of events. The frequency of era boundaries in geologic history supports the postulate that the rare events causing those biotic crises were large bolide-impacts.

Strangelove ocean at era boundaries, terrestrial or extraterrestrial cause

NASA Technical Reports Server (NTRS)

Hsue, Kenneth J.

1988-01-01

Negative perturbations in carbon-isotope value of calcite in pelagic sediments were found at times of biotic crisis, marking horizons which are, or were proposed as era boundaries: Cretaceous/Tertiary (K/T), Permian/Triassic (P/T), and Precambrian/Cambrian (PreC/C). The anomaly was also found at several other mass-extinction horizons, such as terminal Ordovician, Frasnian-Famenian, etc. Studies of K/T boundary indicate that only the planktic fraction of the sediments has the negative isotope anomaly, whereas the benthic fraction has the same value across the boundary. This geochemical signal is thus considered a record of strangelove ocean, or an ocean where isotope fractionation of dissolved carbonate ions in surface waters (by biotic function of planktic organisms) has been significantly reduced because of the drastic reduction of the biomass in the oceans. The reduction of marine biomass at each of the era boundaries was related to chemical pollution of the oceans as a consequence of a catastrophic event; a pH decrease of 0.5 could inhibit the fertility of planktons. Studies of earthquakes, volcanic eruptions, and meteorite-impact occurrences have indicated a linearly inverse log/log relationship between the magnitude and frequency of events. The frequency of era boundaries in geologic history supports the postulate that the rare events causing those biotic crises were large bolide-impacts.

CARBON TETRACHLORIDE TRANSFORMATION IN A MODEL IRON-REDUCING CULTURE: RELATIVE KINETICS OF BIOTIC AND ABIOTIC REACTIONS. (R825958)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Freshwater macroinvertebrate research in western Louisiana: limitations of our knowledge base

NASA Astrophysics Data System (ADS)

Kaller, M.; Hudson, J. D.; Kelso, W. E.; Williams, L. R.

2005-05-01

Western Louisiana streams and rivers represent relatively uncharted waters with regard to their biota, particularly aquatic macroinvertebrates. Whereas statewide taxonomic surveys have been conducted for several taxa (Dryopid Coleoptera, Odonata, and Plecoptera), peer-reviewed studies on macroinvertebrate communities and their structuring factors are few. We present the findings of three different macroinvertebrate community studies in western Louisiana encompassing 1990-2004. These studies investigated large-scale forest cover removal and localized biotic influences on macroinvertebrate communities. These studies generally were inconclusive with regard to abiotic anthropogenic disturbances; instead, strong seasonal and spatial patterns combined with wide tolerances to stream physio-chemistry appeared to be more important factors. However, strong localized biotic effects did appear to significantly alter macroinvertebrate communities. Further, a paucity of classic shredding organisms was noted in each study suggesting a unique community composition in these streams in comparison to neighboring regions. We believe geologic phenomenon may have acted as an evolutionary filter that produced a macroinvertebrate community generally tolerant of abiotic disturbance, but not as of yet, tolerant to biotic disturbances.

Stream salamanders as indicators of stream quality in Maryland, USA

USGS Publications Warehouse

Southerland, M.T.; Jung, R.E.; Baxter, D.P.; Chellman, I.C.; Mercurio, G.; Volstad, J.H.

2004-01-01

Biological indicators are critical to the protection of small, headwater streams and the ecological values they provide. Maryland and other state monitoring programs have determined that fish indicators are ineffective in small streams, where stream salamanders may replace fish as top predators. Because of their life history, physiology, abundance, and ubiquity, stream salamanders are likely representative of biological integrity in these streams. The goal of this study was to determine whether stream salamanders are effective indicators of ecological conditions across biogeographic regions and gradients of human disturbance. During the summers of 2001 and 2002, we intensively surveyed for stream salamanders at 76 stream sites located west of the Maryland Coastal Plain, sites also monitored by the Maryland Biological Stream Survey (MBSS) and City of Gaithersburg. We found 1,584 stream salamanders, including all eight species known in Maryland, using two 15 ? 2 m transects and two 4 m2 quadrats that spanned both stream bank and channel. We performed removal sampling on transects to estimate salamander species detection probabilities, which ranged from 0.67-0.85. Stepwise regressions identified 15 of 52 non-salamander variables, representing water quality, physical habitat, land use, and biological conditions, which best predicted salamander metrics. Indicator development involved (1) identifying reference (non-degraded) and degraded sites (using percent forest, shading, riparian buffer width, aesthetic rating, and benthic macroinvertebrate and fish indices of biotic integrity); (2) testing 12 candidate salamander metrics (representing species richness and composition, abundance, species tolerance, and reproductive function) for their ability to distinguish reference from degraded sites; and (3) combining metrics into an index that effectively discriminated sites according to known stream conditions. Final indices for Highlands, Piedmont, and Non-Coastal Plain regions comprised four metrics: number of species, number of salamanders, number of intolerant salamanders, and number of adult salamanders, producing classification efficiencies between 87% and 90%. Partial validation of these indices was obtained when a test of the number of salamanders metric produced an 82% correct classification of 618 MBSS sites surveyed in 1995-97. This study supports the use of stream salamander monitoring and a composite stream salamander index of biotic integrity (SS-IBI) to determine stream quality in Maryland.

The role of biotic interactions in plant community assembly: What is the community species pool?

NASA Astrophysics Data System (ADS)

Švamberková, Eva; Vítová, Alena; Lepš, Jan

2017-11-01

Differences in plant species composition between a community and its species pool are considered to reflect the effect of community filters. If we define the species pool as a set of species able to reach a site and form a viable population in a given abiotic environment (i.e. to pass the dispersal and abiotic filter), the difference in species composition should correspond to the effect of biotic interactions. However, most of the operational definitions of the species pool are based on co-occurrence patterns and thus also reflect the effect of biotic relationships, including definitions based on functional plant traits, Ellenberg indicator values or Beals index. We conducted two seed introduction experiments in an oligotrophic wet meadow with the aim of demonstrating that many species excluded, according to the above definitions, from a species pool are in fact able to establish there successfully if competition is removed. In sowing experiments, we studied the establishment and survival of species after the removal of competition (i.e. in artificial gaps) and in intact vegetation. We also investigated inter-annual variability of seed germination and seedling establishment and competitive exclusion of sown species. The investigated species also included those from very different habitats (i.e. species with very low corresponding Beals index or Ellenberg indicator values that were different from the target community weighted mean). Many of these species were able to grow in the focal wet meadow if competition was removed, but they did not establish and survive in the intact community. These species are thus not limited by abiotic conditions, but by the biotic filter. We also recorded a great inter-annual variability in seed germination and seedling establishment. Competitive exclusion of species with different ecological requirements could be quite fast (one and half seasons) in some species, but some non-resident species were able to survive several seasons; the resident species were able to persist in competition. Comparison of realized vegetation composition with the corresponding species pool greatly underestimates the potential impact of the biotic filter if the delimitation of the species pool is based on the realized niches of species and co-occurrence patterns.

Adhesive properties of environmental Vibrio alginolyticus strains to biotic and abiotic surfaces.

PubMed

Snoussi, Mejdi; Noumi, Emira; Cheriaa, Jihane; Usai, Donatella; Sechi, Leonardo Antonio; Zanetti, Stefania; Bakhrouf, Amina

2008-10-01

The ability of Vibrio alginolyticus strains isolated from a bathing and fishing area (Khenis, Centre of Tunisia) to adhere to both biotic and abiotic surfaces was evaluated in the present work. The biochemical, physiological and enzymatic activities of all strains was also investigated. Three morphotypes of V. alginolyticus were obtained on Congo red agar and only 14 strains produced black colonies. The majority of strains were able to degrade the skin mucus of both Sparus aurata and Dicentrarchus labrax fishes while the fish mucus preparation of these two specimens exhibits a high level of anti-V. alginolyticus strains. Adhesive properties were observed in 37.5% of the analyzed V. alginolyticus strains to Hep-2 cells and 50% to Caco-2 cells. All strains were able to form a purple pellicule on glass tube when they were stained with Crystal violet. Fifteen percent of V. alginolyticus strains (16/32) were strongly adhesive to polystyrene with a values ranging from 3.04 to 18.25 at 595 nm and only four strains were weak biofilm forming. V. alginolyticus bacterium possess a strong adhesive power to both biotic and inertes surfaces. These proprieties may allow to these strains to persist in this biotope in planctonic state or attached to both biotic and abiotic surfaces.

Influence of solar radiation and biotic interactions on bacterial and eukaryotic communities associated with sewage decomposition in ambient water

EPA Science Inventory

Sewage and ambient water both consist of a highly complex array of bacteria and eukaryotic microbes. When these communities are mixed, the persistence of sewage-derived pathogens in environmental waters can represent a significant public health concern. Solar radiation and biot...

Glacier Lakes Ecosystem Experiment Site: an "Experimental" wilderness

Treesearch

Douglas G. Fox; Anna W. Schoettle; Frank A. Vertucci

1987-01-01

This site, selected to be representative of high-mountain wilderness ecosystems, is being used to study the effects of air pollution and atmospheric deposition In alpine and subalpine, terrestrial and aquatic biotic communities. The research program includes (a) short-term experiments designed to quantify the response of system components hypothesized to be most...

Comparison of oak and sugar maple distribution and regeneration in central Illinois upland oak forests

Treesearch

Peter J. Frey; Scott J. Meiners

2014-01-01

Changes in disturbance frequencies, habitat fragmentation, and other biotic pressures are allowing sugar maple (Acer saccharum) to displace oak (Quercus spp.) in the upland forest understory. The displacement of oaks by sugar maples represents a major management concern throughout the region. We collected seedling microhabitat data...

Herpetology of the American Madrean Archipelago and adjacent valleys

Treesearch

Lawrence L. C. Jones

2005-01-01

Approximately 110 species of amphibians (18 frogs and toads, and 1 salamander) and reptiles (47 snakes, 39 lizards, and 5 turtles) are known from the American Madrean Archipelago and adjacent valleys. The high diversity of the herpetofauna comes from a variety of factors, including a convergence of biotic communities representing deserts, grasslands, and mountains....

The Efficacy of Xylitol, Xylitol-Probiotic and Fluoride Dentifrices in Plaque Reduction and Gingival Inflammation in Children: A Randomised Controlled Clinical Trial.

PubMed

Arat Maden, Eda; Altun, Ceyhan; Açikel, Cengizhan

The present prospective, randomised, placebo-controlled, clinical trial was designed to evaluate the clinical effects of a commercially available dentifrice containing fluoride, xylitol or xylitol-probiotic on the decrease of plaque and gingival inflammation in children between 13 and 15 years of age. Forty-eight adolescents were randomly grouped into three groups of n = 16 each: study group A received xylitol (Xyliwhite) toothpaste; study group B received xylitol-probiotic (Periobiotic) toothpaste; and the control group C received fluoride (Colgate Max Fresh) toothpaste. The subjects were instructed to use the dentifrice determined and a modified Bass brushing technique twice a day for two minutes over a 6-week perioed. Clinical evaluation was performed using a gingival index and a plaque index at baseline and at the end of the 6-week period. From day 0 to 42, reductions in the plaque index were statistically significant in all groups, Colgate Max Fresh, PerioBiotic and Xyliwhite (p-values 0.001, 0.001 and 0.035, respectively), but reductions in the gingival index were statistically significant only in the Colgate Max Fresh and PerioBiotic groups (both with p = 0.001), not in the Xyliwhite group (p = 0.116). PerioBiotic toothpaste was found to be better than Xyliwhite and Colgate Max Fresh toothpastes at reducing plaque and gingival scores. However, statistically significant differences with PerioBiotic and Colgate Max Fresh toothpaste were not observed. It was concluded that PerioBiotic was an all-round dentifrice that produced a significant reduction in both gingivitis and plaque.

Benthic foraminiferal and organic matter compounds as proxies of environmental quality in a tropical coastal lagoon: The Itaipu lagoon (Brazil).

PubMed

Raposo, Débora; Clemente, Iara; Figueiredo, Marcos; Vilar, Amanda; Lorini, Maria Lucia; Frontalini, Fabrizio; Martins, Virgínia; Belart, Pierre; Fontana, Luiz; Habib, Renan; Laut, Lazaro

2018-04-01

Lagoons in the southeast coast of Brazil have experienced eutrophication due to the exponential increase of human population and sewage discharges. Living benthic foraminifera have demonstrated to be good bioindicators of such impacts. This study aims to evaluate the organic matter accumulation effects on the foraminiferal distribution in the Itaipu lagoon (Brazil). On the basis of the biotic and abiotic analyses, three sectors are identified. The Sector I, an inner area, is characterized by high dissolved oxygen values and foraminiferal species with preference for marine conditions, demonstrating the sea influence. The Sector II, in the mangrove margins, is associated to sandy sediment and biopolymers and mainly represented by euryhaline species. The Sector III is marked by low density or absence of living foraminifera and corresponds to a low quality organic matter enriched area (North, Southwest and Centre). Copyright © 2018 Elsevier Ltd. All rights reserved.

Spatially integrative metrics reveal hidden vulnerability of microtidal salt marshes

USGS Publications Warehouse

Ganju, Neil K.; Defne, Zafer; Kirwan, Matthew L.; Fagherazzi, Sergio; D'Alpaos, Andrea; Carniello, Luca

2017-01-01

Salt marshes are valued for their ecosystem services, and their vulnerability is typically assessed through biotic and abiotic measurements at individual points on the landscape. However, lateral erosion can lead to rapid marsh loss as marshes build vertically. Marsh sediment budgets represent a spatially integrated measure of competing constructive and destructive forces: a sediment surplus may result in vertical growth and/or lateral expansion, while a sediment deficit may result in drowning and/or lateral contraction. Here we show that sediment budgets of eight microtidal marsh complexes consistently scale with areal unvegetated/vegetated marsh ratios (UVVR) suggesting these metrics are broadly applicable indicators of microtidal marsh vulnerability. All sites are exhibiting a sediment deficit, with half the sites having projected lifespans of less than 350 years at current rates of sea-level rise and sediment availability. These results demonstrate that open-water conversion and sediment deficits are holistic and sensitive indicators of salt marsh vulnerability.

Spatially integrative metrics reveal hidden vulnerability of microtidal salt marshes

PubMed Central

Ganju, Neil K.; Defne, Zafer; Kirwan, Matthew L.; Fagherazzi, Sergio; D'Alpaos, Andrea; Carniello, Luca

2017-01-01

Salt marshes are valued for their ecosystem services, and their vulnerability is typically assessed through biotic and abiotic measurements at individual points on the landscape. However, lateral erosion can lead to rapid marsh loss as marshes build vertically. Marsh sediment budgets represent a spatially integrated measure of competing constructive and destructive forces: a sediment surplus may result in vertical growth and/or lateral expansion, while a sediment deficit may result in drowning and/or lateral contraction. Here we show that sediment budgets of eight microtidal marsh complexes consistently scale with areal unvegetated/vegetated marsh ratios (UVVR) suggesting these metrics are broadly applicable indicators of microtidal marsh vulnerability. All sites are exhibiting a sediment deficit, with half the sites having projected lifespans of less than 350 years at current rates of sea-level rise and sediment availability. These results demonstrate that open-water conversion and sediment deficits are holistic and sensitive indicators of salt marsh vulnerability. PMID:28112167

Spatially integrative metrics reveal hidden vulnerability of microtidal salt marshes.

PubMed

Ganju, Neil K; Defne, Zafer; Kirwan, Matthew L; Fagherazzi, Sergio; D'Alpaos, Andrea; Carniello, Luca

2017-01-23

Salt marshes are valued for their ecosystem services, and their vulnerability is typically assessed through biotic and abiotic measurements at individual points on the landscape. However, lateral erosion can lead to rapid marsh loss as marshes build vertically. Marsh sediment budgets represent a spatially integrated measure of competing constructive and destructive forces: a sediment surplus may result in vertical growth and/or lateral expansion, while a sediment deficit may result in drowning and/or lateral contraction. Here we show that sediment budgets of eight microtidal marsh complexes consistently scale with areal unvegetated/vegetated marsh ratios (UVVR) suggesting these metrics are broadly applicable indicators of microtidal marsh vulnerability. All sites are exhibiting a sediment deficit, with half the sites having projected lifespans of less than 350 years at current rates of sea-level rise and sediment availability. These results demonstrate that open-water conversion and sediment deficits are holistic and sensitive indicators of salt marsh vulnerability.

Method to grow Actinobacillus pleuropneumoniae biofilm on a biotic surface.

PubMed

Tremblay, Yannick D N; Lévesque, Cynthia; Segers, Ruud P A M; Jacques, Mario

2013-10-20

Actinobacillus pleuropneumoniae is a Gram-negative bacterium and a member of the Pasteurellaceae family. This bacterium is the causative agent of porcine pleuropneumonia, which is a highly contagious respiratory disease causing important economical losses to the worldwide pig industry. It has been shown that A. pleuropneumoniae can form biofilms on abiotic surfaces (plastic and glass). Although in vitro models are extremely useful to gain information on biofilm formation, these models may not be representative of the conditions found at the mucosal surface of the host, which is the natural niche of A. pleuropneumoniae. In this paper, we describe a method to grow A. pleuropneumoniae biofilms on the SJPL cell line, which represents a biotic surface. A non-hemolytic, non-cytotoxic mutant of A. pleuropneumoniae was used in our assays and this allowed the SJPL cell monolayers to be exposed to A. pleuropneumoniae for longer periods. This resulted in the formation of biofilms on the cell monolayer after incubations of 24 and 48 h. The biofilms can be stained with fluorescent probes, such as a lectin against the polymer of N-acetyl-D-glucosamine present in the biofilm matrix, and easily observed by confocal laser scanning microscopy. This is the first protocol that describes the formation of an A. pleuropneumoniae biofilm on a biotic surface. The advantage of this protocol is that it can be used to study biofilm formation in a context of host-pathogen interactions. The protocol could also be adapted to evaluate biofilm inhibitors or the efficacy of antibiotics in the presence of biofilms.

Hydrologic, ecologic, and geomorphic responses of Brewery Creek to construction of a residential subdivision, Dane County, Wisconsin, 1999-2002

USGS Publications Warehouse

Selbig, William R.; Jopke, Peter L.; Marhshall, David W.; Sorge, Michael J.

2004-01-01

Other physical, biological, and ecological surveys including macroinvertebrates, fish, habitat, and geomorphology were done on segments of Brewery Creek affected by the study area. Macroinvertebrate sampling results (Hilsenhoff Biotic Index value, or HBI), on Brewery Creek ranged from 'very good' to 'good' water-quality with no appreciable differences during any phase of construction activity. Results for fish-community composition, however, were within the 'poor' range (Index of Biotic Integrity value, or IBI) during each year of testing. A general absence of intolerant species, with the exception of brown trout, reflects the low IBI values. Habitat values did not change significantly from preconstruction to postconstruction phases. Although installation of a double-celled culvert in Brewery Creek most likely altered the width-to-depth ratio in that reach, the overall habitat rating remained 'fair'. Fluvial geomorphology classifications including channel cross sections, bed- and bank-erosion surveys, and pebble counts did not indicate that stream geomorphic characteristics were altered by home-construction activity in the study area. Increases in fine-grained sediment at various cross sections were attributed to instream erosion processes, such as bank slumping, rather than increases in sediment delivery from the nearby construction site.

A paleoecologic reconstruction of the history of Featherbed Bank, Biscayne National Park, Biscayne Bay, Florida

USGS Publications Warehouse

Stone, Jeffery R.; Cronin, T. M.; Brewster-Wingard, G. L.; Ishman, S.E.; Wardlaw, B.R.; Holmes, C.W.

2000-01-01

Using multiple-proxy biological indicators, a paleoecological history of the past 550 years of Featherbed Bank, Biscayne Bay, has been reconstructed from a short (2.26 m) sediment core. Paleoecological changes in ostracode, mollusc, and foraminifer assemblages show that core SEI297-FB-1 can be divided into three distinctly different zones, which together provide evidence for distinct changes in historical environmental conditions at Featherbed Bank. Assemblages from fossil biotic communities within zone 1, representing approximately 1440 to 1550 AD, are characterized by open-marine biota with relatively limited numbers of epiphytic biota. Molluscan faunal indicators suggest the sediment was capable of supporting infaunal organisms and that faunal richness was relatively limited during this time period. A change in the biotic community occurred around 1550 AD and continued until the late 1800's distinguishing zone 2. Fossil biotic indicators from zone 2 show a strong dominance of epiphytic organisms within all of the biotic communities examined. Foraminifers, molluscs, and ostracodes capable of subsisting in salinities slightly lower than normal marine begin to flourish in this time period, and there is a marked decline in infaunal molluscs. Zone 2 assemblages are replaced around 1900 AD by increased numbers of organisms that typify open-marine conditions and a return to decreased epiphytic assemblages, similar to zone 1. Zone 3 assemblages, however, show some strong dissimilarities from zone 1, including limited infaunal molluscs, increased abundances of the ostracode Malzella floridana, and a significant increase in molluscan faunal richness.

A Global Overview of Exposure Levels and Biological Effects of Trace Elements in Penguins.

PubMed

Espejo, Winfred; Celis, José E; GonzÃlez-Acuña, Daniel; Banegas, Andiranel; Barra, Ricardo; Chiang, Gustavo

2018-01-01

Trace elements are chemical contaminants that can be present almost anywhere on the planet. The study of trace elements in biotic matrices is a topic of great relevance for the implications that it can have on wildlife and human health. Penguins are very useful, since they live exclusively in the Southern Hemisphere and represent about 90% of the biomass of birds of the Southern Ocean. The levels of trace elements (dry weight) in different biotic matrices of penguins were reviewed here. Maps of trace element records in penguins were included. Data on exposure and effects of trace elements in penguins were collected from the literature. The most reported trace elements in penguins are aluminum, arsenic, cadmium, lead, mercury, copper, zinc, and manganese. Trace elements have been measured in 11 of the 18 species of penguins. The most studied biotic matrices are feathers and excreta. Most of the studies have been performed in Antarctica and subantarctic Islands. Little is known about the interaction among metals, which could provide better knowledge about certain mechanisms of detoxification in penguins. Future studies of trace elements in penguins must incorporate other metals such as vanadium, cobalt, nickel, and chromium. Data of metals in the species such as Eudyptes pachyrhynchus, Eudyptes moseleyi, Eudyptes sclateri, Eudyptes robustus, Eudyptes schlegeli, Spheniscus demersus, Spheniscus mendiculus, and Megadyptes antipodes are urged. It is important to correlate levels of metals in different biotic matrices with the effects on different species and in different geographic locations.

Cretaceous-Tertiary boundary in the Antarctic: Climatic cooling precedes biotic crisis

NASA Technical Reports Server (NTRS)

Stott, Lowell D.; Kennett, James P.

1988-01-01

Stable isotopic investigations were conducted on calcareous microfossils across two deep sea Cretaceous-Tertiary boundary sequences on Maud Rise, Weddell Sea, Antarctica. The boundary is taken at the level of massive extinctions in calcareous planktonic microfossils, and coincides with a sharp lithologic change from pure calcareous ooze to calcareous ooze with a large volcanic clay component. The uppermost Maestrichtian is marked by a long-term decrease in delta value of 0 to 18 which spans most of the lower and middle A. mayaroensis Zone and represents a warming trend which culminated in surface water temperatures of about 16 C. At approximately 3 meters below the K-T boundary this warming trend terminates abruptly and benthic and planktonic isotopic records exhibit a rapid increase in delta value of 0 to 18 that continues up to the K-T boundary. The trend towards cooler surface water temperatures stops abruptly at the K-T boundary and delta value of 0 to 18 values remain relatively stable through the Paleocene. Comparison of the Antarctic sequence with the previously documented deep sea records in the South Atlantic reveal shifts of similar magnitude in the latest Maestrichtian. It is indicated that the Southern Ocean underwent the most significant, and apparently permanent, climatic change. The latest Cretaceous oxygen isotopic shift recorded at Maud Rise and other deep sea sites is similar in magnitude to large positive delta valve of 0 to 18 shifts in the middle Eocene, at the Eocene/Oligocene boundary and in the middle Miocene that marked large scale climatic transitions which ultimately lead to cryospheric development of the Antarctic. The climatic shift at the end of the Cretaceous represents one of the most significant climatic transitions recorded in the latest Phanerozoic and had a profound effect on global climate as well as oceanic circulation.

Nutrient concentrations and their relations to the biotic integrity of wadeable streams in Wisconsin

USGS Publications Warehouse

Robertson, Dale M.; Graczyk, David J.; Garrison, Paul J.; Wang, Lizhu; LaLiberte, Gina; Bannerman, Roger

2006-01-01

Excessive nutrient (phosphorus and nitrogen) loss from watersheds is frequently associated with degraded water quality in streams. To reduce this loss, agricultural performance standards and regulations for croplands and livestock operations are being proposed by various States. In addition, the U.S. Environmental Protection Agency is establishing regionally based nutrient criteria that can be refined by each State to determine whether actions are needed to improve a stream's water quality. More confidence in the environmental benefits of the proposed performance standards and nutrient criteria will be possible with a better understanding of the biotic responses to a range of nutrient concentrations in different environmental settings. The U.S. Geological Survey and the Wisconsin Department of Natural Resources collected data from 240 wadeable streams throughout Wisconsin to: 1) describe how nutrient concentrations and biotic-community structure vary throughout the State; 2) determine which environmental characteristics are most strongly related to the distribution of nutrient concentrations; 3) determine reference water-quality and biotic conditions for different areas of the State; 4) determine how the biotic community of streams in different areas of the State respond to changes in nutrient concentrations; 5) determine the best regionalization scheme to describe the patterns in reference conditions and the responses in water quality and the biotic community; and 6) develop new indices to estimate nutrient concentrations in streams from a combination of biotic indices. The ultimate goal of this study is to provide the information needed to guide the development of regionally based nutrient criteria for Wisconsin streams. For total nitrogen (N) and suspended chlorophyll (SCHL) concentrations and water clarity, regional variability in reference conditions and in the responses in water quality to changes in land use are best described by subdividing wadeable streams into two categories: streams in areas with high clay-content soils (Environmental Phosphorus Zone 3, EPZ 3) and streams throughout the rest of the State. The regional variability in the response in total phosphorus (P) concentrations is also best described by subdividing the streams into these two categories; however, little consistent variability was found in reference P concentrations in streams throughout the State. Reference P concentrations are smilar throughout the State (0.03-0.04 mg/L). Reference N concentrations are divided into two categories: 0.6-0.7 mg/L in all streams except those in areas with high clay-content soils, where 0.4 mg/L is more appropriate. Reference SCHL concentrations are divided into two categories: 1.2-1.7 ?g/L in all streams except those in areas with high clay-content soils, where 1.0 ?g/L may be more appropriate. Reference water clarity is divided into two categories: streams in areas with high clay-content soils with a lower reference water clarity (Secchi tube depth, SD, of about 110 cm) and streams throughout the rest of the State (SD greater than or equal to about 115 cm). For each category of the biotic community (SCHL and benthic chlorophyll a concentrations (BCHL), periphytic diatoms, macroinvertebrates, and fish), a few biotic indices were more related to differences in nutrient concentrations than were others. For each of the indices more strongly related to nutrient concentrations, reference conditions were obtained by determining values corresponding to the worst 75th percentile value from a subset of minimally impacted streams (streams having reference nutrient concentrations). By examining the biotic community in streams having either reference P or N concentrations but not both, the relative importance of these two nutrients was determined. For SCHL, P was the more important limiting nutrient; however, for BCHL and all macroinvertebrate indices, it appears that N was the more important nutrient when concent

Benzene-contaminated groundwater remediation using calcium peroxide nanoparticles: synthesis and process optimization.

PubMed

Mosmeri, Hamid; Alaie, Ebrahim; Shavandi, Mahmoud; Dastgheib, Seyed Mohammad Mehdi; Tasharrofi, Saeideh

2017-08-14

Nano-size calcium peroxide (nCaO 2 ) is an appropriate oxygen source which can meet the needs of in situ chemical oxidation (ISCO) for contaminant remediation from groundwater. In the present study, an easy to handle procedure for synthesis of CaO 2 nanoparticles has been investigated. Modeling and optimization of synthesis process was performed by application of response surface methodology (RSM) and central composite rotatable design (CCRD) method. Synthesized nanoparticles were characterized by XRD and FESEM techniques. The optimal synthesis conditions were found to be 5:1, 570 rpm and 10 °C for H 2 O 2 :CaSO 2 ratio, mixing rate and reaction temperature, respectively. Predicted values showed to be in good agreement with experimental results (R 2 values were 0.915 and 0.965 for CaO 2 weight and nanoparticle size, respectively). To study the efficiency of synthesized nanoparticles for benzene removal from groundwater, batch experiments were applied in biotic and abiotic (chemical removal) conditions by 100, 200, 400, and 800 mg/L of nanoparticles within 70 days. Results indicated that application of 400 mg/L of CaO 2 in biotic condition was able to remediate benzene completely from groundwater after 60 days. Furthermore, comparison of biotic and abiotic experiments showed a great potential of microbial stimulation using CaO 2 nanoparticles in benzene remediation from groundwater.

A comparison of algal, macroinvertebrate, and fish assemblage indices for assessing low-level nutrient enrichment in wadeable Ozark streams

USGS Publications Warehouse

Justus, B.G.; Petersen, J.C.; Femmer, S.R.; Davis, J.V.; Wallace, J.E.

2010-01-01

Biotic indices for algae, macroinvertebrates, and fish assemblages can be effective for monitoring stream enrichment, but little is known regarding the value of the three assemblages for detecting perturbance as a consequence of low-level nutrient enrichment. In the summer of 2006, we collected nutrient and biotic samples from 30 wadeable Ozark streams that spanned a nutrient-concentration gradient from reference to moderately enriched conditions. Seventy-three algal metrics, 62 macroinvertebrate metrics, and 60 fish metrics were evaluated for each of the three biotic indices. After a group of candidate metrics had been identified with multivariate analysis, correlation procedures and scatter plots were used to identify the four metrics having strongest relations to a nutrient index calculated from log transformed and normalized total nitrogen and total phosphorus concentrations. The four metrics selected for each of the three biotic indices were: algae-the relative abundance of most tolerant diatoms, the combined relative abundance of three species of Cymbella, mesosaprobic algae percent taxa richness, and the relative abundance of diatoms that are obligate nitrogen heterotrophs; macroinvertebrate-the relative abundance of intolerant organisms, Baetidae relative abundance, moderately tolerant taxa richness, and insect biomass; fish-herbivore and detritivore taxa richness, pool species relative abundance, fish catch per unit effort, and black bass (Micropterus spp.) relative abundance. All three biotic indices were negatively correlated to nutrient concentrations but the algal index had a higher correlation (rho = -0.89) than did the macroinvertebrate and fish indices (rho = -0.63 and -0.58, respectively). Biotic index scores were lowest and nutrient concentrations were highest for streams with basins having the highest poultry and cattle production. Because of the availability of litter for fertilizer and associated increases in grass and hay production, cattle feeding capacity increases with poultry production. Studies are needed that address the synergistic effect of poultry and cattle production on Ozark streams in high production areas before ecological risks can be adequately addressed.

The Real Difference between Biotic and Abiotic Methane

NASA Astrophysics Data System (ADS)

Cao, X.; Bao, H.; Peng, Y.

2017-12-01

Methane has both biotic and abiotic origins, and the identification of these two origins has important implications not only in understanding terrestrial processes but also in searching for extraterrestrial life. Carbon and hydrogen isotopes in methane have been used to identify certain biosignatures, but such efforts often suffer from ambiguity. Recent advancement in our capability in measuring multiply substituted isotopologues of methane (i.e. 13CDH3 and 12CD2H2) has found large 12CD2H2 depletion in abiotic methane. Quantum tunneling has been proposed to account for the apparent abiotic signature. However, quantum tunneling is neither unique to abiotic processes nor consistent with the observed not-so-depleted hydrogen isotope composition. Here we constructed a general kinetic model for methane formation from CO2, and validated it by fitting its parameters to observed 13CDH3, 12CD2H2, and 12CDH3. Our model revealed that the fundamental difference between biotic and abiotic methane isotopic signatures is in the source of hydrogens during methane formation. Hydrogens in biotic methane originate from the stronger carbon-hydrogen and sulfur-hydrogen bonds, while hydrogens in abiotic methane originate from the much weaker metal-hydrogen adsorption bond. This hydrogen source difference results in abiotic methane being more depleted in 12CD2H2 than the biotic one. Our model also shows that the primary kinetic hydrogen isotope effect is at approximately 0.6 for both abiotic and biotic pathways, a normal value further nullifying the role of quantum tunneling. The active and exclusive shuttling of reduced hydrogen via strong chemical bonds like carbon-hydrogen and sulfur-hydrogen in coenzymes is proposed here to be a unique signature of life. In an ironic sense, it is the equilibrated hydrogen isotope composition in the hydrogen donors that distinguishes the living from the non-living.

Mineral Nutrition, Resin Flow and Phloem Phystochemistry in Loblolly Pine

Treesearch

Jefferey M. Warren; H. Lee Allen; Fitzgerald L. Booker

1999-01-01

Southern pine beetles and associated pathogenic fungi represent the largest biotic threat to pine forests in the southeastern USA. The two primary defensive mechanisms of the tree to the beetle-fungal complex are the primary oleoresin flow and the concentrations of preformed and induced secondary compounds. We compared oleoresin flow and concentrations of phloem...

Long-term research at the USDA Forest Service's experimental forests and ranges.

Treesearch

Ariel D. Lugo; Frederick J. Swanson; Olga Ramos González; Mary Beth Adams; Brian Palik; Ronald E. Thill; Dale G. Brockway; Christel Kern; Richard Woodsmith; Robert Musselman

2006-01-01

The network of experimental forests and ranges administered by the U.S. Department of Agriculture Forest Service consists of 77 properties that are representative of most forest cover types and many ecological regions in the Nation. Established as early as 1908, these sites maintain exceptional, long-term databases on environmental dynamics and biotic responses. Early...

Biotic agents that damage black locust in Hungary

Treesearch

Jozsef Toth

2003-01-01

Black locust (Robinia pseudoacacia) plays an important role in Hungarian forestry and represents 21.6% of the total forested area (370 thousand hectares); approximately 19.2% of the area in Hungary is forested. Black locust forests have increased by more than one percent over the last 5 years demonstrating that it is a preferred tree species...

CHARTING A COURSE TOWARD DIAGNOSTIC MONITORING: A CONTINUING REVIEW OF CORAL REEF ATTRIBUTES AND A RESEARCH STRATEGY FOR CREATING CORAL REEF INDEXES OF BIOTIC INTEGRITY. (R825284)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

On the abundance of extraterrestrial life after the Kepler mission

NASA Astrophysics Data System (ADS)

Wandel, Amri

2015-07-01

The data recently accumulated by the Kepler mission have demonstrated that small planets are quite common and that a significant fraction of all stars may have an Earth-like planet within their habitable zone. These results are combined with a Drake-equation formalism to derive the space density of biotic planets as a function of the relatively modest uncertainty in the astronomical data and of the (yet unknown) probability for the evolution of biotic life, F b. I suggest that F b may be estimated by future spectral observations of exoplanet biomarkers. If F b is in the range 0.001-1, then a biotic planet may be expected within 10-100 light years from Earth. Extending the biotic results to advanced life I derive expressions for the distance to putative civilizations in terms of two additional Drake parameters - the probability for evolution of a civilization, F c, and its average longevity. For instance, assuming optimistic probability values (F b~F c~1) and a broadcasting longevity of a few thousand years, the likely distance to the nearest civilizations detectable by searching for intelligent electromagnetic signals is of the order of a few thousand light years. The probability of detecting intelligent signals with present and future radio telescopes is calculated as a function of the Drake parameters. Finally, I describe how the detection of intelligent signals would constrain the Drake parameters.

Land-use intensification causes multitrophic homogenization of grassland communities

NASA Astrophysics Data System (ADS)

Gossner, Martin M.; Lewinsohn, Thomas M.; Kahl, Tiemo; Grassein, Fabrice; Boch, Steffen; Prati, Daniel; Birkhofer, Klaus; Renner, Swen C.; Sikorski, Johannes; Wubet, Tesfaye; Arndt, Hartmut; Baumgartner, Vanessa; Blaser, Stefan; Blüthgen, Nico; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Jorge, Leonardo Ré; Jung, Kirsten; Keyel, Alexander C.; Klein, Alexandra-Maria; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Müller, Jörg; Overmann, Jörg; Pašalić, Esther; Penone, Caterina; Perović, David J.; Purschke, Oliver; Schall, Peter; Socher, Stephanie A.; Sonnemann, Ilja; Tschapka, Marco; Tscharntke, Teja; Türke, Manfred; Venter, Paul Christiaan; Weiner, Christiane N.; Werner, Michael; Wolters, Volkmar; Wurst, Susanne; Westphal, Catrin; Fischer, Markus; Weisser, Wolfgang W.; Allan, Eric

2016-12-01

Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.

Land-use intensification causes multitrophic homogenization of grassland communities.

PubMed

Gossner, Martin M; Lewinsohn, Thomas M; Kahl, Tiemo; Grassein, Fabrice; Boch, Steffen; Prati, Daniel; Birkhofer, Klaus; Renner, Swen C; Sikorski, Johannes; Wubet, Tesfaye; Arndt, Hartmut; Baumgartner, Vanessa; Blaser, Stefan; Blüthgen, Nico; Börschig, Carmen; Buscot, Francois; Diekötter, Tim; Jorge, Leonardo Ré; Jung, Kirsten; Keyel, Alexander C; Klein, Alexandra-Maria; Klemmer, Sandra; Krauss, Jochen; Lange, Markus; Müller, Jörg; Overmann, Jörg; Pašalić, Esther; Penone, Caterina; Perović, David J; Purschke, Oliver; Schall, Peter; Socher, Stephanie A; Sonnemann, Ilja; Tschapka, Marco; Tscharntke, Teja; Türke, Manfred; Venter, Paul Christiaan; Weiner, Christiane N; Werner, Michael; Wolters, Volkmar; Wurst, Susanne; Westphal, Catrin; Fischer, Markus; Weisser, Wolfgang W; Allan, Eric

2016-12-08

Land-use intensification is a major driver of biodiversity loss. Alongside reductions in local species diversity, biotic homogenization at larger spatial scales is of great concern for conservation. Biotic homogenization means a decrease in β-diversity (the compositional dissimilarity between sites). Most studies have investigated losses in local (α)-diversity and neglected biodiversity loss at larger spatial scales. Studies addressing β-diversity have focused on single or a few organism groups (for example, ref. 4), and it is thus unknown whether land-use intensification homogenizes communities at different trophic levels, above- and belowground. Here we show that even moderate increases in local land-use intensity (LUI) cause biotic homogenization across microbial, plant and animal groups, both above- and belowground, and that this is largely independent of changes in α-diversity. We analysed a unique grassland biodiversity dataset, with abundances of more than 4,000 species belonging to 12 trophic groups. LUI, and, in particular, high mowing intensity, had consistent effects on β-diversity across groups, causing a homogenization of soil microbial, fungal pathogen, plant and arthropod communities. These effects were nonlinear and the strongest declines in β-diversity occurred in the transition from extensively managed to intermediate intensity grassland. LUI tended to reduce local α-diversity in aboveground groups, whereas the α-diversity increased in belowground groups. Correlations between the β-diversity of different groups, particularly between plants and their consumers, became weaker at high LUI. This suggests a loss of specialist species and is further evidence for biotic homogenization. The consistently negative effects of LUI on landscape-scale biodiversity underscore the high value of extensively managed grasslands for conserving multitrophic biodiversity and ecosystem service provision. Indeed, biotic homogenization rather than local diversity loss could prove to be the most substantial consequence of land-use intensification.

Unlocking the relationship of biotic integrity of impaired waters to anthropogenic stresses.

PubMed

Novotny, Vladimir; Bartosová, Alena; O'Reilly, Neal; Ehlinger, Timothy

2005-01-01

The Clean Water Act expressed its goals in terms of restoring and preserving the physical, chemical and biological integrity of the Nation's waters. Integrity has been defined as the ability of the water body's ecological system to support and maintain a balanced integrated, adaptive community of organisms comparable to that of a natural biota of the region. Several indices of biotic integrity (IBIs) have been developed to measure quantitatively the biotic composition and, hence, the integrity. Integrity can be impaired by discharges of pollutants from point and nonpoint sources and by other pollution-related to watershed/landscape and channel stresses, including channel and riparian zone modifications and habitat impairment. Various models that link the stressors to the biotic assessment endpoints, i.e., the IBIs, have been presented and discussed. Simple models that link IBIs directly to single or multiple surrogate stressors such as percent imperviousness are inadequate because they may not represent a true cause-effect proximate relationship. Furthermore, some surrogate landscape parameters are irreversible and the relationships cannot be used for development of plans for restoration of the water body integrity. A concept of a layered hierarchical model that will link the watershed, landscape and stream morphology pollution stressors to the biotic assessment endpoints (IBIs) is described. The key groups of structural components of the model are: IBIs and their metrics in the top layer, chemical water and sediment risks and a habitat quality index in the layer below, in-stream concentrations in water and sediments and channel/habitat impairment parameters in the third layer, and watershed/landscaper pollution generating stressors, land use change rates, and hydrology in the lowest layer of stressors. A modified and expanded Maximum Species Richness concept is developed and used to reveal quantitatively the functional relationships between the top two layers of the structural components and parameters of the model.

Determining the factors affecting the distribution of Muscari latifolium, an endemic plant of Turkey, and a mapping species distribution model.

PubMed

Yilmaz, Hatice; Yilmaz, Osman Yalçın; Akyüz, Yaşar Feyza

2017-02-01

Species distribution modeling was used to determine factors among the large predictor candidate data set that affect the distribution of Muscari latifolium , an endemic bulbous plant species of Turkey, to quantify the relative importance of each factor and make a potential spatial distribution map of M. latifolium . Models were built using the Boosted Regression Trees method based on 35 presence and 70 absence records obtained through field sampling in the Gönen Dam watershed area of the Kazdağı Mountains in West Anatolia. Large candidate variables of monthly and seasonal climate, fine-scale land surface, and geologic and biotic variables were simplified using a BRT simplifying procedure. Analyses performed on these resources, direct and indirect variables showed that there were 14 main factors that influence the species' distribution. Five of the 14 most important variables influencing the distribution of the species are bedrock type, Quercus cerris density, precipitation during the wettest month, Pinus nigra density, and northness. These variables account for approximately 60% of the relative importance for determining the distribution of the species. Prediction performance was assessed by 10 random subsample data sets and gave a maximum the area under a receiver operating characteristic curve (AUC) value of 0.93 and an average AUC value of 0.8. This study provides a significant contribution to the knowledge of the habitat requirements and ecological characteristics of this species. The distribution of this species is explained by a combination of biotic and abiotic factors. Hence, using biotic interaction and fine-scale land surface variables in species distribution models improved the accuracy and precision of the model. The knowledge of the relationships between distribution patterns and environmental factors and biotic interaction of M. latifolium can help develop a management and conservation strategy for this species.

General relationships between consumer dispersal, resource dispersal and metacommunity diversity.

PubMed

Haegeman, Bart; Loreau, Michel

2014-02-01

One of the central questions of metacommunity theory is how dispersal of organisms affects species diversity. Here, we show that the diversity-dispersal relationship should not be studied in isolation of other abiotic and biotic flows in the metacommunity. We study a mechanistic metacommunity model in which consumer species compete for an abiotic or biotic resource. We consider both consumer species specialised to a habitat patch, and generalist species capable of using the resource throughout the metacommunity. We present analytical results for different limiting values of consumer dispersal and resource dispersal, and complement these results with simulations for intermediate dispersal values. Our analysis reveals generic patterns for the combined effects of consumer and resource dispersal on the metacommunity diversity of consumer species, and shows that hump-shaped relationships between local diversity and dispersal are not universal. Diversity-dispersal relationships can also be monotonically increasing or multimodal. Our work is a new step towards a general theory of metacommunity diversity integrating dispersal at multiple trophic levels. © 2013 John Wiley & Sons Ltd/CNRS.

Global carbon - nitrogen - phosphorus cycle interactions: A key to solving the atmospheric CO2 balance problem?

NASA Technical Reports Server (NTRS)

Peterson, B. J.; Mellillo, J. M.

1984-01-01

If all biotic sinks of atmospheric CO2 reported were added a value of about 0.4 Gt C/yr would be found. For each category, a very high (non-conservative) estimate was used. This still does not provide a sufficient basis for achieving a balance between the sources and sinks of atmospheric CO2. The bulk of the discrepancy lies in a combination of errors in the major terms, the greatest being in a combination of errors in the major terms, the greatest being in the net biotic release and ocean uptake segments, but smaller errors or biases may exist in calculations of the rate of atmospheric CO2 increase and total fossil fuel use as well. The reason why biotic sinks are not capable of balancing the CO2 increase via nutrient-matching in the short-term is apparent from a comparison of the stoichiometry of the sources and sinks. The burning of fossil fuels and forest biomass releases much more CO2-carbon than is sequestered as organic carbon.

Climate and vegetational regime shifts in the late Paleozoic ice age earth.

PubMed

DiMichele, W A; Montañez, I P; Poulsen, C J; Tabor, N J

2009-03-01

The late Paleozoic earth experienced alternation between glacial and non-glacial climates at multiple temporal scales, accompanied by atmospheric CO2 fluctuations and global warming intervals, often attended by significant vegetational changes in equatorial latitudes of Pangaea. We assess the nature of climate-vegetation interaction during two time intervals: middle-late Pennsylvanian transition and Pennsylvanian-Permian transition, each marked by tropical warming and drying. In case study 1, there is a catastrophic intra-biomic reorganization of dominance and diversity in wetland, evergreen vegetation growing under humid climates. This represents a threshold-type change, possibly a regime shift to an alternative stable state. Case study 2 is an inter-biome dominance change in western and central Pangaea from humid wetland and seasonally dry to semi-arid vegetation. Shifts between these vegetation types had been occurring in Euramerican portions of the equatorial region throughout the late middle and late Pennsylvanian, the drier vegetation reaching persistent dominance by Early Permian. The oscillatory transition between humid and seasonally dry vegetation appears to demonstrate a threshold-like behavior but probably not repeated transitions between alternative stable states. Rather, changes in dominance in lowland equatorial regions were driven by long-term, repetitive climatic oscillations, occurring with increasing intensity, within overall shift to seasonal dryness through time. In neither case study are there clear biotic or abiotic warning signs of looming changes in vegetational composition or geographic distribution, nor is it clear that there are specific, absolute values or rates of environmental change in temperature, rainfall distribution and amount, or atmospheric composition, approach to which might indicate proximity to a terrestrial biotic-change threshold.

The Role of County Surveyors and County Drainage Boards in Addressing Water Quality.

PubMed

Dunn, Mike; Mullendore, Nathan; de Jalon, Silvestre Garcia; Prokopy, Linda Stalker

2016-06-01

Water quality problems stemming from the Midwestern U.S. agricultural landscape have been widely recognized and documented. The Midwestern state of Indiana contains tens of thousands of miles of regulated drains that represent biotic communities that comprise the headwaters of the state's many rivers and creeks. Traditional management, however, reduces these waterways to their most basic function as conveyances, ignoring their role in the ecosystem as hosts for biotic and abiotic processes that actively regulate the fate and transport of nutrients and farm chemicals. Novel techniques and practices such as the two-stage ditch, denitrifying bioreactor, and constructed wetlands represent promising alternatives to traditional management approaches, yet many of these tools remain underutilized. To date, conservation efforts and research have focused on increasing the voluntary adoption of practices among agricultural producers. Comparatively little attention has been paid to the roles of the drainage professionals responsible for the management of waterways and regulated drains. To address this gap, we draw on survey responses from 39 county surveyors and 85 drainage board members operating in Indiana. By examining the backgrounds, attitudes, and actions of these individuals, we consider their role in advocating and implementing novel conservation practices.

Potential for DNA-based ID of Great Lakes fauna: Species inventories vs. barcode libraries

EPA Science Inventory

DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However the abil...

[Validation of two indices of biological integrity (IBI) for the Angulo River subbasin in Central Mexico].

PubMed

Ramírez-Herrejón, Juan Pablo; Mercado-Silva, Norman; Medina-Nava, Martina; Domínguez-Domínguez, Omar

2012-12-01

Efforts to halt freshwater ecosystem degradation in central Mexico can benefit from using bio-monitoring tools that reflect the condition of their biotic integrity. We analyzed the applicability of two fish-based indices of biotic integrity using data from lotic and lentic systems in the Angulo River subbasin (Lerma-Chapala basin). Both independent data from our own collections during two consecutive years, and existing information detailing the ecological attributes of each species, were used to calculate indices of biological integrity for 16 sites in lotic and lentic habitats. We assessed environmental quality by combining independent evaluations water and habitat quality for each site. We found sites with poor, regular and good biotic integrity. Our study did not find sites with good environmental quality. Fish-based IBI scores were strongly and significantly correlated with scores from independent environmental assessment techniques. IBI scores were adequate at representing environmental conditions in most study sites. These results expand the area where a lotic system fish-based IBI can be used, and constitute an initial validation of a lentic system fish-based IBI. Our results suggest that these bio-monitoring tools can be used in future conservation efforts in freshwater ecosystems in the Middle Lerma Basin.

Multivariate analysis of scale-dependent associations between bats and landscape structure

USGS Publications Warehouse

Gorresen, P.M.; Willig, M.R.; Strauss, R.E.

2005-01-01

The assessment of biotic responses to habitat disturbance and fragmentation generally has been limited to analyses at a single spatial scale. Furthermore, methods to compare responses between scales have lacked the ability to discriminate among patterns related to the identity, strength, or direction of associations of biotic variables with landscape attributes. We present an examination of the relationship of population- and community-level characteristics of phyllostomid bats with habitat features that were measured at multiple spatial scales in Atlantic rain forest of eastern Paraguay. We used a matrix of partial correlations between each biotic response variable (i.e., species abundance, species richness, and evenness) and a suite of landscape characteristics to represent the multifaceted associations of bats with spatial structure. Correlation matrices can correspond based on either the strength (i.e., magnitude) or direction (i.e., sign) of association. Therefore, a simulation model independently evaluated correspondence in the magnitude and sign of correlations among scales, and results were combined via a meta-analysis to provide an overall test of significance. Our approach detected both species-specific differences in response to landscape structure and scale dependence in those responses. This matrix-simulation approach has broad applicability to ecological situations in which multiple intercorrelated factors contribute to patterns in space or time. ?? 2005 by the Ecological Society of America.

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

PubMed Central

Walter, Andreas; Knapp, Brigitte A.; Farbmacher, Theresa; Ebner, Christian; Insam, Heribert; Franke‐Whittle, Ingrid H.

2012-01-01

Summary To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year. PMID:22950603

The 'Green Revolution' dwarfing genes play a role in disease resistance in Triticum aestivum and Hordeum vulgare.

PubMed

Saville, R J; Gosman, N; Burt, C J; Makepeace, J; Steed, A; Corbitt, M; Chandler, E; Brown, J K M; Boulton, M I; Nicholson, P

2012-02-01

The Green Revolution dwarfing genes, Rht-B1b and Rht-D1b, encode mutant forms of DELLA proteins and are present in most modern wheat varieties. DELLA proteins have been implicated in the response to biotic stress in the model plant, Arabidopsis thaliana. Using defined wheat Rht near-isogenic lines and barley Sln1 gain of function (GoF) and loss of function (LoF) lines, the role of DELLA in response to biotic stress was investigated in pathosystems representing contrasting trophic styles (biotrophic, hemibiotrophic, and necrotrophic). GoF mutant alleles in wheat and barley confer a resistance trade-off with increased susceptibility to biotrophic pathogens and increased resistance to necrotrophic pathogens whilst the converse was conferred by a LoF mutant allele. The polyploid nature of the wheat genome buffered the effect of single Rht GoF mutations relative to barley (diploid), particularly in respect of increased susceptibility to biotrophic pathogens. A role for DELLA in controlling cell death responses is proposed. Similar to Arabidopsis, a resistance trade-off to pathogens with contrasting pathogenic lifestyles has been identified in monocotyledonous cereal species. Appreciation of the pleiotropic role of DELLA in biotic stress responses in cereals has implications for plant breeding.

A New Sebecid from the Paleogene of Brazil and the Crocodyliform Radiation after the K–Pg Boundary

PubMed Central

Kellner, Alexander W. A.; Pinheiro, André E. P.; Campos, Diogenes A.

2014-01-01

A new crocodyliform, Sahitisuchus fluminensis gen. et sp. nov., is described based on a complete skull, lower jaw and anterior cervical vertebrae collected in the São José de Itaboraí Basin of Rio de Janeiro, Brazil. The specimen is one of the best preserved crocodyliforms from Paleocene deposits recovered so far and represents a sebecosuchian, one of the few clades that survived the Cretaceous-Paleogene biotic crisis. The new taxon is found in the same deposit as an alligatoroid, a group that experienced large diversification in the Paleogene. The sebecosuchian record suggests that after the Cretaceous-Paleogene biotic crisis, the less specialized members of this clade characterized by a higher number of teeth compared to the baurusuchid sebecosuchians survived, some having terrestrial habits while others developed a semi-aquatic life style (e.g., Lorosuchus). Starting in the Eocene, sebecid sebecosuchians became specialized with a more accentuated oreinirostry as observed in Sebecus and in Langstonia, but not showing the typical reduced dentition developed by the Cretaceous baurusuchid sebecosuchians. The basal position of Barinasuchus arveloi, a high-snouted Miocene sebecid, indicates the occurrence of an independent lineage sometime after the K-Pg biotic crisis that developed accentuated oreinirostry, suggesting a more complex history of the post-K-Pg crocodyliform radiation. PMID:24454686

A new sebecid from the paleogene of Brazil and the crocodyliform radiation after the K-Pg boundary.

PubMed

Kellner, Alexander W A; Pinheiro, André E P; Campos, Diogenes A

2014-01-01

A new crocodyliform, Sahitisuchus fluminensis gen. et sp. nov., is described based on a complete skull, lower jaw and anterior cervical vertebrae collected in the São José de Itaboraí Basin of Rio de Janeiro, Brazil. The specimen is one of the best preserved crocodyliforms from Paleocene deposits recovered so far and represents a sebecosuchian, one of the few clades that survived the Cretaceous-Paleogene biotic crisis. The new taxon is found in the same deposit as an alligatoroid, a group that experienced large diversification in the Paleogene. The sebecosuchian record suggests that after the Cretaceous-Paleogene biotic crisis, the less specialized members of this clade characterized by a higher number of teeth compared to the baurusuchid sebecosuchians survived, some having terrestrial habits while others developed a semi-aquatic life style (e.g., Lorosuchus). Starting in the Eocene, sebecid sebecosuchians became specialized with a more accentuated oreinirostry as observed in Sebecus and in Langstonia, but not showing the typical reduced dentition developed by the Cretaceous baurusuchid sebecosuchians. The basal position of Barinasuchus arveloi, a high-snouted Miocene sebecid, indicates the occurrence of an independent lineage sometime after the K-Pg biotic crisis that developed accentuated oreinirostry, suggesting a more complex history of the post-K-Pg crocodyliform radiation.

Catchment-scale determinants of nonindigenous minnow richness in the eastern United States

USGS Publications Warehouse

Peoples, Brandon K.; Midway, Stephen R.; DeWeber, Jefferson T.; Wagner, Tyler

2018-01-01

Understanding the drivers of biological invasions is critical for preserving aquatic biodiversity. Stream fishes make excellent model taxa for examining mechanisms driving species introduction success because their distributions are naturally limited by catchment boundaries. In this study, we compared the relative importance of catchment-scale abiotic and biotic predictors of native and nonindigenous minnow (Cyprinidae) richness in 170 catchments throughout the eastern United States. We compared historic and contemporary cyprinid distributional data to determine catchment-wise native/nonindigenous status for 152 species. Catchment-scale model predictor variables described natural (elevation, precipitation, flow accumulation) and anthropogenic (developed land cover, number of dams) abiotic features, as well as native congener richness. Native congener richness may represent either biotic resistance via interspecific competition, or trait preadaptation according to Darwin's naturalisation hypothesis. We used generalised linear mixed models to examine evidence supporting the relative roles of abiotic and biotic predictors of cyprinid introduction success. Native congener richness was positively correlated with nonindigenous cyprinid richness and was the most important variable predicting nonindigenous cyprinid richness. Mean elevation had a weak positive effect, and effects of other abiotic factors were insignificant and less important. Our results suggest that at this spatial scale, trait preadaptation may be more important than intrageneric competition for determining richness of nonindigenous fishes.

The ‘Green Revolution’ dwarfing genes play a role in disease resistance in Triticum aestivum and Hordeum vulgare

PubMed Central

Saville, R. J.; Gosman, N.; Burt, C. J.; Makepeace, J.; Steed, A.; Corbitt, M.; Chandler, E.; Brown, J. K. M.; Boulton, M. I.; Nicholson, P.

2012-01-01

The Green Revolution dwarfing genes, Rht-B1b and Rht-D1b, encode mutant forms of DELLA proteins and are present in most modern wheat varieties. DELLA proteins have been implicated in the response to biotic stress in the model plant, Arabidopsis thaliana. Using defined wheat Rht near-isogenic lines and barley Sln1 gain of function (GoF) and loss of function (LoF) lines, the role of DELLA in response to biotic stress was investigated in pathosystems representing contrasting trophic styles (biotrophic, hemibiotrophic, and necrotrophic). GoF mutant alleles in wheat and barley confer a resistance trade-off with increased susceptibility to biotrophic pathogens and increased resistance to necrotrophic pathogens whilst the converse was conferred by a LoF mutant allele. The polyploid nature of the wheat genome buffered the effect of single Rht GoF mutations relative to barley (diploid), particularly in respect of increased susceptibility to biotrophic pathogens. A role for DELLA in controlling cell death responses is proposed. Similar to Arabidopsis, a resistance trade-off to pathogens with contrasting pathogenic lifestyles has been identified in monocotyledonous cereal species. Appreciation of the pleiotropic role of DELLA in biotic stress responses in cereals has implications for plant breeding. PMID:22090435

Potential for DNA-based identification of Great Lakes fauna: Match and mismatch between taxa inventories and DNA barcode libraries

EPA Science Inventory

DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to biotic condition assessment and non-native species early-detection monitoring. However, the abi...

New methods for modeling stream temperature using high resolution LiDAR, solar radiation analysis and flow accumulated values

EPA Science Inventory

In-stream temperature directly effects a variety of biotic organisms, communities and processes. Changes in stream temperature can render formally suitable habitat unsuitable for aquatic organisms, particularly native cold water species that are not able to adjust. In order to an...

FISH AND AMPHIBIAN TOLERANCE VALUES AND AN ASSEMBLAGE TOLERANCE INDEX FOR STEAMS AND RIVERS IN THE WESTERN USA

EPA Science Inventory

Aquatic species' tolerances to overall human disturbance are key components of biological assessments of aquatic ecosystems. These tolerance classifications enable development of metrics for use in multimetric indexes, such as the index of biotic integrity (IBI). Usually, species...

Inversion analysis of estimating interannual variability and its uncertainties in biotic and abiotic parameters of a parsimonious physiologically based model after wind disturbance

NASA Astrophysics Data System (ADS)

Toda, M.; Yokozawa, M.; Richardson, A. D.; Kohyama, T.

2011-12-01

The effects of wind disturbance on interannual variability in ecosystem CO2 exchange have been assessed in two forests in northern Japan, i.e., a young, even-aged, monocultured, deciduous forest and an uneven-aged mixed forest of evergreen and deciduous trees, including some over 200 years old using eddy covariance (EC) measurements during 2004-2008. The EC measurements have indicated that photosynthetic recovery of trees after a huge typhoon occurred during early September in 2004 activated annual carbon uptake of both forests due to changes in physiological response of tree leaves during their growth stages. However, little have been resolved about what biotic and abiotic factors regulated interannual variability in heat, water and carbon exchange between an atmosphere and forests. In recent years, an inverse modeling analysis has been utilized as a powerful tool to estimate biotic and abiotic parameters that might affect heat, water and CO2 exchange between the atmosphere and forest of a parsimonious physiologically based model. We conducted the Bayesian inverse model analysis for the model with the EC measurements. The preliminary result showed that the above model-derived NEE values were consistent with observed ones on the hourly basis with optimized parameters by Baysian inversion. In the presentation, we would examine interannual variability in biotic and abiotic parameters related to heat, water and carbon exchange between the atmosphere and forests after disturbance by typhoon.

Historical variability in fire at the ponderosa pine - northern Great Plains prairie ecotone, southeastern Black Hills, South Dakota

Treesearch

Peter M. Brown; Carolyn Hull Sieg

1999-01-01

Ecotones are boundaries between plant assemblages that can represent a physiological or competitive limit of species’ local distributions, usually through one or more biotic or abiotic constraints on species’ resource requirements. However, ecotones also result from the effects of chronic or episodic disturbances, and changes in disturbance regimes may have profound...

Enantiomer fractions of chlordane components in sediment from U.S. Geological Survey sites in lakes and rivers

USGS Publications Warehouse

Ulrich, E.M.; Foreman, W.T.; Van Metre, P.C.; Wilson, J.T.; Rounds, S.A.

2009-01-01

Spatial, temporal, and sediment-type trends in enantiomer signatures were evaluated for cis- and trans-chlordane (CC, TC) in archived core, suspended, and surficial-sediment samples from six lake, reservoir, and river sites across the United States. The enantiomer fractions (EFs) measured in these samples are in good agreement with those reported for sediment, soil, and air samples in previous studies. The chlordane EFs were generally close to the racemic value of 0.5, with CC values ranging from 0.493 to 0.527 (usually >0.5) and TC values from 0.463 to 0.53 (usually <0.5). EF changes with core depth were detected for TC and CC in some cores, with the most non-racemic values near the top of the core. Surficial and suspended sediments generally have EF values similar to the top core layers but are often more non-racemic, indicating that enantioselective degradation is occurring before soils are eroded and deposited into bottom sediments. We hypothesize that rapid losses (desorption or degradation) from suspended sediments of the more bioavailable chlordane fraction during transport and initial deposition could explain the apparent shift to more racemic EF values in surficial and top core sediments. Near racemic CC and TC in the core profiles suggest minimal alteration of chlordane from biotic degradation, unless it is via non-enantioselective processes. EF values for the heptachlor degradate, heptachlor epoxide (HEPX), determined in surficial sediments from one location only were always non-racemic (EF ??? 0.66), were indicative of substantial biotic processing, and followed reported EF trends.

The Evolutionary Ecology of Biotic Association in a Megadiverse Bivalve Superfamily: Sponsorship Required for Permanent Residency in Sediment

PubMed Central

Li, Jingchun; Ó Foighil, Diarmaid; Middelfart, Peter

2012-01-01

Background Marine lineage diversification is shaped by the interaction of biotic and abiotic factors but our understanding of their relative roles is underdeveloped. The megadiverse bivalve superfamily Galeommatoidea represents a promising study system to address this issue. It is composed of small-bodied clams that are either free-living or have commensal associations with invertebrate hosts. To test if the evolution of this lifestyle dichotomy is correlated with specific ecologies, we have performed a statistical analysis on the lifestyle and habitat preference of 121 species based on 90 source documents. Methodology/Principal Findings Galeommatoidea has significant diversity in the two primary benthic habitats: hard- and soft-bottoms. Hard-bottom dwellers are overwhelmingly free-living, typically hidden within crevices of rocks/coral heads/encrusting epifauna. In contrast, species in soft-bottom habitats are almost exclusively infaunal commensals. These infaunal biotic associations may involve direct attachment to a host, or clustering around its tube/burrow, but all commensals locate within the oxygenated sediment envelope produced by the host’s bioturbation. Conclusions/Significance The formation of commensal associations by galeommatoidean clams is robustly correlated with an abiotic environmental setting: living in sediments (). Sediment-dwelling bivalves are exposed to intense predation pressure that drops markedly with depth of burial. Commensal galeommatoideans routinely attain depth refuges many times their body lengths, independent of siphonal investment, by virtue of their host’s burrowing and bioturbation. In effect, they use their much larger hosts as giant auto-irrigating siphon substitutes. The evolution of biotic associations with infaunal bioturbating hosts may have been a prerequisite for the diversification of Galeommatoidea in sediments and has likely been a key factor in the success of this exceptionally diverse bivalve superfamily. PMID:22905116

Mechanistic Processes Controlling Persistent Changes of Forest Canopy Structure After 2005 Amazon Drought

NASA Astrophysics Data System (ADS)

Shi, Mingjie; Liu, Junjie; Zhao, Maosheng; Yu, Yifan; Saatchi, Sassan

2017-12-01

The long-term impact of Amazonian drought on canopy structure has been observed in ground and remote sensing measurements. However, it is still unclear whether it is caused by biotic (e.g., plant structure damage) or environmental (e.g., water deficiency) factors. We used the Community Land Model version 4.5 (CLM4.5) and radar backscatter observations from SeaWinds Scatterometer on board QuikSCAT (QSCAT) satellite to investigate the relative role of biotic and environmental factors in controlling the forest canopy disturbance and recovery processes after the 2005 Amazonian drought. We validated the CLM4.5 simulation of the drought impact and the recovery of leaf carbon (C) pool, an indicator of canopy structure, over southwestern Amazonia with QSCAT backscatter observations, which are sensitive to canopy structure change. We found that the leaf C pool simulated by CLM4.5 recovered to the 2000-2009 mean level (343 g C m-2) in 3 years after a sharp decrease in 2005, consistent with the QSCAT observed slow recovery. Through sensitivity experiments, we found that the slow C recovery was primarily due to biotic factors represented by the canopy damage and reduction of plant C pools. The recovery of soil water and the coupling between water and C pools, which is an environmental factor, only contributes 24% to the leaf C recovery. The results showed (1) the strength of scatterometer backscatter measurements in capturing canopy damage over tropical forests and in validating C cycle models and (2) the biotic factors play the dominant role in regulating the drought induced disturbance and persistent canopy changes in CLM4.5.

Processes influencing the duration and decline of epizootics in Schistocephalus solidus.

PubMed

Heins, David C; Baker, John A; Green, Dillon M

2011-06-01

The interplay of intermediate host fish and plerocercoids of diphyllobothriidean cestodes results in epizootics that are deceptively simple, but conceal complex biotic and abiotic interactions shaping each event independently. Although general descriptions of epizootics and some details of biotic interactions between enemies are known, much remains to be discovered about the abiotic and biotic forces and their interactions driving epizootics. This study shows that the duration of an epizootic of Schistocephalus solidus was sustained by high prevalence, mean intensity, and PI (parasite index-parasite : host biomass ratio) levels among young-of-the-year and 1-yr-old threespine sticklebacks. Many infections and most parasite growth in young-of-the-year fish apparently occurred under the ice during the winter. Few new infections appear to have occurred among 1-yr-old fish, which may live 2 yr and sometimes 3 yr. The decline of the epizootic occurred as the recruitment of 1 to 2-yr-old hosts decreased significantly, followed by reduced infections of young-of-the-year fish. Thus, a major factor influencing parasite population dynamics was reduced transmission (probability of infection) as a result of overwinter host mortality among 1-yr-old fish. Mega-epizootics, named and described herein, appear to represent a "perfect storm" phenomenon dependent on a particular and rare combination of circumstances. Less extreme and more gradual epizootics may be more common and play out in myriad ways, because of complex abiotic and biotic factors influencing both parasite and host populations. The interplay of parasite and host resulting in reciprocal effects upon one another occurs during both the emergence and decline phases of an epizootic.

Disentangling climatic versus biotic drivers of tree range constraints: Broad scale tradeoffs between climate and competion rarely explain local range boundaries

NASA Astrophysics Data System (ADS)

Anderegg, L. D. L.; Hillerislambers, J.

2016-12-01

Accurate prediction of climatically-driven range shifts requires knowledge of the dominant forces constraining species ranges, because climatically controlled range boundaries will likely behave differently from biotically controlled range boundaries in a changing climate. Yet the roles of climatic constraints (due to species physiological tolerance) versus biotic constraints (caused by species interactions) on geographic ranges are largely unknown, infusing large uncertainty into projections of future range shifts. Plant species ranges across strong climatic gradients such as elevation gradients are often assumed to represent a tradeoff between climatic constraints on the harsh side of the range and biotic constraints (often competitive constraints) on the climatically benign side. To test this assumption, we collected tree cores from across the elevational range of the three dominant tree species inhabiting each of three climatically disparate mountain slopes and assessed climatic versus competitive constraints on growth at each species' range margins. Across all species and mountains, we found evidence for a tradeoff between climatic and competitve growth constraints. We also found that some individual species did show an apparent trade-off between a climatic constraint at one range margin and a competitive constraint at the other. However, even these simple elevation gradients resulted in complex interactions between temperature, moisture, and competitive constraints such that a climate-competition tradeoff did not explain range constraints for many species. Our results suggest that tree species can be constrained by a simple trade-off between climate and competition, but that the intricacies of real world climate gradients complicate the application of this theory even in apparently harsh environments, such as near high elevation tree line.

Aquatic biology in Nederlo Creek, southwestern Wisconsin

USGS Publications Warehouse

Kammerer, Phil A.; Lidwin, R.A.; Mason, J.W.; Narf, R.P.

1982-01-01

The aquatic community is diverse and reasonably stable with little indication of environmental disturbance. Aquatic macrophyte population (dominated by Ranunculus aquatilis L., Veronica catenata Penn., and Nasturtium offlcinale) varies little from spring to fall. Periphytic and planktonic algae are predominantly diatoms, with the genus Achnanthes dominating both communities. Most genera of planktonic algae originate in the periphyton, but some true planktonic algae were identified. The benthic invertebrate population is dominated by Trichoptera and is a major food source for trout and forage fish. Biotic index values calculated from benthic invertebrate data indicate that water quality is very good to excellent. The trout population is low and represents only a small part of the total fish population both in biomass and numbers. Brown trout are usually stocked annually in the spring to enhance sport fishing, but by fall most trout are wild. The major environmental factors limiting trout population seem to be insufficient cover, insufficient pool depth and volume, and small spawning areas. The wild trout population is highly dependent on spawning success the previous fall.

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

PubMed Central

2011-01-01

Background Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth. Results A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa). Conclusions This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture. PMID:21752295

How do Humans interact with the Biotic Pump of South America?

NASA Astrophysics Data System (ADS)

Sharma, Ajar; Pande, Saket; Renata Cordeiro Ortigara, Angela; Uhlenbrook, Stefan

2017-04-01

The negative effects of the deforestation have been both advertised and down played. However, the effects are far more tangible than what they seem to be. It has been shown that the change in forest cover causes the rainfall patterns to change as the forests work as so-called Biotic Pumps. This changes the water availability in the area by modifying the water balance. Local water balances affect the changes that may take longer to be visible on the larger scales. The Amazon rain forest, one of the most bio-diverse areas worldwide, is an essential part of the biosphere of South America. However, there are clear links between deforestation carried out for agricultural purposes, specifically, Soybean and Sugarcane and the variability in global food prices. Here we analyse the anthropogenic actions that may influence the biotic pump. Variables such as volatility in commodity prices, risk taking capacities, land availability, government subsidies are used to drive the decision making of farmers. These variables are embedded in a lumped biotic pump model made for Brazil, utilizing data from different sources including MODIS, Centro de Previsão do Tempo e Estudos Climáticos (CPTEC), European Centre for Medium-Range Weather Forecasts (ECMWF). The biotic pump model essentially transports atmospheric moisture downwind, part of which falls as rain. The atmospheric moisture 'upwind' accounts for evaporation, incorporating land cover changes in response to land use decisions made by farmers and rainfall. The model is run for scenarios to demonstrate how rain downwind is affected by upwind land cover and provides first insights in to how much rain and productivity (agriculture) downwind is caused by the Amazonian rain forest upwind We then discuss the value of environmental conservation based on marginal productivity analysis, i.e., finding harmony between the conservation of rainforest and the economic growth of the country.

New methods for modeling stream temperature using high resolution LiDAR, solar radiation analysis and flow accumulated values to predict stream temperature

EPA Science Inventory

In-stream temperature directly effects a variety of biotic organisms, communities and processes. Changes in stream temperature can render formally suitable habitat unsuitable for aquatic organisms, particularly native cold water species that are not able to adjust. In order to...

The multiple stressor ecological risk assessment for the mercury-contaminated South River and upper Shenandoah River using the Bayesian network-relative risk model.

PubMed

Landis, Wayne G; Ayre, Kimberley K; Johns, Annie F; Summers, Heather M; Stinson, Jonah; Harris, Meagan J; Herring, Carlie E; Markiewicz, April J

2017-01-01

We have conducted a regional scale risk assessment using the Bayesian Network Relative Risk Model (BN-RRM) to calculate the ecological risks to the South River and upper Shenandoah River study area. Four biological endpoints (smallmouth bass, white sucker, Belted Kingfisher, and Carolina Wren) and 4 abiotic endpoints (Fishing River Use, Swimming River Use, Boating River Use, and Water Quality Standards) were included in this risk assessment, based on stakeholder input. Although mercury (Hg) contamination was the original impetus for the site being remediated, other chemical and physical stressors were evaluated. There were 3 primary conclusions from the BN-RRM results. First, risk varies according to location, type and quality of habitat, and exposure to stressors within the landscape. The patterns of risk can be evaluated with reasonable certitude. Second, overall risk to abiotic endpoints was greater than overall risk to biotic endpoints. By including both biotic and abiotic endpoints, we are able to compare risk to endpoints that represent a wide range of stakeholder values. Third, whereas Hg reduction is the regulatory priority for the South River, Hg is not the only stressor driving risk to the endpoints. Ecological and habitat stressors contribute risk to the endpoints and should be considered when managing this site. This research provides the foundation for evaluating the risks of multiple stressors of the South River to a variety of endpoints. From this foundation, tools for the evaluation of management options and an adaptive management tools have been forged. Integr Environ Assess Manag 2017;13:85-99. © 2016 SETAC. © 2016 SETAC.

Response of a multi-stressed Mediterranean river to future climate and socio-economic scenarios.

PubMed

Stefanidis, Konstantinos; Panagopoulos, Yiannis; Mimikou, Maria

2018-06-15

Streams and rivers are among the most threatened ecosystems in Europe due to the combined effects of multiple pressures related to anthropogenic activities. Particularly in the Mediterranean region, changes in hydromorphology along with increased nutrient loadings are known to affect the ecological functions and ecosystem services of streams and rivers with the anticipated climate change being likely to further impair their functionality and structure. In this study, we investigated the combined effects of agricultural driven stressors on the ecology and delivered services of the Pinios river basin in Greece under three future world scenarios developed within the EU funded MARS project. Scenarios are based on combinations of Representative Concentration Pathways and Shared Socioeconomic Pathways and refer to early century (2030) and mid-century (2060) representing future climate worlds with particular socioeconomic characteristics. To assess the responses of ecological and ecosystem service indicators to the scenarios we first simulated hydrology and water quality in Pinios with a process-based model. Simulated abiotic stressor parameters (predictors) were linked to two biotic indicators, the macroinvertebrate indicators ASPT and EPT, with empirical modelling based on boosted regression trees and general linear models. Our results showed that the techno world scenario driven by fast economic growth and intensive exploitation of energy resources had the largest impact on both the abiotic status (nutrient loads and concentrations in water) and the biotic indicators. In contrast, the predicted changes under the other two future worlds, consensus and fragmented, were more diverse and were mostly dictated by the projected climate. This work showed that the future scenarios, especially the mid-century ones, had significant impact on both abiotic status and biotic responses underpinning the need for implementing catchment management practices able to mitigate the ecological threat on waters in the long-term. Copyright © 2018 Elsevier B.V. All rights reserved.

Microarray Analysis of Tomato Plants Exposed to the Nonviruliferous or Viruliferous Whitefly Vector Harboring Pepper golden mosaic virus

PubMed Central

Musser, Richard O.; Hum-Musser, Sue M.; Gallucci, Matthew; DesRochers, Brittany; Brown, Judith K.

2014-01-01

Abstract Plants are routinely exposed to biotic and abiotic stresses to which they have evolved by synthesizing constitutive and induced defense compounds. Induced defense compounds are usually made, initially, at low levels; however, following further stimulation by specific kinds of biotic and abiotic stresses, they can be synthesized in relatively large amounts to abate the particular stress. cDNA microarray hybridization was used to identify an array of genes that were differentially expressed in tomato plants 15 d after they were exposed to feeding by nonviruliferous whiteflies or by viruliferous whiteflies carrying Pepper golden mosaic virus (PepGMV) ( Begomovirus, Geminiviridae ). Tomato plants inoculated by viruliferous whiteflies developed symptoms characteristic of PepGMV, whereas plants exposed to nonviruliferous whitefly feeding or nonwounded (negative) control plants exhibited no disease symptoms. The microarray analysis yielded over 290 spotted probes, with significantly altered expression of 161 putative annotated gene targets, and 129 spotted probes of unknown identities. The majority of the differentially regulated “known” genes were associated with the plants exposed to viruliferous compared with nonviruliferous whitefly feeding. Overall, significant differences in gene expression were represented by major physiological functions including defense-, pathogen-, photosynthesis-, and signaling-related responses and were similar to genes identified for other insect–plant systems. Viruliferous whitefly-stimulated gene expression was validated by real-time quantitative polymerase chain reaction of selected, representative candidate genes (messenger RNA): arginase, dehydrin, pathogenesis-related proteins 1 and -4, polyphenol oxidase, and several protease inhibitors. This is the first comparative profiling of the expression of tomato plants portraying different responses to biotic stress induced by viruliferous whitefly feeding (with resultant virus infection) compared with whitefly feeding only and negative control nonwounded plants exposed to neither. These results may be applicable to many other plant–insect–pathogen system interactions. PMID:25525099

Ecological Impacts of Southern Pine Beetle

Treesearch

Maria D. Tchakerian; Robert N. Coulson

2011-01-01

The southern pine beetle (SPB) is the most important biotic disturbance in southern pine forests and causes extensive changes to the forest environment. In this chapter we provide an overview of the ecological impacts of the SPB on forest conditions (the state of the forest) and on forest resources (uses and values associated with the forest). We define ecological...

Consequences of climate change for biotic disturbances in North American forests

Treesearch

Aaron S. Weed; Matthew P. Ayres; Jeffrey A. Hicke

2013-01-01

About one-third of North America is forested. These forests are of incalculable value to human society in terms of harvested resources and ecosystem services and are sensitive to disturbance regimes. Epidemics of forest insects and diseases are the dominant sources of disturbance to North American forests. Here we review current understanding of climatic effects...

Effectiveness of Cooperative Learning and Lecture Demonstration Method on Developing Ecocentric Attitude among Secondary School Students

ERIC Educational Resources Information Center

Kumari, Vijaya S. N.; Umashree, D. K.

2017-01-01

Anthropocentrism and ecocentrism are two ways of understanding an extension of ethics to nature. In an anthropocentric ethic, nature deserves moral consideration because how nature is treated affects humans. In an ecocentric ethic, nature deserves moral consideration because nature has intrinsic value. Ecocentrism focuses on the biotic community…

Risk Assessment as an Environmental Management Tool: Considerations for Freshwater Wetlands

Treesearch

A. Dennis Lemly

1997-01-01

This paper presents a foundation for improving the risk assessment process for freshwater wetlands. Integrating wetland science, i.e., use of an ecosystem-based approach, is the key concept. Each biotic and abiotic wetland component should be identified and its contribution to ecosystem functions and societal values determined when deciding whether a stressor poses an...

Nano-scale investigation of the association of microbial nitrogen residues with iron (hydr)oxides in a forest soil O-horizon

Treesearch

M. Keiluweit; J.J. Bougoure; L. Zeglin; D.D. Myrold; P.K. Weber; J. Pett-Ridge; M. Kleber; P.S. Nico

2012-01-01

Amino sugars in fungal cell walls (such as chitin) represent an important source of nitrogen (N) in many forest soil ecosystems. Despite the importance of this material in soil nitrogen cycling, comparatively little is known about abiotic and biotic controls on and the timescale of its turnover. Part of the reason for this lack of information is the inaccessibility of...

VERAM - Vision and Roadmap for European Raw Materials

NASA Astrophysics Data System (ADS)

Baumgarten, Wibke; Vashev, Boris

2017-04-01

The overall objective of VERAM project is to produce a Vision and Roadmap for European Raw Materials in 2050 based on raw materials research and innovation (R&I) coordination. Two leading European Technology Platforms (ETPs): ETP SMR (Sustainable Minerals Resources) and FTP (Forest Technology Platform) are joining forces to develop a common vison and roadmap with the support of ECTP (European Construction Technology Platform), represented by UNIVPM, SusChem (ETP for Sustainable Chemistry), represented by Cefic, EuMaT (Advanced Materials ETP), represented by VITO, ERAMIN 2, represented by Research Centre JUELICH and WoodWisdom Network Plus represented by the Agency for Renewable Resources (FNR). This partnership provides VERAM with expertise from downstream applications and additional knowledge on non-biotic and biotic raw materials. The project encourages capacity building as well as transfer of knowledge. It expects to provide an innovation reference point for the European Institute of Innovation & Technology (EIT) Raw Materials (formerly the KIC Raw MatTERS), to coordinate the network involved in the European Innovation Partnership (EIP) on Raw Materials Commitments and relevant proposals funded under Horizon 2020. It provides a platform for identifying gaps and complementarities and enables their bridging. VERAM will be able to advise the European Commission and Member States on future research needs and policies to stimulate innovation and assist in overcoming fragmentation in the implementing the EIP Raw Materials Strategic Implementation Plan. VERAM looks for mutually beneficial information exchange, encourages cross-fertilization between actions undertaken by different raw material industries, and expects to accelerate exploitation of breakthrough innovations. One of the main outcomes of the project is the presentation of a common long term 2050 Vision and Roadmap for relevant raw materials including metals, industrial minerals and aggregates and wood. The Vision and Roadmap have the objective of highlighting the path to achieving the European Commission's ambitious target of 80% reduction in CO2 emissions by 2050.

[Estuary health assessment using a benthic-index of biotic integrity in Yangtze Estuary and its adjacent waters].

PubMed

Zhou, Xiao-wei; Wang, Li-ping; Zheng, Bing-hui; Liu, Lu-san; Fu, Qing

2009-01-01

A benthic index of biotic integrity (B-IBI) was developed for application in estuaries health assessment of the Yangtze Estuary and its adjacent waters. Benthic macro-invertebrate samples were collected from 41 stream sites (13 non-degraded stations and 28 degraded stations) in the Yangtze Estuary and its adjacent waters in July, 2005. The analyses of the range of index value distribution, Pearson correlation and judgment ability were performed on fourteen candidate metrics. Six biological metrics were selected for the establishment of B-IBI, which were Shannon-Wiener index, the species number, total density, total biomass, Carapace Animals density percentage and Echinoderms density percentage. B-IBI was obtained by sum up all these indices after which were transformed into a uniform score by using the ratio scoring method. Base on 50 percentile of B-IBI value in reference sites, the criteria of health ranking was determined. The proposed criteria of benthic-index of biotic integrity were as follows: B-IBI > 2.48 was regarded as health, 1.86-2.48 sub-health, 1.24-1.86 fair, 0.62-1.24 poor, and B-IBI < 0.62 very poor. Assessing with these criteria, the results showed that among the 41 sites in Yangtze Estuary and its adjacent waters, 7 sites were health, 2 sites were sub-health, 8 sites were fair, 8 sites were poor and 16 sites were very poor. An independent data set sampled in June of 2006 was used to validate the index, the results indicated that final combined index correctly classified 89% of stations in the validation data set.

Is biotic resistance enhanced by natural variation in diversity?

USGS Publications Warehouse

Grace, James B.; Harrison, Susan P.; Cornell, Howard

2017-01-01

Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the underlying processes by dissecting how biotic resistance to new invaders may be shaped by the same environmental influences that determine diversity and other community properties.In grasslands with heterogeneous soils, we added invaders and removed competitors to analyze the causes of invasion resistance. Abiotic resistance was measured using invader success in the absence of the resident community. Biotic resistance was measured as the reduction in invader success in the presence of the resident community.Invaders were most successful where biotic resistance was lowest and abiotic resistance was highest, confirming the dominant role of biotic resistance. Contrary to theory, though, biotic resistance was highest where both species richness and functional diversity were lowest. In the multivariate framework of a structural equation model, biotic resistance was independent of community diversity, and was highest where fertile soils led to high community biomass.Seed predation slightly augmented biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results.We conclude that in natural systems, diversity may be correlated with invasibility and yet have little effect on biotic resistance to invasion. More generally, the environmental causes of variation in diversity should be considered when examining the potential functional consequences of diversity.

Trophic Magnification of Parabens and Their Metabolites in a Subtropical Marine Food Web.

PubMed

Xue, Xiaohong; Xue, Jingchuan; Liu, Wenbin; Adams, Douglas H; Kannan, Kurunthachalam

2017-01-17

Despite the widespread use of parabens in a range of consumer products, little is known about bioaccumulation of these chemicals in aquatic environments. In this study, six parabens and four of their common metabolites were measured in abiotic (water, sediment) and biotic (fish including sharks, invertebrates, plants) samples collected from a subtropical marine food web in coastal Florida. Methyl paraben (MeP) was found in all abiotic (100%) and a majority of biotic (87%) samples. 4-Hydroxy benzoic acid (4-HB) was the most abundant metabolite, found in 97% of biotic and all abiotic samples analyzed. The food chain accumulation of MeP and 4-HB was investigated for this food web. The trophic magnification factor (TMF) of MeP was estimated to be 1.83, which suggests considerable bioaccumulation and biomagnification of this compound in the marine food web. In contrast, a low TMF value was found for 4-HB (0.30), indicating that this compound is metabolized and excreted along the food web. This is the first study to document the widespread occurrence of parabens and their metabolites in fish, invertebrates, seagrasses, marine macroalgae, mangroves, seawater, and ocean sediments and to elucidate biomagnification potential of MeP in a marine food web.

How far are extraterrestrial life and intelligence after Kepler?

NASA Astrophysics Data System (ADS)

Wandel, Amri

2017-08-01

The Kepler mission has shown that a significant fraction of all stars may have an Earth-size habitable planet. A dramatic support was the recent detection of Proxima Centauri b. Using a Drake-equation like formalism I derive an equation for the abundance of biotic planets as a function of the relatively modest uncertainty in the astronomical data and of the (yet unknown) probability for the evolution of biotic life, Fb. I suggest that Fb may be estimated by future spectral observations of exoplanet biomarkers. It follows that if Fb is not very small, then a biotic planet may be expected within about 10 light years from Earth. Extending this analyses to advanced life, I derive expressions for the distance to putative civilizations in terms of two additional Drake parameters - the probability for evolution of a civilization, Fc, and its average longevity. Assuming "optimistic" values for the Drake parameters, (Fb Fc 1), and a broadcasting duration of a few thousand years, the likely distance to the nearest civilizations detectable by SETI is of the order of a few thousand light years. Finally I calculate the distance and probability of detecting intelligent signals with present and future radio telescopes such as Arecibo and SKA and how it could constrain the Drake parameters.

Biotic resistance to exotic invasions: its role in forest ecosystems, confounding artifacts, and future directions

Treesearch

Gabriela C. Nunez-Mir; Andrew M. Liebhold; Qinfeng Guo; Eckehard G. Brockerhoff; Insu Jo; Kimberly Ordonez; Songlin Fei

2017-01-01

Biotic resistance, the ability of communities to resist exotic invasions, has long attracted interest in the research and management communities. However, inconsistencies exist in various biotic resistance studies and less is known about the current status and knowledge gaps of biotic resistance in forest ecosystems. In this paper, we provide a brief review of the...

An evaluation of freshwater mussel toxicity data in the derivation of water quality guidance and standards for copper

USGS Publications Warehouse

March, F.A.; Dwyer, F.J.; Augspurger, T.; Ingersoll, C.G.; Wang, N.; Mebane, C.A.

2007-01-01

The state of Oklahoma has designated several areas as freshwater mussel sanctuaries in an attempt to provide freshwater mussel species a degree of protection and to facilitate their reproduction. We evaluated the protection afforded freshwater mussels by the U.S. Environmental Protection Agency (U.S. EPA) hardness-based 1996 ambient copper water quality criteria, the 2007 U.S. EPA water quality criteria based on the biotic ligand model and the 2005 state of Oklahoma copper water quality standards. Both the criterion maximum concentration and criterion continuous concentration were evaluated. Published acute and chronic copper toxicity data that met American Society for Testing and Materials guidance for test acceptability were obtained for exposures conducted with glochidia or juvenile freshwater mussels. We tabulated toxicity data for glochidia and juveniles to calculate 20 species mean acute values for freshwater mussels. Generally, freshwater mussel species mean acute values were similar to those of the more sensitive species included in the U.S. EPA water quality derivation database. When added to the database of genus mean acute values used in deriving 1996 copper water quality criteria, 14 freshwater mussel genus mean acute values included 10 of the lowest 15 genus mean acute values, with three mussel species having the lowest values. Chronic exposure and sublethal effects freshwater mussel data available for four species and acute to chronic ratios were used to evaluate the criterion continuous concentration. On the basis of the freshwater mussel toxicity data used in this assessment, the hardness-based 1996 U.S. EPA water quality criteria, the 2005 Oklahoma water quality standards, and the 2007 U.S. EPA water quality criteria based on the biotic ligand model might need to be revised to afford protection to freshwater mussels. ?? 2007 SETAC.

Validation of the Nickel Biotic Ligand Model for Locally Relevant Species in Australian Freshwaters.

PubMed

Peters, Adam; Merrington, Graham; Schlekat, Christian; De Schamphelaere, Karel; Stauber, Jennifer; Batley, Graeme; Harford, Andrew; van Dam, Rick; Pease, Ceiwen; Mooney, Tom; Warne, Michael; Hickey, Chris; Glazebrook, Peter; Chapman, John; Smith, Ross; Krassoi, Rick

2018-06-20

Australian freshwaters have relatively low water hardness and different calcium to magnesium ratios compared with those in Europe. The hardness values of a substantial proportion of Australian freshwaters fall below the application boundary of the existing European nickel Biotic Ligand Models (NiBLMs) of 2 mg Ca/L. Toxicity testing was undertaken using Hydra viridissima to assess the predictive ability of the existing NiBLM for this species in extremely soft waters. This testing revealed an increased competitive effect of calcium and magnesium with nickel for binding to the biotic ligand in soft water (<10 mg CaCO 3 /L) than at higher water hardness. Modifications were made to the NiBLM by increasing the binding constants for Ca and Mg at the biotic ligand to account for softer waters encountered in Australia and the more important competitive effect of calcium and magnesium on nickel toxicity. To validate the modified NiBLM, ecotoxicity testing was performed on five Australian test species in five different natural Australian waters. Overall, no single water chemistry parameter was able to indicate the trends in toxicity to all of the test species. The modified NiBLMs were able to predict the toxicity of nickel to the test species in the validation studies in natural waters better than the existing NiBLMs. This work suggests that the overarching mechanisms defining nickel bioavailability to freshwater species are globally similar, and that NiBLMs can be used in all freshwater systems with minor modifications. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Linking mercury, carbon, and nitrogen stable isotopes in Tibetan biota: Implications for using mercury stable isotopes as source tracers

PubMed Central

Xu, Xiaoyu; Zhang, Qianggong; Wang, Wen-Xiong

2016-01-01

Tibetan Plateau is located at a mountain region isolated from direct anthropogenic sources. Mercury concentrations and stable isotopes of carbon, nitrogen, and mercury were analyzed in sediment and biota for Nam Co and Yamdrok Lake. Biotic mercury concentrations and high food web magnification factors suggested that Tibetan Plateau is no longer a pristine site. The primary source of methylmercury was microbial production in local sediment despite the lack of direct methylmercury input. Strong ultraviolet intensity led to extensive photochemical reactions and up to 65% of methylmercury in water was photo-demethylated before entering the food webs. Biota displayed very high Δ199Hg signatures, with some highest value (8.6%) ever in living organisms. The δ202Hg and Δ199Hg in sediment and biotic samples increased with trophic positions (δ15N) and %methylmercury. Fish total length closely correlated to δ13C and Δ199Hg values due to dissimilar carbon sources and methylmercury pools in different living waters. This is the first mercury isotope study on high altitude lake ecosystems that demonstrated specific isotope fractionations of mercury under extreme environmental conditions. PMID:27151563

Testing the Underlying Chemical Principles of the Biotic Ligand Model (BLM) to Marine Copper Systems: Measuring Copper Speciation Using Fluorescence Quenching.

PubMed

Tait, Tara N; McGeer, James C; Smith, D Scott

2018-01-01

Speciation of copper in marine systems strongly influences the ability of copper to cause toxicity. Natural organic matter (NOM) contains many binding sites which provides a protective effect on copper toxicity. The purpose of this study was to characterize copper binding with NOM using fluorescence quenching techniques. Fluorescence quenching of NOM with copper was performed on nine sea water samples. The resulting stability constants and binding capacities were consistent with literature values of marine NOM, showing strong binding with [Formula: see text] values from 7.64 to 10.2 and binding capacities ranging from 15 to 3110 nmol mg [Formula: see text] Free copper concentrations estimated at total dissolved copper concentrations corresponding to previously published rotifer effect concentrations, in the same nine samples, were statistically the same as the range of free copper calculated for the effect concentration in NOM-free artificial seawater. These data confirms the applicability of fluorescence spectroscopy techniques for NOM and copper speciation characterization in sea water and demonstrates that such measured speciation is consistent with the chemical principles underlying the biotic ligand model approach for bioavailability-based metals risk assessment.

Geographic range velocity and its association with phylogeny and life history traits in North American woody plants.

PubMed

Harnik, Paul G; Maherali, Hafiz; Miller, Joshua H; Manos, Paul S

2018-03-01

The geographic ranges of taxa change in response to environmental conditions. Yet whether rates of range movement (biotic velocities) are phylogenetically conserved is not well known. Phylogenetic conservatism of biotic velocities could reflect similarities among related lineages in climatic tolerances and dispersal-associated traits. We assess whether late Quaternary biotic velocities were phylogenetically conserved and whether they correlate with climatic tolerances and dispersal-associated traits. We used phylogenetic regression and nonparametric correlation to evaluate associations between biotic velocities, dispersal-associated traits, and climatic tolerances for 28 woody plant genera and subgenera in North America. The velocities with which woody plant taxa shifted their core geographic range limits were positively correlated from time step to time step between 16 and 7 ka. The strength of this correlation weakened after 7 ka as the pace of climate change slowed. Dispersal-associated traits and climatic tolerances were not associated with biotic velocities. Although the biotic velocities of some genera were consistently fast and others consistently slow, biotic velocities were not phylogenetically conserved. The rapid late Quaternary range shifts of plants lacking traits that facilitate frequent long-distance dispersal has long been noted (i.e., Reid's Paradox). Our results are consistent with this paradox and show that it remains robust when phylogenetic information is taken into account. The lack of association between biotic velocities, dispersal-associated traits, and climatic tolerances may reflect several, nonmutually exclusive processes, including rare long-distance dispersal, biotic interactions, and cryptic refugia. Because late Quaternary biotic velocities were decoupled from dispersal-associated traits, trait data for genera and subgenera cannot be used to predict longer-term (millennial-scale) floristic responses to climate change.

Differentiating biotic from abiotic methane genesis in hydrothermally active planetary surfaces

PubMed Central

Oze, Christopher; Jones, L. Camille; Goldsmith, Jonas I.; Rosenbauer, Robert J.

2012-01-01

Molecular hydrogen (H2) is derived from the hydrothermal alteration of olivine-rich planetary crust. Abiotic and biotic processes consume H2 to produce methane (CH4); however, the extent of either process is unknown. Here, we assess the temporal dependence and limit of abiotic CH4 related to the presence and formation of mineral catalysts during olivine hydrolysis (i.e., serpentinization) at 200 °C and 0.03 gigapascal. Results indicate that the rate of CH4 production increases to a maximum value related to magnetite catalyzation. By identifying the dynamics of CH4 production, we kinetically model how the H2 to CH4 ratio may be used to assess the origin of CH4 in deep subsurface serpentinization systems on Earth and Mars. Based on our model and available field data, low H2/CH4 ratios (less than approximately 40) indicate that life is likely present and active. PMID:22679287

Differentiating biotic from abiotic methane genesis in hydrothermally active planetary surfaces.

PubMed

Oze, Christopher; Jones, L Camille; Goldsmith, Jonas I; Rosenbauer, Robert J

2012-06-19

Molecular hydrogen (H(2)) is derived from the hydrothermal alteration of olivine-rich planetary crust. Abiotic and biotic processes consume H(2) to produce methane (CH(4)); however, the extent of either process is unknown. Here, we assess the temporal dependence and limit of abiotic CH(4) related to the presence and formation of mineral catalysts during olivine hydrolysis (i.e., serpentinization) at 200 °C and 0.03 gigapascal. Results indicate that the rate of CH(4) production increases to a maximum value related to magnetite catalyzation. By identifying the dynamics of CH(4) production, we kinetically model how the H(2) to CH(4) ratio may be used to assess the origin of CH(4) in deep subsurface serpentinization systems on Earth and Mars. Based on our model and available field data, low H(2)/CH(4) ratios (less than approximately 40) indicate that life is likely present and active.

Faunal assemblages and multi-scale habitat patterns in headwater tributaries of the South Fork Trinity River - an unregulated river embedded within a multiple-use landscape

USGS Publications Warehouse

Welsh, H.H.; Hodgson, G.R.; Duda, J.J.; Emlen, J.M.

2010-01-01

Headwaters can represent 80% of stream kilometers in a watershed, and they also have unique physical and biological properties that have only recently been recognized for their importance in sustaining healthy functioning stream networks and their ecological services. We sampled 60 headwater tributaries in the South Fork Trinity River, a 2,430 km2, mostly forested, multiple-use watershed in northwestern California. Our objectives were: (1) to differentiate unique headwater types using 69 abiotic and vegetation variables measured at three spatial scales, and then to reduce these to informative subsets; (2) determine if distinct biota occupied the different tributary types; (3) determine the environmental attributes associated with the presence and abundance of these biotic assemblages; and (4) using niche modeling, determine key attribute thresholds to illustrate how these biota could be employed as metrics of system integrity and ecological services. Several taxa were sufficiently abundant and widespread to use as bio-indicators: the presence and abundance of steelhead trout (Oncorhynchus mykiss), herpetofauna (reptile and amphibian) species richness, and signal crayfish (Pacifastacus leniusculus) represented different trophic positions, value as commercial resources (steelhead), sensitivity to environmental stress (amphibians), and indicators of biodiversity (herpetofauna species richness). Herpetofauna species richness did not differ, but abundances of steelhead trout, signal crayfish, and amphibian richness all differed significantly among tributary types. Niche models indicated that distribution and abundance patterns in both riparian and aquatic environments were associated with physical and structural attributes at multiple spatial scales, both within and around reaches. The bio-indicators responded to unique sets of attributes, reflecting the high environmental heterogeneity in headwater tributaries across this large watershed. These niche attributes represented a wide range of headwater environments, indicating responses to a number of natural and anthropogenic conditions, and demonstrated the value of using a suite of bio-indicators to elucidate watershed conditions, and to examine numerous disturbances that may influence ecological integrity.

Role of Biotic and Abiotic Processes on Soil CO2 Dynamics in the McMurdo Dry Valleys, Antarctica

NASA Astrophysics Data System (ADS)

Risk, D. A.; Macintyre, C. M.; Lee, C.; Cary, C.; Shanhun, F.; Almond, P. C.

2016-12-01

In the harsh conditions of the Antarctic Dry Valleys, microbial activity has been recorded via measurements of soil carbon dioxide (CO2) concentration and surface efflux. However, high temporal resolution studies in the Dry Valleys have also shown that abiotic solubility-driven processes can strongly influence (and perhaps even dominate) the CO2 dynamics in these low flux environments and suggests that biological activity may be lower than previously thought. In this study, we aim to improve our understanding of CO2 dynamics (biotic and abiotic) in Antarctic Dry Valley soils using long-term automated measurements of soil CO2 surface flux and soil profile concentration at several sites, often at sub-diel frequency. We hypothesize that soil CO2 variations are driven primarily by environmental factors affecting CO2 solubility in soil solution, mainly temperature, and that these processes may even overprint biologic production in representative Dry Valley soils. Monitoring of all sites revealed only one likely biotic CO2 production event, lasting three weeks during the Austral summer and reaching fluxes of 0.4 µmol/m2/s. Under more typical low flux conditions (<0.10 µmol/m2/s) we observed a cyclical daily sink/source pattern consistent with CO2 solubility cycling that would not generally have been evident with normal synoptic afternoon sampling campaigns. Subsurface CO2 monitoring and a lab-controlled Antarctic soil simulation experiment confirmed that abiotic processes are capable of dominating soil CO2 variability. Diel temperature cycles crossing the freezing boundary revealed a dual abiotic cycle of solubility cycling and gas exclusion from ice formation observed only by high temporal frequency measurements (30 min). This work demonstrates a need for a numerical model to partition the dynamic abiotic processes underlying any biotic CO2 production in order to understand potential climate-change induced increases in microbial productivity in terrestrial Antarctica.

Biotic and abiotic factors affecting stemflow variability in downy oak and Scots pine stands in Mediterranean conditions

NASA Astrophysics Data System (ADS)

Cayuela, Carles; Garcia-Estringana, Pablo; Latron, Jérôme; Llorens, Pilar

2015-04-01

Although stemflow is only a small portion of rainfall, it may represent an important local input of water and nutrients at the plant stem. Previous studies have shown that stemflow has a significant influence on hydrological and biogeochemical processes. Stemflow volume is affected by many biotic factors as species, age, branch or bark characteristics. Moreover, the seasonality of the rainfall regime in Mediterranean areas, which includes both frontal rainfall events and short convective storms, can add complexity to the rainfall-stemflow relationship. This work investigates stemflow dynamics and the influence of biotic and abiotic factors on stemflow rates in two Mediterranean stands during the leafed period - from May to October. The monitored stands are a Downy oak forest (Quercus pubescens) and a Scots pine forest (Pinus sylvestris), both located in the Vallcebre research catchments (NE Spain, 42° 12'N, 1° 49'E). The monitoring design of each plot consists of 7 stemflow rings connected to tipping-buckets, bulk rainfall measured in a nearby clearing and meteorological conditions above the canopies. All data were recorded at 5 min interval. Biometric characteristics of the measured trees were also measured. The analysis of 39 rainfall events (65% smaller than 10 mm) shows that stemflow accounted for less than 1% of the bulk rainfall in both stands. Results also show that, on average, the rainfall amount required for the start of the stemflow and the time delay between the beginning of the precipitation and the start of stemflow are higher in the Downy oak forest. As suggested by stemflow funneling ratios, these differences might be linked to the canopy structure and bark water storage capacity of the trees, indicating that during low magnitude events, oaks have more difficulty to reach storage capacity. The role of other biotic and abiotic parameters on stemflow variability in both stands is still under investigation.

Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA

DTIC Science & Technology

2009-05-01

FINAL REPORT Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA SERDP Project ER-1421 MAY 2009 James E. Szecsody...00-2009 4. TITLE AND SUBTITLE Abiotic and Biotic Mechanisms Controlling In Situ Remediation of NDMA 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...investigate whether in situ coupled abiotic/biotic degradation of N-nitrosodimethylamine ( NDMA , an emerging contaminant) could be used as a permeable

Biotic and abiotic factors predicting the global distribution and population density of an invasive large mammal

PubMed Central

Lewis, Jesse S.; Farnsworth, Matthew L.; Burdett, Chris L.; Theobald, David M.; Gray, Miranda; Miller, Ryan S.

2017-01-01

Biotic and abiotic factors are increasingly acknowledged to synergistically shape broad-scale species distributions. However, the relative importance of biotic and abiotic factors in predicting species distributions is unclear. In particular, biotic factors, such as predation and vegetation, including those resulting from anthropogenic land-use change, are underrepresented in species distribution modeling, but could improve model predictions. Using generalized linear models and model selection techniques, we used 129 estimates of population density of wild pigs (Sus scrofa) from 5 continents to evaluate the relative importance, magnitude, and direction of biotic and abiotic factors in predicting population density of an invasive large mammal with a global distribution. Incorporating diverse biotic factors, including agriculture, vegetation cover, and large carnivore richness, into species distribution modeling substantially improved model fit and predictions. Abiotic factors, including precipitation and potential evapotranspiration, were also important predictors. The predictive map of population density revealed wide-ranging potential for an invasive large mammal to expand its distribution globally. This information can be used to proactively create conservation/management plans to control future invasions. Our study demonstrates that the ongoing paradigm shift, which recognizes that both biotic and abiotic factors shape species distributions across broad scales, can be advanced by incorporating diverse biotic factors. PMID:28276519

Serpentinization and Synthesis: Can abiotic and biotic non-volatile organic molecules be identified in the subsurface of the Atlantis Massif?

NASA Astrophysics Data System (ADS)

Hickok, K.; Nguyen, T.; Orcutt, B.; Fruh-Green, G. L.; Wanamaker, E.; Lang, S. Q.

2016-12-01

The high concentrations of hydrogen created during serpentinization can promote the formation of abiotic organic carbon molecules such as methane, formate, short chain hydrocarbons and, in laboratory experiments, larger molecules containing up to 32 carbon atoms. Subsurface archaeal and bacterial communities can use these reduced compounds for metabolic energy. International Ocean Discovery Project Expedition 357 drilled into the Atlantis Massif with the goals of investigating carbon cycling and the presence of life in a zone of active serpentinization. The expedition recovered multiple rock lithologies including gabbros, basalts, carbonate sands, and serpentinites. A subset of these samples are being analyzed to determine if non-volatile organic molecules are produced abiotically in serpentinizing environments and to identify `hot spots' of microbial life in the subsurface. Rock samples of contrasting representative lithologies are being analyzed for the presence of n-alkanes and fatty acids. Preliminary results have so far indicated the presence of alkanes in some samples. The isotopic (13C, 2H) characteristics of these compounds are being compared to a suite of oils, greases, and drilling fluids used during sample collection to distinguish in situ abiotic and biotic signatures from contaminant compounds. Other initial results have shown the efficacy of various sample-handling procedures designed to reduce surface contamination. This study will contribute to the overall understanding of the role serpentinization plays in the global carbon cycle and its implications for pre-biotic chemistry.

Biosynthesis and biological functions of terpenoids in plants.

PubMed

Tholl, Dorothea

2015-01-01

Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.

Biological structure and dynamics of fish assemblages in tributaries of eastern Lake Ontario

USGS Publications Warehouse

McKenna, James E.; Munawar, M.

2003-01-01

Interest in effective management of Great Lakes natural resources and restoration of native populations has stimulated interest in the conditions and ecological role of tributaries in the Great Lakes ecosystem. Rivers of Lake Ontario's eastern basin provide an excellent opportunity to examine important tributaries and their relationship to Lake Ontario. This paper reports on the results of an investigation of fish assemblage structure in lower reaches of the Salmon and Oswego Rivers and at their interfaces with Lake Ontario. These two systems represent conditions near the end points on a continuum from highly disturbed to pristine. They are also of great interest to resource managers for their important fisheries and other economic values. The objective was to identify distinct fish assemblages within these systems and relate their characteristics to biotic and abiotic conditions in an attempt to determine factors responsible for structuring and maintaining those species assemblages. This information is intended to provide baseline information for monitoring the status of these rivers and coastal systems and to aid in the development of models of ecological health.

Multi-regional synthesis of temporal trends in biotic assemblages in streams and rivers of the continental United States

USGS Publications Warehouse

Miller, Matthew P.; Brasher, Anne M.D.; Keenen, Jonathan G.

2013-01-01

Biotic assemblages in aquatic ecosystems are excellent integrators and indicators of changing environmental conditions within a watershed. Therefore, temporal changes in abiotic environmental variables often can be inferred from temporal changes in biotic assemblages. Algae, macroinvertebrate, and fish assemblage data were collected from 91 sampling sites in 4 geographic regions (northeastern/north-central, southeastern, south-central, and western), collectively encompassing the continental United States, from 1993 to 2009 as part of the U.S. Geological Survey National Water-Quality Assessment Program. This report uses a multivariate approach to synthesize temporal trends in biotic assemblages and correlations with relevant abiotic parameters as a function of biotic assemblage, geographic region, and land use. Of the three groups of biota, algal assemblages had temporal trends at the greatest percentage of sites. Of the regions, a greater percentage of sites in the northeastern/north-central and western regions had temporal trends in biotic assemblages. In terms of land use, a greater percentage of watersheds draining agricultural, urban, and undeveloped areas had significant temporal changes in biota, as compared to watersheds with mixed use. Correlations between biotic assemblages and abiotic variables indicate that, in general, macroinvertebrate assemblages correlated with water quality and fish assemblages correlated with physical habitat. Taken together, results indicate that there are regional differences in how individual biotic assemblages (algae, macroinvertebrates, and fish) respond to different abiotic drivers of change.

Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules.

PubMed

Barabás, Béla; Kurdi, Róbert; Zucchi, Claudia; Pályi, Gyula

2018-07-01

Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry. © 2018 Wiley Periodicals, Inc.

Using fish communities to assess streams in Romania: Initial development of an index of biotic integrity

USGS Publications Warehouse

Angermeier, P.L.; Davideanu, G.

2004-01-01

Multimetric biotic indices increasingly are used to complement physicochemical data in assessments of stream quality. We initiated development of multimetric indices, based on fish communities, to assess biotic integrity of streams in two physiographic regions of central Romania. Unlike previous efforts to develop such indices for European streams, our metrics and scoring criteria were selected largely on the basis of empirical relations in the regions of interest. We categorised 54 fish species with respect to ten natural-history attributes, then used this information to compute 32 candidate metrics of five types (taxonomic, tolerance, abundance, reproductive, and feeding) for each of 35 sites. We assessed the utility of candidate metrics for detecting anthropogenic impact based on three criteria: (a) range of values taken, (b) relation to a site-quality index (SQI), which incorporated information on hydrologic alteration, channel alteration, land-use intensity, and water chemistry, and (c) metric redundancy. We chose seven metrics from each region to include in preliminary multimetric indices (PMIs). Both PMIs included taxonomic, tolerance, and feeding metrics, but only two metrics were common to both PMIs. Although we could not validate our PMIs, their strong association with the SQI in each region suggests that such indices would be valuable tools for assessing stream quality and could provide more comprehensive assessments than the traditional approaches based solely on water chemistry.

A multi-criteria targeting approach to neutral grassland conservation.

PubMed

Bayliss, Julian; Helyar, Alice; Lee, John T; Thompson, Stewart

2003-02-01

Resources for creating and managing rare habitats are limited, and a targeting approach aimed at identifying the most viable sites for habitat conservation is therefore desirable. This study developed a multi-criteria targeting approach to site conservation for two rare grassland types, based on a suite of biotic and abiotic factors managed within a Geographical Information System. A number of biotic and abiotic criteria were assessed to evaluate the biodiversity status of grassland sites. Biotic factors included species diversity, species richness and species rarity; and abiotic factors included patch area, position in the ecological unit and the influence of surrounding land use. Each criterion was given equal weighting and a final biodiversity value for each patch was calculated; the patch with the highest cumulative rank score was deemed the patch with the greatest biodiversity. Each site was then examined in relation to agricultural land under the existing management prescriptions of the Upper Thames Tributaries Environmentally Sensitive Area (UTTESA). Sites identified with high biodiversity potential, but currently not included under management prescriptions, were targeted for future inclusion in the ESA scheme. The targeting approach demonstrated how the national Lowland Meadows habitat action plan creation target of 500 ha could be achieved in the UTTESA. The fact that this target figure was so easily attained within this study area highlighted the possible underestimation of national habitat creation targets.

Does natural variation in diversity affect biotic resistance?

USGS Publications Warehouse

Harrison, Susan; Cornell, Howard; Grace, James B.

2015-01-01

Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the key underlying process by dissecting how community diversity is shaped by the same environmental gradients that determine biotic and abiotic resistance to new invaders. In grasslands on highly heterogeneous soils, we used addition of a recent invader, competitor removal and structural equation modelling (SEM) to analyse soil influences on community diversity, biotic and abiotic resistance and invader success. Biotic resistance, measured by reduction in invader success in the presence of the resident community, was negatively correlated with species richness and functional diversity. However, in the multivariate SEM framework, biotic resistance was independent of all forms of diversity and was positively affected by soil fertility via community biomass. Abiotic resistance, measured by invader success in the absence of the resident community, peaked on infertile soils with low biomass and high community diversity. Net invader success was determined by biotic resistance, consistent with this invader's better performance on infertile soils in unmanipulated conditions. Seed predation added slightly to biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. Synthesis. In natural systems, diversity may be correlated with invasibility and yet have no effect on either biotic or abiotic resistance to invasion. More generally, the environmental causes of variation in diversity should not be overlooked when considering the potential functional consequences of diversity.

The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients

PubMed Central

Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

2015-01-01

We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages. PMID:26091266

The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients.

PubMed

Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

2015-01-01

We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages.

Diagenetic Iron Cycling in Ancient Alkaline Saline Lacustrine Sedimentary Rocks: A Case Study on the Jurassic Brushy Basin Member of the Morrison Formation, Colorado Plateau, USA

NASA Astrophysics Data System (ADS)

Potter-McIntyre, S. L.; Chan, M. A.; McPherson, B. J. O. L.

2014-12-01

The upper part of the Brushy Basin Member in the Four Corners region of the U.S. was deposited in an ephemeral alkaline saline lake system with copious input of volcanic ash. The variegated shale formation provides a setting for the study of early diagenetic iron cycling that records the action of alkaline saline fluid chemistries reacting with volcaniclastic sediments in the presence of microbes. A bull's-eye pattern of authigenic minerals with increasing alteration towards the basinal center similar to modern alkaline saline lakes provides evidence for an extreme paleoenvironmental interpretation. The purpose of this research is to document specific factors, such as reactive sediments, microbial influences, and grain size that affect concretion formation and iron cycling in an ancient extreme environment. Three broad diagenetic facies are interpreted by color and associated bioturbation features: red, green and intermediate. Diagenetic facies reflect meter-scale paleotopography: red facies represent shallow water to subaerial, oxidizing conditions; green facies reflect saturated conditions and reducing pore water chemistry shortly after deposition, and intermediate facies represent a combination of the previous two conditions. Evidence of biotic influence is abundant and trace fossils exhibit patterns associated with the diagenetic facies. Red diagenetic facies typically contain burrows and root traces and green diagenetic facies exhibit restricted biotic diversity typically limited to algal molds (vugs). Microbial fossils are well-preserved and are in close proximity to specific iron mineral textures suggesting biotic influence on the crystal morphology. Three categories of concretions are characterized based on mineralogy: carbonate, iron (oxyhydr)oxide and phosphate concretions. Concretion mineralogy and size vary within an outcrop and even within a stratigraphic horizon such that more than one main category is typically present in an outcrop. Variation in concretion mineralogy and morphology within the Brushy Basin Member suggests that alkaline saline fluid chemistries in concert with microbial interaction created diagenetic microenvironments within a larger lake system to influence iron cycling and these reactions can be spatially variable even on 10s of cm scales.

The plant cell wall integrity maintenance mechanism--a case study of a cell wall plasma membrane signaling network.

PubMed

Hamann, Thorsten

2015-04-01

Some of the most important functions of plant cell walls are protection against biotic/abiotic stress and structural support during growth and development. A prerequisite for plant cell walls to perform these functions is the ability to perceive different types of stimuli in both qualitative and quantitative manners and initiate appropriate responses. The responses in turn involve adaptive changes in cellular and cell wall metabolism leading to modifications in the structures originally required for perception. While our knowledge about the underlying plant mechanisms is limited, results from Saccharomyces cerevisiae suggest the cell wall integrity maintenance mechanism represents an excellent example to illustrate how the molecular mechanisms responsible for stimulus perception, signal transduction and integration can function. Here I will review the available knowledge about the yeast cell wall integrity maintenance system for illustration purposes, summarize the limited knowledge available about the corresponding plant mechanism and discuss the relevance of the plant cell wall integrity maintenance mechanism in biotic stress responses. Copyright © 2014 Elsevier Ltd. All rights reserved.

Histolocalization and physico-chemical characterization of dihydrochalcones: Insight into the role of apple major flavonoids.

PubMed

Gaucher, Matthieu; Dugé de Bernonville, Thomas; Lohou, David; Guyot, Sylvain; Guillemette, Thomas; Brisset, Marie-Noëlle; Dat, James F

2013-06-01

Flavonoids, like other metabolites synthesized via the phenylpropanoid pathway, possess a wide range of biological activities including functions in plant development and its interaction with the environment. Dihydrochalcones (mainly phloridzin, sieboldin, trilobatin, phloretin) represent the major flavonoid subgroup in apple green tissues. Although this class of phenolic compounds is found in very large amounts in some tissues (≈200mg/g of leaf DW), their physiological significance remains unclear. In the present study, we highlight their tissue-specific localization in young growing shoots suggesting a specific role in important physiological processes, most notably in response to biotic stress. Indeed, dihydrochalcones could constitute a basal defense, in particular phloretin which exhibits a strong broad-range bactericidal and fungicidal activity. Our results also indicate that sieboldin forms complexes with iron with strong affinity, reinforcing its antioxidant properties and conferring to this dihydrochalcone a potential for iron seclusion and/or storage. The importance of localization and biochemical properties of dihydrochalcones are discussed in view of the apple tree defense strategy against both biotic and abiotic stresses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Biogeochemical reactive transport of carbon, nitrogen and iron in the hyporheic zone

NASA Astrophysics Data System (ADS)

Dwivedi, D.; Steefel, C. I.; Newcomer, M. E.; Arora, B.; Spycher, N.; Hammond, G. E.; Moulton, J. D.; Fox, P. M.; Nico, P. S.; Williams, K. H.; Dafflon, B.; Carroll, R. W. H.

2017-12-01

To understand how biogeochemical processes in the hyporheic zone influence carbon and nitrogen cycling as well as stream biogeochemistry, we developed a biotic and abiotic reaction network and integrated it into a reactive transport simulator - PFLOTRAN. Three-dimensional reactive flow and transport simulations were performed to describe the hyporheic exchange of fluxes from and within an intra-meander region encompassing two meanders of East River in the East Taylor watershed, Colorado. The objectives of this study were to quantify (1) the effect of transience on the export of carbon, nitrogen, and iron; and (2) the biogeochemical transformation of nitrogen and carbon species as a function of the residence time. The model was able to capture reasonably well the observed trends of nitrate and dissolved oxygen values that decreased as well as iron (Fe (II)) values that increased along the meander centerline away from the stream. Hyporheic flow paths create lateral redox zonation within intra-meander regions, which considerably impact nitrogen export into the stream system. Simulation results further demonstrated that low water conditions lead to higher levels of dissolved iron in groundwater, which (Fe (II)> 80%) is exported to the stream on the downstream side during high water conditions. An important conclusion from this study is that reactive transport models representing spatial and temporal heterogeneities are required to identify important factors that contribute to the redox gradients at riverine scales.

Edge effects on foliar stable isotope values in a Madagascan tropical dry forest.

PubMed

Crowley, Brooke E; McGoogan, Keriann C; Lehman, Shawn M

2012-01-01

Edge effects represent an inevitable and important consequence of habitat loss and fragmentation. These effects include changes in microclimate, solar radiation, or temperature. Such abiotic effects can, in turn, impact biotic factors. They can have a substantial impact on species, communities, and ecosystems. Here we examine clinal variations in stable carbon and nitrogen isotope values for trees along an edge-interior gradient in the dry deciduous forest at Ankarafantsika National Park. We predicted that soil respiration and differences in solar irradiance would result in stratified δ¹³C values where leaves collected close to the forest floor would have lower δ¹³C values than those growing higher up in the canopy. We also anticipated that plants growing at the savannah-forest boundary would have higher δ¹³C and δ¹⁵N values than plants growing in the forest interior. As expected, we detected a small but significant canopy effect. Leaves growing below 2 m from the forest floor exhibit δ¹³C values that are, on average, 1.1‰ lower than those growing above this threshold. We did not, however, find any relationship between foliar δ¹³C and distance from the edge. Unpredictably, we detected a striking positive relationship between foliar δ¹⁵N values and increasing distance into the forest interior. Variability in physiology among species, anthropogenic influence, organic input, and rooting depth cannot adequately explain this trend. Instead, this unexpected relationship most likely reflects decreasing nutrient or water availability, or a shift in N-sources with increasing distance from the savannah. Unlike most forest communities, the trees at Ampijoroa are growing in nutrient-limited sands. In addition to being nutrient poor, these well-drained soils likely decrease the amount of soil water available to forest vegetation. Continued research on plant responses to edge effects will improve our understanding of the conservation biology of forest ecosystems in Madagascar.

Edge Effects on Foliar Stable Isotope Values in a Madagascan Tropical Dry Forest

PubMed Central

Crowley, Brooke E.; McGoogan, Keriann C.; Lehman, Shawn M.

2012-01-01

Edge effects represent an inevitable and important consequence of habitat loss and fragmentation. These effects include changes in microclimate, solar radiation, or temperature. Such abiotic effects can, in turn, impact biotic factors. They can have a substantial impact on species, communities, and ecosystems. Here we examine clinal variations in stable carbon and nitrogen isotope values for trees along an edge-interior gradient in the dry deciduous forest at Ankarafantsika National Park. We predicted that soil respiration and differences in solar irradiance would result in stratified δ13C values where leaves collected close to the forest floor would have lower δ13C values than those growing higher up in the canopy. We also anticipated that plants growing at the savannah-forest boundary would have higher δ13C and δ15N values than plants growing in the forest interior. As expected, we detected a small but significant canopy effect. Leaves growing below 2 m from the forest floor exhibit δ13C values that are, on average, 1.1‰ lower than those growing above this threshold. We did not, however, find any relationship between foliar δ13C and distance from the edge. Unpredictably, we detected a striking positive relationship between foliar δ15N values and increasing distance into the forest interior. Variability in physiology among species, anthropogenic influence, organic input, and rooting depth cannot adequately explain this trend. Instead, this unexpected relationship most likely reflects decreasing nutrient or water availability, or a shift in N-sources with increasing distance from the savannah. Unlike most forest communities, the trees at Ampijoroa are growing in nutrient-limited sands. In addition to being nutrient poor, these well-drained soils likely decrease the amount of soil water available to forest vegetation. Continued research on plant responses to edge effects will improve our understanding of the conservation biology of forest ecosystems in Madagascar. PMID:22973460

Edaphic Conditions Regulate Denitrification Directly and Indirectly by Altering Denitrifier Abundance in Wetlands along the Han River, China.

PubMed

Xiong, Ziqian; Guo, Laodong; Zhang, Quanfa; Liu, Guihua; Liu, Wenzhi

2017-05-16

Riparian wetlands play a critical role in retaining nitrogen (N) from upland runoff and improving river water quality, mainly through biological processes such as soil denitrification. However, the relative contribution of abiotic and biotic factors to riparian denitrification capacity remains elusive. Here we report the spatiotemporal dynamics of potential and unamended soil denitrification rates in 20 wetlands along the Han River, an important water source in central China. We also quantified the abundance of soil denitrifying microorganisms using nirK and nirS genes. Results showed that soil denitrification rates were significantly different between riparian and reservoir shoreline wetlands, but not between mountain and lowland wetlands. In addition, soil denitrification rates showed strong seasonality, with higher values in August (summer) and April (spring) but lower values in January (winter). The potential and unamended denitrification rates were positively correlated with edaphic conditions (moisture and carbon concentration), denitrifier abundance, and plant species richness. Path analysis further revealed that edaphic conditions could regulate denitrification rates both directly and indirectly through their effects on denitrifier abundance. Our findings highlight that not only environmental factors, but also biotic factors including denitrifying microorganisms and standing vegetation, play an important role in regulating denitrification rate and N removal capacity in riparian wetlands.

Ecotoxicological assessment of flocculant modified soil for lake restoration using an integrated biotic toxicity index.

PubMed

Wang, Zhibin; Zhang, Honggang; Pan, Gang

2016-06-15

Flocculant modified soils/clays are being increasingly studied as geo-engineering materials for lake restoration and harmful algal bloom control. However, the potential impacts of adding these materials in aquatic ecological systems remain unclear. This study investigated the potential effects of chitosan, cationic starch, chitosan modified soils (MS-C) and cationic starch modified soils (MS-S) on the aquatic organisms by using a bioassay battery. The toxicity potential of these four flocculants was quantitatively assessed using an integrated biotic toxicity index (BTI). The test system includes four aquatic species, namely Chlorella vulgaris, Daphnia magna, Cyprinus carpio and Limnodrilus hoffmeisteri, which represent four trophic levels in the freshwater ecosystem. Results showed that median effect concentrations (EC50) of the MS-C and MS-S were 31-124 times higher than chitosan and cationic starch, respectively. D. magna was the most sensitive species to the four flocculants. Histological examination of C. carpio showed that significant pathological changes were found in gills. Different from chitosan and cationic starch, MS-C and MS-S significantly alleviated the acute toxicities of chitosan and cationic starch. The toxicity order of the four flocculants based on BTI were cationic starch > chitosan > MS-S > MS-C. The results suggested that BTI can be used as a quantitative and comparable indicator to assess biotic toxicity for aquatic geo-engineering materials. Chitosan or cationic starch modified soil/clay materials can be used at their optimal dosage without causing substantial adverse effects to the bioassay battery in aquatic ecosystem. Copyright © 2015 Elsevier Ltd. All rights reserved.

Long-term changes in composition and distribution patterns in the Iberian herpetofaunal communities since the latest Pleistocene

NASA Astrophysics Data System (ADS)

Bisbal-Chinesta, Josep Francesc; Blain, Hugues-Alexandre

2018-03-01

The climate has undergone significant changes since the end of the Last Glacial Maximum and in the course of the Holocene, parallel to important cultural transformations and migrations in the human communities. The faunal record has also suffered the effects of climate change. Amphibians and reptiles in particular have been shown to be highly sensitive because they are very susceptible to temperature alterations due to their ectothermy. This research presents the first approach to the Iberian paleobiogeography of the different species of amphibians and reptiles from the Late Pleistocene (MIS3) to present times, based on a comparative synthesis of the latest research published in recent years and the fossil record of the 58 archaeo-paleontological sites with significant assemblages. The paleoherpetofaunal associations make it possible to establish two major biotic regions during the Late Pleistocene. The first biotic region was located in the center and south of the Iberian Peninsula, with thermophilic species as the most representative taxa. The second biotic region was formed by the Atlantic-Cantabrian facade and the northeast Iberian area, dominated by hygrophilous and Euro-Siberian species, with an absence of Mediterranean species. After the Last Glacial Maximum there was an unprecedented concurrence in the northern Iberian Peninsula of autochthonous taxa from that area with thermophilic species. In the early Holocene, new species with no previous record in the Iberian Peninsula entered northern Iberia from eastern Mediterranean refugia. Finally, the introduction of North African species was the last significant biogeographical change during the Middle-Late Holocene.

Temporal variability in the importance of hydrologic, biotic, and climatic descriptors of dissolved oxygen dynamics in a shallow tidal-marsh creek

NASA Astrophysics Data System (ADS)

Nelson, N.; Munoz-Carpena, R.; Neale, P.; Tzortziou, M.; Megonigal, P.

2017-12-01

Due to strong abiotic forcing, dissolved oxygen (DO) in shallow tidal creeks often disobeys the conventional explanation of general aquatic DO cycling as biologically-regulated. In the present work, we seek to quantify the relative importance of abiotic (hydrologic and climatic), and biotic (primary productivity as represented by chlorophyll-a) descriptors of tidal creek DO. By fitting multiple linear regression models of DO to hourly chlorophyll-a, water quality, hydrology, and weather data collected in a tidal creek of a Chesapeake Bay marsh (Maryland, USA), temporal shifts (summer - early winter) in the relative importance of tidal creek DO descriptors were uncovered. Moreover, this analysis identified an alternative approach to evaluating tidal stage as a driver of DO by dividing stage into two DO-relevant variables: stage above and below bankfull depth. Within the hydrologic variable class, stage below bankfull depth dominated as an important descriptor, thus highlighting the role of pore water drainage and mixing as influential processes forcing tidal creek DO. Study findings suggest that tidal creek DO dynamics are explained by a balance of hydrologic, climatic, and biotic descriptors during warmer seasons due to many of these variables (i.e., chlorophyll-a, water temperature) acting as tracers of estuarine-marsh water mixing; conversely, in early winter months when estuarine and marsh waters differ less distinctly, hydrologic variables increase in relative importance as descriptors of tidal creek DO. These findings underline important distinctions in the underlying mechanisms dictating DO variability in shallow tidal marsh-creek environments relative to open water estuarine systems.

Temporal variability in the importance of hydrologic, biotic, and climatic descriptors of dissolved oxygen dynamics in a shallow tidal-marsh creek

NASA Astrophysics Data System (ADS)

Nelson, Natalie G.; Muñoz-Carpena, Rafael; Neale, Patrick J.; Tzortziou, Maria; Megonigal, J. Patrick

2017-08-01

Due to strong abiotic forcing, dissolved oxygen (DO) in shallow tidal creeks often disobeys the conventional explanation of general aquatic DO cycling as biologically regulated. In the present work, we seek to quantify the relative importance of abiotic (hydrologic and climatic), and biotic (primary productivity as represented by chlorophyll-a) descriptors of tidal creek DO. By fitting multiple linear regression models of DO to hourly chlorophyll-a, water quality, hydrology, and weather data collected in a tidal creek of a Chesapeake Bay marsh (Maryland, USA), temporal shifts (summer-early winter) in the relative importance of tidal creek DO descriptors were uncovered. Moreover, this analysis identified an alternative approach to evaluating tidal stage as a driver of DO by dividing stage into two DO-relevant variables: stage above and below bankfull depth. Within the hydrologic variable class, stage below bankfull depth dominated as an important descriptor, thus highlighting the role of pore water drainage and mixing as influential processes forcing tidal creek DO. Study findings suggest that tidal creek DO dynamics are explained by a balance of hydrologic, climatic, and biotic descriptors during warmer seasons due to many of these variables (i.e., chlorophyll-a, water temperature) acting as tracers of estuarine-marsh water mixing; conversely, in early winter months when estuarine and marsh waters differ less distinctly, hydrologic variables increase in relative importance as descriptors of tidal creek DO. These findings underline important distinctions in the underlying mechanisms dictating DO variability in shallow tidal marsh-creek environments relative to open water estuarine systems.

First steps in developing a multimetric macroinvertebrate index for the Ohio River

USGS Publications Warehouse

Applegate, J.M.; Baumann, P.C.; Emery, E.B.; Wooten, M.S.

2007-01-01

The causes of degradation of aquatic systems are often complex and stem from a variety of human influences. Comprehensive, multimetric biological indices have been developed to quantify this degradation and its effect on aquatic communities, and measure subsequent recovery from anthropogenic stressors. Traditionally, such indices have concentrated on small-to medium-sized streams. Recently, however, the Ohio River Fish Index (ORFIn) was created to assess biotic integrity in the Ohio River. The goal of the present project was to begin developing a companion Ohio River multimetric index using benthic macroinvertebrates. Hester-Dendy multiplate samplers were used to evaluate benthic macroinvertebrate assemblages in relation to a gradient of water quality disturbance, represented by varying distances downstream of industrial and municipal wastewater outfalls in the Ohio River. In August 1999 and 2000, samplers were set every 100 m downstream of outfalls (12 outfalls in 1999, 22 in 2000) for 300-1000 m, as well as at upstream reference sites. Candidate metrics (n = 55) were examined to determine which have potential to detect changes in water quality downstream of outfalls. These individual measures of community structure were plotted against distance downstream of each outfall to determine their response to water quality disturbance. Values at reference and outfall sites were also compared. Metrics that are ecologically relevant and showed a response to outfall disturbance were identified as potentially valuable in a multimetric index. Multiple box plots of index scores indicated greater response to outfall disturbance during periods of low-flow, and longitudinal river-wide trends. Evaluation of other types of anthropogenic disturbance, as well as continued analysis of the effects of chemical water quality on macroinvertebrate communities in future years will facilitate further development of a multimetric benthic macroinvertebrate index to evaluate biotic integrity in the Ohio River. Copyright ?? 2007 John Wiley & Sons, Ltd.

Effects of Four Different Restoration Treatments on the Natural Abundance of 15N Stable Isotopes in Plants

PubMed Central

Temperton, Vicky M.; Märtin, Lea L. A.; Röder, Daniela; Lücke, Andreas; Kiehl, Kathrin

2012-01-01

δ15N signals in plant and soil material integrate over a number of biogeochemical processes related to nitrogen (N) and therefore provide information on net effects of multiple processes on N dynamics. In general little is known in many grassland restoration projects on soil–plant N dynamics in relation to the restoration treatments. In particular, δ15N signals may be a useful tool to assess whether abiotic restoration treatments have produced the desired result. In this study we used the range of abiotic and biotic conditions provided by a restoration experiment to assess to whether the restoration treatments and/or plant functional identity and legume neighborhood affected plant δ15N signals. The restoration treatments consisted of hay transfer and topsoil removal, thus representing increasing restoration effort, from no restoration measures, through biotic manipulation to major abiotic manipulation. We measured δ15N and %N in six different plant species (two non-legumes and four legumes) across the restoration treatments. We found that restoration treatments were clearly reflected in δ15N of the non-legume species, with very depleted δ15N associated with low soil N, and our results suggest this may be linked to uptake of ammonium (rather than nitrate). The two non-legume species differed considerably in their δ15N signals, which may be related to the two species forming different kinds of mycorrhizal symbioses. Plant δ15N signals could clearly separate legumes from non-legumes, but our results did not allow for an assessment of legume neighborhood effects on non-legume δ15N signals. We discuss our results in the light of what the δ15N signals may be telling us about plant–soil N dynamics and their potential value as an indicator for N dynamics in restoration. PMID:22645597

Influence of physiological phenology on the seasonal pattern of ecosystem respiration in deciduous forests.

PubMed

Migliavacca, Mirco; Reichstein, Markus; Richardson, Andrew D; Mahecha, Miguel D; Cremonese, Edoardo; Delpierre, Nicolas; Galvagno, Marta; Law, Beverly E; Wohlfahrt, Georg; Black, T Andrew; Carvalhais, Nuno; Ceccherini, Guido; Chen, Jiquan; Gobron, Nadine; Koffi, Ernest; Munger, J William; Perez-Priego, Oscar; Robustelli, Monica; Tomelleri, Enrico; Cescatti, Alessandro

2015-01-01

Understanding the environmental and biotic drivers of respiration at the ecosystem level is a prerequisite to further improve scenarios of the global carbon cycle. In this study we investigated the relevance of physiological phenology, defined as seasonal changes in plant physiological properties, for explaining the temporal dynamics of ecosystem respiration (RECO) in deciduous forests. Previous studies showed that empirical RECO models can be substantially improved by considering the biotic dependency of RECO on the short-term productivity (e.g., daily gross primary production, GPP) in addition to the well-known environmental controls of temperature and water availability. Here, we use a model-data integration approach to investigate the added value of physiological phenology, represented by the first temporal derivative of GPP, or alternatively of the fraction of absorbed photosynthetically active radiation, for modeling RECO at 19 deciduous broadleaved forests in the FLUXNET La Thuile database. The new data-oriented semiempirical model leads to an 8% decrease in root mean square error (RMSE) and a 6% increase in the modeling efficiency (EF) of modeled RECO when compared to a version of the model that does not consider the physiological phenology. The reduction of the model-observation bias occurred mainly at the monthly time scale, and in spring and summer, while a smaller reduction was observed at the annual time scale. The proposed approach did not improve the model performance at several sites, and we identified as potential causes the plant canopy heterogeneity and the use of air temperature as a driver of ecosystem respiration instead of soil temperature. However, in the majority of sites the model-error remained unchanged regardless of the driving temperature. Overall, our results point toward the potential for improving current approaches for modeling RECO in deciduous forests by including the phenological cycle of the canopy. © 2014 John Wiley & Sons Ltd.

Quantitative patterns between plant volatile emissions induced by biotic stresses and the degree of damage

PubMed Central

Niinemets, Ülo; Kännaste, Astrid; Copolovici, Lucian

2013-01-01

Plants have to cope with a plethora of biotic stresses such as herbivory and pathogen attacks throughout their life cycle. The biotic stresses typically trigger rapid emissions of volatile products of lipoxygenase (LOX) pathway (LOX products: various C6 aldehydes, alcohols, and derivatives, also called green leaf volatiles) associated with oxidative burst. Further a variety of defense pathways is activated, leading to induction of synthesis and emission of a complex blend of volatiles, often including methyl salicylate, indole, mono-, homo-, and sesquiterpenes. The airborne volatiles are involved in systemic responses leading to elicitation of emissions from non-damaged plant parts. For several abiotic stresses, it has been demonstrated that volatile emissions are quantitatively related to the stress dose. The biotic impacts under natural conditions vary in severity from mild to severe, but it is unclear whether volatile emissions also scale with the severity of biotic stresses in a dose-dependent manner. Furthermore, biotic impacts are typically recurrent, but it is poorly understood how direct stress-triggered and systemic emission responses are silenced during periods intervening sequential stress events. Here we review the information on induced emissions elicited in response to biotic attacks, and argue that biotic stress severity vs. emission rate relationships should follow principally the same dose–response relationships as previously demonstrated for different abiotic stresses. Analysis of several case studies investigating the elicitation of emissions in response to chewing herbivores, aphids, rust fungi, powdery mildew, and Botrytis, suggests that induced emissions do respond to stress severity in dose-dependent manner. Bi-phasic emission kinetics of several induced volatiles have been demonstrated in these experiments, suggesting that next to immediate stress-triggered emissions, biotic stress elicited emissions typically have a secondary induction response, possibly reflecting a systemic response. The dose–response relationships can also vary in dependence on plant genotype, herbivore feeding behavior, and plant pre-stress physiological status. Overall, the evidence suggests that there are quantitative relationships between the biotic stress severity and induced volatile emissions. These relationships constitute an encouraging platform to develop quantitative plant stress response models. PMID:23888161

Toxic and Beneficial Potential of Silver Nanoparticles: The Two Sides of the Same Coin.

PubMed

Souza, Lilian Rodrigues Rosa; da Silva, Veronica Santana; Franchi, Leonardo Pereira; de Souza, Tiago Alves Jorge

2018-01-01

Nanotechnology has allowed great changes in chemical, biological and physical properties of metals when compared to their bulk counterparts. Within this context, silver nanoparticles (AgNPs) play a major role due to their unique properties, being widely used in daily products such as fabrics, washing machines, water filters, food and medicine. However, AgNPs can enter cells inducing a "Trojan-horse" type mechanism which potentially leads to cellular autophagy, apoptosis or necrosis. On the other hand, this cytotoxicity mechanism can be optimized to develop drug nanocarriers and anticancer therapies. The increasing use of these NPs entails their release into the environment, damaging ecosystems balance and representing a threat to human health. In this context, the possible deleterious effects that these NPs may represent for the biotic and abiotic ecosystems components represent an obstacle that must be overcome in order to guarantee the safety use of their unique properties.

A Report on the Methods to Associate Variations in Aquatic Biotic Condition to Variations in Stressors

EPA Science Inventory

In this report we present examples of methods that we have used to explore associations between aquatic biotic condition and stressors in two different aquatic systems: estuaries and lakes. We review metrics and indices of biotic condition in lakes and estuaries; discuss some ph...

How will biotic interactions influence climate change-induced range shifts?

PubMed

HilleRisLambers, Janneke; Harsch, Melanie A; Ettinger, Ailene K; Ford, Kevin R; Theobald, Elinore J

2013-09-01

Biotic interactions present a challenge in determining whether species distributions will track climate change. Interactions with competitors, consumers, mutualists, and facilitators can strongly influence local species distributions, but few studies assess how and whether these interactions will impede or accelerate climate change-induced range shifts. In this paper, we explore how ecologists might move forward on this question. We first outline the conditions under which biotic interactions can result in range shifts that proceed faster or slower than climate velocity and result in ecological surprises. Next, we use our own work to demonstrate that experimental studies documenting the strength of biotic interactions across large environmental gradients are a critical first step for understanding whether they will influence climate change-induced range shifts. Further progress could be made by integrating results from these studies into modeling frameworks to predict how or generalize when biotic interactions mediate how changing climates influence range shifts. Finally, we argue that many more case studies like those described here are needed to explore the importance of biotic interactions during climate change-induced range shifts. © 2013 New York Academy of Sciences.

Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions.

PubMed

Holland, J Nathaniel; DeAngelis, Donald L

2009-12-01

Interactions between two populations are often defined by their interaction outcomes; that is, the positive, neutral, or negative effects of species on one another. Yet, signs of outcomes are not absolute, but vary with the biotic and abiotic contexts of interactions. Here, we develop a general theory for transitions between outcomes based on consumer-resource (C-R) interactions in which one or both species exploit the other as a resource. Simple models of C-R interactions revealed multiple equilibria, including one for species coexistence and others for extinction of one or both species, indicating that species' densities alone could determine the fate of interactions. All possible outcomes [(+ +), (+ -), (--), (+ 0), (- 0), (0 0)] of species coexistence emerged merely through changes in parameter values of C-R interactions, indicating that variation in C-R interactions resulting from biotic and abiotic conditions could determine shifts in outcomes. These results suggest that C-R interactions can provide a broad mechanism for understanding context- and density-dependent transitions between interaction outcomes.

Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.

2009-01-01

Interactions between two populations are often defined by their interaction outcomes; that is, the positive, neutral, or negative effects of species on one another. Yet, signs of outcomes are not absolute, but vary with the biotic and abiotic contexts of interactions. Here, we develop a general theory for transitions between outcomes based on consumer-resource (C-R) interactions in which one or both species exploit the other as a resource. Simple models of C-R interactions revealed multiple equilibria, including one for species coexistence and others for extinction of one or both species, indicating that species densities alone could determine the fate of interactions. All possible outcomes (+ +), (+ -), (- -), (+ 0), (- 0), (0 0) of species coexistence emerged merely through changes in parameter values of C-R interactions, indicating that variation in C-R interactions resulting from biotic and abiotic conditions could determine shifts in outcomes. These results suggest that C-R interactions can provide a broad mechanism for understanding context- and density-dependent transitions between interaction outcomes.

Species richness declines and biotic homogenisation have slowed down for NW-European pollinators and plants

PubMed Central

Carvalheiro, Luísa Gigante; Kunin, William E; Keil, Petr; Aguirre-Gutiérrez, Jesus; Ellis, Willem Nicolaas; Fox, Richard; Groom, Quentin; Hennekens, Stephan; Landuyt, Wouter; Maes, Dirk; Meutter, Frank; Michez, Denis; Rasmont, Pierre; Ode, Baudewijn; Potts, Simon Geoffrey; Reemer, Menno; Roberts, Stuart Paul Masson; Schaminée, Joop; WallisDeVries, Michiel F; Biesmeijer, Jacobus Christiaan

2013-01-01

Concern about biodiversity loss has led to increased public investment in conservation. Whereas there is a widespread perception that such initiatives have been unsuccessful, there are few quantitative tests of this perception. Here, we evaluate whether rates of biodiversity change have altered in recent decades in three European countries (Great Britain, Netherlands and Belgium) for plants and flower visiting insects. We compared four 20-year periods, comparing periods of rapid land-use intensification and natural habitat loss (1930–1990) with a period of increased conservation investment (post-1990). We found that extensive species richness loss and biotic homogenisation occurred before 1990, whereas these negative trends became substantially less accentuated during recent decades, being partially reversed for certain taxa (e.g. bees in Great Britain and Netherlands). These results highlight the potential to maintain or even restore current species assemblages (which despite past extinctions are still of great conservation value), at least in regions where large-scale land-use intensification and natural habitat loss has ceased. PMID:23692632

Testing genotypic variation of an invasive plant species in response to soil disturbance and herbivory.

PubMed

Bayliss, Shannon L J; terHorst, Casey P; Lau, Jennifer A

2017-04-01

Herbivores, competitors, and predators can inhibit biological invasions ("biotic resistance" sensu Elton 1959), while disturbance typically promotes biological invasions. Although biotic resistance and disturbance are often considered separately in the invasion literature, these two forces may be linked. One mechanism by which disturbance may facilitate biological invasions is by decreasing the effectiveness of biotic resistance. The effects of both disturbance and biotic resistance may vary across invading genotypes, and genetic variation in the invasive propagule pool may increase the likelihood that some genotypes can overcome biotic resistance or take greater advantage of disturbance. We conducted an experimental field trial in which we manipulated soil disturbance (thatch removal and loosening soil) and the presence of insect herbivores and examined their effects on the invasion success of 44 Medicago polymorpha genotypes. As expected, insecticide reduced leaf damage and increased Medicago fecundity, suggesting that insect herbivores in this system provide some biotic resistance. Soil disturbance increased Medicago fecundity, but did not alter the effectiveness of biotic resistance by insect herbivores. We found significant genetic variation in Medicago in response to disturbance, but not in response to insect herbivores. These results suggest that the ability of Medicago to invade particular habitats depends on the amount of insect herbivory, the history of disturbance in the habitat, and how the specific genotypes in the invader pool respond to these factors.

Linking biotic homogenization to habitat type, invasiveness and growth form of naturalized alien plants in North America

Treesearch

Hong Qian; Qinfeng Guo

2010-01-01

Aim Biotic homogenization is a growing phenomenon and has recently attracted much attention. Here, we analyse a large dataset of native and alien plants in North America to examine whether biotic homogenization is related to several ecological and biological attributes. Location North America (north of Mexico). Methods We assembled...

Regional consequences of a biotic interchange: insights from the Lessepsian invasion

NASA Astrophysics Data System (ADS)

Nawrot, Rafal; Albano, Paolo G.; Chattopadhyay, Devapriya; Zuschin, Martin

2016-04-01

The fossil record provides ample evidence of large-scale biotic interchanges and their pervasive effects on regional biotas, but mechanisms controlling such events are difficult to decipher in deep time. Massive invasion of Indo-Pacific species into the Mediterranean Sea triggered by the opening of the Suez Canal offers a unique opportunity to examine the ecological consequences of breaking down biogeographic barriers. We developed an extensive database of taxonomic composition, body size and ecological characteristics of the Red Sea and Mediterranean bivalve fauna in order to link biotic selectivity of the invasion process with its effects on the recipient biota. Shallow-water occurrence and presence outside the tropical zone in other regions are the strongest predictors of the successful transition through the Suez Canal. Subsequent establishment of alien species in the Mediterranean Sea correlates with early arrival and preference for hard substrates. Finally, large-bodied species and hard-bottom dwellers are over-represented among the invasive aliens that have reached the spread stage and impose a strong impact on native communities. Although body size is important only at the last invasion stage, alien species are significantly larger compared to native Mediterranean bivalves. This reflects biogeographic difference in the body-size distributions of the source and recipient species pools related to the recent geological history of the Mediterranean Sea. Contrary to the general expectations on the effects of temperature on average body size, continued warming of the Mediterranean Sea accelerates the entry of tropical aliens and thus indirectly leads to increase in the proportion of large-bodied species in local communities and the regional biota. Invasion-driven shifts in species composition are stronger in hard-substrate communities, which host a smaller pool of incumbent species and are more susceptible to the establishment of newcomers. Analogous differences between habitats and body-size classes in the invasion levels have been observed in some marine biotic interchanges documented in the fossil record. Further quantitative studies of past invasion events are necessary to test generality of these patterns.

Water-quality, stream-habitat, and biological data for Highland and Marchand Bayous, Galveston County, Texas, 2006-07

USGS Publications Warehouse

Brown, Dexter W.; Mabe, Jeffrey A.; Turco, Michael J.

2008-01-01

Benthic macroinvertebrate and fish data were collected from the same five sites identified for habitat evaluation. Three assessments were done to account for seasonal differences in biotic distribution. Stream-habitat and aquatic biota (benthic macroinvertebrates and fish) were assessed at each site three times during the study to evaluate aquatic life use. A total of 5,126 macroinvertebrate individuals were identified at all sites. During the study, 34 species of fish representing 28 families were collected from all the sites. 

Genomic perspectives in microbial oceanography.

PubMed

DeLong, Edward F; Karl, David M

2005-09-15

The global ocean is an integrated living system where energy and matter transformations are governed by interdependent physical, chemical and biotic processes. Although the fundamentals of ocean physics and chemistry are well established, comprehensive approaches to describing and interpreting oceanic microbial diversity and processes are only now emerging. In particular, the application of genomics to problems in microbial oceanography is significantly expanding our understanding of marine microbial evolution, metabolism and ecology. Integration of these new genome-enabled insights into the broader framework of ocean science represents one of the great contemporary challenges for microbial oceanographers.

Pre-cometary ice composition from hot core chemistry.

PubMed

Tornow, Carmen; Kührt, Ekkehard; Motschmann, Uwe

2005-10-01

Pre-cometary ice located around star-forming regions contains molecules that are pre-biotic compounds or pre-biotic precursors. Molecular line surveys of hot cores provide information on the composition of the ice since it sublimates near these sites. We have combined a hydrostatic hot core model with a complex network of chemical reactions to calculate the time-dependent abundances of molecules, ions, and radicals. The model considers the interaction between the ice and gas phase. It is applied to the Orion hot core where high-mass star formation occurs, and to the solar-mass binary protostar system IRAS 16293-2422. Our calculations show that at the end of the hot core phase both star-forming sites produce the same prebiotic CN-bearing molecules. However, in the Orion hot core these molecules are formed in larger abundances. A comparison of the calculated values with the abundances derived from the observed line data requires a chemically unprocessed molecular cloud as the initial state of hot core evolution. Thus, it appears that these objects are formed at a much younger cloud stage than previously thought. This implies that the ice phase of the young clouds does not contain CN-bearing molecules in large abundances before the hot core has been formed. The pre-biotic molecules synthesized in hot cores cause a chemical enrichment in the gas phase and in the pre-cometary ice. This enrichment is thought to be an important extraterrestrial aspect of the formation of life on Earth and elsewhere.

Mechanisms of biotic resistance across complex life cycles.

PubMed

Rius, Marc; Potter, Elaine E; Aguirre, J David; Stachowicz, John J

2014-01-01

Biotic resistance is the ability of communities to inhibit the establishment, spread or impact of novel species. However, the interactions that underlie biotic resistance depend heavily on the contexts in which species interact. Consequently, studies of biotic resistance that consider single processes, patches, species or life-history stages may provide an incomplete picture of the capacity for communities to resist invasion. Many organisms have multiphasic life cycles, where individuals can occupy distinct niches at different stages of the life history. Generally, studies of biotic resistance focus on interactions within a single life-history stage, and interactions at other life-history stages are overlooked. Here, we demonstrate that different mechanisms of biotic resistance occur across the life history and together limit the invasion success of an introduced marine invertebrate (Ciona intestinalis) in Northern California. We tested the role of interactions (competition and predation) with the resident community in limiting the abundance of Ciona through experiments conducted on fertilization, larval survival, settlement, early postsettlement survival, and the survival of juveniles and adults. Under some circumstances, Ciona became abundant in mid-successional stages and showed more rapid growth rates than a morphologically similar native species, Ascidia ceratodes. However, predators reduced Ciona abundance much more than that of Ascidia at several life stages. Furthermore, Ciona appeared to be a weaker competitor at the adult stage. Early life-history interactions with other sessile species at the fertilization, larval and recruit stages had modest to no effects on Ciona abundance. The presence of biotic resistance mechanisms acting at multiple life stages, and potentially under different conditions, suggests that different components of biotic resistance interact to enhance the resident community's resistance to invasion. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

The Role of Tomato WRKY Genes in Plant Responses to Combined Abiotic and Biotic Stresses

PubMed Central

Bai, Yuling; Sunarti, Sri; Kissoudis, Christos; Visser, Richard G. F.; van der Linden, C. G.

2018-01-01

In the field, plants constantly face a plethora of abiotic and biotic stresses that can impart detrimental effects on plants. In response to multiple stresses, plants can rapidly reprogram their transcriptome through a tightly regulated and highly dynamic regulatory network where WRKY transcription factors can act as activators or repressors. WRKY transcription factors have diverse biological functions in plants, but most notably are key players in plant responses to biotic and abiotic stresses. In tomato there are 83 WRKY genes identified. Here we review recent progress on functions of these tomato WRKY genes and their homologs in other plant species, such as Arabidopsis and rice, with a special focus on their involvement in responses to abiotic and biotic stresses. In particular, we highlight WRKY genes that play a role in plant responses to a combination of abiotic and biotic stresses.

Uncertainty result of biotic index in analysing the water quality of Cikapundung river catchment area, Bandung

NASA Astrophysics Data System (ADS)

Surtikanti, Hertien Koosbandiah

2017-05-01

The Biotic Index was developed in Western Countries in response to the need in water quality evaluation. This method analysis is based on the classification of aquatic macrobenthos as a bioindicator for clean and polluted water. The aim of this study is to compare the analysis of Cikapundung river using 6 different Biotic Indexes. BI Shannon-Weiner, Belgian Biological Index (BBI), Family Biotic Index (FBI), Biological Monitoring Working Party (BMWP), Biological Monitoring Working Party-Average Score Per Taxon (BMWP-ASPT), and A Scoring System for Macroinvertebrate in Australian River (A SIGNAL). Those analysis are compared with Physical Water Index (CPI) which is developed in Indonesia. The result shows that a decreasing water quality is detected upstream to downstream of Cikapundung River. However, based on the CPI analysis result, the BMWP-ASPT biotic index analysis is more comprehensive than other BI in explaining Cikapundung water quality.

Hydrologic, abiotic and biotic interactions: plant density, windspeed, leaf size and groundwater all affect oak water use efficiency

Treesearch

Darin J. Law; Deborah M. Finch

2011-01-01

Plant water use in drylands can be complex due to variation in hydrologic, abiotic and biotic factors, particularly near ephemeral or intermittent streams. Plant use of groundwater may be important but is usually uncertain. Disturbances like fire contribute to complex spatiotemporal heterogeneity. Improved understanding of how such hydrologic, abiotic, and biotic...

Linking macroecology and community ecology: refining predictions of species distributions using biotic interaction networks.

PubMed

Staniczenko, Phillip P A; Sivasubramaniam, Prabu; Suttle, K Blake; Pearson, Richard G

2017-06-01

Macroecological models for predicting species distributions usually only include abiotic environmental conditions as explanatory variables, despite knowledge from community ecology that all species are linked to other species through biotic interactions. This disconnect is largely due to the different spatial scales considered by the two sub-disciplines: macroecologists study patterns at large extents and coarse resolutions, while community ecologists focus on small extents and fine resolutions. A general framework for including biotic interactions in macroecological models would help bridge this divide, as it would allow for rigorous testing of the role that biotic interactions play in determining species ranges. Here, we present an approach that combines species distribution models with Bayesian networks, which enables the direct and indirect effects of biotic interactions to be modelled as propagating conditional dependencies among species' presences. We show that including biotic interactions in distribution models for species from a California grassland community results in better range predictions across the western USA. This new approach will be important for improving estimates of species distributions and their dynamics under environmental change. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Tree Biomass Estimation of Chinese fir (Cunninghamia lanceolata) Based on Bayesian Method

PubMed Central

Zhang, Jianguo

2013-01-01

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most important conifer species for timber production with huge distribution area in southern China. Accurate estimation of biomass is required for accounting and monitoring Chinese forest carbon stocking. In the study, allometric equation was used to analyze tree biomass of Chinese fir. The common methods for estimating allometric model have taken the classical approach based on the frequency interpretation of probability. However, many different biotic and abiotic factors introduce variability in Chinese fir biomass model, suggesting that parameters of biomass model are better represented by probability distributions rather than fixed values as classical method. To deal with the problem, Bayesian method was used for estimating Chinese fir biomass model. In the Bayesian framework, two priors were introduced: non-informative priors and informative priors. For informative priors, 32 biomass equations of Chinese fir were collected from published literature in the paper. The parameter distributions from published literature were regarded as prior distributions in Bayesian model for estimating Chinese fir biomass. Therefore, the Bayesian method with informative priors was better than non-informative priors and classical method, which provides a reasonable method for estimating Chinese fir biomass. PMID:24278198

Tree biomass estimation of Chinese fir (Cunninghamia lanceolata) based on Bayesian method.

PubMed

Zhang, Xiongqing; Duan, Aiguo; Zhang, Jianguo

2013-01-01

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most important conifer species for timber production with huge distribution area in southern China. Accurate estimation of biomass is required for accounting and monitoring Chinese forest carbon stocking. In the study, allometric equation W = a(D2H)b was used to analyze tree biomass of Chinese fir. The common methods for estimating allometric model have taken the classical approach based on the frequency interpretation of probability. However, many different biotic and abiotic factors introduce variability in Chinese fir biomass model, suggesting that parameters of biomass model are better represented by probability distributions rather than fixed values as classical method. To deal with the problem, Bayesian method was used for estimating Chinese fir biomass model. In the Bayesian framework, two priors were introduced: non-informative priors and informative priors. For informative priors, 32 biomass equations of Chinese fir were collected from published literature in the paper. The parameter distributions from published literature were regarded as prior distributions in Bayesian model for estimating Chinese fir biomass. Therefore, the Bayesian method with informative priors was better than non-informative priors and classical method, which provides a reasonable method for estimating Chinese fir biomass.

Performance of biotic indices in comparison to chemical-based Water Quality Index (WQI) in evaluating the water quality of urban river.

PubMed

Wan Abdul Ghani, Wan Mohd Hafezul; Abas Kutty, Ahmad; Mahazar, Mohd Akmal; Al-Shami, Salman Abdo; Ab Hamid, Suhaila

2018-04-19

In order to evaluate the water quality of one of the most polluted urban river in Malaysia, the Penchala River, performance of eight biotic indices, Biomonitoring Working Party (BMWP), BMWP Thai , BMWP Viet , Average Score Per Taxon (ASPT), ASPT Thai , BMWP Viet , Family Biotic Index (FBI), and Singapore Biotic Index (SingScore), was compared. The water quality categorization based on these biotic indices was then compared with the categorization of Malaysian Water Quality Index (WQI) derived from measurements of six water physicochemical parameters (pH, BOD, COD, NH 3 -N, DO, and TSS). The river was divided into four sections: upstream section (recreational area), middle stream 1 (residential area), middle stream 2 (commercial area), and downstream. Abundance and diversity of the macroinvertebrates were the highest in the upstream section (407 individual and H' = 1.56, respectively), followed by the middle stream 1 (356 individual and H' = 0.82). The least abundance was recorded in the downstream section (214 individual). Among all biotic indices, BMWP was the most reliable in evaluating the water quality of this urban river as their classifications were comparable to the WQI. BMWPs in this study have strong relationships with dissolved oxygen (DO) content. Our results demonstrated that the biotic indices were more sensitive towards organic pollution than the WQI. BMWP indices especially BMWP Viet were the most reliable and could be adopted along with the WQI for assessment of water quality in urban rivers.

Specialization in Plant-Hummingbird Networks Is Associated with Species Richness, Contemporary Precipitation and Quaternary Climate-Change Velocity

PubMed Central

Dalsgaard, Bo; Magård, Else; Fjeldså, Jon; Martín González, Ana M.; Rahbek, Carsten; Olesen, Jens M.; Ollerton, Jeff; Alarcón, Ruben; Cardoso Araujo, Andrea; Cotton, Peter A.; Lara, Carlos; Machado, Caio Graco; Sazima, Ivan; Sazima, Marlies; Timmermann, Allan; Watts, Stella; Sandel, Brody; Sutherland, William J.; Svenning, Jens-Christian

2011-01-01

Large-scale geographical patterns of biotic specialization and the underlying drivers are poorly understood, but it is widely believed that climate plays an important role in determining specialization. As climate-driven range dynamics should diminish local adaptations and favor generalization, one hypothesis is that contemporary biotic specialization is determined by the degree of past climatic instability, primarily Quaternary climate-change velocity. Other prominent hypotheses predict that either contemporary climate or species richness affect biotic specialization. To gain insight into geographical patterns of contemporary biotic specialization and its drivers, we use network analysis to determine the degree of specialization in plant-hummingbird mutualistic networks sampled at 31 localities, spanning a wide range of climate regimes across the Americas. We found greater biotic specialization at lower latitudes, with latitude explaining 20–22% of the spatial variation in plant-hummingbird specialization. Potential drivers of specialization - contemporary climate, Quaternary climate-change velocity, and species richness - had superior explanatory power, together explaining 53–64% of the variation in specialization. Notably, our data provides empirical evidence for the hypothesized roles of species richness, contemporary precipitation and Quaternary climate-change velocity as key predictors of biotic specialization, whereas contemporary temperature and seasonality seem unimportant in determining specialization. These results suggest that both ecological and evolutionary processes at Quaternary time scales can be important in driving large-scale geographical patterns of contemporary biotic specialization, at least for co-evolved systems such as plant-hummingbird networks. PMID:21998716

Evaluating robustness in rank-based risk assessments of freshwater ecosystems

USGS Publications Warehouse

Mattson, K.M.; Angermeier, Paul

2007-01-01

Conservation planning aims to protect biodiversity by sustainng the natural physical, chemical, and biological processes within representative ecosystems. Often data to measure these components are inadequate or unavailable. The impact of human activities on ecosystem processes complicates integrity assessments and might alter ecosystem organization at multiple spatial scales. Freshwater conservation targets, such as populations and communities, are influenced by both intrinsic aquatic properties and the surrounding landscape, and locally collected data might not accurately reflect potential impacts. We suggest that changes in five major biotic drivers—energy sources, physical habitat, flow regime, water quality, and biotic interactions—might be used as surrogates to inform conservation planners of the ecological integrity of freshwater ecosystems. Threats to freshwater systems might be evaluated based on their impact to these drivers to provide an overview of potential risk to conservation targets. We developed a risk-based protocol, the Ecological Risk Index (ERI), to identify watersheds with least/most risk to conservation targets. Our protocol combines risk-based components, specifically the frequency and severity of human-induced stressors, with biotic drivers and mappable land- and water-use data to provide a summary of relative risk to watersheds. We illustrate application of our protocol with a case study of the upper Tennessee River basin, USA. Differences in risk patterns among the major drainages in the basin reflect dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among our watersheds. We also found that the relative importance of threats is sensitive to the spatial grain of the analysis. Our case study demonstrates that the ERI is useful for evaluating the frequency and severity of ecosystemwide risk, which can inform local and regional conservation planning.

Dissecting global diversity patterns: examples from the Ordovician Radiation

NASA Technical Reports Server (NTRS)

Miller, A. I.

1997-01-01

Although the history of life has been characterized by intermittent episodes of radiation that can be recognized in global compilations of biodiversity, it does not necessarily follow that these episodes are caused by processes that occurred uniformly around the world. Major diversity increases could be generated by the cumulative effects of different mechanisms operating simultaneously at several geographic or environmental scales. The purpose of this review is to describe ongoing research on the manifestations, at several scales, of the Ordovician Radiation, which was among the most extensive intervals of diversification in the history of life. Through much of the period, diversity was concentrated most heavily near regions of active mountain building and volcanism; differences in diversity patterns from continent to continent, and among regions within continents, reflect this overprint. While this suggests a linkage of the Radiation and tectonic activity, this is by no means the only mediating agent. Outcrop-based research in North America has demonstrated that tectonic activity was detrimental to some biotic elements, in contrast to its effects on other organisms. Moreover, in the Great Basin of North America where the local stratigraphic record is of particularly high quality, biotic transitions characteristic of the period occurred far more rapidly than observed in global compilations of diversity, suggesting that the global rate of transition may represent the aggregate sum of transitions that occurred abruptly, but at different times, around the world. Finally, it has been demonstrated that, in concert with an increase in average age, the environmental and geographic ranges of Ordovician genera both increased significantly through the period, indicating a role for intrinsic factors in producing Ordovician biotic patterns.

Support media can steer methanogenesis in the presence of phenol through biotic and abiotic effects.

PubMed

Poirier, Simon; Déjean, Sébastien; Chapleur, Olivier

2018-09-01

A wide variety of inhibitors can induce anaerobic digester disruption. To avoid performance losses, support media can be used to mitigate inhibitions. However, distinguishing the physico-chemical from the biological mechanisms of such strategies remains delicate. In this framework, the impact of 10  g/L of different types of zeolites and activated carbons (AC) on microbial community dynamics during anaerobic digestion of biowaste in the presence of 1.3 g/L of phenol was evaluated with 16 S rRNA gene sequencing. In the presence of AC, methanogenesis inhibition was rapidly removed due to a decrease of phenol concentration. This abiotic effect related to the physico-chemical properties of AC led to increased final CH4 and CO2 productions by 29-31% compared to digesters incubated without support. Interestingly, although zeolite did not adsorb phenol, final CH4 and CO2 production reached comparable levels as with AC. Nevertheless, compared to digesters incubated without support, methanogenesis lag phase duration was less reduced in the presence of zeolites (5 ± 1 days) than in the presence of activated carbons (12 ± 2 days). Both types of support induced biotic effects. AC and zeolite both allowed the preservation of the major representative archaeal genus of the non-inhibited ecosystem, Methanosarcina. By contrast, they distinctly shaped bacterial populations. OTUs belonging to class W5 became dominant at the expense of OTUs assigned to orders Clostridiales, Bacteroidales and Anaerolinales in the presence of AC. Zeolite enhanced the implantation of OTUs assigned to bacterial phylum Cloacimonetes. This study highlighted that supports can induce biotic and abiotic effects within digesters inhibited with phenol, showing potentialities to enhance anaerobic digestion stability under disrupting conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

The importance of disturbance by fire and other abiotic and biotic factors in driving cheatgrass invasion varies based on invasion stage

Treesearch

Becky K. Kerns; Michelle A. Day

2017-01-01

Disturbances create fluctuations in resource availability that alter abiotic and biotic constraints. Exotic invader response may be due to multiple factors related to disturbance regimes and complex interactions between other small- and largescale abiotic and biotic processes that may vary across invasion stages. We explore how cheatgrass responds to both frequency and...

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

PubMed Central

Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

2013-01-01

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km2 to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere. PMID:22686347

Field Characterization of the Mineralogy and Organic Chemistry of Carbonates from the 2010 Arctic Mars Analog Svalbard Expedition by Evolved Gas Analysis

NASA Technical Reports Server (NTRS)

McAdam, A. C.; Ten Kate, I. L.; Stern, J. C.; Mahaffy, P. R.; Blake, D. F.; Morris, R. V.; Steele, A.; Amundson, H. E. F.

2011-01-01

The 2010 Arctic Mars Analog Svalbard Expedition (AMASE) investigated two geologic settings using methodologies and techniques being developed or considered for future Mars missions, such as the Mars Science Laboratory (MSL), ExoMars, and Mars Sample Return. The Sample Analysis at Mars (SAM) [1] instrument suite, which will be on MSL, consists of a quadrupole mass spectrometer (QMS), a gas chromatograph (GC), and a tunable laser mass spectrometer (TLS); all will be applied to analyze gases created by pyrolysis of samples. During AMASE, a Hiden Evolved Gas Analysis-Mass Spectrometer (EGA-MS) system represented the EGA-MS capability of SAM. Another MSL instrument, CheMin, will use x-ray diffraction (XRD) and x-ray fluorescence (XRF) to perform quantitative mineralogical characterization of samples [e.g., 2]. Field-portable versions of CheMin were used during AMASE. AMASE 2010 focused on two sites that represented biotic and abiotic analogs. The abiotic site was the basaltic Sigurdfjell vent complex, which contains Mars-analog carbonate cements including carbonate globules which are excellent analogs for the globules in the ALH84001 martian meteorite [e.g., 3, 4]. The biotic site was the Knorringfjell fossil methane seep, which featured carbonates precipitated in a methane-supported chemosynthetic community [5]. This contribution focuses on EGA-MS analyses of samples from each site, with mineralogy comparisons to CheMin team results. The results give insight into organic content and organic-mineral associations, as well as some constraints on the minerals present.

A Benthic Community Index for streams in the Northern Lakes and Forests Ecoregion

USGS Publications Warehouse

Butcher, Jason T.; Stewart, Paul M.; Simon, Thomas P.

2003-01-01

Encompassing the northern glaciated section of the Midwest United States, the Northern Lakes and Forests Ecoregion is characterized by mixed conifer and deciduous forests and wetlands. Sites were randomly selected in the ecoregion using the Environmental Protection Agency's Environmental Monitoring and Assessment Program designed to develop an index of biotic integrity for wadeable streams. Macroinvertebrates were sampled during the fall of 1998 and 1999 using a multi-habitat, composite-sample method. Two hundred forty-six invertebrate taxa in 97 families were collected from 94 sites. Ten of 42 candidate metrics satisfied metric selection criteria, including six structural metrics (number of Ephemeroptera taxa, number of Diptera taxa, richness, Shannon-Wiener diversity, percent Trichoptera abundance, and percent Crustacea and Mollusca abundance), two functional metrics (number of Filterer taxa and number of Scraper taxa), and two conditional metrics (number of Ephemeroptera, Trichoptera, and Plecoptera taxa and Hilsenhoff Biotic Index). These metrics were used to develop a Benthic Community Index to assess the biological integrity of wadeable streams in the ecoregion. Index values ranged from 10 to 50, and scores from impaired sites were significantly different than non-impaired sites (P<0.001). Index values were divided into three narrative interpretations of biological integrity (poor, fair, and good). After further testing, the index may provide a useful biological assessment tool for resource managers in the ecoregion.

Environmental Status of the Lake Michigan Region Volume 11. Natural Areas of the Lake Michigan Drainage Basin and Endangered or Threatened Plant and Animal Species

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

Stearns, Forest; Lindsley, Diane

1977-09-01

The accelerating encroachment of human activity on the natural landscape has made many citizens appreciate the need to save representative biotic communities before urbanization and technologically induced change eliminate such communities. Active programs in natural-area preservation a.re now in progress in the four basin states; these programs have strong public support and legislative mandate. Local, state, and federal agencies and private individuals have taken an active interest in protecting select areas as samples of the biotic communities and natural features of the Basin. Most natural areas described in this report have been dedicated or reserved in some fashion. Other areasmore » are being added by the basin states each year. The maintenance of natural communities is closely linked to the preservation of endangered and threatened species of plants and animals which would cease to survive as isolated populations. Under federal regulations, certain plants and animals are listed as endange~ ed or threatened in the Basin. As individual state lists are prepared and investigations proceed, it is probable that many more threatened species will be found.« less

An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism.

PubMed

Mélade, Julien; Wieseke, Nicolas; Ramasindrazana, Beza; Flores, Olivier; Lagadec, Erwan; Gomard, Yann; Goodman, Steven M; Dellagi, Koussay; Pascalis, Hervé

2016-04-12

An eco-epidemiological investigation was carried out on Madagascar bat communities to better understand the evolutionary mechanisms and environmental factors that affect virus transmission among bat species in closely related members of the genus Morbillivirus, currently referred to as Unclassified Morbilli-related paramyxoviruses (UMRVs). A total of 947 bats were investigated originating from 52 capture sites (22 caves, 18 buildings, and 12 outdoor sites) distributed over different bioclimatic zones of the island. Using RT-PCR targeting the L-polymerase gene of the Paramyxoviridae family, we found that 10.5% of sampled bats were infected, representing six out of seven families and 15 out of 31 species analyzed. Univariate analysis indicates that both abiotic and biotic factors may promote viral infection. Using generalized linear modeling of UMRV infection overlaid on biotic and abiotic variables, we demonstrate that sympatric occurrence of bats is a major factor for virus transmission. Phylogenetic analyses revealed that all paramyxoviruses infecting Malagasy bats are UMRVs and showed little host specificity. Analyses using the maximum parsimony reconciliation tool CoRe-PA, indicate that host-switching, rather than co-speciation, is the dominant macro-evolutionary mechanism of UMRVs among Malagasy bats.

Environmental status of the Lake Michigan region. Volume II. Natural areas of the Lake Michigan drainage basin and endangered or threatened plant and animal species

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

Stearns, F.; Lindsley, D.

1977-09-01

The accelerating encroachment of human activity on the natural landscape has made many citizens appreciate the need to save representative biotic communities before urbanization and technologically induced change eliminate such communities. Active programs in natural-area preservation are now in progress in the four basin states; these programs have strong public support and legislative mandate. Local, state, and federal agencies and private individuals have taken an active interest in protecting select areas as samples of the biotic communities and natural features of the Basin. Most natural areas described in this report have been dedicated or reserved in some fashion. Other areasmore » are being added by the basin states each year. The maintenance of natural communities is closely linked to the preservation of endangered and threatened species of plants and animals which would cease to survive as isolated populations. Under federal regulations, certain plants and animals are listed as endangered or threatened in the Basin. As individual state lists are prepared and investigations proceed, it is probable that many more threatened species will be found.« less

Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system.

PubMed

Bonachela, Juan A; Wortel, Meike T; Stenseth, Nils Chr

2017-12-15

The Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

NASA Astrophysics Data System (ADS)

Monard, C.; Gantner, S.; Bertilsson, S.; Hallin, S.; Stenlid, J.

2016-11-01

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

Design, engineering and utility of biotic games.

PubMed

Riedel-Kruse, Ingmar H; Chung, Alice M; Dura, Burak; Hamilton, Andrea L; Lee, Byung C

2011-01-07

Games are a significant and defining part of human culture, and their utility beyond pure entertainment has been demonstrated with so-called 'serious games'. Biotechnology--despite its recent advancements--has had no impact on gaming yet. Here we propose the concept of 'biotic games', i.e., games that operate on biological processes. Utilizing a variety of biological processes we designed and tested a collection of games: 'Enlightenment', 'Ciliaball', 'PAC-mecium', 'Microbash', 'Biotic Pinball', 'POND PONG', 'PolymerRace', and 'The Prisoner's Smellemma'. We found that biotic games exhibit unique features compared to existing game modalities, such as utilizing biological noise, providing a real-life experience rather than virtual reality, and integrating the chemical senses into play. Analogous to video games, biotic games could have significant conceptual and cost-reducing effects on biotechnology and eventually healthcare; enable volunteers to participate in crowd-sourcing to support medical research; and educate society at large to support personal medical decisions and the public discourse on bio-related issues.

The interactions of ants with their biotic environment.

PubMed

Chomicki, Guillaume; Renner, Susanne S

2017-03-15

This s pecial feature results from the symposium 'Ants 2016: ant interactions with their biotic environments' held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this s pecial feature After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts. Using a large molecular clock-dated Formicidae phylogeny, we map the evolutionary origins of different ant clades' interactions with plants, fungi and hemiptera. Ants' biotic interactions provide ideal systems to address fundamental ecological and evolutionary questions about mutualism, coevolution, adaptation and animal communication. © 2017 The Author(s).

The interactions of ants with their biotic environment

PubMed Central

Renner, Susanne S.

2017-01-01

This special feature results from the symposium ‘Ants 2016: ant interactions with their biotic environments’ held in Munich in May 2016 and deals with the interactions between ants and other insects, plants, microbes and fungi, studied at micro- and macroevolutionary levels with a wide range of approaches, from field ecology to next-generation sequencing, chemical ecology and molecular genetics. In this paper, we review key aspects of these biotic interactions to provide background information for the papers of this special feature. After listing the major types of biotic interactions that ants engage in, we present a brief overview of ant/ant communication, ant/plant interactions, ant/fungus symbioses, and recent insights about ants and their endosymbionts. Using a large molecular clock-dated Formicidae phylogeny, we map the evolutionary origins of different ant clades' interactions with plants, fungi and hemiptera. Ants' biotic interactions provide ideal systems to address fundamental ecological and evolutionary questions about mutualism, coevolution, adaptation and animal communication. PMID:28298352

Mechanism of Uranium Reduction and Immobilization in Desulfovibrio vulgaris Biofilms.

PubMed

Stylo, Malgorzata; Neubert, Nadja; Roebbert, Yvonne; Weyer, Stefan; Bernier-Latmani, Rizlan

2015-09-01

The prevalent formation of noncrystalline U(IV) species in the subsurface and their enhanced susceptibility to reoxidation and remobilization, as compared to crystalline uraninite, raise concerns about the long-term sustainability of the bioremediation of U-contaminated sites. The main goal of this study was to resolve the remaining uncertainty concerning the formation mechanism of noncrystalline U(IV) in the environment. Controlled laboratory biofilm systems (biotic, abiotic, and mixed biotic-abiotic) were probed using a combination of U isotope fractionation and X-ray absorption spectroscopy (XAS). Regardless of the mechanism of U reduction, the presence of a biofilm resulted in the formation of noncrystalline U(IV). Our results also show that biotic U reduction is the most effective way to immobilize and reduce U. However, the mixed biotic-abiotic system resembled more closely an abiotic system: (i) the U(IV) solid phase lacked a typically biotic isotope signature and (ii) elemental sulfur was detected, which indicates the oxidation of sulfide coupled to U(VI) reduction. The predominance of abiotic U reduction in our systems is due to the lack of available aqueous U(VI) species for direct enzymatic reduction. In contrast, in cases where bicarbonate is present at a higher concentration, aqueous U(VI) species dominate, allowing biotic U reduction to outcompete the abiotic processes.

Conflict between biotic and climatic selective pressures acting on an extended phenotype in a subarctic, but not temperate, environment.

PubMed

Rohwer, V G; Bonier, F; Martin, P R

2015-10-22

Climatic selective pressures are thought to dominate biotic selective pressures at higher latitudes. However, few studies have experimentally tested how these selective pressures differentially act on traits across latitudes because traits can rarely be manipulated independently of the organism in nature. We overcame this challenge by using an extended phenotype-active bird nests-and conducted reciprocal transplant experiments between a subarctic and temperate site, separated by 14° of latitude. At the subarctic site, biotic selective pressures (nest predation) favoured smaller, non-local temperate nests, whereas climatic selective pressures (temperature) favoured larger local nests, particularly at colder temperatures. By contrast, at the temperate site, climatic and biotic selective pressures acted similarly on temperate and subarctic nests. Our results illustrate a functional trade-off in the subarctic between nest morphologies favoured by biotic versus climatic selective pressures, with climate favouring local nest morphologies. At our temperate site, however, allocative trade-offs in the time and effort devoted to nest construction favour smaller, local nests. Our findings illustrate a conflict between biotic and climatic selective pressures at the northern extremes of a species geographical range, and suggest that trade-offs between trait function and trait elaboration act differentially across latitude to create broad geographic variation in traits. © 2015 The Author(s).

Abiotic vs. biotic influences on habitat selection of coexisting species: Climate change impacts?

USGS Publications Warehouse

Martin, T.E.

2001-01-01

Species are commonly segregated along gradients of microclimate and vegetation. I explore the question of whether segregation is the result of microhabitat partitioning (biotic effects) or choice of differing microclimates (abiotic effects). I explored this question for four ground-nesting bird species that are segregated along a microclimate and vegetation gradient in Arizona. Birds shifted position of their nests on the microhabitat and microclimate gradient in response to changing precipitation over nine years. Similarly, annual bird abundance varied with precipitation across 12 yr. Those shifts in abundance and nesting microhabitat with changing precipitation demonstrate the importance of abiotic influences on bird distributions and habitat choice. However, nest-site shifts and microhabitat use also appear to be influenced by interactions among coexisting species. Moreover, shifts in habitat use by all species caused nest predation (i.e., biotic) costs that increased with increasing distance along the microclimate gradient. These results indicate that abiotic and biotic costs can strongly interact to influence microhabitat choice and abundances of coexisting species. Global climate change impacts have been considered largely in terms of simple distributional shifts, but these results indicate that shifts can also increase biotic costs when species move into habitat types for which they are poorly adapted or that create new biotic interactions.

Conflict between biotic and climatic selective pressures acting on an extended phenotype in a subarctic, but not temperate, environment

PubMed Central

Rohwer, V. G.; Bonier, F.; Martin, P. R.

2015-01-01

Climatic selective pressures are thought to dominate biotic selective pressures at higher latitudes. However, few studies have experimentally tested how these selective pressures differentially act on traits across latitudes because traits can rarely be manipulated independently of the organism in nature. We overcame this challenge by using an extended phenotype—active bird nests—and conducted reciprocal transplant experiments between a subarctic and temperate site, separated by 14° of latitude. At the subarctic site, biotic selective pressures (nest predation) favoured smaller, non-local temperate nests, whereas climatic selective pressures (temperature) favoured larger local nests, particularly at colder temperatures. By contrast, at the temperate site, climatic and biotic selective pressures acted similarly on temperate and subarctic nests. Our results illustrate a functional trade-off in the subarctic between nest morphologies favoured by biotic versus climatic selective pressures, with climate favouring local nest morphologies. At our temperate site, however, allocative trade-offs in the time and effort devoted to nest construction favour smaller, local nests. Our findings illustrate a conflict between biotic and climatic selective pressures at the northern extremes of a species geographical range, and suggest that trade-offs between trait function and trait elaboration act differentially across latitude to create broad geographic variation in traits. PMID:26490789

The abundance of biotic exoplanets and life on planets of Red Dwarf stars

NASA Astrophysics Data System (ADS)

Wandel, Amri; Gale, Joseph

2016-07-01

The Kepler mission has shown that Earthlike planets orbiting within the Habitable Zones of their host stars are common. We derive an expression for the abundance of life bearing (biotic) extra-solar-system planets (exoplanets) in terms of the (yet unknown) probability for the evolution of biotic life. This "biotic probability" may be estimated by future missions and observations, e.g. spectral analyses of the atmospheres of exoplanets, looking for biomarkers. We show that a biotic probability in the range 0.001-1 implies that a biotic planet may be expected within ~10-100 light years from Earth. Of particular interest in the search for exolife are planets orbiting Red Dwarf (RD) stars, the most frequent stellar type. Previous researches suggested that conditions on planets near RDs would be inimical to life, e.g. the Habitable Zone of RDs is small, so their habitable planets would be close enough to be tidally locked. Recent calculations show that this and other properties of RDs, presumed hostile for the evolution of life, are less severe than originally estimated. We conclude that RD planets could be hospitable for the evolution of life as we know it, not less so than planets of solar-type stars. This result, together with the large number of RDs and their Kepler planet-statistics, makes finding life on RD planets ~10-1000 times more likely than on planets of solar-type stars. Our nearest biotic RD-planet is likely to be 2-10 times closer than the nearest solar-type one.

Dissolved and labile concentrations of Cd, Cu, Pb, and Zn in the South Fork Coeur d'Alene River, Idaho: Comparisons among chemical equilibrium models and implications for biotic ligand models

USGS Publications Warehouse

Balistrieri, L.S.; Blank, R.G.

2008-01-01

In order to evaluate thermodynamic speciation calculations inherent in biotic ligand models, the speciation of dissolved Cd, Cu, Pb, and Zn in aquatic systems influenced by historical mining activities is examined using equilibrium computer models and the diffusive gradients in thin films (DGT) technique. Several metal/organic-matter complexation models, including WHAM VI, NICA-Donnan, and Stockholm Humic model (SHM), are used in combination with inorganic speciation models to calculate the thermodynamic speciation of dissolved metals and concentrations of metal associated with biotic ligands (e.g., fish gills). Maximum dynamic metal concentrations, determined from total dissolved metal concentrations and thermodynamic speciation calculations, are compared with labile metal concentrations measured by DGT to assess which metal/organic-matter complexation model best describes metal speciation and, thereby, biotic ligand speciation, in the studied systems. Results indicate that the choice of model that defines metal/organic-matter interactions does not affect calculated concentrations of Cd and Zn associated with biotic ligands for geochemical conditions in the study area, whereas concentrations of Cu and Pb associated with biotic ligands depend on whether the speciation calculations use WHAM VI, NICA-Donnan, or SHM. Agreement between labile metal concentrations and dynamic metal concentrations occurs when WHAM VI is used to calculate Cu speciation and SHM is used to calculate Pb speciation. Additional work in systems that contain wide ranges in concentrations of multiple metals should incorporate analytical speciation methods, such as DGT, to constrain the speciation component of biotic ligand models. ?? 2008 Elsevier Ltd.

Strong biotic influences on regional patterns of climate regulation services

NASA Astrophysics Data System (ADS)

Serna-Chavez, H. M.; Swenson, N. G.; Weiser, M. D.; van Loon, E. E.; Bouten, W.; Davidson, M. D.; van Bodegom, P. M.

2017-05-01

Climate regulation services from forests are an important leverage in global-change mitigation treaties. Like most ecosystem services, climate regulation is the product of various ecological phenomena with unique spatial features. Elucidating which abiotic and biotic factors relate to spatial patterns of climate regulation services advances our understanding of what underlies climate-mitigation potential and its variation within and across ecosystems. Here we quantify and contrast the statistical relations between climate regulation services (albedo and evapotranspiration, primary productivity, and soil carbon) and abiotic and biotic factors. We focus on 16,955 forest plots in a regional extent across the eastern United States. We find the statistical effects of forest litter and understory carbon on climate regulation services to be as strong as those of temperature-precipitation interactions. These biotic factors likely influence climate regulation through changes in vegetation and canopy density, radiance scattering, and decomposition rates. We also find a moderate relation between leaf nitrogen traits and primary productivity at this regional scale. The statistical relation between climate regulation and temperature-precipitation ranges, seasonality, and climatic thresholds highlights a strong feedback with global climate change. Our assessment suggests the expression of strong biotic influences on climate regulation services at a regional, temperate extent. Biotic homogenization and management practices manipulating forest structure and succession will likely strongly impact climate-mitigation potential. The identity, strength, and direction of primary influences differed for each process involved in climate regulation. Hence, different abiotic and biotic factors are needed to monitor and quantify the full climate-mitigation potential of temperate forest ecosystems.

Geoheritage Values at Greenmantle Farm

NASA Astrophysics Data System (ADS)

Etches, J. D.

2009-05-01

The Greenmantle Farm occurrence near Wilberforce, Ontario is a marble feature within the Grenville Province of the Precambrian Shield that hosts a diverse suite of amphibole minerals. The marble is of undetermined petrogenesis, and is possibly either a primary carbonatite intrusion or a derived melt of metasedimentary origin. The site is the type locality for the rare mineral fluorrichterite. Other minerals of note are orthoclase and apatite. Crystal size is relatively large, and all minerals, with the exception of calcite, exhibit generally good to excellent euhedral form. Of note is that the mineral occurrences at this site have not been subjected to any human disturbance including mechanical or hand tool disruption. The site also provides excellent examples of a number of geological features and ecosystem dynamics. In particular, faulting, moisture regime landscape interrelationships, order of crystallization in zoned dykes, and calciphile plant associations are demonstrated. This site represents an exceptional viewing opportunity of an unspoiled mineral occurrence while providing illustrative examples of the interrelationship of abiotic and biotic features. In terms of research, the site will prove to be a valuable subject in regard to amphibole composition, amphibole differentiation in calcareous melts, and will ultimately provide insight into the formation of the occurrence. Determination of what circumstances these marble bodies formed under would add a significant piece of information to the complex history of the Grenville province. This research will be assisted by the completely uncompromised nature of the site. The potential educational value of the site for researchers and grade school students alike is exceptional.

Anoxygenic growth of cyanobacteria on Fe(II) and their associated biosignatures: Implications for biotic contributions to Precambrian Banded Iron Formations

NASA Astrophysics Data System (ADS)

Parenteau, M.; Jahnke, L. L.; Cady, S. L.; Pierson, B.

2011-12-01

Banded Iron Formations (BIFs) are widespread Precambrian sedimentary deposits that accumulated in deep ocean basins or shallow platformal areas with inputs of reduced iron (Fe(II)) and silica from deep ocean hydrothermal activity. There is debate as to whether abiotic or biotic mechanisms were responsible for the oxidation of aqueous Fe(II) and the subsequent accumulation of ferric iron (Fe(III)) mineral assemblages in BIFs. Biotic Fe(II) oxidation could have occurred indirectly as a result of the photosynthetic production of oxygen by cyanobacteria, or could have been directly mediated by anoxygenic phototrophs or chemolithotrophs. The anoxygenic use of Fe(II) as an electron donor for photosynthesis has also been hypothesized in cyanobacteria, representing another biotic mechanism by which Fe(II) could be oxidized in BIFs. This type of photoferrotrophic metabolism may also represent a key step in the evolution of oxygenic photosynthesis. Members of our group have speculated that an intermediate reductant such as Fe(II) could have acted as a transitional electron donor before water. The widespread abundance of Fe(II) in Archean and Neoproterozoic ferruginous oceans would have made it particularly suitable as an electron donor for photosynthesis. We have been searching for modern descendants of such an ancestral "missing link" cyanobacterium in the phototrophic mats at Chocolate Pots, a hot spring in Yellowstone National Park with a constant outflow of anoxic Fe(II)-rich thermal water. Our physiological ecology study of the Synechococcus-Chloroflexi mat using C-14 bicarbonate uptake and autoradiography experiments revealed that the cyanobacteria grow anoxygenically using Fe(II) as an electron donor for photosynthesis in situ. An initial set of similar experiments substituting C-13 bicarbonate as the tracer was used to characterize labeling of the community lipid biomarker signature and confirm the C-14 results. Under light conditions with and without Fe(II), the C-13 label was greatly enriched in the cyanobacterial lipid biomarker n-heptadecane, while dark controls showed no incorporation. No significant incorporation was noted in the Chloroflexi lipid biomarker wax esters, suggesting that Chloroflexus and Roseiflexus grow as photoheterotrophs in these mats. A complimentary study of the microbial biosignatures produced in these mats revealed iron-permineralized carbonaceous microfossils of the candidate photoferrotrophs. Diagnostic lipid biomarkers of the cyanobacteria included n-heptadecane, mid-chain branched mono- and dimethyl analogs and, most notably, 2-methylhopanoids. Wax esters and a long chain tri-unsaturated alkene were proxies for the Chloroflexi. Our work has for the first time identified 2-methylhopanoids in a modern iron-mineralized cyanobacterial mat where the cyanobacteria have been shown to grow anoxygenically using Fe(II) as an electron donor for photosynthesis. We are also currently screening the JGI Yellowstone Community Sequencing Project metagenomic data from this mat for the molecular basis of this type of photoferrotrophic metabolism.

Finger Millet: A "Certain" Crop for an "Uncertain" Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments.

PubMed

Gupta, Sanjay Mohan; Arora, Sandeep; Mirza, Neelofar; Pande, Anjali; Lata, Charu; Puranik, Swati; Kumar, J; Kumar, Anil

2017-01-01

Crop growth and productivity has largely been vulnerable to various abiotic and biotic stresses that are only set to be compounded due to global climate change. Therefore developing improved varieties and designing newer approaches for crop improvement against stress tolerance have become a priority now-a-days. However, most of the crop improvement strategies are directed toward staple cereals such as rice, wheat, maize etc., whereas attention on minor cereals such as finger millet [ Eleusine coracana (L.) Gaertn.] lags far behind. It is an important staple in several semi-arid and tropical regions of the world with excellent nutraceutical properties as well as ensuring food security in these areas even during harsh environment. This review highlights the importance of finger millet as a model nutraceutical crop. Progress and prospects in genetic manipulation for the development of abiotic and biotic stress tolerant varieties is also discussed. Although limited studies have been conducted for genetic improvement of finger millets, its nutritional significance in providing minerals, calories and protein makes it an ideal model for nutrition-agriculture research. Therefore, improved genetic manipulation of finger millets for resistance to both abiotic and biotic stresses, as well as for enhancing nutrient content will be very effective in millet improvement. Key message: Apart from the excellent nutraceutical value of finger millet, its ability to tolerate various abiotic stresses and resist pathogens make it an excellent model for exploring vast genetic and genomic potential of this crop, which provide us a wide choice for developing strategies for making climate resilient staple crops.

Integrating Biogeography with Contemporary Niche Theory.

PubMed

Godsoe, William; Jankowski, Jill; Holt, Robert D; Gravel, Dominique

2017-07-01

There is no consensus on when biotic interactions impact the range limits of species. Starting from MacArthur's use of invasibility to understand how biotic interactions influence coexistence, here we examine how biotic interactions shape species distributions. Range limits emerge from how birth, death, and movement rates vary with the environment. We clarify some basic issues revolving around niche definitions, illustrated with simple resource-consumer theory. We then highlight two different avenues for linking community theory and range theory; the first based on calculating the effects of biotic interactions on range limits across scales and landscape configurations, and the second based on aggregate measures of diffuse interactions and network strength. We conclude with suggestions for a future research agenda. Copyright © 2017 Elsevier Ltd. All rights reserved.

Tropospheric ozone as a fungal elicitor.

PubMed

Zuccarini, Paolo

2009-03-01

Tropospheric ozone has been proven to trigger biochemical plant responses that are similar to the ones induced by an attack of fungal pathogens,i.e. it resembles fungal elicitors.This suggests that ozone can represent a valid tool for the study of stress responses and induction of resistance to pathogens. This review provides an overview of the implications of such a phenomenon for basic and applied research. After an introduction about the environmental implications of tropospheric ozone and plant responses to biotic stresses, the biochemistry of ozone stress is analysed, pointing out its similarities with plant responses to pathogens and its possible applications.

Establishing links between streamflow and ecological integrity in the Sudbury River (Northeastern U.S.)

USGS Publications Warehouse

Roy, Allison; Jane, Stephen F.; Hazelton, Peter D.; Richards, Todd A.; Finn, John T.; Randhir, Timothy O.

2016-01-01

With increased pressure from a growing human population, managers are challenged to understand how novel disturbances (e.g., climate change, increased water withdrawals, urbanization) may affect natural resources. The Sudbury River is a National Wild and Scenic River located in suburban Boston, Massachusetts (Northeastern US) with myriad impairments (e.g., mainstem impoundments, withdrawals, and urbanization) that is under increasing pressure from hydrologic alteration. We sampled fish, mussel, and macroinvertebrate assemblages in the Sudbury River and used species traits to investigate potential effects of past and future flow alteration on biota. Analysis of 33 years of stream gage data indicates continued hydrologic alteration of the Sudbury River, likely related to increased urbanization and water withdrawals over that time. These changes include a roughly 200% increase in rise rates of flows, an approximate 65% decrease in 1-day minimum flows, and a trend towards increasing high flow pulse counts. Biotic sampling in summer of 2014 demonstrated that the Sudbury River is now dominated by generalist species. Of five mussel species sampled, all are generalists in their habitat requirements. Though one mussel species of special concern was sampled, the most abundant species collected were the widespread Eastern elliptio (58%) and Eastern lampmussel (40%). We used the target fish community (TFC) model to assess the degree to which the fish assemblage deviated from that expected for a river with similar zoogeographic and physical features. Overall, the current community has a 22.7% similarity to the TFC. Of the four fluvial specialist species present in the TFC, only fallfish was sampled in our study. While the TFC showed that the historical assemblage was likely dominated by fluvial specialist and fluvial dependent species, the current assemblage is overwhelmingly dominated by macrohabitat generalists (90.6% of fishes sampled). These results are consistent with other studies that show shifts in assemblages from fluvial specialists to habitat generalists with hydrologic alteration. If the current trends continue, it is likely that biotic assemblages will experience increasing pressure from hydrologic alteration. While hydrologic alteration is likely impacting biotic assemblages in the Sudbury River, other factors such as high temperatures, low dissolved oxygen, high nutrients, low availability of high-quality habitat, and poor habitat connectivity may also be negatively impacting biotic assemblages. Comparisons to other rivers and a complete longitudinal habitat survey could help to identify availability of unique habitats and representativeness of this study. While this study suggests impacts of flow on biota, future studies with quantitative, habitat-specific sampling during different flow levels could help to directly identify links between hydrologic alteration and biotic impairment in the Sudbury River.

Sterol glycosyltransferases--the enzymes that modify sterols.

PubMed

Chaturvedi, Pankaj; Misra, Pratibha; Tuli, Rakesh

2011-09-01

Sterols are important components of cell membranes, hormones, signalling molecules and defense-related biotic and abiotic chemicals. Sterol glycosyltransferases (SGTs) are enzymes involved in sterol modifications and play an important role in metabolic plasticity during adaptive responses. The enzymes are classified as a subset of family 1 glycosyltransferases due to the presence of a signature motif in their primary sequence. These enzymes follow a compulsory order sequential mechanism forming a ternary complex. The diverse applications of sterol glycosides, like cytotoxic and apoptotic activity, anticancer activity, medicinal values, anti-stress roles and anti-insect and antibacterial properties, draws attention towards their synthesis mechanisms. Many secondary metabolites are derived from sterol pathways, which are important in defense mechanisms against pathogens. SGTs in plants are involved in changed sensitivity to stress hormones and their agrochemical analogs and changed tolerance to biotic and abiotic stresses. SGTs that glycosylate steroidal hormones, such as brassinosteroids, function as growth and development regulators in plants. In terms of metabolic roles, it can be said that SGTs occupy important position in plant metabolism and may offer future tools for crop improvement.

AMBI indices and multivariate approach to assess the ecological health of Vellar-Coleroon estuarine system undergoing various human activities.

PubMed

Sigamani, Sivaraj; Perumal, Murugesan; Arumugam, Silambarasan; Preetha Mini Jose, H M; Veeraiyan, Bharathidasan

2015-11-15

Estuaries receive a considerable amount of pollutants from various sources. Presently an attempt has been made to assess whether the aquaculture discharges and dredging activities alter the ecological conditions of Vellar-Coleroon estuarine complex. The European Water Framework Directive (WFD) established a framework for the protection of marine waters. In this commission, a variety of indices were used, among them, AMBI (AZTI Marine Biotic Index) indices along with multivariate statistical approach is unique, to assess the ecological status by using macrobenthic communities. Keeping this in view, stations VE-1 and VE-4 in Vellar; CE-6 and CE-7 in Coleroon estuaries showed moderately disturbed with the AMBI values ranging between 3.45 and 3.72. The above said stations were situated near the shrimp farm discharge point and sites of dredging activities. The present study proves that various statistical and biotic indices have great potential in assessing the nature of the ecosystem undergoing various human pressures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments?

PubMed

Fonti, Viviana; Dell'Anno, Antonio; Beolchini, Francesca

2016-09-01

Bioleaching is a consolidated biotechnology in the mining industry and in bio-hydrometallurgy, where microorganisms mediate the solubilisation of metals and semi-metals from mineral ores and concentrates. Bioleaching also has the potential for ex-situ/on-site remediation of aquatic sediments that are contaminated with metals, which represent a key environmental issue of global concern. By eliminating or reducing (semi-)metal contamination of aquatic sediments, bioleaching may represent an environmentally friendly and low-cost strategy for management of contaminated dredged sediments. Nevertheless, the efficiency of bioleaching in this context is greatly influenced by several abiotic and biotic factors. These factors need to be carefully taken into account before selecting bioleaching as a suitable remediation strategy. Here we review the application of bioleaching for sediment bioremediation, and provide a critical view of the main factors that affect its performance. We also discuss future research needs to improve bioleaching strategies for contaminated aquatic sediments, in view of large-scale applications. Copyright © 2016 Elsevier B.V. All rights reserved.

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling.

PubMed

Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

2013-02-01

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Modeling biotic uptake by periphyton and transient hyporrheic storage of nitrate in a natural stream

USGS Publications Warehouse

Kim, Brian K.A.; Jackman, Alan P.; Triska, Frank J.

1992-01-01

To a convection-dispersion hydrologic transport model we coupled a transient storage submodel (Bencala, 1984) and a biotic uptake submodel based on Michaelis-Menten kinetics (Kim et al., 1990). Our purpose was threefold: (1) to simulate nitrate retention in response to change in load in a third-order stream, (2) to differentiate biotic versus hydrologie factors in nitrate retention, and (3) to produce a research tool whose properties are consistent with laboratory and field observations. Hydrodynamic parameters were fitted from chloride concentration during a 20-day chloride-nitrate coinjection (Bencala, 1984), and biotic uptake kinetics were based on flume studies by Kim et al. (1990) and Triska et al. (1983). Nitrate concentration from the 20-day coinjection experiment served as a base for model validation. The complete transport retention model reasonably predicted the observed nitrate concentration. However, simulations which lacked either the transient storage submodel or the biotic uptake submodel poorly predicted the observed nitrate concentration. Model simulations indicated that transient storage in channel and hyporrheic interstices dominated nitrate retention within the first 24 hours, whereas biotic uptake dominated thereafter. A sawtooth function for Vmax ranging from 0.10 to 0.17 μg NO3-N s−1 gAFDM−1 (grams ash free dry mass) slightly underpredicted nitrate retention in simulations of 2–7 days. This result was reasonable since uptake by other nitrate-demanding processes were not included. The model demonstrated how ecosystem retention is an interaction between physical and biotic processes and supports the validity of coupling separate hydrodynamic and reactive submodels to established solute transport models in biological studies of fluvial ecosystems.

Inter-annual variability of carbon fluxes in temperate forest ecosystems: effects of biotic and abiotic factors

NASA Astrophysics Data System (ADS)

Chen, M.; Keenan, T. F.; Hufkens, K.; Munger, J. W.; Bohrer, G.; Brzostek, E. R.; Richardson, A. D.

2014-12-01

Carbon dynamics in terrestrial ecosystems are influenced by both abiotic and biotic factors. Abiotic factors, such as variation in meteorological conditions, directly drive biophysical and biogeochemical processes; biotic factors, referring to the inherent properties of the ecosystem components, reflect the internal regulating effects including temporal dynamics and memory. The magnitude of the effect of abiotic and biotic factors on forest ecosystem carbon exchange has been suggested to vary at different time scales. In this study, we design and conduct a model-data fusion experiment to investigate the role and relative importance of the biotic and abiotic factors for inter-annual variability of the net ecosystem CO2 exchange (NEE) of temperate deciduous forest ecosystems in the Northeastern US. A process-based model (FöBAAR) is parameterized at four eddy-covariance sites using all available flux and biometric measurements. We conducted a "transplant" modeling experiment, that is, cross- site and parameter simulations with different combinations of site meteorology and parameters. Using wavelet analysis and variance partitioning techniques, analysis of model predictions identifies both spatial variant and spatially invariant parameters. Variability of NEE was primarily modulated by gross primary productivity (GPP), with relative contributions varying from hourly to yearly time scales. The inter-annual variability of GPP and NEE is more regulated by meteorological forcing, but spatial variability in certain model parameters (biotic response) has more substantial effects on the inter-annual variability of ecosystem respiration (Reco) through the effects on carbon pools. Both the biotic and abiotic factors play significant roles in modulating the spatial and temporal variability in terrestrial carbon cycling in the region. Together, our study quantifies the relative importance of both, and calls for better understanding of them to better predict regional CO2 exchanges.

The hysteretic evapotranspiration - vapor pressure deficit relation

NASA Astrophysics Data System (ADS)

Zhang, Q.; Manzoni, S.; Katul, G. G.; Porporato, A. M.; Yang, D.

2013-12-01

Diurnal hysteresis between evapotranspiration (ET) and vapor pressure deficit (VPD) was reported in many ecosystems but justification for its onset and magnitude remain incomplete with biotic and abiotic factors invoked as possible explanations. To place these explanations within a mathematical framework, ';rate-dependent' hysteresis originating from a phase angle difference between periodic input and output time series is first considered. Lysimeter evaporation (E) measurements from wet bare soils and model calculations using the Penman equation demonstrate that the E-VPD hysteresis emerges without any biotic effects due to a phase angle difference (or time lag) between net radiation the main driver of E, and VPD. Modulations originating from biotic effects on the ET-VPD hysteresis were then considered. The phase angle difference representation earlier employed was mathematically transformed into a storage problem and applied to the soil-plant system. The transformed system shows that soil moisture storage within the root zone can produce an ET-VPD hysteresis prototypical of those generated by phase-angle differences. To explore the interplay between all the lags in the soil-plant-atmosphere system and phase angle differences among forcing and response variables, a detailed soil-plant-atmosphere continuum (SPAC) model was developed and applied to a grassland ecosystem. The results of the SPAC model suggest that the hysteresis magnitude depends on the radiation-VPD lag. The soil moisture dry-down simulations also suggest that modeled root water potential and leaf water potential are both better indicators of the hysteresis magnitude than soil moisture, suggesting that plant water status is the main factor regulating the hysteretic relation between ET and VPD. Hence, the genesis and magnitude of the ET-VPD hysteresis are controlled directly by both biotic factors and abiotic factors such as time lag between radiation and VPD originating from boundary layer processes. Measured eddy covariance evapotranspiration (ET) and vapor pressure deficit (VPD) time series normalized by their maximum values collected in a grassland ecosystem. The magnitude of the hysteresis is quantified as the area enveloped by the ET-VPD relation (Ahys). The arrows together with time ticks indicate the progression of the diurnal cycle from sunrise to sunset.

Contrasting isotopic signatures between anthropogenic and geogenic Zn and evidence for post-depositional fractionation processes in smelter-impacted soils from Northern France

NASA Astrophysics Data System (ADS)

Juillot, Farid; Maréchal, Chloe; Morin, Guillaume; Jouvin, Delphine; Cacaly, Sylvain; Telouk, Philipe; Benedetti, Marc F.; Ildefonse, Philippe; Sutton, Steve; Guyot, François; Brown, Gordon E., Jr.

2011-05-01

Zinc isotopes have been studied along two smelter-impacted soil profiles sampled near one of the largest Pb and Zn processing plants in Europe located in northern France, about 50 km south of Lille. Mean δ 66Zn values along these two soil profiles range from +0.22 ± 0.17‰ (2 σ) to +0.34 ± 0.17‰ (2 σ) at the lowest horizons and from +0.38 ± 0.45‰ (2 σ) to +0.76 ± 0.14‰ (2 σ) near the surface. The δ 66Zn values in the lowest horizons of the soils are interpreted as being representative of the local geochemical background (mean value +0.31 ± 0.38‰), whereas heavier δ 66Zn values near the surface of the two soils are related to anthropogenic Zn. This anthropogenic Zn occurs in the form of franklinite (ZnFe 2O 4)-bearing slag grains originating from processing wastes at the smelter site and exhibiting δ 66Zn values of +0.81 ± 0.20‰ (2 σ). The presence of franklinite is indicated by EXAFS analysis of the topsoil samples from both soil profiles as well as by micro-XANES analysis of the surface horizon of a third smelter-impacted soil from a distant site. These results indicate that naturally occurring Zn and smelter-derived Zn exhibit significantly different δ 66Zn values, which suggests that zinc isotopes can be used to distinguish between geogenic and anthropogenic sources of Zn in smelter-impacted soils. In addition to a possible influence of additional past sources of light Zn (likely Zn-sulfides and Zn-sulfates directly emitted by the smelter), the light δ 66Zn values in the surface horizons compared to smelter-derived slag materials are interpreted as resulting mainly from fractionation processes associated with biotic and/or abiotic pedological processes (Zn-bearing mineral precipitation, Zn complexation by organic matter, and plant uptake of Zn). This conclusion emphasizes the need for additional Zn isotopic studies before being able to use Zn isotopes to trace sources and pathways of this element in surface environments.

Proposed definition of environmental damage illustrated by the cases of genetically modified crops and invasive species.

PubMed

Bartz, Robert; Heink, Ulrich; Kowarik, Ingo

2010-06-01

The introduction of non-native plant species and the release of genetically modified (GM) crops can induce environmental changes at gene to ecosystem levels. Regulatory frameworks such as the Convention on Biological Diversity or the EU Deliberate Release Directive aim to prevent environmental damage but do not define the term. Although ecologists and conservationists often refer to environmental effects of GM crops or invasive species as damage, most authors do not disclose their normative assumptions or explain why some environmental impacts are regarded as detrimental and others are not. Thus far, a concise definition of environmental damage is missing and is necessary for a transparent assessment of environmental effects or risks. Therefore, we suggest defining environmental damage as a significant adverse effect on a biotic or abiotic conservation resource (i.e., a biotic or abiotic natural resource that is protected by conservational or environmental legislation) that has an impact on the value of the conservation resource, the conservation resource as an ecosystem component, or the sustainable use of the conservation resource. This definition relies on three normative assumptions: only concrete effects on a conservation resource can be damages; only adverse effects that lead to a decrease in the value of the conservation resource can be damages; and only significant adverse effects constitute damage to a conservation resource. Applying this definition within the framework of environmental risk assessment requires further normative determinations, for example, selection of a threshold to distinguish between adverse and significant adverse effects and approaches for assessing the environmental value of conservation resources. Such determinations, however, are not part of the definition of environmental damage. Rather they are part of the definition's operationalization through assessment procedures, which must be grounded in a comprehensible definition of environmental damage.

Analytical approaches used in stream benthic macroinvertebrate biomonitoring programs of State agencies in the United States

USGS Publications Warehouse

Carter, James L.; Resh, Vincent H.

2013-01-01

Biomonitoring programs based on benthic macroinvertebrates are well-established worldwide. Their value, however, depends on the appropriateness of the analytical techniques used. All United States State, benthic macroinvertebrate biomonitoring programs were surveyed regarding the purposes of their programs, quality-assurance and quality-control procedures used, habitat and water-chemistry data collected, treatment of macroinvertebrate data prior to analysis, statistical methods used, and data-storage considerations. State regulatory mandates (59 percent of programs), biotic index development (17 percent), and Federal requirements (15 percent) were the most frequently reported purposes of State programs, with the specific tasks of satisfying the requirements for 305b/303d reports (89 percent), establishment and monitoring of total maximum daily loads, and developing biocriteria being the purposes most often mentioned. Most states establish reference sites (81 percent), but classify them using State-specific methods. The most often used technique for determining the appropriateness of a reference site was Best Professional Judgment (86 percent of these states). Macroinvertebrate samples are almost always collected by using a D-frame net, and duplicate samples are collected from approximately 10 percent of sites for quality assurance and quality control purposes. Most programs have macroinvertebrate samples processed by contractors (53 percent) and have identifications confirmed by a second taxonomist (85 percent). All States collect habitat data, with most using the Rapid Bioassessment Protocol visual-assessment approach, which requires ~1 h/site. Dissolved oxygen, pH, and conductivity are measured in more than 90 percent of programs. Wide variation exists in which taxa are excluded from analyses and the level of taxonomic resolution used. Species traits, such as functional feeding groups, are commonly used (96 percent), as are tolerance values for organic pollution (87 percent). Less often used are tolerance values for metals (28 percent). Benthic data are infrequently modified (34 percent) prior to analysis. Fixed-count subsampling is used widely (83 percent), with the number of organisms sorted ranging from 100 to 600 specimens. Most programs include a step during sample processing to acquire rare taxa (79 percent). Programs calculate from 2 to more than100 different metrics (mean 20), and most formulate a multimetric index (87 percent). Eleven of the 112 metrics reported represent 50 percent of all metrics considered to be useful, and most of these are based on richness or percent composition. Biotic indices and tolerance metrics are most oftenused in the eastern U.S., and functional and habitat-type metrics are most often used in the western U.S. Sixty-nine percent of programs analyze their data in-house, typically performing correlations and regressions, and few use any form of data transformation (34 percent). Fifty-one percent of the programs use multivariate analyses, typically non-metric multi-dimensional scaling. All programs have electronic data storage. Most programs use the Integrated Taxonomic Information System (75 percent) for nomenclature and to update historical data (78 percent). State procedures represent a diversity of biomonitoring approaches which likely compromises comparability among programs. A national-state consensus is needed for: (1) developing methods for the identification of reference conditions and reference sites, (2) standardization in determining and reporting species richness, (3) testing and documenting both the theoretical and mechanistic basis of often-used metrics, (4) development of properly replicated point-source study designs, and (5) curation of benthic macroinvertebrate data, including reference and voucher collections, for successful evaluation of future environmental changes.

Ningaloo Reef: Shallow Marine Habitats Mapped Using a Hyperspectral Sensor

PubMed Central

Kobryn, Halina T.; Wouters, Kristin; Beckley, Lynnath E.; Heege, Thomas

2013-01-01

Research, monitoring and management of large marine protected areas require detailed and up-to-date habitat maps. Ningaloo Marine Park (including the Muiron Islands) in north-western Australia (stretching across three degrees of latitude) was mapped to 20 m depth using HyMap airborne hyperspectral imagery (125 bands) at 3.5 m resolution across the 762 km2 of reef environment between the shoreline and reef slope. The imagery was corrected for atmospheric, air-water interface and water column influences to retrieve bottom reflectance and bathymetry using the physics-based Modular Inversion and Processing System. Using field-validated, image-derived spectra from a representative range of cover types, the classification combined a semi-automated, pixel-based approach with fuzzy logic and derivative techniques. Five thematic classification levels for benthic cover (with probability maps) were generated with varying degrees of detail, ranging from a basic one with three classes (biotic, abiotic and mixed) to the most detailed with 46 classes. The latter consisted of all abiotic and biotic seabed components and hard coral growth forms in dominant or mixed states. The overall accuracy of mapping for the most detailed maps was 70% for the highest classification level. Macro-algal communities formed most of the benthic cover, while hard and soft corals represented only about 7% of the mapped area (58.6 km2). Dense tabulate coral was the largest coral mosaic type (37% of all corals) and the rest of the corals were a mix of tabulate, digitate, massive and soft corals. Our results show that for this shallow, fringing reef environment situated in the arid tropics, hyperspectral remote sensing techniques can offer an efficient and cost-effective approach to mapping and monitoring reef habitats over large, remote and inaccessible areas. PMID:23922921

Environments and extinctions at the K-T boundary in eastern Montana are compatible with an asteroid impact

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

Fastovsky, D.E.; Sheehan, P.M.

1992-01-01

In the terrestrial latest Cretaceous Hell Creek (HC) Formation, both non-biotic events and patterns of extinction and survivorship are consistent with an asteroid impact causing the extinctions. Environments through the last 2--3 million-year interval represented by the HC remained relatively constant: an aggrading coastal lowland dissected by meandering rivers. The K-T boundary occurred during an abrupt change to impeded drainage represented by coals and pond deposits formed under low-energy conditions. Because of the close temporal proximity of the sediments of the Paleocene Cannonball Sea to the K-T boundary in South Dakota, impeded drainage in the earliest Paleocene in eastern Montanamore » may be attributable to riverine base-level changes associated with a renewed transgression of the western interior sea during the K-T transition. Patterns within the biota mirror those of the paleoenvironments. The ecological diversity of HC dinosaurs remains statistically unchanged through HC time. Analyses of vertebrates at the species level indicate a differential extinction in which the terrestrial biota underwent far more extinction than its aquatic counterpart. There is no evidence for changing environments in the upper HC, and there is circumstantial evidence that the latest Cretaceous was a time of renewed transgression rather than regression. Likewise, biotic patterns do not accord with gradual, environmentally driven extinctions. While the paleoenvironmental change that marks the K-T transition in eastern Montana accounts for some of the extinctions, the pattern of differential extinction is concordant with an asteroid impact. In this scenario, aquatic ecosystems and some land-based food chains would be buffered by detritus-based feeding. Terrestrial systems, dependent upon primary productivity, would undergo a short-term loss of resources causing extinctions.« less

Application of Biotic Ligand and Toxic Unit modeling approaches to predict improvements in zooplankton species richness in smelter-damaged lakes near Sudbury, Ontario.

PubMed

Khan, Farhan R; Keller, W Bill; Yan, Norman D; Welsh, Paul G; Wood, Chris M; McGeer, James C

2012-02-07

Using a 30-year record of biological and water chemistry data collected from seven lakes near smelters in Sudbury (Ontario, Canada) we examined the link between reductions of Cu, Ni, and Zn concentrations and zooplankton species richness. The toxicity of the metal mixtures was assessed using an additive Toxic Unit (TU) approach. Four TU models were developed based on total metal concentrations (TM-TU); free ion concentrations (FI-TU); acute LC50s calculated from the Biotic Ligand Model (BLM-TU); and chronic LC50s (acute LC50s adjusted by metal-specific acute-to-chronic ratios, cBLM-TU). All models significantly correlated reductions in metal concentrations to increased zooplankton species richness over time (p < 0.01) with a rank based on r(2) values of cBLM-TU > BLM-TU = FI-TU > TM-TU. Lake-wise comparisons within each model showed that the BLM-TU and cBLM-TU models provided the best description of recovery across all seven lakes. These two models were used to calculate thresholds for chemical and biological recovery using data from reference lakes in the same region. A threshold value of TU = 1 derived from the cBLM-TU provided the most accurate description of recovery. Overall, BLM-based TU models that integrate site-specific water chemistry-derived estimates of toxicity offer a useful predictor of biological recovery.

The use of biotic and abiotic components of Red Sea coastal areas as indicators of ecosystem health.

PubMed

Omar, Wael A; Saleh, Yousef S; Marie, Mohamed-Assem S

2016-03-01

A biomonitoring study was conducted using some biotic (Pomadasys hasta and Lutjanus russellii fish) and abiotic (water and sediment) components of the Red Sea coast of Hodeida, Yemen Republic along two polluted sites (Al-Dawar beach and Urj village) in comparison to a reference site (Al-Nukhailah beach). The studied fish biomarkers included hepatosomatic index (HSI), condition factor (K), scaled mass index (SMI), catalase, glutathione-S-transferase (GST), malondialdehyde (MDA), total protein and albumin. In addition, metals (Fe, Cu, Zn, Pb and Cd) concentrations in water and sediment were measured and sediment pollution assessment was carried out using contamination factor (CF), geoaccumulation index (Igeo), pollution load index (PLI) and enrichment factor (EF). The studied metals concentration in water and sediment samples showed significant increase among the polluted sites in comparison to the reference site. Sediment pollution assessment generally confirmed that Urj village was the most contaminated site followed by Al-Dawar beach. Catalase, GST and MDA proved to be the most responsive biomarkers with increased values of GST and MDA at sites influenced by agricultural, urban and industrial activities while catalase, HSI, K, SMI, total protein and albumin showed the opposite trend. This study recommends monitoring of sediment Igeo and EF values as well as SMI, catalase, GST and MDA as sensitive indicators of different anthropogenic activities and their effects on aquatic ecosystems under complex and different gradients of metal pollution. In addition, P. hasta proved to be more sensitive towards the detected pollution condition.

Effect of water quality and confounding factors on digestive enzyme activities in Gammarus fossarum.

PubMed

Charron, L; Geffard, O; Chaumot, A; Coulaud, R; Queau, H; Geffard, A; Dedourge-Geffard, O

2013-12-01

The feeding activity and subsequent assimilation of the products resulting from food digestion allow organisms to obtain energy for growth, maintenance and reproduction. Among these biological parameters, we studied digestive enzymes (amylase, cellulase and trypsin) in Gammarus fossarum to assess the impact of contaminants on their access to energy resources. However, to enable objective assessment of a toxic effect of decreased water quality on an organisms' digestive capacity, it is necessary to establish reference values based on its natural variability as a function of changing biotic and abiotic factors. To limit the confounding influence of biotic factors, a caging approach with calibrated male organisms from the same population was used. This study applied an in situ deployment at 23 sites of the Rhone basin rivers, complemented by a laboratory experiment assessing the influence of two abiotic factors (temperature and conductivity). The results showed a small effect of conductivity on cellulase activity and a significant effect of temperature on digestive enzyme activity but only at the lowest temperature (7 °C). The experimental conditions allowed us to define an environmental reference value for digestive enzyme activities to select sites where the quality of the water impacted the digestive capacity of the organisms. In addition to the feeding rate, this study showed the relevance of digestive enzymes as biomarkers to be used as an early warning tool to reflect organisms' health and the chemical quality of aquatic ecosystems.

Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry

PubMed Central

Qi, Yanxiang; Liu, Xiaomei; Pu, Jinji

2018-01-01

The NAC transcription factors involved plant development and response to various stress stimuli. However, little information is available concerning the NAC family in the woodland strawberry. Herein, 37 NAC genes were identified from the woodland strawberry genome and were classified into 13 groups based on phylogenetic analysis. And further analyses of gene structure and conserved motifs showed closer relationship of them in every subgroup. Quantitative real-time PCR evaluation different tissues revealed distinct spatial expression profiles of the FvNAC genes. The comprehensive expression of FvNAC genes revealed under abiotic stress (cold, heat, drought, salt), signal molecule treatments (H2O2, ABA, melatonin, rapamycin), biotic stress (Colletotrichum gloeosporioides and Ralstonia solanacearum). Expression profiles derived from quantitative real-time PCR suggested that 5 FvNAC genes responded dramatically to the various abiotic and biotic stresses, indicating their contribution to abiotic and biotic stresses resistance in woodland strawberry. Interestingly, FvNAC genes showed greater extent responded to the cold treatment than other abiotic stress, and H2O2 exhibited a greater response than ABA, melatonin, and rapamycin. For biotic stresses, 3 FvNAC genes were up-regulated during infection with C. gloeosporioides, while 6 FvNAC genes were down-regulated during infection with R. solanacearum. In conclusion, this study identified candidate FvNAC genes to be used for the genetic improvement of abiotic and biotic stress tolerance in woodland strawberry. PMID:29897926

Separating the role of biotic interactions and climate in determining adaptive response of plants to climate change.

PubMed

Tomiolo, Sara; Van der Putten, Wim H; Tielbörger, Katja

2015-05-01

Altered rainfall regimes will greatly affect the response of plant species to climate change. However, little is known about how direct effects of changing precipitation on plant performance may depend on other abiotic factors and biotic interactions. We used reciprocal transplants between climatically very different sites with simultaneous manipulation of soil, plant population origin, and neighbor conditions to evaluate local adaptation and possible adaptive response of four Eastern Mediterranean annual plant species to climate change. The effect of site on plant performance was negligible, but soil origin had a strong effect on fecundity, most likely due to differential water retaining ability. Competition by neighbors strongly reduced fitness. We separated the effects of the abiotic and biotic soil properties on plant performance by repeating the field experiment in a greenhouse under homogenous environmental conditions and including a soil biota manipulation treatment. As in the field, plant performance differed among soil origins and neighbor treatments. Moreover, we found plant species-specific responses to soil biota that may be best explained by the differential sensitivity to negative and positive soil biota effects. Overall, under the conditions of our experiment with two contrasting sites, biotic interactions had a strong effect on plant fitness that interacted with and eventually overrode climate. Because climate and biotic interactions covary, reciprocal transplants and climate gradient studies should consider soil biotic interactions and abiotic conditions when evaluating climate change effects on plant performance.

Sulfate-reducing bacteria lower sulfur-mediated pitting corrosion under conditions of oxygen ingress.

PubMed

Johnston, Shawna L; Voordouw, Gerrit

2012-08-21

The effect of oxygen ingress into sour water containing dissolved sulfide on the production of sulfur and polysulfide (S-PS) and associated iron corrosion was investigated. Biotic (active SRB present), abiotic (autoclaved SRB present), and chemical (no bacteria present) conditions were compared. Under biotic conditions formation of S-PS was only seen at a high ratio of oxygen to sulfide (R(OS)) of 1 to 2.4. General corrosion rates increased 10-fold to 0.10 mm/yr under these conditions. Under abiotic and chemical conditions S-PS formation increased over the entire range of R(OS) with general corrosion rates reaching 0.06 mm/yr. Although general corrosion rates were thus highest under biotic conditions, biotically corroded coupons showed much less pitting corrosion. Maximum pit depth increased to 40-80 μm with increasing R(OS) for coupons incubated for 1 month under abiotic or chemical conditions but not for biotically incubated coupons (10 μm). This appeared to be related to the properties and size of the sulfur formed, which was hydrophobic and in excess of 10 μm under chemical or abiotic conditions and hydrophilic and 0.5 to 1 μm under biotic conditions. Hence, perhaps contrary to expectation, SRB lowered pitting corrosion rates under conditions of oxygen ingress due to their ability to respire oxygen and produce a less aggressive form of sulfur. Microbial control, which is usually required in sour systems, may be counterproductive under these conditions.

Soil heterogeneity in Mojave Desert shrublands: Biotic and abiotic processes

NASA Astrophysics Data System (ADS)

Caldwell, Todd G.; Young, Michael H.; McDonald, Eric V.; Zhu, Jianting

2012-09-01

Geological and ecological processes play critical roles in the evolution of desert piedmonts. Feedback between fast cyclic biotic and slow cumulative pedogenic processes on arid alluvial fan systems results in a heterogeneous landscape of interspace and canopy microsites. Defining the spatial extent between these processes will allow a better connection to ecosystem service and climate change. We use a soil chronosequence in the Mojave Desert and high spatial resolution infiltrometer measurements along transects radiating from canopies of perennial shrubs to assess the extent of biotic and abiotic processes and the heterogeneity of soil properties in arid shrublands. Results showed higher saturated conductivity under vegetation regardless of surface age, but it was more conspicuous on older, developed soils. At proximal locations to the shrub, bulk density, soil structure grade, silt, and clay content significantly increased radially from the canopy, while sand and organic material decreased. Soil properties at distal locations 2-5 times the canopy radius had no significant spatial correlation. The extent of the biotic influence of the shrub was 1.34 ± 0.32 times the canopy radius. Hydraulic properties were weakly correlated in space, but 75% of the variance could be attributed to sand content, soil structure grade, mean-particle diameter, and soil organic material, none of which are exclusively biotic or abiotic. The fast cyclic biotic processes occurring under vegetation are clearly overprinted on slow cumulative abiotic processes, resulting in the deterministic variability observed at the plant scale.

Field and remote sensing for findings on the functions and evolutions of deltas

NASA Astrophysics Data System (ADS)

Taramelli, A.; Valentini, E.

2013-12-01

In a rapidly changing environment we realise that traditional knowledge of physical processes (both biotic and a-biotic) is insufficient to adequately deal with societal threats and opportunities particularly in low laying deltas, such changes to environments as a result of urbanization or changes to ecosystems as a result of climate change. Pattern formation and strong bio-morphological interactions are a striking features in deltas: vegetation distribution has been observed to be related with tidal channel network, with wind/wave forces as well as with the urbanization and natural built, but the relationship between the relevant biological, physical and anthropogenic processes are fairly unexplored. Through the combination of spaceborne optical and SAR imagery, we derived both ecological and morphological parameters, to be integrated for a multi-temporal analysis of the dominant processes and trends in a specific delta. Based on inter annual and intra annual time series of fractional abundance from multispectral imagery, the vegetation phenology in urbanized, non urbanized and buffer zones of the Po delta and adjoin wetlands were calculated and the relationship between them and the major physical drivers was studied. The results highlight that over time, the dynamics of different subsystems represents a balance between inputs (forcing agents like climate) and natural responses (related responses like the vegetation evolution) relevant to urbanization. Basically the urbanization is strongly linked with the phenology and spatial patterns of vegetation cover and not with the channel distribution. Agricultural and farmers uses are in fact the urban edges and they didn't changed obviously if seasonal trends are subtracted from the inter-annual ones. Changes in buffer zones if they were closer to urban or agricultural areas were observed different from the adjoining coastal areas. Finally the uncertainties calculation of the Delta system (i.e. subsidence rates or erosion rates) using new monitoring techniques such as satellite remote sensing shows to be a specific added value that could be used for simulations over varying time scales and it should be considered as a potential ';add in' for an integrated management approach that could be exported in major delta (i.e. Mekong).

Methane clumped isotopes in the Songliao Basin (China): New insights into abiotic vs. biotic hydrocarbon formation

NASA Astrophysics Data System (ADS)

Shuai, Yanhua; Etiope, Giuseppe; Zhang, Shuichang; Douglas, Peter M. J.; Huang, Ling; Eiler, John M.

2018-01-01

Abiotic hydrocarbon gas, typically generated in serpentinized ultramafic rocks and crystalline shields, has important implications for the deep biosphere, petroleum systems, the carbon cycle and astrobiology. Distinguishing abiotic gas (produced by chemical reactions like Sabatier synthesis) from biotic gas (produced from degradation of organic matter or microbial activity) is sometimes challenging because their isotopic and molecular composition may overlap. Abiotic gas has been recognized in numerous locations on the Earth, although there are no confirmed instances where it is the dominant source of commercially valuable quantities in reservoir rocks. The deep hydrocarbon reservoirs of the Xujiaweizi Depression in the Songliao Basin (China) have been considered to host significant amounts of abiotic methane. Here we report methane clumped-isotope values (Δ18) and the isotopic composition of C1-C3 alkanes, CO2 and helium of five gas samples collected from those Xujiaweizi deep reservoirs. Some geochemical features of these samples resemble previously suggested identifiers of abiotic gas (13C-enriched CH4; decrease in 13C/12C ratio with increasing carbon number for the C1-C4 alkanes; abundant, apparently non-biogenic CO2; and mantle-derived helium). However, combining these constraints with new measurements of the clumped-isotope composition of methane and careful consideration of the geological context, suggests that the Xujiaweizi depression gas is dominantly, if not exclusively, thermogenic and derived from over-mature source rocks, i.e., from catagenesis of buried organic matter at high temperatures. Methane formation temperatures suggested by clumped-isotopes (167-213 °C) are lower than magmatic gas generation processes and consistent with the maturity of local source rocks. Also, there are no geological conditions (e.g., serpentinized ultramafic rocks) that may lead to high production of H2 and thus abiotic production of CH4 via CO2 reduction. We propose that the Songliao gas is representative of an atypical type of thermogenic gas that can be mistaken for abiotic gas. Such gases may be encountered more frequently in future exploration of deep or over-mature petroleum systems.

Protein synthesis inhibition activity by strawberry tissue protein extracts during plant life cycle and under biotic and abiotic stresses.

PubMed

Polito, Letizia; Bortolotti, Massimo; Mercatelli, Daniele; Mancuso, Rossella; Baruzzi, Gianluca; Faedi, Walther; Bolognesi, Andrea

2013-07-25

Ribosome-inactivating proteins (RIPs), enzymes that are widely distributed in the plant kingdom, inhibit protein synthesis by depurinating rRNA and many other polynucleotidic substrates. Although RIPs show antiviral, antifungal, and insecticidal activities, their biological and physiological roles are not completely understood. Additionally, it has been described that RIP expression is augmented under stressful conditions. In this study, we evaluated protein synthesis inhibition activity in partially purified basic proteins (hereafter referred to as RIP activity) from tissue extracts of Fragaria × ananassa (strawberry) cultivars with low (Dora) and high (Record) tolerance to root pathogens and fructification stress. Association between the presence of RIP activity and the crop management (organic or integrated soil), growth stage (quiescence, flowering, and fructification), and exogenous stress (drought) were investigated. RIP activity was found in every tissue tested (roots, rhizomes, leaves, buds, flowers, and fruits) and under each tested condition. However, significant differences in RIP distribution were observed depending on the soil and growth stage, and an increase in RIP activity was found in the leaves of drought-stressed plants. These results suggest that RIP expression and activity could represent a response mechanism against biotic and abiotic stresses and could be a useful tool in selecting stress-resistant strawberry genotypes.

Use of carbon isotope analysis to understand semi-arid erosion dynamics and long-term semi-arid land degradation.

PubMed

Turnbull, Laura; Brazier, Richard E; Wainwright, John; Dixon, Liz; Bol, Roland

2008-06-01

Many semi-arid areas worldwide are becoming degraded, in the form of C(4) grasslands being replaced by C(3) shrublands, which causes an increase in surface runoff and erosion, and altered nutrient cycling, which may affect global biogeochemical cycling. The prevention or control of vegetation transitions is hindered by a lack of understanding of their temporal and spatial dynamics, particularly in terms of interactions between biotic and abiotic processes. This research investigates (1) the effects of soil erosion on the delta(13)C values of soil organic matter (SOM) throughout the soil profile and its implications for reconstructing vegetation change using carbon-isotope analysis and (2) the spatial properties of erosion over a grass-shrub transition to increase understanding of biotic-abiotic interactions by using delta(13)C signals of eroded material as a sediment tracer. Results demonstrate that the soils over grass-shrub transitions are not in steady state. A complex interplay of factors determines the input of SOM to the surface horizon of the soil and its subsequent retention and turnover through the soil profile. A positive correlation between event runoff and delta(13)C signatures of eroded sediment was found in all plots. This indicates that the delta(13)C signatures of eroded sediment may provide a means of distinguishing between changes in erosion dynamics over runoff events of different magnitudes and over different vegetation types. The development of this technique using delta(13)C signatures of eroded sediment provides a new means of furthering existing understanding of erosion dynamics over vegetation transitions. This is critical in terms of understanding biotic-abiotic feedbacks and the evolution of areas subject to vegetation change in semi-arid environments. John Wiley & Sons, Ltd

Finger Millet: A “Certain” Crop for an “Uncertain” Future and a Solution to Food Insecurity and Hidden Hunger under Stressful Environments

PubMed Central

Gupta, Sanjay Mohan; Arora, Sandeep; Mirza, Neelofar; Pande, Anjali; Lata, Charu; Puranik, Swati; Kumar, J.; Kumar, Anil

2017-01-01

Crop growth and productivity has largely been vulnerable to various abiotic and biotic stresses that are only set to be compounded due to global climate change. Therefore developing improved varieties and designing newer approaches for crop improvement against stress tolerance have become a priority now-a-days. However, most of the crop improvement strategies are directed toward staple cereals such as rice, wheat, maize etc., whereas attention on minor cereals such as finger millet [Eleusine coracana (L.) Gaertn.] lags far behind. It is an important staple in several semi-arid and tropical regions of the world with excellent nutraceutical properties as well as ensuring food security in these areas even during harsh environment. This review highlights the importance of finger millet as a model nutraceutical crop. Progress and prospects in genetic manipulation for the development of abiotic and biotic stress tolerant varieties is also discussed. Although limited studies have been conducted for genetic improvement of finger millets, its nutritional significance in providing minerals, calories and protein makes it an ideal model for nutrition-agriculture research. Therefore, improved genetic manipulation of finger millets for resistance to both abiotic and biotic stresses, as well as for enhancing nutrient content will be very effective in millet improvement. Key message: Apart from the excellent nutraceutical value of finger millet, its ability to tolerate various abiotic stresses and resist pathogens make it an excellent model for exploring vast genetic and genomic potential of this crop, which provide us a wide choice for developing strategies for making climate resilient staple crops. PMID:28487720

Temporal Dynamics of Abiotic and Biotic Factors on Leaf Litter of Three Plant Species in Relation to Decomposition Rate along a Subalpine Elevation Gradient

PubMed Central

Zhu, Jianxiao; Yang, Wanqin; He, Xinhua

2013-01-01

Relationships between abiotic (soil temperature and number of freeze-thaw cycles) or biotic factors (chemical elements, microbial biomass, extracellular enzymes, and decomposer communities in litter) and litter decomposition rates were investigated over two years in subalpine forests close to the Qinghai-Tibet Plateau in China. Litterbags with senescent birch, fir, and spruce leaves were placed on the forest floor at 2,704 m, 3,023 m, 3,298 m, and 3,582 m elevation. Results showed that the decomposition rate positively correlated with soil mean temperature during the plant growing season, and with the number of soil freeze-thaw cycles during the winter. Concentrations of soluble nitrogen (N), phosphorus (P) and potassium (K) had positive effects but C:N and lignin:N ratios had negative effects on the decomposition rate (k), especially during the winter. Meanwhile, microbial biomass carbon (MBC), N (MBN), and P (MBP) were positively correlated with k values during the first growing season. These biotic factors accounted for 60.0% and 56.4% of the variation in decomposition rate during the winter and the growing season in the first year, respectively. Specifically, litter chemistry (C, N, P, K, lignin, C:N and lignin:N ratio) independently explained 29.6% and 13.3%, and the microbe-related factors (MBC, MBN, MBP, bacterial and fungal biomass, sucrase and ACP activity) explained 22.9% and 34.9% during the first winter and the first growing season, respectively. We conclude that frequent freeze-thaw cycles and litter chemical properties determine the winter decomposition while microbe-related factors play more important roles in determining decomposition in the subsequent growing season. PMID:23620803

Habitability for Complex Life and the Development and Self-Limitations of the Biotic Enhancement of Weathering

NASA Astrophysics Data System (ADS)

Schwartzman, D. W.; Volk, T.

2014-12-01

We submit that the tightly coupled coevolution of biota and climate is a critical driver of the self-organization of the biosphere over geologic time. The long-term carbon biogeochemical cycle includes a major influence of biology relevant to climatic, namely the biotic enhancement of weathering (BEW). According to a meta-analysis of field and experimental evidence, the likely magnitude of the present BEW is roughly two orders of magnitude, the culmination of its progressive increase over geologic time. Within the context of modeling this long-term cycle, this value can be used to estimate the likely abiotic temperature history of the Earth's surface, assuming plausible initial temperatures, and histories of volcanic outgassing and continental crust growth. The result of this modeling is that the Earth would have been habitable for thermophilic life (growing above 50 deg C) for the past 4.4 billion years, but not for low-temperature life, including plants and animals. Hence biospheric cooling due to biotic actions allowed the emergence of complex life. Much larger increases in BEW are self-limiting, since the atmospheric CO2 level would plunge below the lower limit potentially for photosynthesis, thereby driving a decline in the biological productivity and global BEW, related to reduced plant and soil activities, with the system being kept at this threshold or going back to higher CO2 levels, with scenarios dependent on volcanic outgassing and solar inputs. We will present astrobiological implications of this modeling. References: Schwartzman D (1999, 2002) Life, Temperature, and the Earth: The Self Organizing Biosphere. Columbia Univ. Press; Schwartzman, D. (2013) Keynote: The Geobiology of Weathering: The 13th Hypothesis. Goldschmidt Conference. (Schwartzman D. and Brantley S. (2013) Mineral. Mag. 77(5): 2170); Volk T (1998) Gaia's Body: Toward a Physiology of Earth. Copernicus.

FRET-based glucose imaging identifies glucose signalling in response to biotic and abiotic stresses in rice roots.

PubMed

Zhu, Qingdong; Wang, Li; Dong, Qianli; Chang, Shu; Wen, Kexin; Jia, Shenghua; Chu, Zhilin; Wang, Hanmeng; Gao, Ping; Zhao, Heping; Han, Shengcheng; Wang, Yingdian

2017-08-01

Glucose is the primary energy provider and the most important sugar-signalling molecule, regulating metabolites and modulating gene expression from unicellular yeast to multicellular plants and animals. Therefore, monitoring intracellular glucose levels temporally and spatially in living cells is an essential step for decoding the glucose signalling in response to biotic and abiotic stresses. In this study, the genetically encoded FRET (Förster resonance energy transfer) nanosensors, FLIPglu-2μ∆13 and FLIPglu-600μΔ13, were used to measure cytosolic glucose dynamics in rice plants. First, we found that the FRET signal decreased in response to external glucose in a concentration-dependent manner. The glucose concentration at which the cytosolic level corresponded to the K 0.5 value for FLIPglu-2μΔ13 was approximately 10.05μM, and that for FLIPglu-600μΔ13 was 0.9mM, respectively. The substrate selectivity of nanosensors for glucose and its analogues is D-Glucose>2-deoxyglucose>3-O-methylglucose>L-Glucose. We further showed that the biotic elicitors (flg22 and chitin) and the abiotic elicitors (osmotic stress, salinity and extreme temperature) induce the intracellular glucose increases in the detached root segments of transgenic rice containing FLIPglu-2μΔ13 in a stimulus-specific manner, but not in FLIPglu-600μΔ13 transgenic lines. These results demonstrated that FRET nanosensors can be used to detect increases in intracellular glucose within the physiological range of 0.2-20μM in response to various stimuli in transgenic rice root cells, which indicated that intracellular glucose may act as a potential secondary messenger to connect extracellular stimuli with cellular physiological responses in plants. Copyright © 2017 Elsevier GmbH. All rights reserved.

Ecological study of peat landforms in Canada and Alaska

NASA Technical Reports Server (NTRS)

Glaser, Paul H.

1989-01-01

Over 20 percent of the land surface of Canada and Alaska is covered by peatlands, which may be defined as any waterlogged ecosystem with a minimum thickness of 20 cm of organic matter in the soil. Past investigations have demonstrated the value of aerial photographs in identifying the major vegetation types and analyzing the biotic and hydrogeologic processes that control the development of these peatlands. In the present study, LANDSAT TM imagery was used in conjunction with field studies to determine the utility of this satellite sensor for detecting these important processes. Although the vegetation landforms within these major peat basins are visible on aerial photographs, LANDSAT TM imagery provides essential new evidence for their analysis. Spectral data from the LANDSAT TM system provides: (1) synoptic views of the patterns across large portions of these peat basins, indicating important physiographic controls on peatland development, (2) more sensitive detection of the major vegetation types, allowing rapid quantitative estimates to be made of their distribution and aerial extent, (3) discrimination of bog areas with potentially rapid or slow rates of peat accumulation, (4) identification of discharge zones for groundwater, which apparently represents the most important source of alkalinity in these peat basins, and (5) detection of flow patterns in water tracks that appear nearly uniform on standard aerial photographs.

Temperature rise and parasitic infection interact to increase the impact of an invasive species.

PubMed

Laverty, Ciaran; Brenner, David; McIlwaine, Christopher; Lennon, Jack J; Dick, Jaimie T A; Lucy, Frances E; Christian, Keith A

2017-04-01

Invasive species often detrimentally impact native biota, e.g. through predation, but predicting such impacts is difficult due to multiple and perhaps interacting abiotic and biotic context dependencies. Higher mean and peak temperatures, together with parasites, might influence the impact of predatory invasive host species additively, synergistically or antagonistically. Here, we apply the comparative functional response methodology (relationship between resource consumption rate and resource supply) in one experiment and conduct a second scaled-up mesocosm experiment to assess any differential predatory impacts of the freshwater invasive amphipod Gammarus pulex, when uninfected and infected with the acanthocephalan Echinorhynchus truttae, at three temperatures representative of current and future climate. Individual G. pulex showed Type II predatory functional responses. In both experiments, infection was associated with higher maximum feeding rates, which also increased with increasing temperatures. Additionally, infection interacted with higher temperatures to synergistically elevate functional responses and feeding rates. Parasitic infection also generally increased Q 10 values. We thus suggest that the differential metabolic responses of the host and parasite to increasing temperatures drives the synergy between infection and temperature, elevating feeding rates and thus enhancing the ecological impact of the invader. Copyright © 2017 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

A probabilistic model for silver bioaccumulation in aquatic systems and assessment of human health risks

USGS Publications Warehouse

Warila, James; Batterman, Stuart; Passino-Reader, Dora R.

2001-01-01

Silver (Ag) is discharged in wastewater effluents and is also a component in a proposed secondary water disinfectant. A steady-state model was developed to simulate bioaccumulation in aquatic biota and assess ecological and human health risks. Trophic levels included phytoplankton, invertebrates, brown trout, and common carp. Uptake routes included water, food, or sediment. Based on an extensive review of the literature, distributions were derived for most inputs for use in Monte Carlo simulations. Three scenarios represented ranges of dilution and turbidity. Compared with the limited field data available, median estimates of Ag in carp (0.07-2.1 Iμg/g dry weight) were 0.5 to 9 times measured values, and all measurements were within the predicted interquartile range. Median Ag concentrations in biota were ranked invertebrates > phytoplankton > trout > carp. Biotic concentrations were highest for conditions of low dilution and low turbidity. Critical variables included Ag assimilation eficiency, specific feeding rate, and the phytoplankton bioconcentration factor. Bioaccumulation of Ag seems unlikely to result in txicity to aquatic biota and humans consuming fish. Although the highest predicted Ag concentrations in water (>200 ng/L) may pose chronic risks to early survival and development of salmonids and risks of argyria to subsistence fishers, these results occur under highly conservative conditions.

Managing shifting species: Ancient DNA reveals conservation conundrums in a dynamic world.

PubMed

Waters, Jonathan M; Grosser, Stefanie

2016-11-01

The spread of exotic species represents a major driver of biological change across the planet. While dispersal and colonization are natural biological processes, we suggest that the failure to recognize increasing rates of human-facilitated self-introductions may represent a threat to native lineages. Notably, recent biogeographic analyses have revealed numerous cases of biological range shifts in response to anthropogenic impacts and climate change. In particular, ancient DNA analyses have revealed several cases in which lineages traditionally thought to be long-established "natives" are in fact recent colonizers. Such range expansion events have apparently occurred in response to human-mediated native biodiversity declines and ecosystem change, particularly in recently colonized, isolated ecosystems such as New Zealand. While such events can potentially boost local biodiversity, the spread of exotic lineages may also hasten the decline of indigenous species, so it is essential that conservation managers recognize these rapid biotic shifts.​. © 2016 WILEY Periodicals, Inc.

Shrubline but not treeline advance matches climate velocity in montane ecosystems of south-central Alaska.

PubMed

Dial, Roman J; Smeltz, T Scott; Sullivan, Patrick F; Rinas, Christina L; Timm, Katriina; Geck, Jason E; Tobin, S Carl; Golden, Trevor S; Berg, Edward C

2016-05-01

Tall shrubs and trees are advancing into many tundra and wetland ecosystems but at a rate that often falls short of that predicted due to climate change. For forest, tall shrub, and tundra ecosystems in two pristine mountain ranges of Alaska, we apply a Bayesian, error-propagated calculation of expected elevational rise (climate velocity), observed rise (biotic velocity), and their difference (biotic inertia). We show a sensitive dependence of climate velocity on lapse rate and derive biotic velocity as a rigid elevational shift. Ecosystem presence identified from recent and historic orthophotos ~50 years apart was regressed on elevation. Biotic velocity was estimated as the difference between critical point elevations of recent and historic logistic fits divided by time between imagery. For both mountain ranges, the 95% highest posterior density of climate velocity enclosed the posterior distributions of all biotic velocities. In the Kenai Mountains, mean tall shrub and climate velocities were both 2.8 m y(-1). In the better sampled Chugach Mountains, mean tundra retreat was 1.2 m y(-1) and climate velocity 1.3 m y(-1). In each mountain range, the posterior mode of tall woody vegetation velocity (the complement of tundra) matched climate velocity better than either forest or tall shrub alone, suggesting competitive compensation can be important. Forest velocity was consistently low at 0.1-1.1 m y(-1), indicating treeline is advancing slowly. We hypothesize that the high biotic inertia of forest ecosystems in south-central Alaska may be due to competition with tall shrubs and/or more complex climate controls on the elevational limits of trees than tall shrubs. Among tall shrubs, those that disperse farthest had lowest inertia. Finally, the rapid upward advance of woody vegetation may be contributing to regional declines in Dall's sheep (Ovis dalli), a poorly dispersing alpine specialist herbivore with substantial biotic inertia due to dispersal reluctance. © 2015 John Wiley & Sons Ltd.

Biotic interactions mediate the expansion of black mangrove (Avicennia germinans) into salt marshes under climate change.

PubMed

Guo, Hongyu; Zhang, Yihui; Lan, Zhenjiang; Pennings, Steven C

2013-09-01

Many species are expanding their distributions to higher latitudes due to global warming. Understanding the mechanisms underlying these distribution shifts is critical for better understanding the impacts of climate changes. The climate envelope approach is widely used to model and predict species distribution shifts with changing climates. Biotic interactions between species, however, may also influence species distributions, and a better understanding of biotic interactions could improve predictions based solely on climate envelope models. Along the northern Gulf of Mexico coast, USA, subtropical black mangrove (Avicennia germinans) at the northern limit of its distribution grows sympatrically with temperate salt marsh plants in Florida, Louisiana, and Texas. In recent decades, freeze-free winters have led to an expansion of black mangrove into salt marshes. We examined how biotic interactions between black mangrove and salt marsh vegetation along the Texas coast varied across (i) a latitudinal gradient (associated with a winter-temperature gradient); (ii) the elevational gradient within each marsh (which creates different marsh habitats); and (iii) different life history stages of black mangroves (seedlings vs. juvenile trees). Each of these variables affected the strength or nature of biotic interactions between black mangrove and salt marsh vegetation: (i) Salt marsh vegetation facilitated black mangrove seedlings at their high-latitude distribution limit, but inhibited black mangrove seedlings at lower latitudes; (ii) mangroves performed well at intermediate elevations, but grew and survived poorly in high- and low-marsh habitats; and (iii) the effect of salt marsh vegetation on black mangroves switched from negative to neutral as black mangroves grew from seedlings into juvenile trees. These results indicate that the expansion of black mangroves is mediated by complex biotic interactions. A better understanding of the impacts of climate change on ecological communities requires incorporating context-dependent biotic interactions into species range models. © 2013 John Wiley & Sons Ltd.

U. S. EPA’S APPROACH FOR CHLORINATED SOLVENTS

EPA Science Inventory

The approach for chlorinated solvents is similar to the approach for petroleum hydrocarbons. However, there are more mechanisms of removal, including reductive dechlorination (biotic or abiotic), dehydrochloroelimination (abiotic), and hydrolysis (biotic or abiotic). As a resul...

Climate change and the past, present, and future of biotic interactions.

PubMed

Blois, Jessica L; Zarnetske, Phoebe L; Fitzpatrick, Matthew C; Finnegan, Seth

2013-08-02

Biotic interactions drive key ecological and evolutionary processes and mediate ecosystem responses to climate change. The direction, frequency, and intensity of biotic interactions can in turn be altered by climate change. Understanding the complex interplay between climate and biotic interactions is thus essential for fully anticipating how ecosystems will respond to the fast rates of current warming, which are unprecedented since the end of the last glacial period. We highlight episodes of climate change that have disrupted ecosystems and trophic interactions over time scales ranging from years to millennia by changing species' relative abundances and geographic ranges, causing extinctions, and creating transient and novel communities dominated by generalist species and interactions. These patterns emerge repeatedly across disparate temporal and spatial scales, suggesting the possibility of similar underlying processes. Based on these findings, we identify knowledge gaps and fruitful areas for research that will further our understanding of the effects of climate change on ecosystems.

Leaf δ13C variability with elevation, slope aspect, and precipitation in the southwest United States

USGS Publications Warehouse

Van De Water, Peter K.; Leavitt, Steven W.; Betancourt, Julio L.

2002-01-01

Leaves from several desert and woodland species, including gymnosperms and angiosperms with both C3 and C4 physiology, were analyzed to detect trends in δ13Cleaf with elevation and slope aspect along two transects in southeastern Utah and south-central New Mexico, USA. The main difference between the two transects is the steeper elevational gradient for mean annual and summer precipitation in the southern transect. For any given species, we found that isotopic differences between individual plants growing at the same site commonly equal differences measured for plants along the entire altitudinal gradient. In C3 plants, δ13Cleaf values become slightly enriched at the lowest elevations, the opposite of trends identified in more humid regions. Apparently, increasing water-use efficiency with drought stress offsets the influence of other biotic and abiotic factors that operate to decrease isotopic discrimination with elevation. For some species shared by the two transects (e.g., Pinus edulis and Cercocarpus montanus), δ13Cleaf values are dramatically depleted at sites that receive more than 550 mm mean annual precipitation, roughly the boundary (pedalfer-pedocal) at which soils commonly fill to field capacity in summer and carbonates are leached. We hypothesize that, in summer-wet areas, this may represent the boundary at which drought stress overtakes other factors in determining the sign of δ13Cleaf with elevation. The opposition of isotopic trends with elevation in arid versus humid regions cautions against standard correction for elevation in comparative studies of δ13Cleaf.

Annual grass invasion in sagebrush-steppe: The relative importance of climate, soil properties and biotic interactions

USGS Publications Warehouse

Bansal, Sheel; Sheley, Roger L.

2016-01-01

The invasion by winter-annual grasses (AGs) such as Bromus tectorum into sagebrush steppe throughout the western USA is a classic example of a biological invasion with multiple, interacting climate, soil and biotic factors driving the invasion, although few studies have examined all components together. Across a 6000-km2 area of the northern Great Basin, we conducted a field assessment of 100 climate, soil, and biotic (functional group abundances, diversity) factors at each of 90 sites that spanned an invasion gradient ranging from 0 to 100 % AG cover. We first determined which biotic and abiotic factors had the strongest correlative relationships with AGs and each resident functional group. We then used regression and structural equation modeling to explore how multiple ecological factors interact to influence AG abundance. Among biotic interactions, we observed negative relationships between AGs and biodiversity, perennial grass cover, resident species richness, biological soil crust cover and shrub density, whereas perennial and annual forb cover, tree cover and soil microbial biomass had no direct linkage to AG. Among abiotic factors, AG cover was strongly related to climate (increasing cover with increasing temperature and aridity), but had weak relationships with soil factors. Our structural equation model showed negative effects of perennial grasses and biodiversity on AG cover while integrating the negative effects of warmer climate and positive influence of belowground processes on resident functional groups. Our findings illustrate the relative importance of biotic interactions and climate on invasive abundance, while soil properties appear to have stronger relationships with resident biota than with invasives.

Biogeography of Anurans from the Poorly Known and Threatened Coastal Sandplains of Eastern Brazil.

PubMed

Xavier, Ariane Lima; Guedes, Thaís Barreto; Napoli, Marcelo Felgueiras

2015-01-01

The east coast of Brazil comprises an extensive area inserted in the Tropical Atlantic Domain and is represented by sandy plains of beach ridges commonly known as Restingas. The coastal environments are unique and house a rich amphibian fauna, the geographical distribution patterns of which are incipient. Biogeographical studies can explain the current distributional patterns and provide the identification of natural biogeographical units. These areas are important in elucidating the evolutionary history of the taxa and the areas where they occur. The aim of this study was to seek natural biogeographical units in the Brazilian sandy plains of beach ridges by means of distribution data of amphibians and to test the main predictions of the vicariance model to explain the patterns found. We revised and georeferenced data on the geographical distribution of 63 anuran species. We performed a search for latitudinal distribution patterns along the sandy coastal plains of Brazil using the non-metric multidimensional scaling method (NMDS) and the biotic element analysis to identify natural biogeographical units. The results showed a monotonic variation in anuran species composition along the latitudinal gradient with a break in the clinal pattern from 23°S to 25°S latitude (states of Rio de Janeiro to São Paulo). The major predictions of the vicariance model were corroborated by the detection of four biotic elements with significantly clustered distribution and by the presence of congeneric species distributed in distinct biotic elements. The results support the hypothesis that vicariance could be one of the factors responsible for the distribution patterns of the anuran communities along the sandy coastal plains of eastern Brazil. The results of the clusters are also congruent with the predictions of paleoclimatic models made for the Last Glacial Maximum of the Pleistocene, such as the presence of historical forest refugia and biogeographical patterns already detected for amphibians in the Atlantic Rainforest.

Ecosystem development in roadside grasslands: biotic control, plant–soil interactions and dispersal limitations

PubMed Central

García-Palacios, Pablo; Bowker, Matthew A.; Maestre, Fernando T.; Soliveres, Santiago; Valladares, Fernando; Papadopoulos, Jorge; Escudero, Adrián

2015-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant–soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0–2, 7–9 and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts [BSCs], and soil microbial functional diversity [soil microorganisms] affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant–soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: 1) maintain well-conserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, 2) increase BSC cover in areas under strong erosion risk, to avoid soil loss, and 3) enhance soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. PMID:22073661

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

PubMed Central

Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

2016-01-01

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species interactions and environmental filtering are important for structuring microbial communities but emphasize the need for more research into these interactions. PMID:27065966

Interactive biotic and abiotic regulators of soil carbon cycling: evidence from controlled climate experiments on peatland and boreal soils.

PubMed

Briones, María Jesús I; McNamara, Niall P; Poskitt, Jan; Crow, Susan E; Ostle, Nicholas J

2014-09-01

Partially decomposed plant and animal remains have been accumulating in organic soils (i.e. >40% C content) for millennia, making them the largest terrestrial carbon store. There is growing concern that, in a warming world, soil biotic processing will accelerate and release greenhouse gases that further exacerbate climate change. However, the magnitude of this response remains uncertain as the constraints are abiotic, biotic and interactive. Here, we examined the influence of resource quality and biological activity on the temperature sensitivity of soil respiration under different soil moisture regimes. Organic soils were sampled from 13 boreal and peatland ecosystems located in the United Kingdom, Ireland, Spain, Finland and Sweden, representing a natural resource quality range of C, N and P. They were incubated at four temperatures (4, 10, 15 and 20 °C) at either 60% or 100% water holding capacity (WHC). Our results showed that chemical and biological properties play an important role in determining soil respiration responses to temperature and moisture changes. High soil C : P and C : N ratios were symptomatic of slow C turnover and long-term C accumulation. In boreal soils, low bacterial to fungal ratios were related to greater temperature sensitivity of respiration, which was amplified in drier conditions. This contrasted with peatland soils which were dominated by bacterial communities and enchytraeid grazing, resulting in a more rapid C turnover under warmer and wetter conditions. The unexpected acceleration of C mineralization under high moisture contents was possibly linked to the primarily role of fermented organic matter, instead of oxygen, in mediating microbial decomposition. We conclude that to improve C model simulations of soil respiration, a better resolution of the interactions occurring between climate, resource quality and the decomposer community will be required. © 2014 John Wiley & Sons Ltd.

Recovery vs. Restructuring: Establishing Ecologic Patterns in Early and Middle Triassic Paleocommunities (Invited)

NASA Astrophysics Data System (ADS)

Fraiser, M.; Dineen, A.; Sheehan, P.

2013-12-01

Published data has been interpreted as indicating that marine ecological devastation following the end-Permian mass extinction was protracted and may have lasted 5 million years into the Middle Triassic (Anisian). However, a review of previous literature shows that understanding of biotic recovery is typically based on only a few components of the ecosystem, such as on taxonomic diversity, a single genus/phylum, or facies. Typically, paleocommunities are considered fully recovered when dominance and diversity are regained and normal ecosystem functioning has resumed. However, in addition to the biodiversity crash at the end of the Permian, taxonomic and ecologic structure also changed,with the extinction marking the faunal shift from brachiopod-rich Paleozoic Evolutionary Fauna (EF) to the mollusc-rich Modern EF. This suggests that the extreme reorganizational nature of the Triassic does not adhere to the standard definition of recovery, which is a return to previous conditions. Thus, we propose the term 'restructuring' to describe this interval, as Early and Middle Triassic communities might not exhibit the typical characteristics of a 'normal' Permian one. To more fully characterize Triassic ecologic restructuring, paleoecologists should take into account functional diversity and redundancy. We quantified functional richness and regularity in four different paleocommunities from classic Permian and Triassic sections. Functional richness was low in paleocommunities after the end-Permian mass extinction, but increased to high levels by the Middle Triassic. In contrast, functional regularity was low in the Middle Permian, but high in all the Triassic paleocommunities. The change from low to high functional regularity/redundancy at the P/T boundary may be a factor of the highly stressful Triassic environmental conditions (i.e. anoxia, hypercapnia), as high regularity in a community can boost survival in harsh environments. Parameters such as these will more accurately establish if the biotic patterns represent either failed biotic restructuring or a fully restructured marine community adapted to harsh Triassic environments.

Integrating human impacts and ecological integrity into a risk-based protocol for conservation planning

USGS Publications Warehouse

Mattson, K.M.; Angermeier, P.L.

2007-01-01

Conservation planning aims to protect biodiversity by sustainng the natural physical, chemical, and biological processes within representative ecosystems. Often data to measure these components are inadequate or unavailable. The impact of human activities on ecosystem processes complicates integrity assessments and might alter ecosystem organization at multiple spatial scales. Freshwater conservation targets, such as populations and communities, are influenced by both intrinsic aquatic properties and the surrounding landscape, and locally collected data might not accurately reflect potential impacts. We suggest that changes in five major biotic drivers-energy sources, physical habitat, flow regime, water quality, and biotic interactions-might be used as surrogates to inform conservation planners of the ecological integrity of freshwater ecosystems. Threats to freshwater systems might be evaluated based on their impact to these drivers to provide an overview of potential risk to conservation targets. We developed a risk-based protocol, the Ecological Risk Index (ERI), to identify watersheds with least/most risk to conservation targets. Our protocol combines risk-based components, specifically the frequency and severity of human-induced stressors, with biotic drivers and mappable land- and water-use data to provide a summary of relative risk to watersheds. We illustrate application of our protocol with a case study of the upper Tennessee River basin, USA. Differences in risk patterns among the major drainages in the basin reflect dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among our watersheds. We also found that the relative importance of threats is sensitive to the spatial grain of the analysis. Our case study demonstrates that the ERI is useful for evaluating the frequency and severity of ecosystemwide risk, which can inform local and regional conservation planning. ?? 2006 Springer Science+Business Media, Inc.

Biogeography of Anurans from the Poorly Known and Threatened Coastal Sandplains of Eastern Brazil

PubMed Central

Xavier, Ariane Lima; Guedes, Thaís Barreto; Napoli, Marcelo Felgueiras

2015-01-01

The east coast of Brazil comprises an extensive area inserted in the Tropical Atlantic Domain and is represented by sandy plains of beach ridges commonly known as Restingas. The coastal environments are unique and house a rich amphibian fauna, the geographical distribution patterns of which are incipient. Biogeographical studies can explain the current distributional patterns and provide the identification of natural biogeographical units. These areas are important in elucidating the evolutionary history of the taxa and the areas where they occur. The aim of this study was to seek natural biogeographical units in the Brazilian sandy plains of beach ridges by means of distribution data of amphibians and to test the main predictions of the vicariance model to explain the patterns found. We revised and georeferenced data on the geographical distribution of 63 anuran species. We performed a search for latitudinal distribution patterns along the sandy coastal plains of Brazil using the non-metric multidimensional scaling method (NMDS) and the biotic element analysis to identify natural biogeographical units. The results showed a monotonic variation in anuran species composition along the latitudinal gradient with a break in the clinal pattern from 23°S to 25°S latitude (states of Rio de Janeiro to São Paulo). The major predictions of the vicariance model were corroborated by the detection of four biotic elements with significantly clustered distribution and by the presence of congeneric species distributed in distinct biotic elements. The results support the hypothesis that vicariance could be one of the factors responsible for the distribution patterns of the anuran communities along the sandy coastal plains of eastern Brazil. The results of the clusters are also congruent with the predictions of paleoclimatic models made for the Last Glacial Maximum of the Pleistocene, such as the presence of historical forest refugia and biogeographical patterns already detected for amphibians in the Atlantic Rainforest. PMID:26047484

Ecological coassociations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle.

PubMed

Garrick, Ryan C; Nason, John D; Fernández-Manjarrés, Juan F; Dyer, Rodney J

2013-06-01

Ecologically interacting species may have phylogeographical histories that are shaped both by features of their abiotic landscape and by biotic constraints imposed by their coassociation. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species.This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of codistributed free-living animals (e.g. herpetofauna and small mammals). Thus, 'plant-like' patterns should be discernible in host-specific insect herbivores. Here, we investigate the population history of a monophagous bark beetle, Araptus attenuatus, and consider drivers of phylogeographical patterns in the light of previous work on its host plant, Euphorbia lomelii. Using a combination of phylogenetic, coalescent-simulation-based and exploratory analyses of mitochondrial DNA sequences and nuclear genotypic data, we found that the evolutionary history of A. attenuatus exhibits similarities to its host plant that are attributable to both biotic and abiotic processes. Southward range expansion and recent colonization of continental Sonora from the Baja peninsula appear to be unique to this taxon pair and probably reflect influences of the host plant. On the other hand, abiotic factors with landscape level influences on a diverse suite of codistributed arid-adapted taxa, such as Plio- and Pleistocene-aged marine incursions in the region, also left genetic signatures in beetle and host plant populations. Superimposed on these similarities, bark beetle-specific patterns and processes were also evident: our data revealed two secondarily sympatric,reproductively isolated genetic lineages, as well as a previously unrecognized mid peninsular warm desert refuge. Taken together, this work illustrates that the evolutionary history of species-specific insect herbivores may represent a mosaic of influences,including—but not limited to—those imposed by the host plant.

Diversity and Biotic Homogenization of Urban Land-Snail Faunas in Relation to Habitat Types and Macroclimate in 32 Central European Cities

PubMed Central

Horsák, Michal; Lososová, Zdeňka; Čejka, Tomáš; Juřičková, Lucie; Chytrý, Milan

2013-01-01

The effects of non-native species invasions on community diversity and biotic homogenization have been described for various taxa in urban environments, but not for land snails. Here we relate the diversity of native and non-native land-snail urban faunas to urban habitat types and macroclimate, and analyse homogenization effects of non-native species across cities and within the main urban habitat types. Land-snail species were recorded in seven 1-ha plots in 32 cities of ten countries of Central Europe and Benelux (224 plots in total). Each plot represented one urban habitat type characterized by different management and a specific disturbance regime. For each plot, we obtained January, July and mean annual temperature and annual precipitation. Snail species were classified into either native or non-native. The effects of habitat type and macroclimate on the number of native and non-native species were analysed using generalized estimating equations; the homogenization effect of non-native species based on the Jaccard similarity index and homogenization index. We recorded 67 native and 20 non-native species. Besides being more numerous, native species also had much higher beta diversity than non-natives. There were significant differences between the studied habitat types in the numbers of native and non-native species, both of which decreased from less to heavily urbanized habitats. Macroclimate was more important for the number of non-native than native species; however in both cases the effect of climate on diversity was overridden by the effect of urban habitat type. This is the first study on urban land snails documenting that non-native land-snail species significantly contribute to homogenization among whole cities, but both the homogenization and diversification effects occur when individual habitat types are compared among cities. This indicates that the spread of non-native snail species may cause biotic homogenization, but it depends on scale and habitat type. PMID:23936525

Diversity and biotic homogenization of urban land-snail faunas in relation to habitat types and macroclimate in 32 central European cities.

PubMed

Horsák, Michal; Lososová, Zdeňka; Čejka, Tomáš; Juřičková, Lucie; Chytrý, Milan

2013-01-01

The effects of non-native species invasions on community diversity and biotic homogenization have been described for various taxa in urban environments, but not for land snails. Here we relate the diversity of native and non-native land-snail urban faunas to urban habitat types and macroclimate, and analyse homogenization effects of non-native species across cities and within the main urban habitat types. Land-snail species were recorded in seven 1-ha plots in 32 cities of ten countries of Central Europe and Benelux (224 plots in total). Each plot represented one urban habitat type characterized by different management and a specific disturbance regime. For each plot, we obtained January, July and mean annual temperature and annual precipitation. Snail species were classified into either native or non-native. The effects of habitat type and macroclimate on the number of native and non-native species were analysed using generalized estimating equations; the homogenization effect of non-native species based on the Jaccard similarity index and homogenization index. We recorded 67 native and 20 non-native species. Besides being more numerous, native species also had much higher beta diversity than non-natives. There were significant differences between the studied habitat types in the numbers of native and non-native species, both of which decreased from less to heavily urbanized habitats. Macroclimate was more important for the number of non-native than native species; however in both cases the effect of climate on diversity was overridden by the effect of urban habitat type. This is the first study on urban land snails documenting that non-native land-snail species significantly contribute to homogenization among whole cities, but both the homogenization and diversification effects occur when individual habitat types are compared among cities. This indicates that the spread of non-native snail species may cause biotic homogenization, but it depends on scale and habitat type.

Ecosystem development in roadside grasslands: Biotic control, plant-soil interactions, and dispersal limitations

USGS Publications Warehouse

Garcia-Palacios, P.; Bowker, M.A.; Maestre, F.T.; Soliveres, S.; Valladares, F.; Papadopoulos, J.; Escudero, A.

2011-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant-soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0-2, 7-9, and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts (BSCs), and soil microbial functional diversity (soil microorganisms) affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control, and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant-soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: (1) maintaining wellconserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, (2) increasing BSC cover in areas under strong erosion risk, to avoid soil loss, and (3) enhancing soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. ?? 2011 by the Ecological Society of America.

A framework to assess the impacts of climate change on stream health indicators in Michigan watersheds

NASA Astrophysics Data System (ADS)

Woznicki, S. A.; Nejadhashemi, A. P.; Tang, Y.; Wang, L.

2016-12-01

Climate change is projected to alter watershed hydrology and potentially amplify nonpoint source pollution transport. These changes have implications for fish and macroinvertebrates, which are often used as measures of aquatic ecosystem health. By quantifying the risk of adverse impacts to aquatic ecosystem health at the reach-scale, watershed climate change adaptation strategies can be developed and prioritized. The objective of this research was to quantify the impacts of climate change on stream health in seven Michigan watersheds. A process-based watershed model, the Soil and Water Assessment Tool (SWAT), was linked to adaptive neuro-fuzzy inferenced (ANFIS) stream health models. SWAT models were used to simulate reach-scale flow regime (magnitude, frequency, timing, duration, and rate of change) and water quality variables. The ANFIS models were developed based on relationships between the in-stream variables and sampling points of four stream health indicators: the fish index of biotic integrity (IBI), macroinvertebrate family index of biotic integrity (FIBI), Hilsenhoff biotic index (HBI), and number of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa. The combined SWAT-ANFIS models extended stream health predictions to all watershed reaches. A climate model ensemble from the Coupled Model Intercomparison Project Phase 5 (CMIP5) was used to develop projections of changes to flow regime (using SWAT) and stream health indicators (using ANFIS) from a baseline of 1980-2000 to 2020-2040. Flow regime variables representing variability, duration of extreme events, and timing of low and high flow events were sensitive to changes in climate. The stream health indicators were relatively insensitive to changing climate at the watershed scale. However, there were many instances of individual reaches that were projected to experience declines in stream health. Using the probability of stream health decline coupled with the magnitude of the decline, maps of vulnerable stream ecosystems were developed, which can be used in the watershed management decision-making process.

Biotic Invasions: Causes, Epidemiology, Global Consequences and Control

EPA Pesticide Factsheets

The module provides a link to an article in a series of articles in Issues in Ecology. This article presents information on biotic invaders, their destruction, controlling their detriment and the effects aquaculture is having on world fish supplies.

Olivine Weathering: Abiotic Versus Biotic Processes as Possible Biosignatures

NASA Technical Reports Server (NTRS)

Longazo, T. G.; Wentworth, S. J.; McKay, D. S.; Southam, G.; Clemett, S. J.

2001-01-01

A preliminary study to determine how abiotic versus biotic processes affect the weathering of olivine crystals. Perhaps the differences between these weathering processes could be used as biosignatures. Additional information is contained in the original extended abstract.

BIOTIC AND ABIOTIC CONTRIBUTIONS TO REDUCTIVE TRANSFORMATION OF ORGANIC POLLUTANTS

EPA Science Inventory

The relative contributions of biotic and abiotic reductive transformation reactions were probed in two anoxic freshwater sediments by following the transformation of nitrobenzene, and 2,4 dichlorophenol (compounds with different one electron reduction potentials). The sediments d...

Influence of Disturbance on Soil Respiration in Biologically Crusted Soil during the Dry Season

PubMed Central

Feng, Wei; Zhang, Yu-qing; Wu, Bin; Zha, Tian-shan; Jia, Xin; Qin, Shu-gao; Shao, Chen-xi; Liu, Jia-bin; Lai, Zong-rui; Fa, Ke-yu

2013-01-01

Soil respiration (Rs) is a major pathway for carbon cycling and is a complex process involving abiotic and biotic factors. Biological soil crusts (BSCs) are a key biotic component of desert ecosystems worldwide. In desert ecosystems, soils are protected from surface disturbance by BSCs, but it is unknown whether Rs is affected by disturbance of this crust layer. We measured Rs in three types of disturbed and undisturbed crusted soils (algae, lichen, and moss), as well as bare land from April to August, 2010, in Mu Us desert, northwest China. Rs was similar among undisturbed soils but increased significantly in disturbed moss and algae crusted soils. The variation of Rs in undisturbed and disturbed soil was related to soil bulk density. Disturbance also led to changes in soil organic carbon and fine particles contents, including declines of 60–70% in surface soil C and N, relative to predisturbance values. Once BSCs were disturbed, Q 10 increased. Our findings indicate that a loss of BSCs cover will lead to greater soil C loss through respiration. Given these results, understanding the disturbance sensitivity impact on Rs could be helpful to modify soil management practices which promote carbon sequestration. PMID:24453845

Biotic transitions in global marine diversity

NASA Technical Reports Server (NTRS)

Miller, A. I.

1998-01-01

Long-term transitions in the composition of Earth's marine biota during the Phanerozoic have historically been explained in two different ways. One view is that they were mediated through biotic interactions among organisms played out over geologic time. The other is that mass extinctions transcended any such interactions and governed diversity over the long term by resetting the relative diversities of higher taxa. However, a growing body of evidence suggests that macroevolutionary processes effecting biotic transitions during background times were not fundamentally different from those operating during mass extinctions. Physical perturbations at many geographic scales combined to produce the long-term trajectory of Phanerozoic diversity.

Effect of Temperature on the Biotic Potential of Honeybee Microsporidia▿

PubMed Central

Martín-Hernández, Raquel; Meana, Aránzazu; García-Palencia, Pilar; Marín, Pilar; Botías, Cristina; Garrido-Bailón, Encarna; Barrios, Laura; Higes, Mariano

2009-01-01

The biological cycle of Nosema spp. in honeybees depends on temperature. When expressed as total spore counts per day after infection, the biotic potentials of Nosema apis and N. ceranae at 33°C were similar, but a higher proportion of immature stages of N. ceranae than of N. apis were seen. At 25 and 37°C, the biotic potential of N. ceranae was higher than that of N. apis. The better adaptation of N. ceranae to complete its endogenous cycle at different temperatures clearly supports the observation of the different epidemiological patterns. PMID:19233948

Effect of temperature on the biotic potential of honeybee microsporidia.

PubMed

Martín-Hernández, Raquel; Meana, Aránzazu; García-Palencia, Pilar; Marín, Pilar; Botías, Cristina; Garrido-Bailón, Encarna; Barrios, Laura; Higes, Mariano

2009-04-01

The biological cycle of Nosema spp. in honeybees depends on temperature. When expressed as total spore counts per day after infection, the biotic potentials of Nosema apis and N. ceranae at 33 degrees C were similar, but a higher proportion of immature stages of N. ceranae than of N. apis were seen. At 25 and 37 degrees C, the biotic potential of N. ceranae was higher than that of N. apis. The better adaptation of N. ceranae to complete its endogenous cycle at different temperatures clearly supports the observation of the different epidemiological patterns.

Seasonal fecundity is not related to geographic position ...

EPA Pesticide Factsheets

AimSixty-five years ago, Theodosius Dobzhansky suggested that individuals of a species face greater challenges from abiotic stressors at high latitudes and from biotic stressors at their low-latitude range edges. This idea has been expanded to the hypothesis that species’ ranges are limited by abiotic and biotic stressors at high and low latitudes, respectively. Support has been found in many systems, but this hypothesis has almost never been tested with demographic data. We present an analysis of fecundity across the breeding range of a species as a test of this hypothesis.Location575 km of tidal marshes in the northeastern United States.MethodsWe monitored saltmarsh sparrow (Ammodramus caudacutus) nests at twenty-three sites from Maine to New Jersey, USA. With data from 840 nests, we calculated daily nest failure probabilities due to competing abiotic (flooding) and biotic (depredation) stressors.ResultsWe observed that abiotic stress (nest flooding probability) was greater than biotic stress (nest depredation probability) at the high-latitude range edge of saltmarsh sparrows, consistent with Dobzhansky’s hypothesis. Similarly, biotic stress decreased with increasing latitude throughout the range, whereas abiotic stress was not predicted by latitude alone. Instead, nest flooding probability was best predicted by date, maximum high tide, and extremity of rare flooding events.Main conclusionsOur results provide support for Dobzhansky’s hypothesis across th

Experimental reduction in interaction intensity strongly affects biotic selection.

PubMed

Sletvold, Nina; Ågren, Jon

2016-11-01

The link between biotic interaction intensity and strength of selection is of fundamental interest for understanding biotically driven diversification and predicting the consequences of environmental change. The strength of selection resulting from biotic interactions is determined by the strength of the interaction and by the covariance between fitness and the trait under selection. When the relationship between trait and absolute fitness is constant, selection strength should be a direct function of mean population interaction intensity. To test this prediction, we excluded pollinators for intervals of different length to induce five levels of pollination intensity within a single plant population. Pollen limitation (PL) increased from 0 to 0.77 across treatments, accompanied by a fivefold increase in the opportunity for selection. Trait-fitness covariance declined with PL for number of flowers, but varied little for other traits. Pollinator-mediated selection on plant height, corolla size, and spur length increased by 91%, 34%, and 330%, respectively, in the most severely pollen-limited treatment compared to open-pollinated plants. The results indicate that realized biotic selection can be predicted from mean population interaction intensity when variation in trait-fitness covariance is limited, and that declines in pollination intensity will strongly increase selection on traits involved in the interaction. © 2016 by the Ecological Society of America.

Urbanization influences on aquatic communities in northeastern Illinois streams

USGS Publications Warehouse

Fitzpatrick, F.A.; Harris, M.A.; Arnold, T.L.; Richards, K.D.

2004-01-01

Biotic indices and sediment trace element concentrations for 43 streams in northeastern Illinois (Chicago area) from the 1980s and 1990s were examined along an agricultural to urban land cover gradient to explore the relations among biotic integrity, sediment chemistry, and urbanization. The Illinois fish Alternative Index of Biotic Integrity (AIBI) ranged from poor to excellent in agricultural/rural streams, but streams with more than 10 percent watershed urban land (about 500 people/mi2) had fair or poor index scores. A macroinvertebrate index (MBI) showed similar trends. A qualitative habitat index (PIBI) did not correlate to either urban indicator. The AIBI and MBI correlated with urban associated sediment trace element concentrations. Elevated copper concentrations in sediment occurred in streams with greater than 40 percent watershed urban land. The number of intolerant fish species and modified index of biotic integrity scores increased in some rural, urbanizing, and urban streams from the 1980s to 1990s, with the largest increases occurring in rural streams with loamy/sandy surficial deposits. However, smaller increases also occurred in urban streams with clayey surficial deposits and over 50 percent watershed urban land. These data illustrate the potentially complex spatial and temporal relations among biotic integrity, sediment chemistry, watershed urban land, population density, and regional and local geologic setting.

Evaluating adequacy of the representative stream reach used in invertebrate monitoring programs

USGS Publications Warehouse

Rabeni, C.F.; Wang, N.; Sarver, R.J.

1999-01-01

Selection of a representative stream reach is implicitly or explicitly recommended in many biomonitoring protocols using benthic invertebrates. We evaluated the adequacy of sampling a single stream reach selected on the basis of its appearance. We 1st demonstrated the precision of our within-reach sampling. Then we sampled 3 or 4 reaches (each ~20x mean width) within an 8-16 km segment on each of 8 streams in 3 ecoregions and calculated 4 common metrics: 1) total taxa; 2) Ephemeroptera, Plecoptera, and Trichoptera taxa; 3) biotic index; and 4) Sharmon's diversity index. In only 6% of possible cases was the coefficient of variation for any of the metrics reduced >10% by sampling additional reaches. Sampling a 2nd reach on a stream improved the ability to detect impairment by an average of only 9.3%. Sampling a 3rd reach on a stream additionally improved ability to detect impairment by only 4.5%. We concluded that a single well-chosen reach, if adequately sampled, can be representative of an entire stream segment, and sampling additional reaches within a segment may not be cost effective.

Senescence Meets Dedifferentiation

PubMed Central

Givaty Rapp, Yemima; Ransbotyn, Vanessa; Grafi, Gideon

2015-01-01

Senescence represents the final stage of leaf development but is often induced prematurely following exposure to biotic and abiotic stresses. Leaf senescence is manifested by color change from green to yellow (due to chlorophyll degradation) or to red (due to de novo synthesis of anthocyanins coupled with chlorophyll degradation) and frequently culminates in programmed death of leaves. However, the breakdown of chlorophyll and macromolecules such as proteins and RNAs that occurs during leaf senescence does not necessarily represent a one-way road to death but rather a reversible process whereby senescing leaves can, under certain conditions, re-green and regain their photosynthetic capacity. This phenomenon essentially distinguishes senescence from programmed cell death, leading researchers to hypothesize that changes occurring during senescence might represent a process of trans-differentiation, that is the conversion of one cell type to another. In this review, we highlight attributes common to senescence and dedifferentiation including chromatin structure and activation of transposable elements and provide further support to the notion that senescence is not merely a deterioration process leading to death but rather a unique developmental state resembling dedifferentiation. PMID:27135333

Geomorpho-Landscapes

NASA Astrophysics Data System (ADS)

Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

2014-05-01

Landscape is the object of human perceptions, being the image of spatial organization of elements and structures: mankind lives the first approach with the environment, viewing and feeling the landscape. Many definitions of landscape have been given over time: in this case we refer to the Landscape defined as the result of interaction among physical, biotic and anthropic phenomena acting in a different spatial-temporal scale (Foreman & Godron) Following an Aristotelic approach in studying nature, we can assert that " Shape is synthesis": so it is possible to read the land features as the expression of the endogenous and exogenous processes that mould earth surfaces; moreover, Landscape is the result of the interaction of natural and cultural components, and conditions the spatial-temporal development of a region. The study of the Landscape offers results useful in order to promote sustainable development, ecotourism, enhancement of natural and cultural heritage, popularization of the scientific knowledge. In Italy, a very important GIS-based tool to represent the territory is the "Carta della Natura" ("Map of Nature", presently coordinated by the ISPRA) that aims at assessing the state of the whole Italian territory, analyzing Landscape. The methodology follows a holistic approach, taking into consideration all the components of a landscape and then integrating the information. Each individual landscape, studied at different scales, shows distinctive elements: structural, which depend on physical form and specific spatial organization; functional, which depend on relationships created between biotic and abiotic elements, and dynamic, which depend on the successive evolution of the structure. The identification of the landscape units, recognized at different scales of analysis, allows an evaluation of the state of the land, referring to the dual risk/resource which characterizes the Italian country. An interesting opportunity is to discover those areas of unusual value -referring to biodiversity, geodiversity, culture- which can be considered as a special heritage. Starting from the concept of Geomorphosite, a geomorphologic landform with a scientific, cultural and socio-economical value (Panizza 2001), we propose a further definition, useful in the preliminary steps of the landscape analysis: "geomorpho-landscape" as a spatial object or component of a geological landscape, whose geo-morphological evolution, linked to the geological setting, are elements of aesthetical, semiological as well as historical and cultural value. The structure of the landscape is represented by the physical shape and spatial organization, in dynamic way: it is necessary to provide a readout of the landscape components that supplements the geo-morphological, lithological, geodiversity data (Lugeri et alii, 2012). The concept of "geomorpho-landscape" is conceived to address the need to describe by a synthetic approach the geological processes emerging at the landscape scale, allowing to link spatial patterns to geological processes Each geo-form has in itself geological, geo-morphological, landmark, historical and cultural features, of such special relevance, that they can be defined in terms of scientific quality, rarity, aesthetic appeal and educational and cultural value. Reference List AMADIO V. (2003). Analisi di sistemi e progetti di paesaggio. Franco Angeli, Milano, pp 236 AMADIO V, AMADEI M, BAGNAIA R, DI BUCCI D, LAURETI L, LISI A, LUGERI FR, LUGERI N. (2002). The role of Geomorphology in Landscape Ecology: The Landscape Unit Map of Italy', Scale 1: 250,000 ("Carta della Natura" Project). In: Allison RJ (ed) Applied Geomorphology: theory and practice. John Wiley & Sons, London, pp 265-282 APAT (2003). Carta della natura alla scala 1:250,000: metodologie di realizzazione. APAT, Manuali e linee guida 17/2003, Roma, pp 103 LUGERI F.R., FARABOLLINI P., GRAVIANO G. & AMADIO V. (2012). Geoheritage: Nature and culture in a landscape approach. European Geologist, 34, 23-28. (ISSN 1028-267X) FORMAN R.T.T. & GODRON M. (1986). Landscape ecology. John Wiley and Sons, NewYork, pp 620 PANIZZA M. (2001). Geomorphosites: concepts, methods and example of geomorphological survey. Chinese Science Bulletin, Suppl. Bd, 4-6, p 46

A compendium of transcription factor and Transcriptionally active protein coding gene families in cowpea (Vigna unguiculata L.).

PubMed

Misra, Vikram A; Wang, Yu; Timko, Michael P

2017-11-22

Cowpea (Vigna unguiculata (L.) Walp.) is the most important food and forage legume in the semi-arid tropics of sub-Saharan Africa where approximately 80% of worldwide production takes place primarily on low-input, subsistence farm sites. Among the major goals of cowpea breeding and improvement programs are the rapid manipulation of agronomic traits for seed size and quality and improved resistance to abiotic and biotic stresses to enhance productivity. Knowing the suite of transcription factors (TFs) and transcriptionally active proteins (TAPs) that control various critical plant cellular processes would contribute tremendously to these improvement aims. We used a computational approach that employed three different predictive pipelines to data mine the cowpea genome and identified over 4400 genes representing 136 different TF and TAP families. We compare the information content of cowpea to two evolutionarily close species common bean (Phaseolus vulgaris), and soybean (Glycine max) to gauge the relative informational content. Our data indicate that correcting for genome size cowpea has fewer TF and TAP genes than common bean (4408 / 5291) and soybean (4408/ 11,065). Members of the GROWTH-REGULATING FACTOR (GRF) and Auxin/indole-3-acetic acid (Aux/IAA) gene families appear to be over-represented in the genome relative to common bean and soybean, whereas members of the MADS (Minichromosome maintenance deficient 1 (MCM1), AGAMOUS, DEFICIENS, and serum response factor (SRF)) and C2C2-YABBY appear to be under-represented. Analysis of the AP2-EREBP APETALA2-Ethylene Responsive Element Binding Protein (AP2-EREBP), NAC (NAM (no apical meristem), ATAF1, 2 (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon)), and WRKY families, known to be important in defense signaling, revealed changes and phylogenetic rearrangements relative to common bean and soybean that suggest these groups may have evolved different functions. The availability of detailed information on the coding capacity of the cowpea genome and in particular the various TF and TAP gene families will facilitate future comparative analysis and development of strategies for controlling growth, differentiation, and abiotic and biotic stress resistances of cowpea.

River Quality Investigations, Part 1: Some Diversity and Biotic Indices.

ERIC Educational Resources Information Center

Hewitt, G.

1991-01-01

The following indices for assessing river water quality are described: Shannon-Weiner Diversity Index, Sorenson Quotient of Similarity, Czekanowski's Index of Similarity, Trent Biotic Index, Chandler Score, and Biological Monitoring Working Party Score. Their advantages and disadvantages are outlined. (Author)

Evaluating temporal changes in stream condition in three New Jersey rive basins by using an index of biotic integrity

USGS Publications Warehouse

Chang, Ming; Kennen, Jonathan G.; Del Corso, Ellyn

2000-01-01

An index of biotic integrity (!B!) modified for New Jersey streams was used to compare changes in stream condition from the 1970s to the 1990s in Delaware, Passaic, and Raritan River Basins. Stream condition was assessed at 88 sampling locations. Mean IBI scores for all basins increased from the 1970s to the 1990s, but the stream-condition category improved (from fair to good) only for the Delaware River Basin. The number of benthic insectivores and the proportion of insectivorous cyprinds increased in all three basins; however, the number of white suckers decreased significantly only in the Delaware River Basin. Results of linear-regression analysis indicate a significant correlation between the percentage of altered land in the basin and change in IBI score (1970s to 1990s) for Delaware River sites. Results of analysis of variance of the rank-transformed IBI scores for the 1970s and 1990s indicate that the three basins was equal in the 1970s. Results of a multiple-comparison test demonstrated that the 1990s IBI values for the Delaware River Basin differed significantly from those for the Passaic and Raritan River Basins. Many factors, such as the imposition of the more stringent standards on water-water and industrial discharges during the 1980s and changes in land-use practices, likely contributed to the change in the Delaware River Basin. A general increase in IBI values for the Passaic, Raritan, and Delaware River Basins over the past 25 years appears to reflect overall improvements in water quality.

Influence of Environmental Factors on Biotic Responses to Nutrient Enrichment in Agricultural Streams1

PubMed Central

Maret, Terry R; Konrad, Christopher P; Tranmer, Andrew W

2010-01-01

The influence of environmental factors on biotic responses to nutrients was examined in three diverse agricultural regions of the United States. Seventy wadeable sites were selected along an agricultural land use gradient while minimizing natural variation within each region. Nutrients, habitat, algae, macroinvertebrates, and macrophyte cover were sampled during a single summer low-flow period in 2006 or 2007. Continuous stream stage and water temperature were collected at each site for 30 days prior to sampling. Wide ranges of concentrations were found for total nitrogen (TN) (0.07-9.61 mg/l) and total phosphorus (TP) (<0.004-0.361 mg/l), but biotic responses including periphytic and sestonic chlorophyll a (RCHL and SCHL, respectively), and percent of stream bed with aquatic macrophyte (AQM) growth were not strongly related to concentrations of TN or TP. Pearson’s coefficient of determination (R2) for nutrients and biotic measures across all sites ranged from 0.08 to 0.32 and generally were not higher within each region. The biotic measures (RCHL, SCHL, and AQM) were combined in an index to evaluate eutrophic status across sites that could have different biotic responses to nutrient enrichment. Stepwise multiple regression identified TN, percent canopy, median riffle depth, and daily percent change in stage as significant factors for the eutrophic index (R2 = 0.50, p < 0.001). A TN threshold of 0.48 mg/l was identified where eutrophic index scores became less responsive to increasing TN concentrations, for all sites. Multiple plant growth indicators should be used when evaluating eutrophication, especially when streams contain an abundance of macrophytes. PMID:22457568

Biotic resistance to invasion along an estuarine gradient

PubMed Central

Hovel, Kevin A.

2010-01-01

Biotic resistance is the ability of native communities to repel the establishment of invasive species. Predation by native species may confer biotic resistance to communities, but the environmental context under which this form of biotic resistance occurs is not well understood. We evaluated several factors that influence the distribution of invasive Asian mussels (Musculista senhousia) in Mission Bay, a southern California estuary containing an extensive eelgrass (Zostera marina) habitat. Asian mussels exhibit a distinct spatial pattern of invasion, with extremely high densities towards the back of Mission Bay (up to 4,000 m−2) in contrast with near-complete absence at sites towards the front of the bay. We established that recruits arrived at sites where adult mussels were absent and found that dense eelgrass does not appear to preclude Asian mussel growth and survival. Mussel survival and growth were high in predator-exclusion plots throughout the bay, but mussel survival was low in the front of the bay when plots were open to predators. Additional experiments revealed that consumption by spiny lobsters (Panulirus interruptus) and a gastropod (Pteropurpura festiva) likely are the primary factors responsible for resistance to Asian mussel invasion. However, biotic resistance was dependent on location within the estuary (for both species) and also on the availability of a hard substratum (for P. festiva). Our findings indicate that biotic resistance in the form of predation may be conferred by higher order predators, but that the strength of resistance may strongly vary across estuarine gradients and depend on the nature of the locally available habitat. Electronic supplementary material The online version of this article (doi:10.1007/s00442-010-1700-7) contains supplementary material, which is available to authorized users. PMID:20602118

Carbonate-platform response to the Toarcian Oceanic Anoxic Event in the southern hemisphere: Implications for climatic change and biotic platform demise

NASA Astrophysics Data System (ADS)

Han, Zhong; Hu, Xiumian; Kemp, David B.; Li, Juan

2018-05-01

The Toarcian Oceanic Anoxic Event (T-OAE, ∼183 Ma) was a profound short-term environmental perturbation associated with the large-scale release of 13C-depleted carbon into the global ocean-atmosphere system, which resulted in a significant negative carbon-isotope excursion (CIE). The general lack of characteristic T-OAE records outside of the northern hemisphere means that the precise environmental effects and significance of this event are uncertain. Many biotic carbonate platforms of the northern hemisphere western Tethys drowned or shifted to non-skeletal platforms during the early Toarcian. However, southern hemisphere records of Toarcian carbonate platforms are rare, and thus the extent and significance of biotic platform demise during the T-OAE is unclear. Here we present high-resolution geochemical and sedimentological data across two Pliensbachian-Toarcian shallow-water carbonate-platform sections exposed in the Tibetan Himalaya. These sections were located paleogeographically on the open southeastern tropical Tethyan margin in the southern hemisphere. The T-OAE in the Tibetan Himalaya is marked by a negative CIE in organic matter. Our sedimentological analysis of the two sections reveals an abundance of storm deposits within the T-OAE interval, which emphasizes a close link between warming and tropical storms during the T-OAE event, in line with evidence recently provided from western Tethyan sections of the northern hemisphere. In addition, our analysis also reveals extensive biotic carbonate-platform demise by drowning or changing to non-skeletal carbonates coincident with the onset of the CIE. Taken together, our results suggest that rapid and pervasive seawater warming in response to carbon release likely played a significant role in sudden biotic carbonate platform demise, and suppression/postponement of biotic platform re-development along the whole tropical/subtropical Tethyan margin.

Competition magnifies the impact of a pesticide in a warming world by reducing heat tolerance and increasing autotomy.

PubMed

Op de Beeck, Lin; Verheyen, Julie; Stoks, Robby

2018-02-01

There is increasing concern that standard laboratory toxicity tests may be misleading when assessing the impact of toxicants, because they lack ecological realism. Both warming and biotic interactions have been identified to magnify the effects of toxicants. Moreover, while biotic interactions may change the impact of toxicants, toxicants may also change the impact of biotic interactions. However, studies looking at the impact of biotic interactions on the toxicity of pesticides and vice versa under warming are very scarce. Therefore, we tested how warming (+4 °C), intraspecific competition (density treatment) and exposure to the pesticide chlorpyrifos, both in isolation and in combination, affected mortality, cannibalism, growth and heat tolerance of low- and high-latitude populations of the damselfly Ischnura elegans. Moreover, we addressed whether toxicant exposure, potentially in interaction with competition and warming, increased the frequency of autotomy, a widespread antipredator mechanism. Competition increased the toxicity of chlorpyrifos and made it become lethal. Cannibalism was not affected by chlorpyrifos but increased at high density and under warming. Chlorpyrifos reduced heat tolerance but only when competition was high. This is the first demonstration that a biotic interaction can be a major determinant of 'toxicant-induced climate change sensitivity'. Competition enhanced the impact of chlorpyrifos under warming for high-latitude larvae, leading to an increase in autotomy which reduces fitness in the long term. This points to a novel pathway how transient pesticide pulses may cause delayed effects on populations in a warming world. Our results highlight that the interplay between biotic interactions and toxicants have a strong relevance for ecological risk assessment in a warming polluted world. Copyright © 2017 Elsevier Ltd. All rights reserved.

Does scale matter? A systematic review of incorporating biological realism when predicting changes in species distributions.

PubMed

Record, Sydne; Strecker, Angela; Tuanmu, Mao-Ning; Beaudrot, Lydia; Zarnetske, Phoebe; Belmaker, Jonathan; Gerstner, Beth

2018-01-01

There is ample evidence that biotic factors, such as biotic interactions and dispersal capacity, can affect species distributions and influence species' responses to climate change. However, little is known about how these factors affect predictions from species distribution models (SDMs) with respect to spatial grain and extent of the models. Understanding how spatial scale influences the effects of biological processes in SDMs is important because SDMs are one of the primary tools used by conservation biologists to assess biodiversity impacts of climate change. We systematically reviewed SDM studies published from 2003-2015 using ISI Web of Science searches to: (1) determine the current state and key knowledge gaps of SDMs that incorporate biotic interactions and dispersal; and (2) understand how choice of spatial scale may alter the influence of biological processes on SDM predictions. We used linear mixed effects models to examine how predictions from SDMs changed in response to the effects of spatial scale, dispersal, and biotic interactions. There were important biases in studies including an emphasis on terrestrial ecosystems in northern latitudes and little representation of aquatic ecosystems. Our results suggest that neither spatial extent nor grain influence projected climate-induced changes in species ranges when SDMs include dispersal or biotic interactions. We identified several knowledge gaps and suggest that SDM studies forecasting the effects of climate change should: 1) address broader ranges of taxa and locations; and 1) report the grain size, extent, and results with and without biological complexity. The spatial scale of analysis in SDMs did not affect estimates of projected range shifts with dispersal and biotic interactions. However, the lack of reporting on results with and without biological complexity precluded many studies from our analysis.

A direct-gradient multivariate index of biotic condition

USGS Publications Warehouse

Miranda, Leandro E.; Aycock, J.N.; Killgore, K. J.

2012-01-01

Multimetric indexes constructed by summing metric scores have been criticized despite many of their merits. A leading criticism is the potential for investigator bias involved in metric selection and scoring. Often there is a large number of competing metrics equally well correlated with environmental stressors, requiring a judgment call by the investigator to select the most suitable metrics to include in the index and how to score them. Data-driven procedures for multimetric index formulation published during the last decade have reduced this limitation, yet apprehension remains. Multivariate approaches that select metrics with statistical algorithms may reduce the level of investigator bias and alleviate a weakness of multimetric indexes. We investigated the suitability of a direct-gradient multivariate procedure to derive an index of biotic condition for fish assemblages in oxbow lakes in the Lower Mississippi Alluvial Valley. Although this multivariate procedure also requires that the investigator identify a set of suitable metrics potentially associated with a set of environmental stressors, it is different from multimetric procedures because it limits investigator judgment in selecting a subset of biotic metrics to include in the index and because it produces metric weights suitable for computation of index scores. The procedure, applied to a sample of 35 competing biotic metrics measured at 50 oxbow lakes distributed over a wide geographical region in the Lower Mississippi Alluvial Valley, selected 11 metrics that adequately indexed the biotic condition of five test lakes. Because the multivariate index includes only metrics that explain the maximum variability in the stressor variables rather than a balanced set of metrics chosen to reflect various fish assemblage attributes, it is fundamentally different from multimetric indexes of biotic integrity with advantages and disadvantages. As such, it provides an alternative to multimetric procedures.

Elucidating the Role of Carbon Sources on Abiotic and Biotic Release of Arsenic into Cambodian Aquifers

NASA Astrophysics Data System (ADS)

Koeneke, M.

2017-12-01

Arsenic (As) is a naturally occurring contaminant in Cambodia that has been contaminating well-water sources of millions of people. Commonly, studies look into the biotic factors that cause the arsenic to be released from aquifer sediments to groundwater. However, abiotic release of As from sediments, though little studied, may also play key roles in As contamination of well water. The goal of this research is to quantitatively compare organic-carbon mediated abiotic and biotic release of arsenic from sediments to groundwater. Batch anaerobic incubation experiments under abiotic (sodium azide used to immobilize microbes) and biotic conditions were conducted using Cambodian aquifer sediments, four different organic carbon sources (sodium lactate, sodium citrate, sodium oxalate, and humic acid), and six different carbon concentrations (0, 1, 2.5, 5, 10, 25mg C/L). Dissolved arsenic, iron(Fe), and manganese(Mn) concentrations in the treatments were measured 112 days . In addition, sediment and solution carbon solution was measured . Collectively, these show how different carbon sources, different carbon concentrations, and how abiotic and biotic factors impact the release of arsenic from Cambodian sediments into aquifers. Overall, an introduction of organic carbon to the soil increases the amount of As released from the sediment. The biotic + abiotic and abiotic conditions seemed to play a minimal role in the amount of As released. Dissolved species analysis showed us that 100% of the As was As(V), Our ICP-MS results vary due to the heterogeneity of samples, but when high levels are Fe are seen in solution, we also see high levels of As. We also see higher As concentrations when there is a smaller amount of Mn in solution.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

PubMed

Krishnan S, Gopala; Waters, Daniel L E; Henry, Robert J

2014-01-01

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Characterizing Feedback Control Mechanisms in Nonlinear Microbial Models of Soil Organic Matter Decomposition by Stability Analysis

NASA Astrophysics Data System (ADS)

Georgiou, K.; Tang, J.; Riley, W. J.; Torn, M. S.

2014-12-01

Soil organic matter (SOM) decomposition is regulated by biotic and abiotic processes. Feedback interactions between such processes may act to dampen oscillatory responses to perturbations from equilibrium. Indeed, although biological oscillations have been observed in small-scale laboratory incubations, the overlying behavior at the plot-scale exhibits a relatively stable response to disturbances in input rates and temperature. Recent studies have demonstrated the ability of microbial models to capture nonlinear feedbacks in SOM decomposition that linear Century-type models are unable to reproduce, such as soil priming in response to increased carbon input. However, these microbial models often exhibit strong oscillatory behavior that is deemed unrealistic. The inherently nonlinear dynamics of SOM decomposition have important implications for global climate-carbon and carbon-concentration feedbacks. It is therefore imperative to represent these dynamics in Earth System Models (ESMs) by introducing sub-models that accurately represent microbial and abiotic processes. In the present study we explore, both analytically and numerically, four microbe-enabled model structures of varying levels of complexity. The most complex model combines microbial physiology, a non-linear mineral sorption isotherm, and enzyme dynamics. Based on detailed stability analysis of the nonlinear dynamics, we calculate the system modes as functions of model parameters. This dependence provides insight into the source of state oscillations. We find that feedback mechanisms that emerge from careful representation of enzyme and mineral interactions, with parameter values in a prescribed range, are critical for both maintaining system stability and capturing realistic responses to disturbances. Corroborating and expanding upon the results of recent studies, we explain the emergence of oscillatory responses and discuss the appropriate microbe-enabled model structure for inclusion in ESMs.

Influence of water chemistry and natural organic matter on active and passive uptake of inorganic mercury by gills of rainbow trout (Oncorhynchus mykiss).

PubMed

Klinck, Joel; Dunbar, Michael; Brown, Stephanie; Nichols, Joel; Winter, Anna; Hughes, Christopher; Playle, Richard C

2005-03-25

To distinguish physiologically regulated uptake from passive uptake of inorganic Hg in fish, rainbow trout (Oncorhynchus mykiss) were exposed to inorganic Hg (0.5, 1, or 2 microM total Hg) in ion-poor water with various treatments. Addition of ions to the water (mM concentrations of Ca, K, Cl) did not consistently alter Hg accumulation by trout gills, although there was a trend to higher Hg accumulation at higher ion concentrations. The apical Ca channel blockers Verapamil and lanthanum also did not consistently affect Hg accumulation by trout gills. Pre-treatment of trout with the Na channel blocker Phenamil decreased Hg uptake by about half. These results suggest a combination of physiologically regulated and passive uptake of Hg by trout gills. Strong complexing agents of Hg (EDTA, NTA, ethylenediamine, cysteine) decreased Hg-binding by trout gills in a dose-dependent manner. From these data, a conditional equilibrium binding constant for Hg to the gills was estimated as logK(Hg-gill) = 18.0, representing very strong binding of Hg to the gills. This value is a first step in creating a biotic ligand model (BLM) for inorganic Hg and fish. Natural organic matter (2-10 mg C/L) also decreased Hg-binding by trout gills, although mM concentrations of Na, K, and Cl interfered with this effect. At low concentrations of these ions, natural organic matter samples isolated from various sources bound Hg to similar degrees, as judged by Hg accumulation by trout gills. A conditional binding constant to natural organic matter (NOM) was estimated as logK(Hg-NOM) = 18.0 with about 0.5 micromol binding sites per mg C, representing strong binding of Hg to NOM.

NABS RESPONSE OF A MULTI-METRIC FISH BIOTIC INDEX TO SPECIES DECLINES

EPA Science Inventory

Multi-metric indices of biotic integrity (IBI) are commonly used to compare fish communities among streams, but ability to monitor trends within streams is largely unknown. We assessed the IBI trend detection ability using simulations which progressively degraded the fish assembl...

Using biotechnology and genomics to improve biotic and abiotic stress in apple

USDA-ARS?s Scientific Manuscript database

Genomic sequencing, molecular biology, and transformation technologies are providing valuable tools to better understand the complexity of how plants develop, function, and respond to biotic and abiotic stress. These approaches should complement but not replace a solid understanding of whole plant ...

Electrofishing distance needed to estimate consistent Index of Biotic Integrity (IBI) scores in raftable Oregon rivers

EPA Science Inventory

An important issue surrounding assessment of riverine fish assemblages is the minimum amount of sampling distance needed to adequately determine biotic condition. Determining adequate sampling distance is important because sampling distance affects estimates of fish assemblage c...

Are biotic indices sensitive to river toxicants? A comparison of metrics based on diatoms and macro-invertebrates.

PubMed

Blanco, S; Bécares, E

2010-03-01

Biotic indices based on macro-invertebrates and diatoms are frequently used to diagnose ecological quality in watercourses, but few published works have assessed their effectiveness as biomonitors of the concentration of micropollutants. A biological survey performed at 188 sites in the basin of the River Duero in north-western Spain. Nineteen diatom and six macro-invertebrate indices were calculated and compared with the concentrations of 37 different toxicants by means of a correlation analysis. Several chemical variables analysed correlated significantly with at least one biotic index. Sládecek's diatom index and the number of macro-invertebrate families exhibited particularly high correlation coefficients. Methods based on macro-invertebrates performed better in detecting biocides, while diatom indices showed stronger correlations with potentially toxic elements such as heavy metals. All biotic indices, and particularly diatom indices, were especially sensitive to the concentration of fats and oils and trichloroethene. Copyright 2010 Elsevier Ltd. All rights reserved.

The search for a topographic signature of life.

PubMed

Dietrich, William E; Perron, J Taylor

2006-01-26

Landscapes are shaped by the uplift, deformation and breakdown of bedrock and the erosion, transport and deposition of sediment. Life is important in all of these processes. Over short timescales, the impact of life is quite apparent: rock weathering, soil formation and erosion, slope stability and river dynamics are directly influenced by biotic processes that mediate chemical reactions, dilate soil, disrupt the ground surface and add strength with a weave of roots. Over geologic time, biotic effects are less obvious but equally important: biota affect climate, and climatic conditions dictate the mechanisms and rates of erosion that control topographic evolution. Apart from the obvious influence of humans, does the resulting landscape bear an unmistakable stamp of life? The influence of life on topography is a topic that has remained largely unexplored. Erosion laws that explicitly include biotic effects are needed to explore how intrinsically small-scale biotic processes can influence the form of entire landscapes, and to determine whether these processes create a distinctive topography.

Patterns of Abundance of Seagrasses and Associated Infaunal Communities at Inhaca Island, Mozambique

NASA Astrophysics Data System (ADS)

Paula, J.; Fidalgo Ecosta, P.; Martins, A.; Gove, D.

2001-09-01

This study was conducted at Inhaca Island, south Mozambique, and focused on three different seagrass associations, dominated respectively by Thalassodendron ciliatum, Thalassia hemprichii and Zostera capensis. The main objective of this study was to compare the three seagrass associations, in what concerns vegetal and associated infaunal communities biomass. The approach was a nested design, which intended to provide information on seasonal effects and variability at decreasing spatial scales. Nested ANOVA was performed for all biological and porewater parameters and a cluster analysis of different biotic and abiotic parameters was performed. Nutrient concentration was consistently higher during the dry period as well as mean values of organic matter. Consistently lower values of chlorophyll a (chl a) were obtained at T. hemprichii meadow sites and the highest values were found at Z. capensis meadow. Phaeopigments have shown an opposite pattern when compared to chl a, and average values were consistently higher during the dry season. There were no net differences of seagrass standing crop during both sampled seasons, however at meadow level major differences were found, and higher biomass was obtained at T. ciliatum meadow, followed by T. hemprichii. Mean values of epibiota have shown that higher biomass was obtained at T. ciliatum meadow, the remaining meadows presented very low values. Meiofauna biomass showed fluctuations between seagrass meadows, stations and also between seasons. Macrofauna biomass showed clear fluctuations between seasons, being strongly more homogeneous during the dry season and highly variable in the wet season. ANOVA results have shown different significance at the different levels of the analysis, suggesting different spatial and temporal patterns and interactions between parameters. The dendrogram produced two main groups of variables, the first one comprised of OM, phaeopigments, nitrites, nitrates, meiofauna, grain size and chl a. The second group comprises pH, macrofauna, ammonia, both seagrass components and epibiota on above-ground seagrass fraction. These two groups of parameters may correspond to different functional components of the seagrass ecosystem. The sediment biotic structure seems largely dependent on detritus-based chains, and has a high degree of spatial variability. On the other hand, macrofauna seems to be more related to the direct influence of seagrass standing crop, probably caused by the increased habitat complexity provided by higher seagrass biomass.

Protectiveness of water quality criteria for copper in western United States waters relative to predicted olfactory responses in juvenile Pacific salmon.

PubMed

DeForest, David K; Gensemer, Robert W; Van Genderen, Eric J; Gorsuch, Joseph W

2011-07-01

Copper (Cu) can impair olfaction in juvenile Pacific salmon (as well as other fishes), thus potentially inhibiting the ability of juveniles to avoid predators or to find food. Because Cu is commonly elevated in stormwater runoff in urban environments, storm events may result in elevated Cu concentrations in salmon-bearing streams. Accordingly, there is concern that existing Cu criteria, which were not derived using data for olfactory-related endpoints, may not be adequately protective of juvenile salmon. However, a modification of the US Environmental Protection Agency (USEPA) biotic ligand model (BLM) for deriving site-specific Cu criteria was recently proposed, which accounted for the sensitivity of olfactory endpoints. The modification was based on olfactory inhibition in juvenile coho salmon (Oncorhynchus kisutch) exposed to Cu in various combinations of pH, hardness, alkalinity, and dissolved organic carbon (DOC) concentrations. We used that olfactory-based BLM to derive 20% inhibition concentrations (IC20) values for Cu for 133 stream locations in the western United States. The olfactory BLM-based IC20 values were compared to the existing hardness-based Cu criteria and the USEPA's BLM-based Cu criteria for these representative natural waters of the western United States. Of the 133 sampling locations, mean hardness-dependent acute and chronic Cu criteria were below the mean olfactory-based BLM IC20 value in 122 (92%) and 129 (97%) of the waters, respectively (i.e., <20% olfactory impairment would have been predicted at the mean hardness-based Cu criteria concentrations). Waters characterized by a combination of high hardness and very low DOC were most likely to have hardness-based Cu criteria that were higher than the olfactory-based BLM IC20 values, because DOC strongly influences Cu bioavailability in the BLM. In all waters, the USEPA's current BLM-based criteria were below the mean olfactory-based BLM IC20 values, indicating that the USEPA's BLM-based criteria are protective of olfactory impairment in juvenile salmon. Copyright © 2011 SETAC.

Why do trees die? Characterizing the drivers of background tree mortality.

PubMed

Das, Adrian J; Stephenson, Nathan L; Davis, Kristin P

2016-10-01

The drivers of background tree mortality rates-the typical low rates of tree mortality found in forests in the absence of acute stresses like drought-are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the "ambient" or "random" background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from one another. Finally, beyond the current emphasis on folivory and leaf defenses, studies of broad-scale gradients in the nature and strength of biotic interactions should also include biotic attacks on, and defenses of, tree stems and roots. © 2016 by the Ecological Society of America.

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress

PubMed Central

2013-01-01

Background Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and susceptible varieties of Oryza sativa. A comparative analysis to fungal, parasite and viral infection in rice is also presented. Results Within 24 h of Xoo inoculation, significant reduction of cell wall components and induction of several signalling components, membrane bound receptor kinases and specific WRKY and NAC transcription factors was prominent, providing a framework for how the presence of this pathogen was signalled and response mounted. Extensive comparative analyses of various other pathogen responses, including in response to infection with another bacterium (Xoc), resistant and susceptible parasite infection, fungal, and viral infections, led to a proposed model for the rice biotic stress response. In this way, a conserved induction of calcium signalling functions, and specific WRKY and NAC transcription factors, was identified in response to all biotic stresses. Comparison of these responses to abiotic stress (cold, drought, salt, heat), enabled the identification of unique genes responsive only to bacterial infection, 240 genes responsive to both abiotic and biotic stress, and 135 genes responsive to biotic, but not abiotic stresses. Functional significance of a number of these genes, using genetic inactivation or over-expression, has revealed significant stress-associated phenotypes. While only a few antagonistic responses were observed between biotic and abiotic stresses, e.g. for a number of endochitinases and kinase encoding genes, some of these may be crucial in explaining greater pathogen infection and damage under abiotic stresses. Conclusions The analyses presented here provides a global view of the responses to multiple stresses, further validates known resistance-associated genes, and highlights new potential target genes, some lineage specific to rice, that play important roles in response to stress, providing a roadmap to develop varieties of rice that are more resistant to multiple biotic and abiotic stresses, as encountered in nature. PMID:23398910

Why do trees die? Characterizing the drivers of background tree mortality

USGS Publications Warehouse

Das, Adrian J.; Stephenson, Nathan L.; Davis, Kristin P.

2016-01-01

The drivers of background tree mortality rates—the typical low rates of tree mortality found in forests in the absence of acute stresses like drought—are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the “ambient” or “random” background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from one another. Finally, beyond the current emphasis on folivory and leaf defenses, studies of broad-scale gradients in the nature and strength of biotic interactions should also include biotic attacks on, and defenses of, tree stems and roots.

Foliar damage beyond species distributions is partly explained by distance dependent interactions with natural enemies.

PubMed

Katz, Daniel S W; Ibáñez, Inés

2016-09-01

Plant distributions are expected to shift in response to climate change, and range expansion dynamics will be shaped by the performance of individuals at the colonizing front. These plants will encounter new biotic communities beyond their range edges, and the net outcome of these encounters could profoundly affect colonization success. However, little is known about how biotic interactions vary across range edges and this has hindered efforts to predict changes in species distributions in response to climate change. In contrast, a rich literature documents how biotic interactions within species ranges vary according to distance to and density of conspecific individuals. Here, we test whether this framework can be extended to explain how biotic interactions differ beyond range edges, where conspecific adults are basically absent. To do so, we planted seven species of trees along a 450-km latitudinal gradient that crossed the current distributional range of five of these species and monitored foliar disease and invertebrate herbivory over 5 yr. Foliar disease and herbivory were analyzed as a function of distance to and density of conspecific and congeneric trees at several spatial scales. We found that within species ranges foliar disease was lower for seedlings that were farther from conspecific adults for Acer rubrum, Carya glabra, Quercus alba, and Robinia pseudoacacia. Beyond range edges, there was even less foliar disease for C. glabra, Q. alba, and R. pseudoacacia (A. rubrum was not planted outside its range). Liriodendron tulipifera did not experience reduced disease within or beyond its range. In contrast, Quercus velutina displayed significant but idiosyncratic patterns in disease at varying distances from conspecifics. Patterns of distance dependent herbivory across spatial scales was generally weak and in some cases negative (i.e., seedlings farther from conspecific adults had more herbivory). Overall, we conclude that differences in biotic interactions across range edges can be thought of as a spatial extension to the concept of distance dependent biotic interactions. This framework also provides the basis for general predictions of how distance dependent biotic interactions will change across range edges in other systems. © 2016 by the Ecological Society of America.

The Great American Biotic Interchange: Dispersals, Tectonics, Climate, Sea Level and Holding Pens

PubMed Central

2010-01-01

The biotic and geologic dynamics of the Great American Biotic Interchange are reviewed and revised. Information on the Marine Isotope Stage chronology, sea level changes as well as Pliocene and Pleistocene vegetation changes in Central and northern South America add to a discussion of the role of climate in facilitating trans-isthmian exchanges. Trans-isthmian land mammal exchanges during the Pleistocene glacial intervals appear to have been promoted by the development of diverse non-tropical ecologies. Electronic supplementary material The online version of this article (doi:10.1007/s10914-010-9144-8) contains supplementary material, which is available to authorized users. PMID:21125025

Proteomic dissection of plant responses to various pathogens.

PubMed

Fang, Xianping; Chen, Jianping; Dai, Liangying; Ma, Huasheng; Zhang, Hengmu; Yang, Jian; Wang, Fang; Yan, Chengqi

2015-05-01

During their growth and development, plants are vulnerable to the effects of a variety of pathogens. Proteomics technology plays an important role in research studies of plant defense mechanisms by mining the expression changes of proteins in response to various biotic stresses. This review article provides a comprehensive overview of the latest developments in international proteomic research on plant biotic stress. It summarizes the methods commonly used in plant proteomic research to investigate biotic stress, analyze the protein responses of plants in adverse conditions, and reviews the applications of proteomics combined with transgenic technology in plant protection. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DETERMINATION OF CONDITION CATEGORIES FOR BIOTIC INDICES USING POWER ANALYSIS

EPA Science Inventory

Multimetric biotic indices are often used in bioassessment programs to determine the condition of water resources. These indices are typically divided into a number of condition tiers (e.g., good, poor). However, the number of tiers is often based on professional judgement. We u...

SENSITIVITY OF INDICES OF BIOTIC INTEGRITY TO SIMULATED FISH ASSEMBLAGE CHANGES - 2

EPA Science Inventory

Multi-metric indices of biotic integrity (IBI) are commonly used to compare fish communities among streams, but their ability to monitor trends within streams is largely unknown. We assessed the IBI trend detection ability using simulations which progressively degraded the fish a...

SENSITIVITY OF INDICES OF BIOTIC INTEGRITY TO SIMULATED FISH ASSEMBLAGE CHANGES

EPA Science Inventory

Multi-metric indices of biotic integrity (IBI) are commonly used to assess condition of stream fish assemblages, but their ability to monitor trends within streams over time is largely unknown. We assessed the trend detection ability of two IBI formulations (one with traditional ...

Electrofishing Effort Required to Estimate Biotic Condition in Southern Idaho Rivers

EPA Science Inventory

An important issue surrounding biomonitoring in large rivers is the minimum sampling effort required to collect an adequate number of fish for accurate and precise determinations of biotic condition. During the summer of 2002, we sampled 15 randomly selected large-river sites in...

THE INFLUENCE OF SUBURBAN LAND USE ON HABITAT AND BIOTIC INTEGRITY OF COASTAL RHODE ISLAND STREAMS

EPA Science Inventory

Watershed land use in suburban areas can affect stream biota through degradation of instream habitat, water quality, and riparian vegetation. By monitoring stream biotic communities in various geographic regions, we can better understand and conserve our watershed ecosystems. The...

Immobilization of uranium and arsenic by injectible iron and hydrogen stimulated autotrophic sulphate reduction

NASA Astrophysics Data System (ADS)

Burghardt, D.; Simon, E.; Knöller, K.; Kassahun, A.

2007-12-01

The main object of the study was the development of a long-term efficient and inexpensive in-situ immobilization technology for uranium (U) and arsenic (As) in smaller and decentralized groundwater discharges from abandoned mining processing sites. Therefore, corrosion of grey cast iron (gcFe) and nano-scale iron particles (naFe) as well as hydrogen stimulated autotrophic sulphate reduction (aSR) were investigated. Two column experiments with sulphate reducing bacterias (SRB) (biotic gcFe , biotic naFe) and one abiotic gcFe-column experiment were performed. In the biotic naFe column, no particle translocation was observed and a temporary but intensive naFe corrosion indicated by a decrease in Eh, a pH increase and H 2 evolution. Decreasing sulphate concentrations and 34S enrichment in the column effluent indicated aSR. Fe(II) retention could be explained by siderite and consequently FeS precipitation by geochemical modeling (PhreeqC). U and As were completely immobilised within the biotic naFe column. In the biotic gcFe column, particle entrapment in open pore spaces resulted in a heterogeneous distribution of Fe-enriched zones and an increase in permeability due to preferential flow. However, Fe(II) concentrations in the effluent indicated a constant and lasting gcFe corrosion. An efficient immobilization was found for As, but not for U.

Influence of environmental factors on biotic responses to nutrient enrichment in agricultural streams

USGS Publications Warehouse

Maret, Terry R.; Konrad, Christopher P.; Tranmer, Andrew W.

2010-01-01

The influence of environmental factors on biotic responses to nutrients was examined in three diverse agricultural regions of the United States. Seventy wadeable sites were selected along an agricultural land use gradient while minimizing natural variation within each region. Nutrients, habitat, algae, macroinvertebrates, and macrophyte cover were sampled during a single summer low-flow period in 2006 or 2007. Continuous stream stage and water temperature were collected at each site for 30 days prior to sampling. Wide ranges of concentrations were found for total nitrogen (TN) (0.07-9.61 mg/l) and total phosphorus (TP) (R2) for nutrients and biotic measures across all sites ranged from 0.08 to 0.32 and generally were not higher within each region. The biotic measures (RCHL, SCHL, and AQM) were combined in an index to evaluate eutrophic status across sites that could have different biotic responses to nutrient enrichment. Stepwise multiple regression identified TN, percent canopy, median riffle depth, and daily percent change in stage as significant factors for the eutrophic index (R2 = 0.50, p < 0.001). A TN threshold of 0.48 mg/l was identified where eutrophic index scores became less responsive to increasing TN concentrations, for all sites. Multiple plant growth indicators should be used when evaluating eutrophication, especially when streams contain an abundance of macrophytes.

Early biotic stress detection in tomato (Solanum lycopersicum) by BVOC emissions.

PubMed

Kasal-Slavik, Tina; Eschweiler, Julia; Kleist, Einhard; Mumm, Roland; Goldbach, Heiner E; Schouten, Alexander; Wildt, Jürgen

2017-12-01

We investigated impacts of early and mild biotic stress on Biogenic Volatile Organic Compounds (BVOC) emissions from tomato in order to test their potential for early (biotic) stress detection. Tomato plants were exposed to two common fungal pathogens, Botrytis cinerea and Oidium neolycopesici and the sap-sucking aphid Myzus persicae. Furthermore, plants were exposed to methyl jasmonate (MeJA) in order to identify BVOC emissions related to activation of jasmonic acid (JA) signalling pathway. These emissions where then used as a reference for identifying active JA signalling pathway in plants at early stages of biotic stress. After infection by the necrotrophic fungus B. cinerea, changes in BVOC emissions indicated that tomato plants had predominantly activated the jasmonic acid (JA) signalling pathway. The plants were able to modify their defence pathways in order to overcome fungal infection. When tomato plants were infected with the biotrophic fungus O. neolycopersici, only minor changes in BVOC emissions were observed with additional emissions of the sesquiterpene α-copaene. α-copaene emissions allowed the identification of general biotic stress in the plants, without pinpointing the actual triggered defence pathway. BVOC emissions during M. persicae attack had changed before the occurrence of visual symptoms. Despite low infestation rates, plants emitted methyl salicylate indicating activation of the SA-mediated defence pathway. Copyright © 2017 Elsevier Ltd. All rights reserved.

How does the multifaceted plant hormone salicylic acid combat disease in plants and are similar mechanisms utilized in humans?

PubMed

Dempsey, D'Maris Amick; Klessig, Daniel F

2017-03-23

Salicylic acid (SA) is an important plant hormone that regulates many aspects of plant growth and development, as well as resistance to (a)biotic stress. Efforts to identify SA effector proteins have revealed that SA binds to and alters the activity of multiple plant proteins-this represents a shift from the paradigm that hormones mediate their functions via one or a few receptors. SA and its derivatives also have multiple targets in animals; some of these proteins, like their plant counterparts, are associated with pathological processes. Together, these findings suggest that SA exerts its defense-associated effects in both kingdoms via a large number of targets.

Diversity of Holocene life forms in fossil glacier ice

PubMed Central

Willerslev, Eske; Hansen, Anders J.; Christensen, Bent; Steffensen, Jørgen Peder; Arctander, Peter

1999-01-01

Studies of biotic remains of polar ice caps have been limited to morphological identification of plant pollen and spores. By using sensitive molecular techniques, we now demonstrate a much greater range of detectable organisms; from 2000- and 4000-year-old ice-core samples, we obtained and characterized 120 clones that represent at least 57 distinct taxa and reveal a diversity of fungi, plants, algae, and protists. The organisms derive from distant sources as well as from the local arctic environment. Our results suggest that additional taxa may soon be readily identified, providing a plank for future studies of deep ice cores and yielding valuable information about ancient communities and their change over time. PMID:10393940

Selective environmental stress from sulphur emitted by continental flood basalt eruptions

NASA Astrophysics Data System (ADS)

Schmidt, Anja; Skeffington, Richard; Thordarson, Thorvaldur; Self, Stephen; Forster, Piers; Rap, Alexandru; Ridgwell, Andy; Fowler, David; Wilson, Marjorie; Mann, Graham; Wignall, Paul; Carslaw, Ken

2016-04-01

Several biotic crises during the past 300 million years have been linked to episodes of continental flood basalt volcanism, and in particular to the release of massive quantities of magmatic sulphur gas species. Flood basalt provinces were typically formed by numerous individual eruptions, each lasting years to decades. However, the environmental impact of these eruptions may have been limited by the occurrence of quiescent periods that lasted hundreds to thousands of years. Here we use a global aerosol model to quantify the sulphur-induced environmental effects of individual, decade-long flood basalt eruptions representative of the Columbia River Basalt Group, 16.5-14.5 million years ago, and the Deccan Traps, 65 million years ago. For a decade-long eruption of Deccan scale, we calculate a decadal-mean reduction in global surface temperature of 4.5 K, which would recover within 50 years after an eruption ceased unless climate feedbacks were very different in deep-time climates. Acid mists and fogs could have caused immediate damage to vegetation in some regions, but acid-sensitive land and marine ecosystems were well-buffered against volcanic sulphur deposition effects even during century-long eruptions. We conclude that magmatic sulphur from flood basalt eruptions would have caused a biotic crisis only if eruption frequencies and lava discharge rates had been high and sustained for several centuries at a time.

Selective environmental stress from sulphur emitted by continental flood basalt eruptions

NASA Astrophysics Data System (ADS)

Schmidt, Anja; Skeffington, Richard A.; Thordarson, Thorvaldur; Self, Stephen; Forster, Piers M.; Rap, Alexandru; Ridgwell, Andy; Fowler, David; Wilson, Marjorie; Mann, Graham W.; Wignall, Paul B.; Carslaw, Kenneth S.

2016-01-01

Several biotic crises during the past 300 million years have been linked to episodes of continental flood basalt volcanism, and in particular to the release of massive quantities of magmatic sulphur gas species. Flood basalt provinces were typically formed by numerous individual eruptions, each lasting years to decades. However, the environmental impact of these eruptions may have been limited by the occurrence of quiescent periods that lasted hundreds to thousands of years. Here we use a global aerosol model to quantify the sulphur-induced environmental effects of individual, decade-long flood basalt eruptions representative of the Columbia River Basalt Group, 16.5-14.5 million years ago, and the Deccan Traps, 65 million years ago. For a decade-long eruption of Deccan scale, we calculate a decadal-mean reduction in global surface temperature of 4.5 K, which would recover within 50 years after an eruption ceased unless climate feedbacks were very different in deep-time climates. Acid mists and fogs could have caused immediate damage to vegetation in some regions, but acid-sensitive land and marine ecosystems were well-buffered against volcanic sulphur deposition effects even during century-long eruptions. We conclude that magmatic sulphur from flood basalt eruptions would have caused a biotic crisis only if eruption frequencies and lava discharge rates had been high and sustained for several centuries at a time.

Redox chemistry changes in the Panthalassic Ocean linked to the end-Permian mass extinction and delayed Early Triassic biotic recovery

NASA Astrophysics Data System (ADS)

Zhang, Guijie; Zhang, Xiaolin; Hu, Dongping; Li, Dandan; Algeo, Thomas J.; Farquhar, James; Henderson, Charles M.; Qin, Liping; Shen, Megan; Shen, Danielle; Schoepfer, Shane D.; Chen, Kefan; Shen, Yanan

2017-02-01

The end-Permian mass extinction represents the most severe biotic crisis for the last 540 million years, and the marine ecosystem recovery from this extinction was protracted, spanning the entirety of the Early Triassic and possibly longer. Numerous studies from the low-latitude Paleotethys and high-latitude Boreal oceans have examined the possible link between ocean chemistry changes and the end-Permian mass extinction. However, redox chemistry changes in the Panthalassic Ocean, comprising ˜85-90% of the global ocean area, remain under debate. Here, we report multiple S-isotopic data of pyrite from Upper Permian-Lower Triassic deep-sea sediments of the Panthalassic Ocean, now present in outcrops of western Canada and Japan. We find a sulfur isotope signal of negative Δ33S with either positive δ34S or negative δ34S that implies mixing of sulfide sulfur with different δ34S before, during, and after the end-Permian mass extinction. The precise coincidence of the negative Δ33S anomaly with the extinction horizon in western Canada suggests that shoaling of H2S-rich waters may have driven the end-Permian mass extinction. Our data also imply episodic euxinia and oscillations between sulfidic and oxic conditions during the earliest Triassic, providing evidence of a causal link between incursion of sulfidic waters and the delayed recovery of the marine ecosystem.

Stream denitrification across biomes and its response to anthropogenic nitrate loading

USGS Publications Warehouse

Mulholland, P.J.; Helton, A.M.; Poole, G.C.; Hall, R.O.; Hamilton, S.K.; Peterson, B.J.; Tank, J.L.; Ashkenas, L.R.; Cooper, L.W.; Dahm, Clifford N.; Dodds, W.K.; Findlay, S.E.G.; Gregory, S.V.; Grimm, N. B.; Johnson, S.L.; McDowell, W.H.; Meyer, J.L.; Valett, H.M.; Webster, J.R.; Arango, C.P.; Beaulieu, J.J.; Bernot, M.J.; Burgin, A.J.; Crenshaw, C.L.; Johnson, L.T.; Niederlehner, B.R.; O'Brien, J. M.; Potter, J.D.; Sheibley, R.W.; Sobota, D.J.; Thomas, S.M.

2008-01-01

Anthropogenic addition of bioavailable nitrogen to the biosphere is increasing and terrestrial ecosystems are becoming increasingly nitrogen-saturated, causing more bioavailable nitrogen to enter groundwater and surface waters. Large-scale nitrogen budgets show that an average of about 20-25 per cent of the nitrogen added to the biosphere is exported from rivers to the ocean or inland basins, indicating that substantial sinks for nitrogen must exist in the landscape. Streams and rivers may themselves be important sinks for bioavailable nitrogen owing to their hydrological connections with terrestrial systems, high rates of biological activity, and streambed sediment environments that favour microbial denitrification. Here we present data from nitrogen stable isotope tracer experiments across 72 streams and 8 regions representing several biomes. We show that total biotic uptake and denitrification of nitrate increase with stream nitrate concentration, but that the efficiency of biotic uptake and denitrification declines as concentration increases, reducing the proportion of in-stream nitrate that is removed from transport. Our data suggest that the total uptake of nitrate is related to ecosystem photosynthesis and that denitrification is related to ecosystem respiration. In addition, we use a stream network model to demonstrate that excess nitrate in streams elicits a disproportionate increase in the fraction of nitrate that is exported to receiving waters and reduces the relative role of small versus large streams as nitrate sinks. ??2008 Nature Publishing Group.

Phytoplankton dynamics of a subtropical reservoir controlled by the complex interplay among hydrological, abiotic, and biotic variables.

PubMed

Kuo, Yi-Ming; Wu, Jiunn-Tzong

2016-12-01

This study was conducted to identify the key factors related to the spatiotemporal variations in phytoplankton abundance in a subtropical reservoir from 2006 to 2010 and to assist in developing strategies for water quality management. Dynamic factor analysis (DFA), a dimension-reduction technique, was used to identify interactions between explanatory variables (i.e., environmental variables) and abundance (biovolume) of predominant phytoplankton classes. The optimal DFA model significantly described the dynamic changes in abundances of predominant phytoplankton groups (including dinoflagellates, diatoms, and green algae) at five monitoring sites. Water temperature, electrical conductivity, water level, nutrients (total phosphorus, NO 3 -N, and NH 3 -N), macro-zooplankton, and zooplankton were the key factors affecting the dynamics of aforementioned phytoplankton. Therefore, transformations of nutrients and reactions between water quality variables and aforementioned processes altered by hydrological conditions may also control the abundance dynamics of phytoplankton, which may represent common trends in the DFA model. The meandering shape of Shihmen Reservoir and its surrounding rivers caused a complex interplay between hydrological conditions and abiotic and biotic variables, resulting in phytoplankton abundance that could not be estimated using certain variables. Additional water quality and hydrological variables at surrounding rivers and monitoring plans should be executed a few days before and after reservoir operations and heavy storm, which would assist in developing site-specific preventive strategies to control phytoplankton abundance.

Framework for Derivation of Water Quality Criteria Using the Biotic Ligand Model: Copper as a Case Study.

PubMed

Gondek, John C; Gensemer, Robert W; Claytor, Carrie A; Canton, Steven P; Gorsuch, Joseph W

2018-06-01

Acceptance of the Biotic Ligand Model (BLM) to derive aquatic life criteria, for metals in general and copper in particular, is growing amongst regulatory agencies worldwide. Thus, it is important to ensure that water quality data are used appropriately and consistently in deriving such criteria. Here we present a suggested BLM implementation framework (hereafter referred to as "the Framework") to help guide the decision-making process when designing sampling and analysis programs for use of the BLM to derive water quality criteria applied on a site-specific basis. Such a framework will help inform stakeholders on the requirements needed to derive BLM-based criteria, and thus, ensure the appropriate types and amount of data are being collected and interpreted. The Framework was developed for calculating BLM-based criteria when data are available from multiple sampling locations on a stream. The Framework aspires to promote consistency when applying the BLM across datasets of disparate water quality, data quantity, and spatial and temporal representativeness, and is meant to be flexible to maximize applicability over a wide range of scenarios. Therefore, the Framework allows for a certain level of interpretation and adjustment to address the issues unique to each dataset. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

DEVELOPMENT AND EVALUATION OF A MACROINVERTEBRATE BIOTIC INTEGRITY INDEX (MBII) FOR REGIONALLY ASSESSING MID-ATLANTIC HIGHLANDS STREAMS

EPA Science Inventory

The multimetric Macroinvertebrate Biotic Integrity Index (MBII) was developed from data collected at 574 wadeable stream reaches in the Mid-Atlantic Highlands region (MAHR) by the USEPA's Environmental Monitoring and Assessment Program (EMAP). Over 100 candidate metrics were eval...

BOOTSTRAPPING AND MONTE CARLO METHODS OF POWER ANALYSIS USED TO ESTABLISH CONDITION CATEGORIES FOR BIOTIC INDICES

EPA Science Inventory

Biotic indices have been used ot assess biological condition by dividing index scores into condition categories. Historically the number of categories has been based on professional judgement. Alternatively, statistical methods such as power analysis can be used to determine the ...

Subtropical Biotic Fringing Reefs as Ecological Laboratories.

ERIC Educational Resources Information Center

Hunt, Jeffrey W.

1980-01-01

Describes a 16-week course in marine biology involving a class-coordinated investigation of a subtropical biotic fringing reef of Hawaii. Describes in detail the development of preliminary hypotheses regarding general cause-effect relationships on the reef, and the exploration of specific areas, such as chemical or physical factors. (CS)

Using the index of biotic integrity (IBI) to measure environmental quality in warmwater streams of Wisconsin.

Treesearch

John Lyons

1992-01-01

Describes an index based on attributes of fish assemblages that has proven effective in assessing biotic integrity and environmental health in intermediate-sized, warmwater (i.e., too warm for salmonids) streams and rivers of Wisconsin. Provides detailed guidelines for applying this index.

DEVELOPMENT OF A FISH INDEX OF BIOTIC INTEGRITY FOR ASSESSING WADEABLE STREAMS IN WEST VIRGINIA

EPA Science Inventory

We used Environmental Monitoring Assessment Program (EMAP) data from the Mid-Atlantic Highlands Assessment (MAHA) to develop an Index of Biotic Integrity (IBI) for West Virginia (WV). Standard techniques were used to evaluate a candidate pool of 58 fish assemblage metrics. Resp...

LANDSCAPE INFLUENCES ON IN-STREAM BIOTIC INTEGRITY: USE OF MACROINVERTEBRATE METRICS TO IDENTIFY LANDSCAPE STRESSORS IN HEADWATER CATCHMENTS

EPA Science Inventory

The biotic integrity of streams is profoundly influenced by quantitative and qualitative features in the landscape of the surrounding catchment. In this study, aquatic macroinvertebrate metrics (e.g., relative abundance of Ephemeroptera, Trichoptera, and/or Plecoptera taxa, or t...

USE OF PERIPHYTON ASSEMBLAGE DATA AS AN INDEX OF BIOTIC INTEGRITY

EPA Science Inventory

Periphyton assemblages data collected from 233 stream site-visits (49 in 1993, 56 in 1994, and 128 in 1995) throughout the Mid-Appalachian region were used to develop a periphyton index of biotic integrity (PIBI} based on 1) algal genera richness; 2)the relative abundances of dia...

PREDICTING SEDIMENT METAL TOXICITY USING A SEDIMENT BIOTIC LIGAND MODEL: METHODOLOGY AND INITIAL APPLICATION

EPA Science Inventory

An extension of the simultaneously extracted metals/acid-volatile sulfide (SEM/AVS) procedure is presented that predicts the acute and chronic sediment metals effects concentrations. A biotic ligand model (BLM) and a pore water–sediment partitioning model are used to predict the ...

Regulation of Specialized Metabolism by WRKY Transcription Factors

PubMed Central

Schluttenhofer, Craig; Yuan, Ling

2015-01-01

WRKY transcription factors (TFs) are well known for regulating plant abiotic and biotic stress tolerance. However, much less is known about how WRKY TFs affect plant-specialized metabolism. Analysis of WRKY TFs regulating the production of specialized metabolites emphasizes the values of the family outside of traditionally accepted roles in stress tolerance. WRKYs with conserved roles across plant species seem to be essential in regulating specialized metabolism. Overall, the WRKY family plays an essential role in regulating the biosynthesis of important pharmaceutical, aromatherapy, biofuel, and industrial components, warranting considerable attention in the forthcoming years. PMID:25501946

Structural diversity: a multi-dimensional approach to assess recreational services in urban parks.

PubMed

Voigt, Annette; Kabisch, Nadja; Wurster, Daniel; Haase, Dagmar; Breuste, Jürgen

2014-05-01

Urban green spaces provide important recreational services for urban residents. In general, when park visitors enjoy "the green," they are in actuality appreciating a mix of biotic, abiotic, and man-made park infrastructure elements and qualities. We argue that these three dimensions of structural diversity have an influence on how people use and value urban parks. We present a straightforward approach for assessing urban parks that combines multi-dimensional landscape mapping and questionnaire surveys. We discuss the method as well the results from its application to differently sized parks in Berlin and Salzburg.

Predicting toxic effects of copper on aquatic biota in mineralized areas by using the Biotic Ligand Model

USGS Publications Warehouse

Smith, Kathleen S.; Ranville, James F.; Adams, M.; Choate, LaDonna M.; Church, Stan E.; Fey, David L.; Wanty, Richard B.; Crock, James G.

2006-01-01

The chemical speciation of metals influences their biological effects. The Biotic Ligand Model (BLM) is a computational approach to predict chemical speciation and acute toxicological effects of metals on aquatic biota. Recently, the U.S. Environmental Protection Agency incorporated the BLM into their regulatory water-quality criteria for copper. Results from three different laboratory copper toxicity tests were compared with BLM predictions for simulated test-waters. This was done to evaluate the ability of the BLM to accurately predict the effects of hardness and concentrations of dissolved organic carbon (DOC) and iron on aquatic toxicity. In addition, we evaluated whether the BLM and the three toxicity tests provide consistent results. Comparison of BLM predictions with two types of Ceriodaphnia dubia toxicity tests shows that there is fairly good agreement between predicted LC50 values computed by the BLM and LC50 values determined from the two toxicity tests. Specifically, the effect of increasing calcium concentration (and hardness) on copper toxicity appears to be minimal. Also, there is fairly good agreement between the BLM and the two toxicity tests for test solutions containing elevated DOC, for which the LC50 is 3-to-5 times greater (less toxic) than the LC50 for the lower-DOC test water. This illustrates the protective effects of DOC on copper toxicity and demonstrates the ability of the BLM to predict these protective effects. In contrast, for test solutions with added iron there is a decrease in LC50 values (increase in toxicity) in results from the two C. dubia toxicity tests, and the agreement between BLM LC50 predictions and results from these toxicity tests is poor. The inability of the BLM to account for competitive iron binding to DOC or DOC fractionation may be a significant shortcoming of the BLM for predicting site- specific water-quality criteria in streams affected by iron-rich acidic drainage in mined and mineralized areas.

Microbial ecology studies at two coal mine refuse sites in Illinois

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

Miller, R. M.; Cameron, R. E.

An investigation was made of the microflora associated with coal refuse at two abandoned mines in the midwestern United States. Information was gathered for both the edaphic and the biotic composition of the refuse material. Emphasis was placed on heterotrophic and autotrophic components as to numbers, kinds, and physiological groups. The presence of chemolithotrophs was also investigated. The relationship between abiotic and biotic components in regard to distribution of bacteria, fungi, and algae is discussed. Information presented in this report will be utilized in assessing trends and changes in microbial numbers and composition related to manipulations of the edaphic andmore » biotic ecosystem components associated with reclamation of the refuse piles.« less

Detection of Geothermal Phosphite Using High Performance Liquid Chromatography

PubMed Central

Pech, Herbe; Henry, Amanda; Khachikian, Crist S.; Salmassi, Tina M.; Hanrahan, Grady; Foster, Krishna L.

2009-01-01

Little is known about the pre-biotic mechanisms that initiated the bioavailability of phosphorus, an element essential to life. A better understanding of phosphorus speciation in modern earth environments representative of early earth, may help to elucidate the origins of bioavailable phosphorus. This paper presents the first quantitative measurements of phosphite in a pristine geothermal pool representative of early earth. Phosphite and phosphate were initially identified and quantified in geothermal pool and stream samples at Hot Creek Gorge near Mammoth Lakes, California using suppressed conductivity ion chromatography. Results confirmed the presence of 0.06 ± 0.02 μM of phosphite and 0.05 ± 0.01 μM of phosphate in a geothermal pool. In the stream, phosphite concentrations were below detection limit (0.04 μM) and phosphate was measured at 1.06 ± 0.36 μM. The presence of phosphite in the geothermal pool was confirmed using both chemical oxidation and ion chromatography/mass spectrometry. PMID:19921877

Invasion by native tree species prevents biotic homogenization in novel forests of Puerto Rico

Treesearch

Oscar J. Abelleira Martinez

2010-01-01

There is concern that secondary forests dominated by introduced species, known as novel forests, increase taxonomical similarity between localities and lead to biotic homogenization in human dominated landscapes. In Puerto Rico, agricultural abandonment has given way to novel forests dominated by the introduced African tulip tree Spathodea campanulata Beauv. (...

Utilizing genetic resources and precision agriculture to enhance resistance to biotic and abiotic stress in watermelon

USDA-ARS?s Scientific Manuscript database

Originally from Africa, watermelon is a staple crop in South Carolina and rich source of important phytochemicals that promote human health. As a result of many years of domestication and selection for desired fruit quality, modern watermelon cultivars are susceptible to biotic and abiotic stress. T...

Evidence of biotic resistance to invasions in forests of the Eastern USA

Treesearch

Basil V. Iannone III; Kevin M. Potter; Kelly-Ann Dixon Hamil; Whitney Huang; Hao Zhang; Qinfeng Guo; Christopher M. Oswalt; Christopher W. Woodall; Songlin Fei

2016-01-01

Context Detecting biotic resistance to biological invasions across large geographic areas may require acknowledging multiple metrics of niche usage and potential spatial heterogeneity in associations between invasive and native species diversity and dominance.Objectives Determine (1) if native communities are ...

SEWAGE DECOMPOSITION IN AMBIENT WATER: INFLUENCE OF SOLARRADIATION AND BIOTIC INTERACTIONS ON MICROORGANISM COMMUNITIES AND BACTEROIDALES REAL-TIME QUANTITATIVE PCR MEASUREMENTS - poster

EPA Science Inventory

AIMS: Sewage and ambient water both consist of a highly complex array of bacteria and eukaryotic microbes. When these communities are mixed, solar radiation and biotic interactions (predation and competition) can influence pathogen decay based on experiments targeting indicator ...

Sewage Decomposition in Ambient Water: Influence of Solarradiation and Biotic Interactions on Microorganism Communities and Bacteroidales Real-Time Quantitative PCR Measurements - poster/abstract

EPA Science Inventory

AIMS: Sewage and ambient water both consist of a highly complex array of bacteria and eukaryotic microbes. When these communities are mixed, solar radiation and biotic interactions (predation and competition) can influence pathogen decay based on experiments targeting indicator ...

Effects of landscape and riparian condition on a fish index of biotic integrity in a large southeastern Brazil river

EPA Science Inventory

Environmental conditions of a large river in southeastern Brazil were assessed by evaluating fish assemblage structure (index of biotic integrity, IBI), landscape use (forest, pasture, urban area, and tributary water) and riparian condition. A survey of the 338 km-long middle rea...

Biotic and abiotic mechanisms in the establishment of northern red oak seedlings: a review

Treesearch

Linda S. Gribko; Thomas M. Schuler; W. Mark Ford

2002-01-01

This review of literature pertaining to the biotic and abiotic mechanisms in the establishment of northern red oak seedlings is designed to aid forest managers and researchers interested in sustaining the oak component of the eastern and central hardwood forest regions. Recommendations for future research are presented.

Durango diversity panel: abiotic and biotic stress characterization and potential for introducing new germplasm into East Africa

USDA-ARS?s Scientific Manuscript database

The Durango Diversity Panel (DDP) consists of 192 old and newly released US and Canadian cultivars and germplasm lines in the pinto, great northern, red, and pink bean market classes. The Durango Race provides genetic diversity for drought stress tolerance, and biotic stress resistance. Much disea...

Climate drivers of bark beetle outbreak dynamics in Norway spruce forests

Treesearch

Lorenzo Marini; Bjorn Okland; Anna Maria Jonsson; Barbara Bentz; Allan Carroll; Beat Forster; Jean-Claude Gregoire; Rainer Hurling; Louis Michel Nageleisen; Sigrid Netherer; Hans Peter Ravn; Aaron Weed; Martin Schroeder

2017-01-01

Bark beetles are among the most devastating biotic agents affecting forests globally and several species are expected to be favored by climate change. Given the potential interactions of insect outbreaks with other biotic and abiotic disturbances, and the potentially strong impact of changing disturbance regimes on forest resources, investigating climatic drivers of...

Advanced Analytical Methodologies Based on Raman Spectroscopy to Detect Prebiotic and Biotic Molecules: Applicability in the Study of the Martian Nakhlite NWA 6148 Meteorite

NASA Astrophysics Data System (ADS)

Madariaga, J. M.; Torre-Fdez, I.; Ruiz-Galende, P.; Aramendia, J.; Gomez-Nubla, L.; Fdez-Ortiz de Vallejuelo, S.; Maguregui, M.; Castro, K.; Arana, G.

2018-04-01

Advanced methodologies based on Raman spectroscopy are proposed to detect prebiotic and biotic molecules in returned samples from Mars: (a) optical microscopy with confocal micro-Raman, (b) the SCA instrument, (c) Raman Imaging. Examples for NWA 6148.

A STRUCTURED APPROACH FOR DEVELOPING INDICES OF BIOTIC INTEGRITY: THREE EXAMPLES FROM STREAMS AND RIVERS IN THE WESTERN USA

EPA Science Inventory

In the late 1990s the Environmental Monitoring and Assessment Program of the U.S. Environmental Protection Agency developed a structured set of tests to evaluate and facilitate selection of metrics for indices of biotic integrity (IBIs). These IBIs were designed to be applicable ...

DEVELOPMENT AND EVALUATION OF A FISH ASSEMBLAGE INDEX OF BIOTIC INTEGRITY FOR NORTHWESTERN GREAT PLAINS STREAMS

EPA Science Inventory

Quantitative indicators of biological integrity are needed for streams in the Great Plains of North America, but it was not known if the Index of Biotic Integrity (IBI) approach would be effective in this semi-arid region. Great Plains streams have a depauperate and tolerant i...

Recommended reference genes for quantitative PCR analysis in soybean have variable stabilities during diverse biotic stresses

USDA-ARS?s Scientific Manuscript database

For real-time reverse transcription-PCR (qRT-PCR) in soybean, reference genes in different tissues, developmental stages, various cultivars, and under stress conditions have been suggested but their usefulness for research on soybean under various biotic stresses occurring in North-Central U.S. is n...

Site-scale disturbance and habitat development best predict an index of amphibian biotic integrity in Ohio shrub and forested wetlands

USGS Publications Warehouse

Micacchion, Mick; Stapanian, Martin A.; Adams, Jean V.

2015-01-01

We determined the best predictors of an index of amphibian biotic integrity calculated from 54 shrub and forested wetlands in Ohio, USA using a two-step sequential holdout validation procedure. We considered 13 variables as predictors: four metrics of wetland condition from the Ohio Rapid Assessment Method (ORAM), a wetland vegetation index of biotic integrity, and eight metrics from a landscape disturbance index. For all iterations, the best model included the single ORAM metric that assesses habitat alteration, substrate disturbance, and habitat development within a wetland. Our results align with results of similar studies that have associated high scores for wetland vegetation indices of biotic integrity with low habitat alteration and substrate disturbance within wetlands. Thus, implementing similar management practices (e.g., not removing downed woody debris, retaining natural morphological features, decreasing nutrient input from surrounding agricultural lands) could concurrently increase ecological integrity of both plant and amphibian communities in a wetland. Further, our results have the unexpected effect of making progress toward a more unifying theory of ecological indices.

Relative Importance of Biotic and Abiotic Forces on the Composition and Dynamics of a Soft-Sediment Intertidal Community

PubMed Central

Barbeau, Myriam A.

2016-01-01

Top-down, bottom-up, middle-out and abiotic factors are usually viewed as main forces structuring biological communities, although assessment of their relative importance, in a single study, is rarely done. We quantified, using multivariate methods, associations between abiotic and biotic (top-down, bottom-up and middle-out) variables and infaunal population/community variation on intertidal mudflats in the Bay of Fundy, Canada, over two years. Our analysis indicated that spatial structural factors like site and plot accounted for most of the community and population variation. Although we observed a significant relationship between the community/populations and the biotic and abiotic variables, most were of minor importance relative to the structural factors. We suggest that community and population structure were relatively uncoupled from the structuring influences of biotic and abiotic factors in this system because of high concentrations of resources that sustain high densities of infauna and limit exploitative competition. Furthermore, we hypothesize that the infaunal community primarily reflects stochastic spatial events, namely a “first come, first served” process. PMID:26790098

Environmental Maternal Effects Mediate the Resistance of Maritime Pine to Biotic Stress

PubMed Central

Vivas, María; Zas, Rafael; Sampedro, Luis; Solla, Alejandro

2013-01-01

The resistance to abiotic stress is increasingly recognised as being impacted by maternal effects, given that environmental conditions experienced by parent (mother) trees affect stress tolerance in offspring. We hypothesised that abiotic environmental maternal effects may also mediate the resistance of trees to biotic stress. The influence of maternal environment and maternal genotype and the interaction of these two factors on early resistance of Pinus pinaster half-sibs to the Fusarium circinatum pathogen was studied using 10 mother genotypes clonally replicated in two contrasting environments. Necrosis length of infected seedlings was 16% shorter in seedlings grown from favourable maternal environment seeds than in seedlings grown from unfavourable maternal environment seeds. Damage caused by F. circinatum was mediated by maternal environment and maternal genotype, but not by seed mass. Mechanisms unrelated to seed provisioning, perhaps of epigenetic nature, were probably involved in the transgenerational plasticity of P. pinaster, mediating its resistance to biotic stress. Our findings suggest that the transgenerational resistance of pines due to an abiotic stress may interact with the defensive response of pines to a biotic stress. PMID:23922944

Influence of canopy traits on spatio-temporal variability of throughfall in Mediterranean Downy oak and Scots pine stands

NASA Astrophysics Data System (ADS)

Llorens, Pilar; Garcia-Estringana, Pablo; Latron, Jérôme; Molina, Antonio J.; Gallart, Francesc

2014-05-01

The spatio-temporal variability of throughfall is the result of the interaction of biotic factors, related to the canopy traits, and abiotic factors, linked to the meteorological conditions. This variability may lead to significant differences in the volume of water and solutes that reach the ground in each location, and beyond in the hydrological and biogeochemical dynamics of forest soils. Two forest stands in Mediterranean climatic conditions were studied to analyse the role of biotic and abiotic factors in the temporal and spatial redistribution of throughfall. The monitored stands are a Downy oak forest (Quercus pubescens) and a Scots pine forest (Pinus sylvestris), both located in the Vallcebre research catchments (NE Spain, 42º 12'N, 1º 49'E). The study plots are representative of Mediterranean mountain areas with spontaneous afforestation by Scots pine as a consequence of the abandonment of agricultural terraces, formerly covered by Downy oaks. The monitoring design of each plot consisted of a set of 20 automatic rain recorders and 40 automatic soil moisture probes located below the canopy. 100 hemispheric photographs of the canopy were used to place the instruments at representative locations (in terms of canopy cover) within the plot. Bulk rainfall, stemflow and meteorological conditions above the forest cover were also automatically recorded. Canopy cover as well as biometric characteristics of the plots were also regularly measured. The results indicate a temporal persistence of throughfall in both stands, as observed elsewhere. However, for the oak plot the seasonal evolution of canopy traits added additional variability, with higher variability in summer and different locations of wet and dry spots depending on the season. Furthermore, this work investigates the influence of canopy structure on the spatial variability of throughfall by analysing a large set of forest parameters, from main canopy traits to detailed leaves and wood characteristics. The analysis includes the consideration of the interaction of main abiotic factors with canopy traits.

Carica papaya microRNAs are responsive to Papaya meleira virus infection.

PubMed

Abreu, Paolla M V; Gaspar, Clicia G; Buss, David S; Ventura, José A; Ferreira, Paulo C G; Fernandes, Patricia M B

2014-01-01

MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya.

Carica papaya MicroRNAs Are Responsive to Papaya meleira virus Infection

PubMed Central

Abreu, Paolla M. V.; Gaspar, Clicia G.; Buss, David S.; Ventura, José A.; Ferreira, Paulo C. G.; Fernandes, Patricia M. B.

2014-01-01

MicroRNAs are implicated in the response to biotic stresses. Papaya meleira virus (PMeV) is the causal agent of sticky disease, a commercially important pathology in papaya for which there are currently no resistant varieties. PMeV has a number of unusual features, such as residence in the laticifers of infected plants, and the response of the papaya to PMeV infection is not well understood. The protein levels of 20S proteasome subunits increase during PMeV infection, suggesting that proteolysis could be an important aspect of the plant defense response mechanism. To date, 10,598 plant microRNAs have been identified in the Plant miRNAs Database, but only two, miR162 and miR403, are from papaya. In this study, known plant microRNA sequences were used to search for potential microRNAs in the papaya genome. A total of 462 microRNAs, representing 72 microRNA families, were identified. The expression of 11 microRNAs, whose targets are involved in 20S and 26S proteasomal degradation and in other stress response pathways, was compared by real-time PCR in healthy and infected papaya leaf tissue. We found that the expression of miRNAs involved in proteasomal degradation increased in response to very low levels of PMeV titre and decreased as the viral titre increased. In contrast, miRNAs implicated in the plant response to biotic stress decreased their expression at very low level of PMeV and increased at high PMeV levels. Corroborating with this results, analysed target genes for this miRNAs had their expression modulated in a dependent manner. This study represents a comprehensive identification of conserved miRNAs inpapaya. The data presented here might help to complement the available molecular and genomic tools for the study of papaya. The differential expression of some miRNAs and identifying their target genes will be helpful for understanding the regulation and interaction of PMeV and papaya. PMID:25072834

Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL

PubMed Central

Biselli, Chiara; Bagnaresi, Paolo; Faccioli, Primetta; Hu, Xinkun; Balcerzak, Margaret; Mattera, Maria G.; Yan, Zehong; Ouellet, Therese; Cattivelli, Luigi; Valè, Giampiero

2018-01-01

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus. PMID:29434615

Development of a macrophyte-based index of biotic integrity for Minnesota lakes

USGS Publications Warehouse

Beck, M.W.; Hatch, L.K.; Vondracek, B.; Valley, R.D.

2010-01-01

Traditional approaches for managing aquatic resources have often failed to account for effects of anthropogenic disturbances on biota that are not directly reflected by chemical and physical proxies of environmental condition. The index of biotic integrity (IBI) is a potentially effective assessment method to integrate ecological, functional, and structural aspects of aquatic systems. A macrophyte-based IBI was developed for Minnesota lakes to assess the ability of aquatic plant communities to indicate environmental condition. The index was developed using quantitative point intercept vegetation surveys for 97 lakes that represent a range of limnological and watershed characteristics. We followed an approach similar to that used in Wisconsin to develop the aquatic macrophyte community index (AMCI). Regional adaptation of the AMCI required the identification of species representative of macrophyte communities in Minnesota. Metrics and scaling methods were also substantially modified to produce a more empirically robust index. Regression analyses indicated that IBI scores reflected statewide differences in lake trophic state (R2 = 0.57, F = 130.3, df = 1, 95, p < 0.005), agricultural (R2 = 0.51, F = 83.0, df = 1, 79, p < 0.005), urban (R2 = 0.22, F = 23.0, df = 1, 79, p < 0.005), and forested land uses (R2 = 0.51, F = 84.7, df = 1, 79, p < 0.005), and county population density (R2 = 0.14, F = 16.6, df = 1, 95, p < 0.005). Variance partitioning analyses using multiple regression models indicated a unique response of the IBI to human-induced stress separate from a response to natural lake characteristics. The IBI was minimally affected by differences in sample point density as indicated by Monte Carlo analyses of reduced sampling effort. Our analysis indicates that a macrophyte IBI calibrated for Minnesota lakes could be useful for identifying differences in environmental condition attributed to human-induced stress gradients. ?? 2010 Elsevier Ltd.

Integration of biotic ligand models (BLM) and bioaccumulation kinetics into a mechanistic framework for metal uptake in aquatic organisms.

PubMed

Veltman, Karin; Huijbregts, Mark A J; Hendriks, A Jan

2010-07-01

Both biotic ligand models (BLM) and bioaccumulation models aim to quantify metal exposure based on mechanistic knowledge, but key factors included in the description of metal uptake differ between the two approaches. Here, we present a quantitative comparison of both approaches and show that BLM and bioaccumulation kinetics can be merged into a common mechanistic framework for metal uptake in aquatic organisms. Our results show that metal-specific absorption efficiencies calculated from BLM-parameters for freshwater fish are highly comparable, i.e. within a factor of 2.4 for silver, cadmium, copper, and zinc, to bioaccumulation-absorption efficiencies for predominantly marine fish. Conditional affinity constants are significantly related to the metal-specific covalent index. Additionally, the affinity constants of calcium, cadmium, copper, sodium, and zinc are significantly comparable across aquatic species, including molluscs, daphnids, and fish. This suggests that affinity constants can be estimated from the covalent index, and constants can be extrapolated across species. A new model is proposed that integrates the combined effect of metal chemodynamics, as speciation, competition, and ligand affinity, and species characteristics, as size, on metal uptake by aquatic organisms. An important direction for further research is the quantitative comparison of the proposed model with acute toxicity values for organisms belonging to different size classes.

Diesel pollution biodegradation: synergetic effect of Mycobacterium and filamentous fungi.

PubMed

Li, You-Qing; Liu, Hong-Fang; Tian, Zhen-Le; Zhu, Li-Hua; Wu, Ying-Hui; Tang, He-Qing

2008-06-01

To biodegrade the diesel pollution in aqueous solution inoculated with Mycobacterium and filamentous fungi. Bacteria sampled from petroleum hydrocarbons contaminated sites in Karamay Oilfield were isolated and identified as Mycobacterium hyalinum (MH) and cladosporium. Spectrophotometry and gas chromatography (GC) were used to analyze of the residual concentrations of diesel oil and its biodegradation products. From the GC data, the values of apparent biodegradation ratio of the bacterial strain MH to diesel oil were close to those obtained in the control experiments. Moreover, the number of MH did not increase with degradation time. However, by using n-octadecane instead of diesel oil, the real biotic degradation ratio increased to 20.9% over 5 days of degradation. Cladosporium strongly biodegraded diesel oil with a real degradation ratio of up to 34% after 5 days treatment. When the two strains were used simultaneously, a significant synergistic effect between them resulted in almost complete degradation of diesel oil, achieving a total diesel removal of 99% over 5 days of treatment, in which one part of about 80% and another part of about 19% were attributed to biotic and abiotic processes, respectively. The observed synergistic effect was closely related to the aromatics-degrading ability of Cladosporium, which favored the growth of MH and promoted the bioavailability of diesel oil.

Abiotic and biotic dynamics during the initial stages of high solids switchgrass degradation.

PubMed

Fontenelle, L T; Corgie, S C; Walker, L P

2011-07-01

An understanding of the underlying dynamics of how biotic variables drive changes in abiotic parameters in the early stages of biomass biodegradation is essential for better control of the process. Probe hybridization was used to quantitatively study the growth of bacteria, yeast and fungi for three levels of initial moisture content (60, 65 and 75% MC) over a period of 64 h. Changes in abiotic parameters were also documented. By 64 h, samples were significantly differentiated both in temporal and spatial dimension, proving that considerable changes had occurred in these initial stages. Maximum carbon (C) conversion occurred in the 75% MC reactor at a peak value of 49%, with 40% and 37% in the 65 and 60% MC reactors, respectively. Higher temperature, higher pH, higher rates of O2 consumption and CO2 evolution were also observed in the highest moisture reactor; suggesting that of the three MCs studied, 75% MC was the optimal one for the process. MC during the process also proved to be important because it greatly influenced variation in the spatial dimension, further underscoring the importance of characterizing changes with bed height. Most importantly, we were able to positively correlate the rate of substrate degradation with bacterial biomass levels and highlight the critical role of bacteria in biological decomposition.

A proposal to conserve black-footed ferrets and the prairie dog ecosystem

USGS Publications Warehouse

Miller, Brian; Wemmer, Christen; Biggins, Dean; Reading, Richard P.

1990-01-01

Prairie dogs (Cynomys spp.) have been poisoned throughout this century because of grazing competition with livestock. Recent evidence showed these early claims were exaggerated, but animal control was already entrenched in government policy. As a result, ongoing government subsidized poisoning has reduced prairie dogs to about 2% of their former distribution. The reduction of prairie dogs diminished species diversity in the arid grasslands of North America, including the potential extinction of the black-footed ferret (Mustela nigripes). Cost-benefit analysis revealed that poisoning costs more than any grazing benefits accrued. This analysis did not consider the long-term costs of reversing ecosystem degradation, the intangible value of biological diversity as a public benefit, or the depletion of biotic resources as a loss of actual or potential wealth. The government presently finances the poisoning policy and the preservation of endangered species like the black-footed ferret, two apparently conflicting programs. We, therefore, propose an integrated management plan that considers both interests. We propose that federal monies allocated to the poisoning program be converted into a rebate for ranchers who manage livestock while preserving the prairie dog community. This would redirect funds and personnel already allocated to prairie dog eradication to an incentive for ranchers who manage for livestock and wildlife. Livestock interests and grassland biotic diversity would both benefit.

Differences found in the macroinvertebrate community composition in the presence or absence of the invasive alien crayfish, Orconectes hylas

USGS Publications Warehouse

Freeland-Riggert, Brandye T.; Cairns, Stefan H.; Poulton, Barry C.; Riggert, Chris M.

2016-01-01

Introductions of alien species into aquatic ecosystems have been well documented, including invasions of crayfish species; however, little is known about the effects of these introductions on macroinvertebrate communities. The woodland crayfish (Orconectes hylas (Faxon)) has been introduced into the St. Francis River watershed in southeast Missouri and has displaced populations of native crayfish. The effects of O. hylas on macroinvertebrate community composition were investigated in a fourth-order Ozark stream at two locations, one with the presence of O. hylas and one without. Significant differences between sites and across four sampling periods and two habitats were found in five categories of benthic macroinvertebrate metrics: species richness, percent/composition, dominance/diversity, functional feeding groups, and biotic indices. In most seasons and habitat combinations, the invaded site had significantly higher relative abundance of riffle beetles (Coleoptera: Elmidae), and significantly lower Missouri biotic index values, total taxa richness, and both richness and relative abundance of midges (Diptera: Chironomidae). Overall study results indicate that some macroinvertebrate community differences due to the O. hylas invasion were not consistent between seasons and habitats, suggesting that further research on spatial and temporal habitat use and feeding ecology of Ozark crayfish species is needed to improve our understanding of the effects of these invasions on aquatic communities.

The niche, biogeography and species interactions

PubMed Central

Wiens, John J.

2011-01-01

In this paper, I review the relevance of the niche to biogeography, and what biogeography may tell us about the niche. The niche is defined as the combination of abiotic and biotic conditions where a species can persist. I argue that most biogeographic patterns are created by niche differences over space, and that even ‘geographic barriers’ must have an ecological basis. However, we know little about specific ecological factors underlying most biogeographic patterns. Some evidence supports the importance of abiotic factors, whereas few examples exist of large-scale patterns created by biotic interactions. I also show how incorporating biogeography may offer new perspectives on resource-related niches and species interactions. Several examples demonstrate that even after a major evolutionary radiation within a region, the region can still be invaded by ecologically similar species from another clade, countering the long-standing idea that communities and regions are generally ‘saturated’ with species. I also describe the somewhat paradoxical situation where competition seems to limit trait evolution in a group, but does not prevent co-occurrence of species with similar values for that trait (called here the ‘competition–divergence–co-occurrence conundrum’). In general, the interface of biogeography and ecology could be a major area for research in both fields. PMID:21768150

Genomic Tools in Groundnut Breeding Program: Status and Perspectives

PubMed Central

Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

2016-01-01

Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

An exploratory analysis of Indiana and Illinois biotic ...

EPA Pesticide Factsheets

EPA recognizes the importance of nutrient criteria in protecting designated uses from eutrophication effects associated with elevated phosphorus and nitrogen in streams and has worked with states over the past 12 years to assist them in developing nutrient criteria. Towards that end, EPA has provided states and tribes with technical guidance to assess nutrient impacts and to develop criteria. EPA published recommendations in 2000 on scientifically defensible empirical approaches for setting numeric criteria. EPA also published eco-regional criteria recommendations in 2000-2001 based on a frequency distribution approach meant to approximate reference condition concentrations. In 2010, EPA elaborated on one of these empirical approaches (i.e., stressor-response relationships) for developing nutrient criteria. The purpose of this report was to conduct exploratory analyses of state datasets from Illinois and Indiana to determine threshold values for nutrients and chlorophyll a that could guide Indiana and Illinois criteria development. Box and whisker plots were used to compare nutrient and chlorophyll a concentrations between Illinois and Indiana. Stressor response analyses, using piece-wise linear regression and change-point analysis (Illinois only) were conducted to determine thresholds of change in relationships between nutrients and biotic assemblages. Impact stmt: The purpose of this report was to conduct exploratory analyses of state datasets from Illinois

ANALYSIS OF BIOTIC AND ABIOTIC FACTORS INFLUENCING THE OCCURRENCE OF WEST NILE VIRUS INFECTION IN TUNISIA.

PubMed

Ben Hassine, Th; Calistri, P; Ippoliti, C; Conte, A; Danzetta, M L; Bruno, R; Lelli, R; Bejaoui, M; Hammami, S

2014-01-01

Eco-climatic conditions are often associated with the occurrence of West Nile Disease (WND) cases. Among the complex set of biotic and abiotic factors influencing the emergence and spread of this vector-borne disease, two main variables have been considered to have a great influence on the probability of West Nile Virus (WNV) introduction and circulation in Tunisia: the presence of susceptible bird populations and the existence of geographical areas where the environmental and climatic conditions are more favourable to mosquito multiplications. The aim of this study was to identify and classify the climatic and environmental variables possibly associated with the occurrence of WNVhuman cases in Tunisia. The following environmental and climatic variables have been considered: wetlands and humid areas, Normalised Difference Vegetation Index (NDVI), temperatures and elevation. A preliminary analysis for the characterization of main variables associated with areas with a history of WNV human cases in Tunisia between 1997 and 2011 has been made. This preliminary analysis clearly indicates the closeness to marshes ecosystem, where migratory bird populations are located, as an important risk factor for WNV infection. On the contrary the temperature absolute seems to be not a significant factor in Tunisian epidemiological situation. In relation to NDVI values, more complex considerations should be made.

Differences Found in the Macroinvertebrate Community Composition in the Presence or Absence of the Invasive Alien Crayfish, Orconectes hylas

PubMed Central

Freeland-Riggert, Brandye T.

2016-01-01

Introductions of alien species into aquatic ecosystems have been well documented, including invasions of crayfish species; however, little is known about the effects of these introductions on macroinvertebrate communities. The woodland crayfish (Orconectes hylas (Faxon)) has been introduced into the St. Francis River watershed in southeast Missouri and has displaced populations of native crayfish. The effects of O. hylas on macroinvertebrate community composition were investigated in a fourth-order Ozark stream at two locations, one with the presence of O. hylas and one without. Significant differences between sites and across four sampling periods and two habitats were found in five categories of benthic macroinvertebrate metrics: species richness, percent/composition, dominance/diversity, functional feeding groups, and biotic indices. In most seasons and habitat combinations, the invaded site had significantly higher relative abundance of riffle beetles (Coleoptera: Elmidae), and significantly lower Missouri biotic index values, total taxa richness, and both richness and relative abundance of midges (Diptera: Chironomidae). Overall study results indicate that some macroinvertebrate community differences due to the O. hylas invasion were not consistent between seasons and habitats, suggesting that further research on spatial and temporal habitat use and feeding ecology of Ozark crayfish species is needed to improve our understanding of the effects of these invasions on aquatic communities. PMID:26986207

A proposal to conserve black-footed ferrets and the prairie dog ecosystem

NASA Astrophysics Data System (ADS)

Miller, Brian; Wemmer, Christen; Biggins, Dean; Reading, Richard

1990-11-01

Prairie dogs ( Cynomys spp.) have been poisoned throughout this century because of grazing competition with livestock. Recent evidence showed these early claims were exaggerated, but animal control was already entrenched in government policy. As a result, ongoing government subsidized poisoning has reduced prairie dogs to about 2% of their former distribution. The reduction of prairie dogs diminished species diversity in the arid grasslands of North America, including the potential extinction of the black-footed ferret ( Mustela nigripes). Cost-benefit analysis revealed that poisoning costs more than any grazing benefits accrued. This analysis did not consider the long-term costs of reversing ecosystem degradation, the intangible value of biological diversity as a public benefit, or the depletion of biotic resources as a loss of actual or potential wealth. The government presently finances the poisoning policy and the preservation of endangered species like the black-footed ferret, two apparently conflicting programs. We, therefore, propose an integrated management plan that considers both interests. We propose that federal monies allocated to the poisoning program be converted into a rebate for ranchers who manage livestock while preserving the prairie dog community. This would redirect funds and personnel already allocated to prairie dog eradication to an incentive for ranchers who manage for livestock and wildlife. Livestock interests and grassland biotic diversity would both benefit.

The hysteretic evapotranspiration—Vapor pressure deficit relation

NASA Astrophysics Data System (ADS)

Zhang, Quan; Manzoni, Stefano; Katul, Gabriel; Porporato, Amilcare; Yang, Dawen

2014-02-01

Diurnal hysteresis between evapotranspiration (ET) and vapor pressure deficit (VPD) was reported in many ecosystems, but justification for its onset and magnitude remains incomplete with biotic and abiotic factors invoked as possible explanations. To place these explanations within a holistic framework, the occurrence of hysteresis was theoretically assessed along a hierarchy of model systems where both abiotic and biotic components are sequentially added. Lysimeter evaporation (E) measurements and model calculations using the Penman equation were used to investigate the effect of the time lag between net radiation and VPD on the hysteresis in the absence of any biotic effects. Modulations from biotic effects on the ET-VPD hysteresis were then added using soil-plant-atmosphere models of different complexities applied to a grassland ecosystem. The results suggest that the hysteresis magnitude depends on the radiation-VPD lag, while the plant and soil water potentials are both key factors modulating the hysteretic ET-VPD relation as soil moisture declines. In particular, larger hysteresis magnitude is achieved at less negative leaf water potential, root water potential, and soil water potential. While plant hydraulic capacitance affects the leaf water potential-ET relation, it has negligible effects on the ET-VPD hysteresis. Therefore, the genesis and magnitude of the ET-VPD hysteresis are controlled directly by both abiotic factors such as soil water availability, biotic factors (leaf and root water potentials, which in turn depend on soil moisture), and the time lag between radiation and VPD.

Biotic soil crusts in relation to topography, cheatgrass, and fire in the Columbia Basin, Washington

USGS Publications Warehouse

Ponzetti, Jeanne; McCune, B.; Pyke, David A.

2007-01-01

We studied lichen and bryophyte soil crust communities in a large public grazing allotment within a sagebrush steppe ecosystem in which the biotic soil crusts are largely intact. The allotment had been rested from grazing for 12 years, but experienced an extensive series of wildfires. In the 350, 4 ?? 0.5 m plots, stratified by topographic position, we found 60 species or species groups that can be distinguished in the field with a hand lens, averaging 11.5 species groups per plot. Lichen and bryophyte soil crust communities differed among topographic positions. Draws were the most disturbed, apparently from water erosion in a narrow channel and mass wasting from the steepened sides. Presumably because of this disturbance, draws had the lowest average species richness of all the topographic strata we examined. Biotic crust species richness and cover were inversely related to cover of the invasive annual, cheatgrass (Bromus tectorum), and positively related to cover of native bunchgrasses. Integrity of the biotic crust was more strongly related to cheatgrass than to fire. In general, we observed good recovery of crusts following fire, but only in those areas dominated by perennial bunchgrasses. We interpret the resilience of the biotic crust, in this case, to the low abundance of cheatgrass, low amounts of soil disturbance and high moss cover. These fires have not resulted in an explosion of the cheatgrass population, perhaps because of the historically low levels of livestock grazing.

Local shifts in floral biotic interactions in habitat edges and their effect on quantity and quality of plant offspring

PubMed Central

Fenu, Giuseppe; Bernardo, Liliana

2017-01-01

Abstract Spatial shifts in insect fauna due to ecological heterogeneity can severely constrain plant reproduction. Nonetheless, data showing effects of insect visit patterns and intensity of mutualistic and/or antagonistic plant–insect interactions on plant reproduction over structured ecological gradients remain scarce. We investigated how changes in flower-visitor abundance, identity and behaviour over a forest-open habitat gradient affect plant biotic interactions, and quantitative and qualitative fitness in the edge-specialist Dianthus balbisii. Composition and behaviour of the insects visiting flowers of D. balbisii strongly varied over the study gradient, influencing strength and patterns of plant biotic interactions (i.e. herbivory and pollination likelihood). Seed set comparison in free- and manually pollinated flowers suggested spatial variations in the extent of quantitative pollen limitation, which appeared more pronounced at the gradient extremes. Such variations were congruent to patterns of flower visit and plant biotic interactions. The analyses on seed and seedling viability evidenced that spatial variation in amount and type of pollinators, and frequency of herbivory affected qualitative fitness of D. balbisii by influencing selfing and outcrossing rates. Our work emphasizes the role of plant biotic interactions as a fine-scale mediator of plant fitness in ecotones, highlighting that optimal plant reproduction can take place into a restricted interval of the ecological gradients occurring at forest edges. Reducing the habitat complexity typical of such transition contexts can threat edge-adapted plants. PMID:28775831

White-tailed deer are a biotic filter during community assembly, reducing species and phylogenetic diversity.

PubMed

Begley-Miller, Danielle R; Hipp, Andrew L; Brown, Bethany H; Hahn, Marlene; Rooney, Thomas P

2014-06-09

Community assembly entails a filtering process, where species found in a local community are those that can pass through environmental (abiotic) and biotic filters and successfully compete. Previous research has demonstrated the ability of white-tailed deer (Odocoileus virginianus) to reduce species diversity and favour browse-tolerant plant communities. In this study, we expand on our previous work by investigating deer as a possible biotic filter altering local plant community assembly. We used replicated 23-year-old deer exclosures to experimentally assess the effects of deer on species diversity (H'), richness (SR), phylogenetic community structure and phylogenetic diversity in paired browsed (control) and unbrowsed (exclosed) plots. Additionally, we developed a deer-browsing susceptibility index (DBSI) to assess the vulnerability of local species to deer. Deer browsing caused a 12 % reduction in H' and 17 % reduction in SR, consistent with previous studies. Furthermore, browsing reduced phylogenetic diversity by 63 %, causing significant phylogenetic clustering. Overall, graminoids were the least vulnerable to deer browsing based on DBSI calculations. These findings demonstrate that deer are a significant driver of plant community assembly due to their role as a selective browser, or more generally, as a biotic filter. This study highlights the importance of knowledge about the plant tree of life in assessing the effects of biotic filters on plant communities. Application of such knowledge has considerable potential to advance our understanding of plant community assembly. Published by Oxford University Press on behalf of the Annals of Botany Company.

Plant Hormesis Management with Biostimulants of Biotic Origin in Agriculture.

PubMed

Vargas-Hernandez, Marcela; Macias-Bobadilla, Israel; Guevara-Gonzalez, Ramon G; Romero-Gomez, Sergio de J; Rico-Garcia, Enrique; Ocampo-Velazquez, Rosalia V; Alvarez-Arquieta, Luz de L; Torres-Pacheco, Irineo

2017-01-01

Over time plants developed complex mechanisms in order to adapt themselves to the environment. Plant innate immunity is one of the most important mechanisms for the environmental adaptation. A myriad of secondary metabolites with nutraceutical features are produced by the plant immune system in order to get adaptation to new environments that provoke stress (stressors). Hormesis is a phenomenon by which a stressor (i.e., toxins, herbicides, etc.) stimulates the cellular stress response, including secondary metabolites production, in order to help organisms to establish adaptive responses. Hormetins of biotic origin (i.e., biostimulants or biological control compounds), in certain doses might enhance plant performance, however, in excessive doses they are commonly deleterious. Biostimulants or biological control compounds of biotic origin are called "elicitors" that have widely been studied as inducers of plant tolerance to biotic and abiotic stresses. The plant response toward elicitors is reminiscent of hormetic responses toward toxins in several organisms. Thus, controlled management of hormetic responses in plants using these types of compounds is expected to be an important tool to increase nutraceutical quality of plant food and trying to minimize negative effects on yields. The aim of this review is to analyze the potential for agriculture that the use of biostimulants and biological control compounds of biotic origin could have in the management of the plant hormesis. The use of homolog DNA as biostimulant or biological control compound in crop production is also discussed.

Plant Hormesis Management with Biostimulants of Biotic Origin in Agriculture

PubMed Central

Vargas-Hernandez, Marcela; Macias-Bobadilla, Israel; Guevara-Gonzalez, Ramon G.; Romero-Gomez, Sergio de J.; Rico-Garcia, Enrique; Ocampo-Velazquez, Rosalia V.; Alvarez-Arquieta, Luz de L.; Torres-Pacheco, Irineo

2017-01-01

Over time plants developed complex mechanisms in order to adapt themselves to the environment. Plant innate immunity is one of the most important mechanisms for the environmental adaptation. A myriad of secondary metabolites with nutraceutical features are produced by the plant immune system in order to get adaptation to new environments that provoke stress (stressors). Hormesis is a phenomenon by which a stressor (i.e., toxins, herbicides, etc.) stimulates the cellular stress response, including secondary metabolites production, in order to help organisms to establish adaptive responses. Hormetins of biotic origin (i.e., biostimulants or biological control compounds), in certain doses might enhance plant performance, however, in excessive doses they are commonly deleterious. Biostimulants or biological control compounds of biotic origin are called “elicitors” that have widely been studied as inducers of plant tolerance to biotic and abiotic stresses. The plant response toward elicitors is reminiscent of hormetic responses toward toxins in several organisms. Thus, controlled management of hormetic responses in plants using these types of compounds is expected to be an important tool to increase nutraceutical quality of plant food and trying to minimize negative effects on yields. The aim of this review is to analyze the potential for agriculture that the use of biostimulants and biological control compounds of biotic origin could have in the management of the plant hormesis. The use of homolog DNA as biostimulant or biological control compound in crop production is also discussed. PMID:29081787

Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae)

PubMed Central

Mestre, Alexandre; Aguilar-Alberola, Josep A; Baldry, David; Balkis, Husamettin; Ellis, Adam; Gil-Delgado, Jose A; Grabow, Karsten; Klobučar, Göran; Kouba, Antonín; Maguire, Ivana; Martens, Andreas; Mülayim, Ayşegül; Rueda, Juan; Scharf, Burkhard; Soes, Menno; S Monrós, Juan; Mesquita-Joanes, Francesc

2013-01-01

In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa. PMID:24455152

Does prescribed burning result in biotic homogenization of coastal heathlands?

PubMed

Velle, Liv Guri; Nilsen, Liv Sigrid; Norderhaug, Ann; Vandvik, Vigdis

2014-05-01

Biotic homogenization due to replacement of native biodiversity by widespread generalist species has been demonstrated in a number of ecosystems and taxonomic groups worldwide, causing growing conservation concern. Human disturbance is a key driver of biotic homogenization, suggesting potential conservation challenges in seminatural ecosystems, where anthropogenic disturbances such as grazing and burning are necessary for maintaining ecological dynamics and functioning. We test whether prescribed burning results in biotic homogenization in the coastal heathlands of north-western Europe, a seminatural landscape where extensive grazing and burning has constituted the traditional land-use practice over the past 6000 years. We compare the beta-diversity before and after fire at three ecological scales: within local vegetation patches, between wet and dry heathland patches within landscapes, and along a 470 km bioclimatic gradient. Within local patches, we found no evidence of homogenization after fire; species richness increased, and the species that entered the burnt Calluna stands were not widespread specialists but native grasses and herbs characteristic of the heathland system. At the landscapes scale, we saw a weak homogenization as wet and dry heathland patches become more compositionally similar after fire. This was because of a decrease in habitat-specific species unique to either wet or dry habitats and postfire colonization by a set of heathland specialists that established in both habitat types. Along the bioclimatic gradient, species that increased after fire generally had more specific environmental requirements and narrower geographical distributions than the prefire flora, resulting in a biotic 'heterogenisation' after fire. Our study demonstrates that human disturbance does not necessarily cause biotic homogenization, but that continuation of traditional land-use practices can instead be crucial for the maintenance of the diversity and ecological function of a seminatural ecosystem. The species that established after prescribed burning were heathland specialists with relatively narrow geographical ranges. © 2013 John Wiley & Sons Ltd.

Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae).

PubMed

Mestre, Alexandre; Aguilar-Alberola, Josep A; Baldry, David; Balkis, Husamettin; Ellis, Adam; Gil-Delgado, Jose A; Grabow, Karsten; Klobučar, Göran; Kouba, Antonín; Maguire, Ivana; Martens, Andreas; Mülayim, Ayşegül; Rueda, Juan; Scharf, Burkhard; Soes, Menno; S Monrós, Juan; Mesquita-Joanes, Francesc

2013-12-01

In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa.

Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales

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

Wu, Jin; Guan, Kaiyu; Hayek, Matthew

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance-derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light-use efficiency associated with changes in the parameters themselves. Our fitted model wasmore » able to explain most of the variability in GEP at hourly (R 2 = 0.77) to interannual (R 2 = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light-use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing biotic from environmental variability can help to resolve debates about environmental limitations to tropical forest photosynthesis. For example, we found that biotically regulated canopy photosynthetic light-use efficiency (associated with leaf phenology) increased with sunlight during dry seasons (consistent with light but not water limitation of canopy development) but that realized GEP was nonetheless lower relative to its potential efficiency during dry than wet seasons (consistent with water limitation of photosynthesis in given assemblages of leaves). Lastly, this work highlights the importance of accounting for differential regulation of GEP at different timescales and of identifying the underlying feedbacks and adaptive mechanisms.« less

Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales

DOE PAGES

Wu, Jin; Guan, Kaiyu; Hayek, Matthew; ...

2016-09-19

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance-derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light-use efficiency associated with changes in the parameters themselves. Our fitted model wasmore » able to explain most of the variability in GEP at hourly (R 2 = 0.77) to interannual (R 2 = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light-use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing biotic from environmental variability can help to resolve debates about environmental limitations to tropical forest photosynthesis. For example, we found that biotically regulated canopy photosynthetic light-use efficiency (associated with leaf phenology) increased with sunlight during dry seasons (consistent with light but not water limitation of canopy development) but that realized GEP was nonetheless lower relative to its potential efficiency during dry than wet seasons (consistent with water limitation of photosynthesis in given assemblages of leaves). Lastly, this work highlights the importance of accounting for differential regulation of GEP at different timescales and of identifying the underlying feedbacks and adaptive mechanisms.« less

Partitioning controls on Amazon forest photosynthesis between environmental and biotic factors at hourly to interannual timescales.

PubMed

Wu, Jin; Guan, Kaiyu; Hayek, Matthew; Restrepo-Coupe, Natalia; Wiedemann, Kenia T; Xu, Xiangtao; Wehr, Richard; Christoffersen, Bradley O; Miao, Guofang; da Silva, Rodrigo; de Araujo, Alessandro C; Oliviera, Raimundo C; Camargo, Plinio B; Monson, Russell K; Huete, Alfredo R; Saleska, Scott R

2017-03-01

Gross ecosystem productivity (GEP) in tropical forests varies both with the environment and with biotic changes in photosynthetic infrastructure, but our understanding of the relative effects of these factors across timescales is limited. Here, we used a statistical model to partition the variability of seven years of eddy covariance-derived GEP in a central Amazon evergreen forest into two main causes: variation in environmental drivers (solar radiation, diffuse light fraction, and vapor pressure deficit) that interact with model parameters that govern photosynthesis and biotic variation in canopy photosynthetic light-use efficiency associated with changes in the parameters themselves. Our fitted model was able to explain most of the variability in GEP at hourly (R 2  = 0.77) to interannual (R 2  = 0.80) timescales. At hourly timescales, we found that 75% of observed GEP variability could be attributed to environmental variability. When aggregating GEP to the longer timescales (daily, monthly, and yearly), however, environmental variation explained progressively less GEP variability: At monthly timescales, it explained only 3%, much less than biotic variation in canopy photosynthetic light-use efficiency, which accounted for 63%. These results challenge modeling approaches that assume GEP is primarily controlled by the environment at both short and long timescales. Our approach distinguishing biotic from environmental variability can help to resolve debates about environmental limitations to tropical forest photosynthesis. For example, we found that biotically regulated canopy photosynthetic light-use efficiency (associated with leaf phenology) increased with sunlight during dry seasons (consistent with light but not water limitation of canopy development) but that realized GEP was nonetheless lower relative to its potential efficiency during dry than wet seasons (consistent with water limitation of photosynthesis in given assemblages of leaves). This work highlights the importance of accounting for differential regulation of GEP at different timescales and of identifying the underlying feedbacks and adaptive mechanisms. © 2016 John Wiley & Sons Ltd.

Effects of multi-scale environmental characteristics on agricultural stream biota in eastern Wisconsin

USGS Publications Warehouse

Fitzpatrick, F.A.; Scudder, B.C.; Lenz, B.N.; Sullivan, D.J.

2001-01-01

The U.S. Geological Survey examined 25 agricultural streams in eastern Wisconsin to determine relations between fish, invertebrate, and algal metrics and multiple spatial scales of land cover, geologic setting, hydrologic, aquatic habitat, and water chemistry data. Spearman correlation and redundancy analyses were used to examine relations among biotic metrics and environmental characteristics. Riparian vegetation, geologic, and hydrologic conditions affected the response of biotic metrics to watershed agricultural land cover but the relations were aquatic assemblage dependent. It was difficult to separate the interrelated effects of geologic setting, watershed and buffer land cover, and base flow. Watershed and buffer land cover, geologic setting, reach riparian vegetation width, and stream size affected the fish IBI, invertebrate diversity, diatom IBI, and number of algal taxa; however, the invertebrate FBI, percentage of EPT, and the diatom pollution index were more influenced by nutrient concentrations and flow variability. Fish IBI scores seemed most sensitive to land cover in the entire stream network buffer, more so than watershed-scale land cover and segment or reach riparian vegetation width. All but one stream with more than approximately 10 percent buffer agriculture had fish IBI scores of fair or poor. In general, the invertebrate and algal metrics used in this study were not as sensitive to land cover effects as fish metrics. Some of the reach-scale characteristics, such as width/depth ratios, velocity, and bank stability, could be related to watershed influences of both land cover and geologic setting. The Wisconsin habitat index was related to watershed geologic setting, watershed and buffer land cover, riparian vegetation width, and base flow, and appeared to be a good indicator of stream quality. Results from this study emphasize the value of using more than one or two biotic metrics to assess water quality and the importance of environmental characteristics at multiple scales.

Short-term alteration of biotic and abiotic components of the pelagic system in a shallow bay produced by a strong natural hypoxia event.

PubMed

Hernández-Miranda, Eduardo; Veas, Rodrigo; Anabalón, Valeria; Quiñones, Renato A

2017-01-01

In January 2008 there was an intensive and extensive upwelling event in the southern Humboldt Current System. This event produced an intrusion of water with low dissolved oxygen into Coliumo Bay, which caused massive mortality and the beaching of pelagic and benthic organisms, including zooplankton. During this event, which lasted 3 to 5 days, we studied and evaluated the effect of the hypoxic water in the bay on the abundance of macrozooplankton, nanoplankton and microphytoplankton, the concentration of several nutrients and hydrographic conditions. At the beginning of the hypoxia event the water column had very low dissolved oxygen concentrations (<0.5 mL O2 L-1), low temperatures and high salinity which are characteristics of the oxygen minimum zone from the Humboldt Current System. Redox, pH, nitrate, phosphate, silicate and chlorophyll-a values were the lowest, while nitrate and the phaeopigment values were the highest. The N:P ratio was below 16, and the abundance of nano- and microphytoplankton were at their lowest, the latter also with the lowest proportion of live organisms. Macrozooplankton had the greatest abundance during hypoxia, dominated mainly by crustacean, fish eggs and amphipods. The hypoxia event generated a strong short-term alteration of all biotic and abiotic components of the pelagic system in Coliumo Bay and the neighboring coastal zone. These negative effects associated with strong natural hypoxia events could have important consequences for the productivity and ecosystem functioning of the coastal zone of the Humboldt Current System if, as suggested by several models, winds favorable to upwelling should increase due to climate change. The effects of natural hypoxia in this coastal zone can be dramatic especially for pelagic and benthic species not adapted to endure conditions of low dissolved oxygen.

Of Paleo-Genes and Perch: What if an “Alien” Is Actually a Native?

PubMed Central

Stager, J. Curt; Sporn, Lee Ann; Johnson, Melanie; Regalado, Sean

2015-01-01

Documenting whether a biotic taxon is native or alien to an ecosystem has theoretical value for ecological and evolutionary studies, and has practical value because it can potentially identify a taxon as a desirable component of an ecosystem or target it for removal. In some cases, however, such background information is inadequate or unavailable. Here we use paleo-DNA to re-evaluate the historical status of yellow perch in the 6 million acre Adirondack State Park of northern New York. Yellow perch DNA in a 2200-year sediment record reveals a long-term native status for these supposedly alien fish and challenges assumptions that they necessarily exclude native trout from upland lakes. Similar approaches could be applied to other species with uncertain historical distributions and could help to identify unrecognized pockets of biodiversity. PMID:25751263

Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in Medicago truncatula

PubMed Central

Naoumkina, Marina A; He, XianZhi; Dixon, Richard A

2008-01-01

Background Exposure of Medicago truncatula cell suspension cultures to pathogen or wound signals leads to accumulation of various classes of flavonoid and/or triterpene defense molecules, orchestrated via a complex signalling network in which transcription factors (TFs) are essential components. Results In this study, we analyzed TFs responding to yeast elicitor (YE) or methyl jasmonate (MJ). From 502 differentially expressed TFs, WRKY and AP2/EREBP gene families were over-represented among YE-induced genes whereas Basic Helix-Loop-Helix (bHLH) family members were more over-represented among the MJ-induced genes. Jasmonate ZIM-domain (JAZ) transcriptional regulators were highly induced by MJ treatment. To investigate potential involvement of WRKY TFs in signalling, we expressed four Medicago WRKY genes in tobacco. Levels of soluble and wall bound phenolic compounds and lignin were increased in all cases. WRKY W109669 also induced tobacco endo-1,3-β-glucanase (NtPR2) and enhanced the systemic defense response to tobacco mosaic virus in transgenic tobacco plants. Conclusion These results confirm that Medicago WRKY TFs have broad roles in orchestrating metabolic responses to biotic stress, and that they also represent potentially valuable reagents for engineering metabolic changes that impact pathogen resistance. PMID:19102779

Preliminary global paleogeographic maps through the Greenhouse-Icehouse transition: forcing of the Drake Passage and Asian Monsoons.

NASA Astrophysics Data System (ADS)

Poblete, Fernando; Dupont-Nivet, Guillaume; Licht, Alexis; van Hinsbergen, Douwe; Roperch, Pierrick; Guillocheau, Francois; Baby, Guillaume; Baatsen, Michiel

2017-04-01

Paleogeographic maps are essential for understanding Earth dynamics. They provide the necessary boundary conditions for climate and geodynamic modeling, surface processes and biotic interactions. In particular, the opening and closing of ocean gateways and the growth of major mountain belts are major drivers of climate changes and biotic interchange. However, the timing and spatial extent of such events are highly controversial and regularly questioned by new data. As part of the ERC "MAGIC" project focusing on Asian Monsoons during the Icehouse to Greenhouse transition we thus produced a set of worldwide Cenozoic paleogeographic maps in the period time between 60 to 20 Ma, with a set of boundary conditions specific to the India-Asia collision zone and the Drake Passage. The creation of a paleogeographic map followed a rigorous and reproductively methodology that integrates paleobathymetric, paleoshoreline and paleotopographic data into a coherent plate tectonic model using the open source software GPlates. (1) We use the model provided by Seton et al. (2012) as a first order tectonic model modified to integrate the full restoration of five regions: the Andes, the Scotia Arc, Africa, The Mediterranean Sea and the Tibet-Himalayan collision zone. (2) The paleobathymetry was provided by Müller et al. (2008) using age-depth relationships and assuming symmetric ridge spreading. (3) Paleoshoreline maps were modified according to the fossil database from fossilworks.org and the geological record and were used to represent the boundary between terrestrial and marine paleo-environments. (4) To reconstruct paleoelevations, the most controversial task, we compiled a wide range of data including stable isotope, leaf physiognomy, and thermochronology combined with regional fossil and geological records (tectonic setting) and geomorphological data. Finally, we use the open source GMT software and a set of masks to modify the current Earth relief model (ETOPO) according to the estimated paleoelevation for specific region at each period of time. Our approach specifically takes into account the evolution of continental margins. Paleotopographic evolution is coupled with the evolving shape of continents. Considering the constant addition of new data and models, the value of this method is to generate a progressive paleorelief model of the Earth that can be easily compared and updated with new data.

A Mediterranean free-floating peat mire hosts microbial communities shared by cold latitude habitats

NASA Astrophysics Data System (ADS)

Concheri, Giuseppe; Stevanato, Piergiorgio; Zaccone, Claudio; Shotyk, William; D'Orazio, Valeria; Miano, Teodoro; Lobianco, Daniela; Piffanelli, Pietro; Rizzi, Valeria; Ferrandi, Chiara; Squartini, Andrea

2017-04-01

The microbiological features of a peculiar and hitherto unexplored environment, i.e., a 4m-deep, free-floating peat island located within the Posta Fibreno lake (central Italy), were analyzed via DNA-based techniques. Methods included RealTime PCR targeting for nitrogen (N) cycle genes (nitrification from eubacteria and archaea, denitrification, N fixation), and Next Generation Sequencing (NGS) using an Illumina platform of prokaryotic (16S) and eukaryotic (ITS) amplicons to assess community members identity and abundance. Two depths were sampled at ca. 40 and 280 cm from the surface, the former corresponding to a portion of Sphagnum residues accumulated less than 30 yrs ago above the water level, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520-1660 AD. Bacterial gene abundances for the N cycle were consistently higher in the deeper sample. Sequencing analyses allowed identifying for the surface sample 1738 prokaryotic and 310 eukaryotic Operational Taxonomic Units (OTUs), while, for the deeper sample, the corresponding values were 2026 and 291 respectively. There was a very limited taxa overlap between the two layers' communities in which dominant taxa featured two different sulphate-reducing Deltaproteobacteria for prokaryotes. For eukaryotes, the surface sample was dominated by the Neobulgaria (Ascomycota) genus, while in the deeper one three quarters of the ITS reads were featured by a taxon observed in Antarctic lakes. The functional guilds represented pertain mostly to species involved in slow organic matter degradation and contexts in which dissolved organic carbon contains one-atom compounds, supportive of methylotrophy and methanogenesis. The identity of taxa partitioning between the acidic surface layer and the neutral core is very reminiscent of the differences reported between bogs and fens peatland types respectively, supporting the view of Posta Fibreno as a hybrid between the two main models. A remarkable feature is the coincidence of most taxa observed with database subjects isolated from mires and lakes in boreal/polar environments in spite of the fact that Posta Fibreno is located in sub-Mediterranean climate conditions. This instance suggests a common ecological feature linking peat-forming mires and habitats alike, in which the process factor would rule in determining the biotic composition in spite of the macroclimatic and geographical variables. The principle offers interpretive clues for a deeper understanding of a number of other biotic-environmental interplay contexts.

Hierarchical patterns of symbiotic orchid germination linked to adult proximity and environmental gradients

Treesearch

Jeffrey M. Diez

2007-01-01

The recruitment stage can be critical in determining plant population dynamics, as juveniles encounter a range of abiotic and biotic stressors in the environments where they land after dispersal, and often experience high mortality rates. Although both abiotic and biotic constraints on recruitment are often assumed to operate at multiple scales, these relationships are...

Evaluation of habitat suitability index models for assessing biotic resources

Treesearch

John C. Rennie; Joseph D. Clark; James M. Sweeney

2000-01-01

Existing habitat suitability index (HSI) models are evaluated for assessing the biotic resources on Champion International Corporation (CIC) lands with data from a standard and an expanded timber inventory. Forty HSI models for 34 species that occur in the Southern Appalachians have been identified from the literature. All of the variables for 14 models are provided (...

Pathways and mechanisms for removal of dissolved organic carbon from leaf leachate in streams

Treesearch

Clifford N. Dahm

1981-01-01

Removal of dissolved organic carbon (DOC) from water resulting from adsorption and microbial uptake was examined to determine the importance of biotic and abiotic pathways. Physical–chemical adsorption to components of the stream sediment or water and biotic assimilation associated with the microbial population was determined in recirculating chambers utilizing...

Analysis of the U.S. forest tolerance patterns depending on current and future temperature and precipitation

Treesearch

Jean Lienard; John Harrison; Nikolay Strigul

2015-01-01

Forested ecosystems are shaped by climate, soil and biotic interactions, resulting in constrained spatial distribution of species and biomes. Tolerance traits of species determine their fundamental ecological niche, while biotic interactions narrow tree distributions to the realized niche. In particular, shade, drought and waterlogging tolerances have been well-...

Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress

USDA-ARS?s Scientific Manuscript database

Here we argue for a research initiative on gene-for-gene (g-f-g) interactions between wheat and its parasites. One aim is to begin a conversation between the disparate communities of plant pathology and entomology. Another is to understand how responses to biotic stress are integrated in an import...

Environmental and biotic controls over aboveground biomass throughout a tropical rainforest

Treesearch

G.P. Asner; R.F. Hughes; T.A. Varga; D.E. Knapp; T. Kennedy-Bowdoin

2009-01-01

The environmental and biotic factors affecting spatial variation in canopy three-dimensional (3-D) structure and aboveground tree biomass (AGB) are poorly understood in tropical rain forests. We combined field measurements and airborne light detection and ranging (lidar) to quantify 3-D structure and AGB across a 5,016 ha rain forest reserve on the...

Biotic resistance: Exclusion of native rodent consumers releases populations of a weak invader

Treesearch

Dean E. Pearson; Teal Potter; John L. Maron

2012-01-01

Biotic resistance is a commonly invoked hypothesis to explain why most exotic plant species naturalize at low abundance. Although numerous studies have documented negative impacts of native consumers on exotic plant performance, longer-term multi-generation studies are needed to understand how native consumer damage to exotics translates to their population-level...

Climate, trees, pests, and weeds: Change, uncertainty, and biotic stressors in eastern US national park forests

Treesearch

Nicholas A. Fisichelli; Scott R. Abella; Matthew Peters; Frank J. Krist

2014-01-01

The US National Park Service (NPS) manages over 8900 km2 of forest area in the eastern United States where climate change and nonnative species are altering forest structure, composition, and processes. Understanding potential forest change in response to climate, differences in habitat projections among models (uncertainty), and nonnative biotic...

DEVELOPMENT OF A FISH INDEX OF BIOTIC INTEGRITY TO ASSESS THE CONDITION OF WEST VIRGINIA STREAMS: TECHNICAL SUPPORT DOCUMENT

EPA Science Inventory

This report documents the development of a fish index of biotic integrity (IBI) for wadeable streams in West Virginia and to determine the applicability of the IBI in streams with different thermal regimes. The IBI will be developed using fish data collected at EMAP sites from 1...

Conceptual assessment framework for forested wetland restoration: the Pen Branch experience

Treesearch

Randy K. Kolka; E. A. Nelson; C. C. Trettin

2000-01-01

Development of an assessment framework and associated indicators that can be used to evaluate the effectiveness of a wetland restoration is critical to demonstrating the sustainability of restored sites. Current wetland restoration assessment techniques such as the index of biotic integrity (IBI) or the hydrogeomorphic method (HGM) generally focus on either the biotic...

Changes in free amino acids and polyamine levels in Satsuma leaves in response to Asian citrus psyllid infestation and water stress

USDA-ARS?s Scientific Manuscript database

The effects of biotic and abiotic stresses on changes in amino acids and polyamine levels in Satsuma orange (Citrus unshiu; cultivar Owari) leaves were investigated. Asian citrus psyllids (Diaphorina citri (Kuwayama) (ACP) infestation was used to induce biotic stress while a water deficit was impos...

Utilizing genetic diversity in the desert watermelon citrullus colocynthis for enhancing watermelon cultivars for resistance to biotic and abiotic stress

USDA-ARS?s Scientific Manuscript database

Wide genetic diversity exists among the desert watermelon Citrullus colocynthis (L.) Schrad. (CC) accessions collected in the deserts of northern Africa, the Middle East, and Asia. Because of their resistance to biotic and abiotic stresses, there can be a viable source of genes used for enhancing wa...

Wetland habitat disturbance best predicts metrics of an amphibian index of biotic integrity

USGS Publications Warehouse

Stapanian, Martin A.; Micacchion, Mick; Adams, Jean V.

2015-01-01

Regression and classification trees were used to identify the best predictors of the five component metrics of the Ohio Amphibian Index of Biotic Integrity (AmphIBI) in 54 wetlands in Ohio, USA. Of the 17 wetland- and surrounding landscape-scale variables considered, the best predictor for all AmphIBI metrics was habitat alteration and development within the wetland. The results were qualitatively similar to the best predictors for a wetland vegetation index of biotic integrity, suggesting that similar management practices (e.g., reducing or eliminating nutrient enrichment from agriculture, mowing, grazing, logging, and removing down woody debris) within the boundaries of the wetland can be applied to effectively increase the quality of wetland vegetation and amphibian communities.

A new sediment core from the early Aptian OAE1a: the Cau section (Prebetic Zone, Spain)

NASA Astrophysics Data System (ADS)

Alejandro Ruiz-Ortiz, Pedro; Castro, José Manuel; de Gea, Ginés A.; Jarvis, Ian; Loeser, Hannes; Molina, José Miguel; Nieto, Luis Miguel; Pancost, Richard; Quijano, María Luisa; Reolid, Matías; Skelton, Peter; Weissert, Helmut

2016-04-01

The occurrence of time intervals of enhanced deposition of organic matter (OM) during the Cretaceous, defined as Oceanic Anoxic Events (OAE), reflect abrupt changes in global carbon cycling. The exemplary Aptian OAE1a (120 Ma), is recorded in all the main ocean basins and associated with massive burial of OM in marine sediments [1]. OAE1a is concomitant with the 'nannoconid crisis', which represents a major biotic turnover [2], and also with widespread demise of carbonate platforms [1]. Much research has been done on the OAE1a from different sections in the world over the last decades, since the definition of the C-isotope stratigraphy of the event [3]. Notwithstanding, high-resolution studies across the entire event will be crucial to elucidate the precise timing and rates of the different environmental and biotic changes involved. In order to perform high-resolution studies, drill-cores can represent the best option. Previous cores with successful scientific results has been performed in two reference sections, the Cismon Apti-core [4], and more recently in La Bédoule [5]. Here we present a new drill-core from southern Spain, the Cau section core, drilled in the last quarter of 2015. The Cau section is located in the easternmost part of the Prebetic Zone (Betic Cordillera), which represents the platform deposits of the Southern Iberian Palaeomargin. The lower Aptian of the Cau section is represented by an hemipelagic unit (Almadich Formation, ca. 200 m thick), deposited in a highly subsiding sector of a tilted block, located in the distal parts of the Prebetic Platform. Previous studies of the early Aptian of the Cau section have focused on the stratigraphy, bioevents, C-isotope stratigraphy, and organic and elemental geochemistry [6], [7], among others. A recent study on the Cau section based on biomarkers has presented a detailed record of the PCO2, [8]. All these studies reveal that the Cau section represents an excellent site to investigate the OAE1a, based on its exceptional thickness and stratigraphic continuity, the quality and preservation of fossils and the geochemical signatures. Acknowledgements: This work is a contribution of the research project CGL2014-55274-P (Gov. of Spain). [1] Föllmi (2012). Cret. Res. 35, 230-257. [2] Erba et al. (2010). Science. 329, 428-432. [3] Menegatti et al. (1998). Paleoceanography 13, 530-545. [4] Erba et al. (1999). Jour. For. Res. 29, 371-391. [5] Lorenzen et al. (2013). Cret. Res. 39, 6-16. [6] Gea et al. (2003) Palaeo3. 200, 207-219. [7] Quijano et al. (2012). Palaeo3. 365-366, 276-293. [8] Naafs et al. (2016). Nat. Geosc. DOI: 10.1038/NGEO2627.

Contamination of estuarine water, biota, and sediment by halogenated organic compounds: A field study

USGS Publications Warehouse

Pereira, W.E.; Rostad, C.E.; Chiou, C.T.; Brinton, T.I.; Barber, L.B.; Demcheck, D.K.; Demas, C.R.

1988-01-01

Studies conducted in the vicinity of an industrial outfall in the Calcasieu River estuary, Louisiana, have shown that water, bottom and suspended sediment, and four different species of biota are contaminated with halogenated organic compounds (HOC) including haloarenes. A "salting-out" effect in the estuary moderately enhanced the partitioning tendency of the contaminants into biota and sediments. Contaminant concentrations in water, suspended sediments, and biota were found to be far below the values predicted on the basis of the assumption of phase equilibria with respect to concentrations in bottom sediment. Relative concentration factors of HOC between biota (catfish) and bottom sediment increased with increasing octanol/estuarine water partition coefficients (Kow*), maximizing at log Kow* of about 5, although these ratios were considerably less than equilibrium values. In contrast, contaminant concentrations in water, biota, and suspended sediments were much closer to equilibrium values. Bioconcentration factors of HOC determined on the basis of lipid content for four different biotic species correlated reasonably well with equilibrium triolein/water partition coefficients (Ktw).

The Legacy of Invasive Species on Ecosystem Carbon Dynamics in a Restored Tallgrass Prairie

NASA Astrophysics Data System (ADS)

Matamala, R.; Graham, S.; Cook, D.; Gonzalez-Meler, M.

2008-12-01

Restoration of degraded grassland and prairie ecosystems represents a target sink for offsetting rising atmospheric CO2 levels by increasing carbon sequestration in C-depleted soils, as two-thirds of the biomass is allocated belowground. When considering controls on ecosystem C cycling, biodiversity-led productivity has the potential to be a strong biotic influence. However, invasive species can disrupt ecosystem processes by exhibiting functional characteristics which are distinct from their native counterparts. Invasibility has been linked to disturbance history, which might lead to additional vulnerability of managed lands. The restoration of tallgrass prairie at Fermilab, Batavia, IL, is a known C sink, accruing soil organic matter at rates 43 g C m-2 y-1 during the past 20 years. This rate integrates environmental, climatic and vegetation variations that occurred over this period. Typically, the tallgrass prairie is dominated by warm season grasses and forbs with sporadic but recurrent years when invasive species increase productivity. We measured net ecosystem exchange, net ecosystem production (NEP) and soil C at a 19- year-old restored tallgrass prairie in a four year study where plant species dominance varied. In the first year, the prairie restoration was a strong C sink with a NEP 438 g C m-2 despite a pronounced spring drought. During the second year, dominance of the invasive biannual Melilotus alba L., led to a shorter growing season that resulted on a 47% reduction in NEP from the previous year. NEP did not recover in the third year, even when M. alba was present but not dominant and a number of prairie species re-emerged, showing the legacy of the previous year disturbance. At this time soil C for all years and a fourth NEP year is being analyzed. These data suggest that biotic factors can exert large memory effects on NEP and possibly influence the sink capacity of restored ecosystems. Management strategies should aim to control biotic limitations to NEP in order to maximize long term C sequestration of restorations.

The Shorezone Functionality Index applied to Central Europe lakes.

NASA Astrophysics Data System (ADS)

Zennaro, Barbara; Siligardi, Maurizio

2013-04-01

While most of earlier indices were characterized by a particular analysis, for example to the water itself (chemical analyses) or the biotic environment (biotic extended index), the Lake Shorezone Functionality Index (SFI) looks at the overall status of the lacustrine environment, extending out from the lake itself to also include the surrounding territory and watershed topography. Biotic and abiotic parameters are collected in the field with an ecological point of view to evaluate the buffering capacity of riparian vegetation, the complexity and artificiality of the shoreline, the anthropogenic use of the surrounding territory, and the way the inputs from the watershed enter the lake. Each shore stretch with similar parameters is evaluated in the field with a different form. The parameters collected are then run into a dedicated software (SFINX02) that will assigned a functionality level ranging from excellent to bad (divided into 5 categories as suggested from the WFD 2000/60/CE). The same software can also be used to model different scenarios, offering therefore a toll to foresee the impacts that public or private work may have on the lake, or to plan tailored restoration actions. The data transferred into a GIS environment is used to carry out further spatial analysis and to easily display the results in maps. The SFI reports, thematic maps and brochures give specific indications on what actions are needed to improve the functionality of the lake and to avoid stress to the lake. Therefore this index can be used to plan, monitor and evaluate restoration efforts. The SFI index is easily surveyed, speedily and economically, and it evaluates the state of the environment, assists in the identification of the causes of deterioration and represents a powerful tool that can be used for sustainable planning and management. To date, the Shorezone Functionality Index (created in 2009) has been used within the Eulakes and Silmas European projects in Italy (Lake Garda, Idro, Levico, Caldonazzo), Austria (Lake Neusiedl, Wothersee and MillstatterSee), Slovenia (Lake Bohinj), Poland (Lake Charzykowskie) and Hungary (Lake Balaton), and in Chile on lakes of the Araucania region (Lake Villarica, Boho).

The Earth Microbiome Project and Global Systems Biology

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

Gilbert, Jack A.; Jansson, Janet K.; Knight, Rob

Recently, we published the first large-scale analysis of data from the Earth Microbiome Project (1, 2), a truly multidisciplinary research program involving more than 500 scientists and 27,751 samples acquired from 43 countries. These samples represent myriad specimen types and span a wide range of biotic and abiotic factors, geographic locations, and physicochemical properties. The database (https://qiita.ucsd.edu/emp/) is still growing, with over 90,000 amplicon datasets, >500 metagenomic runs, and metabolomics datasets from a similar number of samples. Importantly, the techniques, data and analytical tools are all standardized and publicly accessible, providing a framework to support research at a scale ofmore » integration that just 7 years ago seemed impossible.« less

Induction of phenolic compounds in Hypericum perforatum L. cells by Colletotrichum gloeosporioides elicitation.

PubMed

Conceição, Luis F R; Ferreres, Federico; Tavares, Rui M; Dias, Alberto C P

2006-01-01

Changes in phenolic metabolism after elicitation with Colletotrichum gloeosporioides (CG) has been studied in Hypericum perforatum L. (HP) cell suspension cultures. Soluble phenolics were analysed by HPLC-DAD and HPLC-DAD-MS/MS. HP cultures elicited with the CG elicitor showed a significant increase in xanthone accumulation. Xanthone accumulation increased twelve fold when the cells were primed with methyl-jasmonate (MeJ) or salicylic acid (SA), before elicitation. HP cultures exposed only to MeJ produced a set of flavonoids, the flavones which represent a substantial part (approx. 40%) of the total flavonoids accumulated in these cells. The possible importance of xanthones as a component of defence mechanism of HP against biotic stress is discussed.

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

NASA Astrophysics Data System (ADS)

Nowak, Martin E.; Schwab, Valérie F.; Lazar, Cassandre S.; Behrendt, Thomas; Kohlhepp, Bernd; Totsche, Kai Uwe; Küsel, Kirsten; Trumbore, Susan E.

2017-08-01

Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria) and biotic factors influence the δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in the δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes in 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water-rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13C and 14C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface-derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface-derived carbon sources.

Mismatch in microbial food webs: predators but not prey perform better in their local biotic and abiotic conditions.

PubMed

Parain, Elodie C; Gravel, Dominique; Rohr, Rudolf P; Bersier, Louis-Félix; Gray, Sarah M

2016-07-01

Understanding how trophic levels respond to changes in abiotic and biotic conditions is key for predicting how food webs will react to environmental perturbations. Different trophic levels may respond disproportionately to change, with lower levels more likely to react faster, as they typically consist of smaller-bodied species with higher reproductive rates. This response could cause a mismatch between trophic levels, in which predators and prey will respond differently to changing abiotic or biotic conditions. This mismatch between trophic levels could result in altered top-down and bottom-up control and changes in interaction strength. To determine the possibility of a mismatch, we conducted a reciprocal-transplant experiment involving Sarracenia purpurea food webs consisting of bacterial communities as prey and a subset of six morphologically similar protozoans as predators. We used a factorial design with four temperatures, four bacteria and protozoan biogeographic origins, replicated four times. This design allowed us to determine how predator and prey dynamics were altered by abiotic (temperature) conditions and biotic (predators paired with prey from either their local or non-local biogeographic origin) conditions. We found that prey reached higher densities in warmer temperature regardless of their temperature of origin. Conversely, predators achieved higher densities in the temperature condition and with the prey from their origin. These results confirm that predators perform better in abiotic and biotic conditions of their origin while their prey do not. This mismatch between trophic levels may be especially significant under climate change, potentially disrupting ecosystem functioning by disproportionately affecting top-down and bottom-up control.

Effect of biotic and abiotic factors on inter- and intra-event variability in stemflow rates in oak and pine stands in a Mediterranean mountain area

NASA Astrophysics Data System (ADS)

Cayuela, C.; Llorens, P.; Sánchez-Costa, E.; Levia, D. F.; Latron, J.

2018-05-01

Stemflow, despite being a small proportion of gross rainfall, is an important and understudied flux of water in forested areas. Recent studies have highlighted its complexity and relative importance for understanding soil and groundwater recharge. Stemflow dynamics offer an insight into how rain water is stored and released from the stems of trees to the soil. Past attempts have been made to understand the variability of stemflow under different types of vegetation, but rather few studies have focused on the combined influence of biotic and abiotic factors on inter and intra-storm stemflow variability, and none in Mediterranean climates. This study presents stemflow data collected at high temporal resolution for two species with contrasting canopies and bark characteristics: Quercus pubescens Willd. (downy oak) and Pinus sylvestris L. (Scots pine) in the Vallcebre research catchments (NE of Spain, 42° 12‧N, 1° 49‧E). The main objective was to understand how the interaction of biotic and abiotic factors affected stemflow dynamics. Mean stemflow production was low for both species (∼1% of incident rainfall) and increased with rainfall amount. However, the magnitude of the response depended on the combination of multiple biotic and abiotic factors. Both species produced similar stemflow volumes and the largest differences were found among trees of the same species. The combined analysis of biotic and abiotic factors showed that funneling ratios and stemflow dynamics were highly influenced by the interaction of rainfall intensity and tree size.

Comparative transcriptome analysis of pepper (Capsicum annuum) revealed common regulons in multiple stress conditions and hormone treatments.

PubMed

Lee, Sanghyeob; Choi, Doil

2013-09-01

Global transcriptome analysis revealed common regulons for biotic/abiotic stresses, and some of these regulons encoding signaling components in both stresses were newly identified in this study. In this study, we aimed to identify plant responses to multiple stress conditions and discover the common regulons activated under a variety of stress conditions. Global transcriptome analysis revealed that salicylic acid (SA) may affect the activation of abiotic stress-responsive genes in pepper. Our data indicate that methyl jasmonate (MeJA) and ethylene (ET)-responsive genes were primarily activated by biotic stress, while abscisic acid (ABA)-responsive genes were activated under both types of stresses. We also identified differentially expressed gene (DEG) responses to specific stress conditions. Biotic stress induces more DEGs than those induced by abiotic and hormone applications. The clustering analysis using DEGs indicates that there are common regulons for biotic or abiotic stress conditions. Although SA and MeJA have an antagonistic effect on gene expression levels, SA and MeJA show a largely common regulation as compared to the regulation at the DEG expression level induced by other hormones. We also monitored the expression profiles of DEG encoding signaling components. Twenty-two percent of these were commonly expressed in both stress conditions. The importance of this study is that several genes commonly regulated by both stress conditions may have future applications for creating broadly stress-tolerant pepper plants. This study revealed that there are complex regulons in pepper plant to both biotic and abiotic stress conditions.

Habitat selection, facilitation, and biotic settlement cues affect distribution and performance of coral recruits in French Polynesia.

PubMed

Price, Nichole

2010-07-01

Habitat selection can determine the distribution and performance of individuals if the precision with which sites are chosen corresponds with exposure to risks or resources. Contrastingly, facilitation can allow persistence of individuals arriving by chance and potentially maladapted to local abiotic conditions. For marine organisms, selection of a permanent attachment site at the end of their larval stage or the presence of a facilitator can be a critical determinant of recruitment success. In coral reef ecosystems, it is well known that settling planula larvae of reef-building corals use coarse environmental cues (i.e., light) for habitat selection. Although laboratory studies suggest that larvae can also use precise biotic cues produced by crustose coralline algae (CCA) to select attachment sites, the ecological consequences of biotic cues for corals are poorly understood in situ. In a field experiment exploring the relative importance of biotic cues and variability in habitat quality to recruitment of hard corals, pocilloporid and acroporid corals recruited more frequently to one species of CCA, Titanoderma prototypum, and significantly less so to other species of CCA; these results are consistent with laboratory assays from other studies. The provision of the biotic cue accurately predicted coral recruitment rates across habitats of varying quality. At the scale of CCA, corals attached to the "preferred" CCA experienced increased survivorship while recruits attached elsewhere had lower colony growth and survivorship. For reef-building corals, the behavioral selection of habitat using chemical cues both reduces the risk of incidental mortality and indicates the presence of a facilitator.

Developing a Phytoplankton Biotic Index as an Indicator of Freshwater Inflow within a Subtropical Estuary

NASA Astrophysics Data System (ADS)

Steichen, J. L.; Quigg, A.; Lucchese, A.; Preischel, H.

2016-02-01

Freshwater inflows drive the water and sediment quality in coastal bays and estuaries influencing the ecosystem and health of the biological community. Phytoplankton accessory pigments (used as a proxy for major taxonomic groups) have been utilized to develop a biotic index of physical, chemical and biotic disturbances in Chesapeake Bay (USA) and other estuarine systems. In this study we have used the Chesapeake Bay - Phytoplankton Index of Biotic Integrity model as a guide in developing an index for Galveston Bay, TX (USA) as an indicator of sufficient freshwater inflow to a subtropical estuary. Multivariate statistical analyses were run using PRIMER-E+PERMANOVA to determine the correlations between phytoplankton accessory pigment concentrations and a suite of abiotic factors associated with freshwater inflow (salinity, DIN, PO4, secchi). Phytoplankton pigment concentrations and water quality parameters were collected across Galveston Bay on a monthly basis from 2008-2013. In the upper region of the bay nearest the river source Dinophyceae, Cryptophyceae (winter (Dec-Feb)) and Chlorophyceae (winter and spring (Mar-May)) were significantly correlated to freshwater inflow and nutrient concentrations PO4 (p<0.05). Increased concentrations of Bacillariophyceae and Cyanophyceae (summer (Jun-Aug)) were significantly correlated to lower concentrations of DIN (p<0.05). Near the mouth of the estuary there was a significant correlation between the increase in Bacillariophyceae, Cyanophyceae, Cryptophyceae and Dinophyceae with decreasing PO4 (p<0.05). Within the dynamic system of Galveston Bay we are working to apply a Phytoplankton Index of Biotic Integrity as a means of monitoring the biological health of this ecologically and economically important estuarine ecosystem.

Spatial variation in abiotic and biotic factors in a floodplain determine anuran body size and growth rate at metamorphosis.

PubMed

Indermaur, Lukas; Schmidt, Benedikt R; Tockner, Klement; Schaub, Michael

2010-07-01

Body size at metamorphosis is a critical trait in the life history of amphibians. Despite the wide-spread use of amphibians as experimental model organisms, there is a limited understanding of how multiple abiotic and biotic factors affect the variation in metamorphic traits under natural conditions. The aim of our study was to quantify the effects of abiotic and biotic factors on spatial variation in the body size of tadpoles and size at metamorphosis of the European common toad (Bufo b. spinosus). Our study population was distributed over the riverbed (active tract) and the fringing riparian forest of a natural floodplain. The riverbed had warm ponds with variable hydroperiod and few predators, whereas the forest had ponds with the opposite characteristics. Spatial variation in body size at metamorphosis was governed by the interactive effects of abiotic and biotic factors. The particular form of the interaction between water temperature and intraspecific tadpole density suggests that abiotic factors laid the foundation for biotic factors: intraspecific density decreased growth only at high temperature. Predation and intraspecific density jointly reduced metamorphic size. Interspecific density had a negligible affect on body size at metamorphosis, suggesting weak inter-anuran interactions in the larval stage. Population density at metamorphosis was about one to two orders of magnitudes higher in the riverbed ponds than in the forest ponds, mainly because of lower tadpole mortality. Based on our results, we conclude that ponds in the riverbed appear to play a pivotal role for the population because tadpole growth and survival is best in this habitat.

Temperature, precipitation and biotic interactions as determinants of tree seedling recruitment across the tree line ecotone.

PubMed

Tingstad, Lise; Olsen, Siri Lie; Klanderud, Kari; Vandvik, Vigdis; Ohlson, Mikael

2015-10-01

Seedling recruitment is a critical life history stage for trees, and successful recruitment is tightly linked to both abiotic factors and biotic interactions. In order to better understand how tree species' distributions may change in response to anticipated climate change, more knowledge of the effects of complex climate and biotic interactions is needed. We conducted a seed-sowing experiment to investigate how temperature, precipitation and biotic interactions impact recruitment of Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) seedlings in southern Norway. Seeds were sown into intact vegetation and experimentally created gaps. To study the combined effects of temperature and precipitation, the experiment was replicated across 12 sites, spanning a natural climate gradient from boreal to alpine and from sub-continental to oceanic. Seedling emergence and survival were assessed 12 and 16 months after sowing, respectively, and above-ground biomass and height were determined at the end of the experiment. Interestingly, very few seedlings were detected in the boreal sites, and the highest number of seedlings emerged and established in the alpine sites, indicating that low temperature did not limit seedling recruitment. Site precipitation had an overall positive effect on seedling recruitment, especially at intermediate precipitation levels. Seedling emergence, establishment and biomass were higher in gap plots compared to intact vegetation at all temperature levels. These results suggest that biotic interactions in the form of competition may be more important than temperature as a limiting factor for tree seedling recruitment in the sub- and low-alpine zone of southern Norway.

Effects of Abiotic and Biotic Stresses on the Internalization and Dissemination of Human Norovirus Surrogates in Growing Romaine Lettuce

PubMed Central

DiCaprio, Erin; Purgianto, Anastasia

2015-01-01

Human norovirus (NoV) is the major causative agent of fresh-produce-related outbreaks of gastroenteritis; however, the ecology and persistence of human NoV in produce systems are poorly understood. In this study, the effects of abiotic and biotic stresses on the internalization and dissemination of two human NoV surrogates (murine norovirus 1 [MNV-1] and Tulane virus [TV]) in romaine lettuce were determined. To induce abiotic stress, romaine lettuce was grown under drought and flood conditions that mimic extreme weather events, followed by inoculation of soil with MNV-1 or TV. Independently, lettuce plants were infected with lettuce mosaic virus (LMV) to induce biotic stress, followed by inoculation with TV. Plants were grown for 14 days, and viral titers in harvested tissues were determined by plaque assays. It was found that drought stress significantly decreased the rates of both MNV-1 and TV internalization and dissemination. In contrast, neither flood stress nor biotic stress significantly impacted viral internalization or dissemination. Additionally, the rates of TV internalization and dissemination in soil-grown lettuce were significantly higher than those for MNV-1. Collectively, these results demonstrated that (i) human NoV surrogates can be internalized via roots and disseminated to shoots and leaves of romaine lettuce grown in soil, (ii) abiotic stress (drought) but not biotic stress (LMV infection) affects the rates of viral internalization and dissemination, and (iii) the type of virus affects the efficiency of internalization and dissemination. This study also highlights the need to develop effective measures to eliminate internalized viruses in fresh produce. PMID:25956773

Assessing the ecological effects of water stress and pollution in a temporary river - Implications for water management.

PubMed

Karaouzas, Ioannis; Smeti, Evangelia; Vourka, Aikaterini; Vardakas, Leonidas; Mentzafou, Aggeliki; Tornés, Elisabet; Sabater, Sergi; Muñoz, Isabel; Skoulikidis, Nikolaos Th; Kalogianni, Eleni

2018-03-15

Temporary rivers are dynamic and complex ecosystems that are widespread in arid and semi-arid regions, such as the Mediterranean. Biotic communities adapted in their intermittent nature could withstand recurrent drought events. However, anthropogenic disturbances in the form of water stress and chemical pollution challenge biota with unpredictable outcomes, especially in view of climate change. In this study we assess the response of the biotic community of a temporary river to environmental stressors, focusing on water stress and pollution. Towards this aim, several metrics of four biotic groups (diatoms, macrophytes, macroinvertebrates and fish) were applied. All biotic groups responded to a pollution gradient mainly driven by land use, distinct functional groups of all biota responded to water stress (a response related to the rheophilic nature of the species and their resistance to shear stress), while the combined effects of water stress and pollution were apparent in fish. Biotic groups presented a differential temporal response to water stress, where diatom temporal assemblage patterns were explained by water stress variables of short-time response (15days), while the responses of the other biota were associated to longer time periods. There were two time periods of fish response, a short (15days) and a long-time response (60-75days). When considering management decisions, our results indicate that, given the known response of river biota to pollution, biomonitoring of temporary rivers should also involve metrics that can be utilized as early warnings of water stress. Copyright © 2017 Elsevier B.V. All rights reserved.

Lethally Hot Temperatures During the Early Triassic Greenhouse

NASA Astrophysics Data System (ADS)

Sun, Yadong; Joachimski, Michael M.; Wignall, Paul B.; Yan, Chunbo; Chen, Yanlong; Jiang, Haishui; Wang, Lina; Lai, Xulong

2012-10-01

Global warming is widely regarded to have played a contributing role in numerous past biotic crises. Here, we show that the end-Permian mass extinction coincided with a rapid temperature rise to exceptionally high values in the Early Triassic that were inimical to life in equatorial latitudes and suppressed ecosystem recovery. This was manifested in the loss of calcareous algae, the near-absence of fish in equatorial Tethys, and the dominance of small taxa of invertebrates during the thermal maxima. High temperatures drove most Early Triassic plants and animals out of equatorial terrestrial ecosystems and probably were a major cause of the end-Smithian crisis.

Proceedings of the California Forest Soils Council Conference on Forest Soils Biology and Forest Management

Treesearch

Robert F. Powers; Donald L. Hauxwell; Gary M. Nakamura

2000-01-01

Biotic properties of forest soil are the linkages connecting forest vegetation with an inert rooting medium to create a dynamic, functioning ecosystem. But despite the significance of these properties, managers have little awareness of the biotic world beneath their feet. Much of our working knowledge of soil biology seems anchored in myth and misunderstanding. To...

Biotic diversity interfaces with urbanization in the Lake Tahoe basin

Treesearch

Patricia N. Manley; Dennis D. Murphy; Lori A. Campbell; Kirsten E. Heckmann; Susan Merideth; Sean A. Parks; Monte P. Sanford; Matthew D. Schlesinger

2006-01-01

In the Lake Tahoe Basin, the retention of native ecosystems within urban areas may greatly enhance the landscape’s ability to maintain biotic diversity. Our study of plant, invertebrate and vertebrate species showed that many native species were present in remnant forest stands in developed areas; however, their richness and abundance declined in association with...

Dissecting the sea wheatgrass genome to transfer biotic stress resistance and abiotic stress tolerance into wheat

USDA-ARS?s Scientific Manuscript database

Wheat production is facing numerous challenges from biotic and abiotic stresses. Alien gene transfer has been an effective approach for wheat germplasm enhancement. Sea wheatgrass (SWG) (Thinopyrum junceiforme, 2n = 4x = 28, genomes J1J1J2J2) is a distant relative of wheat and a relatively untapped ...

Biotic and abiotic factors influencing infestation levels of the arundo leafminer, Lasioptera donacis, in its native range in Mediterranean Europe

USDA-ARS?s Scientific Manuscript database

Lasioptera donacis is a biological control agent of Arundo donax, which is an invasive weed in the riparian habitats of the Rio Grande Basin of Texas and Northern Mexico. Field research was conducted in the native range of L. donacis in Mediterranean Europe to evaluate the biotic and abiotic factor...

Rodent seed predation as a biotic filter influencing exotic plant abundance and distribution

Treesearch

D. E. Pearson; J. L. Hierro; M. Chiuffo; D. Villarreal

2014-01-01

Biotic resistance is commonly invoked to explain why many exotic plants fail to thrive in introduced ranges, but the role of seed predation as an invasion filter is understudied. Abiotic conditions may also influence plant populations and can interact with consumers to determine plant distributions, but how these factors jointly influence invasions is poorly understood...

Past tree influence and prescribed fire mediate biotic interactions and community reassembly in a grassland-restoration experiment

Treesearch

Charles B. Halpern; Joseph A. Antos; Donald McKenzie; Annette M. Olson; Lara Souza

2016-01-01

1. Woody plant encroachment of grasslands is occurring globally, with profound ecological consequences. Attempts to restore herbaceous dominance may fail if the woody state is resilient or if intervention leads to an alternate, undesirable state. Restoration outcomes often hinge on biotic interactions – particularly on priority effects that inhibit or promote community...

Tree invasion of a montane meadow complex: temporal trends, spatial patterns, and biotic interactions

Treesearch

Charles B. Halpern; Joseph A. Antos; Janine M. Rice; Ryan D. Haugo; Nicole L. Lang

2010-01-01

We combined spatial point pattern analysis, population age structures, and a time-series of stem maps to quantify spatial and temporal patterns of conifer invasion over a 200-yr period in three plots totaling 4 ha. In combination, spatial and temporal patterns of establishment suggest an invasion process shaped by biotic interactions, with facilitation promoting...

Effects of biotic disturbances on forest carbon cycling in the United States and Canada

Treesearch

Jeffrey A. Hicke; Craig D. Allen; Ankur R. Desai; Michael C. Dietze; Ronald J. Hall; Edward H. Hogg; Daniel M. Kashian; David Moore; Kenneth F. Raffa; Rona N. Sturrock; James Vogelmann

2011-01-01

Forest insects and pathogens are major disturbance agents that have affected millions of hectares in North America in recent decades, implying significant impacts to the carbon (C) cycle. Here, we review and synthesize published studies of the effects of biotic disturbances on forest C cycling in the United States and Canada. Primary productivity in stands was reduced...

A potential conflict between preserving regional plant diversity and biotic resistance to an invasive grass, Microstegium vimineum

Treesearch

J. Stephen Brewer

2010-01-01

The relevance of diversity-biotic resistance studies to conservation of biodiversity could be improved by simultaneously examining the drivers of regional diversity and their effects on local species diversity and invasion. Using path analysis, I examined direct and indirect effects of various abiotic factors (i.e., flooding, treefall gaps, soil texture, proximity to...

Can plant-natural enemy communication withstand disruption by biotic and abiotic factors?

PubMed

Clavijo McCormick, Andrea

2016-12-01

The attraction of natural enemies towards herbivore-induced plant volatiles is a well-documented phenomenon. However, the majority of published studies are carried under optimal water and nutrient regimes and with just one herbivore. But what happens when additional levels of ecological complexity are added? Does the presence of a second herbivore, microorganisms, and abiotic stress interfere with plant-natural enemy communication? or is communication stable enough to withstand disruption by additional biotic and abiotic factors?Investigating the effects of these additional levels of ecological complexity is key to understanding the stability of tritrophic interactions in natural ecosystems and may aid to forecast the impact of environmental disturbances on these, especially in climate change scenarios, which are often associated with modifications in plant and arthropod species distribution and increased levels of abiotic stress.This review explores the literature on natural enemy attraction to herbivore-induced volatiles when, besides herbivory, plants are challenged by additional biotic and abiotic factors.The aim of this review was to establish the impact of different biotic and abiotic factors on plant-natural enemy communication and to highlight critical aspects to guide future research efforts.

Effect of mining activities in biotic communities of Villa de la Paz, San Luis Potosi, Mexico.

PubMed

Espinosa-Reyes, Guillermo; González-Mille, Donaji J; Ilizaliturri-Hernández, César A; Mejía-Saavedra, Jesús; Cilia-López, V Gabriela; Costilla-Salazar, Rogelio; Díaz-Barriga, Fernando

2014-01-01

Mining is one of the most important industrial activities worldwide. During its different stages numerous impacts are generated to the environment. The activities in the region have generated a great amount of mining residues, which have caused severe pollution and health effects in both human population and biotic components. The aim of this paper was to assess the impact of mining activities on biotic communities within the district of Villa de la Paz. The results showed that the concentrations of As and Pb in soil were higher than the national regulations for urban or agricultural areas. The bioavailability of these metals was certified by the presence of them in the roots of species of plants and in kidneys and livers of wild rodents. In regard to the community analysis, the sites that were located close to the mining district of Villa de la Paz registered a lower biological diversity, in both plants and wild rodents, aside from showing a change in the species composition of plant communities. The results of this study are evidence of the impact of mining on biotic communities, and the need to take into account the wildlife in the assessment of contaminated sites.

Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model.

PubMed

Lany, Nina K; Zarnetske, Phoebe L; Schliep, Erin M; Schaeffer, Robert N; Orians, Colin M; Orwig, David A; Preisser, Evan L

2018-05-01

A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions. © 2018 by the Ecological Society of America.

Effect of Mining Activities in Biotic Communities of Villa de la Paz, San Luis Potosi, Mexico

PubMed Central

Espinosa-Reyes, Guillermo; González-Mille, Donaji J.; Ilizaliturri-Hernández, César A.; Mejía-Saavedra, Jesús; Cilia-López, V. Gabriela; Costilla-Salazar, Rogelio; Díaz-Barriga, Fernando

2014-01-01

Mining is one of the most important industrial activities worldwide. During its different stages numerous impacts are generated to the environment. The activities in the region have generated a great amount of mining residues, which have caused severe pollution and health effects in both human population and biotic components. The aim of this paper was to assess the impact of mining activities on biotic communities within the district of Villa de la Paz. The results showed that the concentrations of As and Pb in soil were higher than the national regulations for urban or agricultural areas. The bioavailability of these metals was certified by the presence of them in the roots of species of plants and in kidneys and livers of wild rodents. In regard to the community analysis, the sites that were located close to the mining district of Villa de la Paz registered a lower biological diversity, in both plants and wild rodents, aside from showing a change in the species composition of plant communities. The results of this study are evidence of the impact of mining on biotic communities, and the need to take into account the wildlife in the assessment of contaminated sites. PMID:24592381

Transcriptional profiling unravels potential metabolic activities of the olive leaf non-glandular trichome

PubMed Central

Koudounas, Konstantinos; Manioudaki, Maria E.; Kourti, Anna; Banilas, Georgios; Hatzopoulos, Polydefkis

2015-01-01

The olive leaf trichomes are multicellular peltate hairs densely distributed mainly at the lower leaf epidermis. Although, non-glandular, they have gained much attention since they significantly contribute to abiotic and biotic stress tolerance of olive leaves. The exact mechanisms by which olive trichomes achieve these goals are not fully understood. They could act as mechanical barrier but they also accumulate high amounts of flavonoids among other secondary metabolites. However, little is currently known about the exact compounds they produce and the respective metabolic pathways. Here we present the first EST analysis from olive leaf trichomes by using 454-pyrosequencing. A total of 5368 unigenes were identified out of 7258 high quality reads with an average length of 262 bp. Blast search revealed that 27.5% of them had high homologies to known proteins. By using Blast2GO, 1079 unigenes (20.1%) were assigned at least one Gene Ontology (GO) term. Most of the genes were involved in cellular and metabolic processes and in binding functions followed by catalytic activity. A total of 521 transcripts were mapped to 67 KEGG pathways. Olive trichomes represent a tissue of highly unique transcriptome as per the genes involved in developmental processes and the secondary metabolism. The results indicate that mature olive trichomes are trancriptionally active, mainly through the potential production of enzymes that contribute to phenolic compounds with important roles in biotic and abiotic stress responses. PMID:26322070

Development and validation of a macroinvertebrate index of biotic integrity (IBI) for assessing urban impacts to Northern California freshwater wetlands.

PubMed

Lunde, Kevin B; Resh, Vincent H

2012-06-01

Despite California policies requiring assessment of ambient wetland condition and compensatory wetland mitigations, no intensive monitoring tools have been developed to evaluate freshwater wetlands within the state. Therefore, we developed standardized, wadeable field methods to sample macroinvertebrate communities and evaluated 40 wetlands across Northern California to develop a macroinvertebrate index of biotic integrity (IBI). A priori reference sites were selected with minimal urban impacts, representing a best-attainable condition. We screened 56 macroinvertebrate metrics for inclusion in the IBI based on responsiveness to percent urbanization. Eight final metrics were selected for inclusion in the IBI: percent three dominant taxa; scraper richness; percent Ephemeroptera, Odonata, and Trichoptera (EOT); EOT richness; percent Tanypodinae/Chironomidae; Oligochaeta richness; percent Coleoptera; and predator richness. The IBI (potential range 0-100) demonstrated significant discriminatory power between the reference (mean = 69) and impacted wetlands (mean = 28). It also declined with increasing percent urbanization (R (2) = 0.53, p < 0.005) among wetlands in an independent validation dataset (n = 14). The IBI was robust in showing no significant bias with environmental gradients. This IBI is a functional tool to determine the ecological condition at urban (stormwater and flood control ponds), as well as rural freshwater wetlands (stockponds, seasonal wetlands, and natural ponds). Biological differences between perennial and non-perennial wetlands suggest that developing separate indicators for these wetland types may improve applicability, although the existing data set was not sufficient for exploring this option.

Ecogeographical Variation in Skull Shape of South-American Canids: Abiotic or Biotic Processes?

PubMed

de Moura Bubadué, Jamile; Cáceres, Nilton; Dos Santos Carvalho, Renan; Meloro, Carlo

Species morphological changes can be mutually influenced by environmental or biotic factors, such as competition. South American canids represent a quite recent radiation of taxa that evolved forms very disparate in phenotype, ecology and behaviour. Today, in the central part of South America there is one dominant large species (the maned wolf, Chrysocyon brachyurus ) that directly influence sympatric smaller taxa via interspecific killing. Further south, three species of similar sized foxes ( Lycalopex spp.) share the same habitats. Such unique combination of taxa and geographic distribution makes South American dogs an ideal group to test for the simultaneous impact of climate and competition on phenotypic variation. Using geometric morphometrics, we quantified skull size and shape of 431 specimens belonging to the eight extant South American canid species: Atelocynus microtis , Cerdocyon thous , Ch. brachyurus , Lycalopex culpaeus , L. griseus , L. gymnocercus , L. vetulus and Speothos venaticus . South American canids are significantly different in both skull size and shape. The hypercarnivorous bush dog is mostly distinct in shape from all the other taxa while a degree of overlap in shape-but not size-occurs between species of the genus Lycalopex . Both climate and competition impacts interspecific morphological variation. We identified climatic adaptations as the main driving force of diversification for the South American canids. Competition has a lower degree of impact on their skull morphology although it might have played a role in the past, when canid community was richer in morphotypes.

Evaulation of the Quality of an Aquatic Habitat on the Drietomica River

NASA Astrophysics Data System (ADS)

Stankoci, Ivan; Jariabková, Jana; Macura, Viliam

2014-03-01

The ecological status of a river is influenced by many factors, of which the most important are fauna and flora; in this paper they are defined as a habitat. During the years 2004, 2005, 2006 and 2011, research on the hydroecological quality of a habitat was evaluated in the reference section of the Drietomica River. Drietomica is a typical representative river of the Slovak flysch area and is located in the region of the White Carpathians in the northwestern part of Slovakia. In this article the results of modeling a microhabitat by means of the Instream Flow Incremental Methodology (IFIM) are presented. For the one-dimensional modeling, the River Habitat Simulation System (RHABSIM) was used to analyse the interaction between a water flow, the morphology of a riverbed, and the biological components of the environment. The habitat ´s hydroecological quality was evaluated after detailed ichthyological, topographical and hydro-morphological surveys. The main step was assessing the biotic characteristics of the habitat through the suitability curves for the Brown trout (Salmo trutta m. fario). Suitability curves are a graphic representation of the main biotic and abiotic preferences of a microhabitat's components. The suitability curves were derived for the depth, velocity, fish covers and degree of the shading. For evaluating the quality of the aquatic habitat, 19 fish covers were closely monitored and evaluated. The results of the Weighted Usable Area (WUA = f (Q)) were evaluated from a comprehensive assessment of the referenced reach of the Drietomica River.

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

DOE PAGES

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; ...

2015-06-23

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. In this study, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanismsmore » at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. Lastly, they also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.« less

Microbial- and thiosulfate-mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury

PubMed Central

Vázquez-Rodríguez, Adiari I.; Hansel, Colleen M.; Zhang, Tong; Lamborg, Carl H.; Santelli, Cara M.; Webb, Samuel M.; Brooks, Scott C.

2015-01-01

Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment. PMID:26157421

In silico identification and characterization of the MAPK family members of unicellular model eukaryote Tetrahymena thermophila.

PubMed

Yıldız, Mehmet Taha; Arslanyolu, Muhittin

2014-10-01

The biological function and evolutionary diversity of the mitogen-activated protein kinase (MAPK) family have mostly been studied in fungi, animals and plants, with very limited information from lower eukaryotes. This study aimed to describe the MAPKs of unicellular Tetrahymena thermophila. Eight members of the T. thermophila MAPK (TtMPK) gene family, in addition to previously reported TtMPK1, TtMPK2 and TtMPK3, were identified bioinformatically using a T. thermophila genome database. Phylogenetic analysis assigned the TtMPKs into two major groups, ERK1/2-like (TtMPK1, 2, 3, 5, 6, 7, 8, and 9) as stress-responsive MAPKs for biotic and abiotic stresses, and ERK7/8-like (TtMPK4, 10, and 11) as cell-cycle-associated protein kinases for biotic factors. Semi-quantitative RT-PCR analysis of the TtMPKs showed high mRNA expression at 30°C; however, only TtMPK5 and TtMPK6 showed high expression at 37°C. Osmotic shock by 100mM NaCl only increased the expression of TtMPK2, whereas 20mM NaCl reduced the expression of all MPKs to almost zero. The results suggested that T. thermophila MAPKs are among the closest representatives of the ancestors of the eukaryotic MAPK family. Although no functional characterization of MPKs was performed, this study is the first report of the genome-wide MAPK family in T. thermophila. Copyright © 2014 Elsevier GmbH. All rights reserved.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

The impact of biotic/abiotic interfaces in mineral nutrient cycling: A study of soils of the Santa Cruz chronosequence, California

USGS Publications Warehouse

White, A.F.; Schulz, M.S.; Vivit, D.V.; Bullen, T.D.; Fitzpatrick, J.

2012-01-01

Biotic/abiotic interactions between soil mineral nutrients and annual grassland vegetation are characterized for five soils in a marine terrace chronosequence near Santa Cruz, California. A Mediterranean climate, with wet winters and dry summers, controls the annual cycle of plant growth and litter decomposition, resulting in net above-ground productivities of 280-600gm -2yr -1. The biotic/abiotic (A/B) interface separates seasonally reversible nutrient gradients, reflecting biological cycling in the shallower soils, from downward chemical weathering gradients in the deeper soils. The A/B interface is pedologically defined by argillic clay horizons centered at soil depths of about one meter which intensify with soil age. Below these horizons, elevated solute Na/Ca, Mg/Ca and Sr/Ca ratios reflect plagioclase and smectite weathering along pore water flow paths. Above the A/B interface, lower cation ratios denote temporal variability due to seasonal plant nutrient uptake and litter leaching. Potassium and Ca exhibit no seasonal variability beneath the A/B interface, indicating closed nutrient cycling within the root zone, whereas Mg variability below the A/B interface denotes downward leakage resulting from higher inputs of marine aerosols and lower plant nutrient requirements.The fraction of a mineral nutrient annually cycled through the plants, compared to that lost from pore water discharge, is defined their respective fluxes F j,plants=q j,plants/(q j,plants+q j,discharge) with average values for K and Ca (F K,plants=0.99; F Ca,plants=0.93) much higher than for Mg and Na (F Mg,plants 0.64; F Na,plants=0.28). The discrimination against Rb and Sr by plants is described by fractionation factors (K Sr/Ca=0.86; K Rb/K=0.83) which are used in Rayleigh fractionation-mixing calculations to fit seasonal patterns in solute K and Ca cycling. K Rb/K and K24Mg/22Mg values (derived from isotope data in the literature) fall within fractionation envelopes bounded by inputs from rainfall and mineral weathering. K Sr/Ca and K44Ca/40Ca fractionation factors fall outside these envelopes indicating that Ca nutrient cycling is closed to these external inputs. Small net positive K and Ca fluxes (6-14molm -2yr -1), based on annual mass balances, indicate that the soils are accumulating mineral nutrients, probably as a result of long-term environmental disequilibrium. ?? 2011.

Higher predation risk for insect prey at low latitudes and elevations.

PubMed

Roslin, Tomas; Hardwick, Bess; Novotny, Vojtech; Petry, William K; Andrew, Nigel R; Asmus, Ashley; Barrio, Isabel C; Basset, Yves; Boesing, Andrea Larissa; Bonebrake, Timothy C; Cameron, Erin K; Dáttilo, Wesley; Donoso, David A; Drozd, Pavel; Gray, Claudia L; Hik, David S; Hill, Sarah J; Hopkins, Tapani; Huang, Shuyin; Koane, Bonny; Laird-Hopkins, Benita; Laukkanen, Liisa; Lewis, Owen T; Milne, Sol; Mwesige, Isaiah; Nakamura, Akihiro; Nell, Colleen S; Nichols, Elizabeth; Prokurat, Alena; Sam, Katerina; Schmidt, Niels M; Slade, Alison; Slade, Victor; Suchanková, Alžběta; Teder, Tiit; van Nouhuys, Saskya; Vandvik, Vigdis; Weissflog, Anita; Zhukovich, Vital; Slade, Eleanor M

2017-05-19

Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic trend in attack rates by birds or mammals. These matching gradients at global and regional scales suggest consistent drivers of biotic interaction strength, a finding that needs to be integrated into general theories of herbivory, community organization, and life-history evolution. Copyright © 2017, American Association for the Advancement of Science.

Global warming, elevational range shifts, and lowland biotic attrition in the wet tropics.

PubMed

Colwell, Robert K; Brehm, Gunnar; Cardelús, Catherine L; Gilman, Alex C; Longino, John T

2008-10-10

Many studies suggest that global warming is driving species ranges poleward and toward higher elevations at temperate latitudes, but evidence for range shifts is scarce for the tropics, where the shallow latitudinal temperature gradient makes upslope shifts more likely than poleward shifts. Based on new data for plants and insects on an elevational transect in Costa Rica, we assess the potential for lowland biotic attrition, range-shift gaps, and mountaintop extinctions under projected warming. We conclude that tropical lowland biotas may face a level of net lowland biotic attrition without parallel at higher latitudes (where range shifts may be compensated for by species from lower latitudes) and that a high proportion of tropical species soon faces gaps between current and projected elevational ranges.

Spectroscopic Studies of Pre-Biotic Carbon Chemistry

NASA Technical Reports Server (NTRS)

Blake, Geoffrey A.

2003-01-01

As described in the original proposal and in our progress reports, research in the Blake group supported by the Exobiology program seeks to understand the pre-biotic chemistry of carbon along with that of other first- and second-row elements from the earliest stages of star formation through the development of planetary systems. The major tool used is spectroscopy, and the program has observational, laboratory, and theoretical components. The observational and theoretical programs are concerned primarily with a quantitative assessment of the chemical budgets of the biogenic elements in the circumstellar environment of forming stars and planetary systems, while the laboratory work is focused on the complex species that characterize the pre-biotic chemistry of carbon. We outline below our results over the past year acquired, in part, with Exobiology support.

Variability in winter climate and winter extremes reduces population growth of an alpine butterfly.

PubMed

Roland, Jens; Matter, Stephen F

2013-01-01

We examined the long-term, 15-year pattern of population change in a network of 21 Rocky Mountain populations of Parnassius smintheus butterflies in response to climatic variation. We found that winter values of the broadscale climate variable, the Pacific Decadal Oscillation (PDO) index, were a strong predictor of annual population growth, much more so than were endogenous biotic factors related to population density. The relationship between PDO and population growth was nonlinear. Populations declined in years with extreme winter PDO values, when there were either extremely warm or extremely cold sea surface temperatures in the eastern Pacific relative to that in the western Pacific. Results suggest that more variable winters, and more frequent extremely cold or warm winters, will result in more frequent decline of these populations, a pattern exacerbated by the trend for increasingly variable winters seen over the past century.

Agricultural lands preservation: a sociology of survival

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

White, T.S.

1983-01-01

This is a rural sociological study investigating the viability of agricultural lands use-values and rural communities in the context of the structure of US agriculture. It outlines the theoretical foundation, ideology, and praxis of a sociology of survival. It is undertaken within the framework of environmental sociology, which focuses on the dynamic interpenetration of social and biotic systems. The concepts of carrying capacity, sustained multiple-use yield, and land-use compatibility and their significance are discussed. The phenomenon of phantom carrying capacity is explored, and its ominous portent noted; but the astonishing potential of agricultural lands to produce huge net gains inmore » use values and in real carrying capacity is affirmed. The theory of unlimited resources, substitution, and market-allocation is falsified. Absolute shortages of renewable and nonrenewable resources are documented, and the necessity for population control, conservation, expanded sustained-yield production, and social allocation is established.« less

The influence of biotic and abiotic factors on (137)Cs accumulation in higher fungi after the accident at Chernobyl NPP.

PubMed

Zarubina, N

2016-09-01

Levels of soil contamination with (137)Cs, the belonging of fungi to a certain ecological group, the localization depth of the main part of mycelium in soil are the primary factors influencing the value of (137)Cs specific activity in higher fungi after the accident at Chernobyl NPP. It has been found that the value of (137)Cs specific activity in fungi of one species could vary by more than 10 times during a vegetation period. A correlation between the changes of (137)Cs content in fungi during the vegetation period and the amount of precipitates during various periods preceding the collection of samples has not been determined. An assumption has been proposed stating dependence between peculiarities of mycelium growth during the vegetation period and the changes of (137)Cs specific activity in fungi. Copyright © 2015 Elsevier Ltd. All rights reserved.

Benthic response to water quality and biotic pressures in lower south San Francisco Bay, Alviso Slough, and Coyote Creek

USGS Publications Warehouse

Parchaso, Francis; Thompson, Janet K.; Crauder, Jeff S.; Anduaga, Rosa I.; Pearson, Sarah A.

2015-12-22

Bivalve biomass is elevated in summer and fall relative to the spring and winter except in Artesian Slough, where bivalves did not establish a signifcant presence. Presence of certain species contributes to the prey value of the community to predators. Potamocorbula amurensis is a shallow-burrowing bivalve and hence is easy prey for bottom-feeding predators. In contrast, Macoma petalum is a deposit feeder and can burrow deeper into the substrate than Potamocorbula amurensis, making it harder to be preyed upon. The quantitative importance of such predator-prey relationships on phytoplankton dynamics requires further investigation. There were also more amphipods in the sloughs in March 2014; this group is another potential contributor to the benthic-pelagic biomass balance. There is no observed reason for Artesian Slough to have low bivalve biomass values and high amphipod abundances. 

Principles of Chemical Biology: From Sexy Fatty Acids and EBV probes to Anti-Acid Antibiotic via Post-Biotics and Host-Microbe Metabolic Complementarity.

PubMed

2017-06-22

This month: The role of fatty acids in sex determination; a probe to monitor and inhibit EBNA1 at the same time; a biological role for post-biotics; what happens when you mix microbes, hosts, and drugs; and an antibiotic that cross-protects with acid. Copyright © 2017. Published by Elsevier Ltd.

A summary of the benthic-invertebrate and fish-community data from streams in the Indianapolis metropolitan area, Indiana, 1981-2012

USGS Publications Warehouse

Voelker, David C.; Bunch, Aubrey R.; Dobrowolski, Edward G.; Shoda, Megan E.

2015-01-01

Beginning in 1994, the Ephemeroptera, Plecoptera, and Trichoptera (EPT) Index and Hilsenhoff Biotic Index (HBI) were calculated. Beginning in 1999, the Invertebrate Community Index (ICI) also was calculated from the benthic-invertebrate data. Fish-community data were collected periodically from 1999 to 2012, from which an Index of Biotic Integrity (IBI) was calculated.

Chapter 6: Above Ground Deterioration of Wood and Wood-Based Materials

Treesearch

Grant Kirker; Jerrold Winandy

2014-01-01

Wood as a material has unique properties that make it ideal for above ground exposure in a wide range of structural and non-strucutral applications. However, no material is without limitations. Wood is a bio-polymer which is subject to degradative processes, both abiotic and biotic. This chapter is a general summary of the abiotic and biotic factors that impact service...

Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change [includes Supporting Information

Treesearch

Seth J. Wenger; Daniel J. Isaak; Charlie Luce; Helen M. Neville; Kurt D. Fausch; Jason B. Dunham; Daniel C. Dauwalter; Michael K. Young; Marketa M. Elsner; Bruce E. Rieman; Alan F. Hamlet; Jack E. Williams

2011-01-01

Broad-scale studies of climate change effects on freshwater species have focused mainly on temperature, ignoring critical drivers such as flow regime and biotic interactions. We use downscaled outputs from general circulation models coupled with a hydrologic model to forecast the effects of altered flows and increased temperatures on four interacting species of trout...

SERDP ER-1376 Enhancement of In Situ Bioremediation of Energetic Compounds by Coupled Abiotic/Biotic Processes:Final Report for 2004 - 2006

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

Szecsody, James E.; Comfort, Steve; Fredrickson, Herbert L.

2007-08-07

This project was initiated by SERDP to quantify processes and determine the effectiveness of abiotic/biotic mineralization of energetics (RDX, HMX, TNT) in aquifer sediments by combinations of biostimulation (carbon, trace nutrient additions) and chemical reduction of sediment to create a reducing environment. Initially it was hypothesized that a balance of chemical reduction of sediment and biostimulation would increase the RDX, HMX, and TNT mineralization rate significantly (by a combination of abiotic and biotic processes) so that this abiotic/biotic treatment may be a more efficient for remediation than biotic treatment alone in some cases. Because both abiotic and biotic processes aremore » involved in energetic mineralization in sediments, it was further hypothesized that consideration for both abiotic reduction and microbial growth was need to optimize the sediment system for the most rapid mineralization rate. Results show that there are separate optimal abiotic/biostimulation aquifer sediment treatments for RDX/HMX and for TNT. Optimal sediment treatment for RDX and HMX (which have chemical similarities and similar degradation pathways) is mainly chemical reduction of sediment, which increased the RDX/HMX mineralization rate 100 to150 times (relative to untreated sediment), with additional carbon or trace nutrient addition, which increased the RDX/HMX mineralization rate an additional 3 to 4 times. In contrast, the optimal aquifer sediment treatment for TNT involves mainly biostimulation (glucose addition), which stimulates a TNT/glucose cometabolic degradation pathway (6.8 times more rapid than untreated sediment), degrading TNT to amino-intermediates that irreversibly sorb (i.e., end product is not CO2). The TNT mass migration risk is minimized by these transformation reactions, as the triaminotoluene and 2,4- and 2,6-diaminonitrotoluene products that irreversibly sorb are no longer mobile in the subsurface environment. These transformation rates are increased 13 times further by chemical reduction of sediment. Dithionite reduction alone is not an effective treatment for TNT (intermediates that irreversibly sorb are not produced), even though the TNT degradation rate (to 2- or 4-aminodinitrotoluene) increases.« less

Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms

NASA Astrophysics Data System (ADS)

Druschel, Gregory K.; Emerson, David; Sutka, R.; Suchecki, P.; Luther, George W., III

2008-07-01

Neutrophilic iron oxidizing bacteria (FeOB) must actively compete with rapid abiotic processes governing Fe(II) oxidation and as a result have adapted to primarily inhabit low-O 2 environments where they can more successfully compete with abiotic Fe(II) oxidation. The spatial distribution of these microorganisms can be observed through the chemical gradients they affect, as measured using in situ voltammetric analysis for dissolved Fe(II), Fe(III), O 2, and FeS (aq). Field and laboratory determination of the chemical environments inhabited by the FeOB were coupled with detailed kinetic competition studies for abiotic and biotic oxidation processes using a pure culture of FeOB to quantify the geochemical niche these organisms inhabit. In gradient culture tubes, the maximum oxygen levels, which were associated with growth bands of Sideroxydans lithotrophicus (ES-1, a novel FeOB), were 15-50 μM. Kinetic measurements made on S. lithotrophicus compared biotic/abiotic (killed control) Fe oxidation rates. The biotic rate can be a significant and measurable fraction of the total Fe oxidation rate below O 2 concentrations of approximately 50 μM, but biotic Fe(II) oxidation (via the biotic/abiotic rate comparison) becomes difficult to detect at higher O 2 levels. These results are further supported by observations of conditions supporting FeOB communities in field settings. Variablity in cell densities and cellular activity as well as variations in hydrous ferrous oxide mineral quantities significantly affect the laboratory kinetic rates. The microbial habitat (or geochemical niche) where FeOB are active is thus largely controlled by the competition between abiotic and biotic kinetics, which are dependent on Fe(II) concentration, P O2, temperature and pH in addition to the surface area of hydrous ferric oxide minerals and the cell density/activity of FeOB. Additional field and lab culture observations suggest a potentially important role for the iron-sulfide aqueous molecular cluster, FeS (aq), in the overall cycling of iron associated with the environments these microorganisms inhabit.

Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement.

PubMed

Tandon, Gitanjali; Jaiswal, Sarika; Iquebal, M A; Kumar, Sunil; Kaur, Sukhdeep; Rai, Anil; Kumar, Dinesh

2015-01-01

Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. In angiosperm plants, lipase-like protein phytoalexin deficient 4 (PAD4) is well known to be essential for systemic resistance against biotic stress. PAD4 functions together with its interacting partner protein enhanced disease susceptibility 1 (EDS1) to promote salicylic acid (SA)-dependent and SA-independent defense pathway. Existence and structure of key protein of systemic resistance EDS1 and PAD4 are not known in grapes. Before SA pathway studies are taken in grape, molecular evidence of EDS1: PAD4 complex is to be established. To establish this, EDS1 protein sequence was retrieved from NCBI and homologous PAD4 protein was generated using Arabidopsis thaliana as template and conserved domains were confirmed. In this study, computational methods were used to model EDS1 and PAD4 and simulated the interactions of EDS1 and PAD4. Since no structural details of the proteins were available, homology modeling was employed to construct three-dimensional structures. Further, molecular dynamic simulations were performed to study the dynamic behavior of the EDS1 and PAD4. The modeled proteins were validated and subjected to molecular docking analysis. Molecular evidence of stable complex of EDS1:PAD4 in grape supporting SA defense pathway in response to biotic stress is reported in this study. If SA defense pathway genes are explored, then markers of genes involved can play pivotal role in grape variety development especially against biotic stress leading to higher productivity.

Anthropogenic disturbance homogenizes seagrass fish communities.

PubMed

Iacarella, Josephine C; Adamczyk, Emily; Bowen, Dan; Chalifour, Lia; Eger, Aaron; Heath, William; Helms, Sibylla; Hessing-Lewis, Margot; Hunt, Brian P V; MacInnis, Andrew; O'Connor, Mary I; Robinson, Clifford L K; Yakimishyn, Jennifer; Baum, Julia K

2018-05-01

Anthropogenic activities have led to the biotic homogenization of many ecological communities, yet in coastal systems this phenomenon remains understudied. In particular, activities that locally affect marine habitat-forming foundation species may perturb habitat and promote species with generalist, opportunistic traits, in turn affecting spatial patterns of biodiversity. Here, we quantified fish diversity in seagrass communities across 89 sites spanning 6° latitude along the Pacific coast of Canada, to test the hypothesis that anthropogenic disturbances homogenize (i.e., lower beta-diversity) assemblages within coastal ecosystems. We test for patterns of biotic homogenization at sites within different anthropogenic disturbance categories (low, medium, and high) at two spatial scales (within and across regions) using both abundance- and incidence-based beta-diversity metrics. Our models provide clear evidence that fish communities in high anthropogenic disturbance seagrass areas are homogenized relative to those in low disturbance areas. These results were consistent across within-region comparisons using abundance- and incidence-based measures of beta-diversity, and in across-region comparisons using incidence-based measures. Physical and biotic characteristics of seagrass meadows also influenced fish beta-diversity. Biotic habitat characteristics including seagrass biomass and shoot density were more differentiated among high disturbance sites, potentially indicative of a perturbed environment. Indicator species and trait analyses revealed fishes associated with low disturbance sites had characteristics including stenotopy, lower swimming ability, and egg guarding behavior. Our study is the first to show biotic homogenization of fishes across seagrass meadows within areas of relatively high human impact. These results support the importance of targeting conservation efforts in low anthropogenic disturbance areas across land- and seascapes, as well as managing anthropogenic impacts in high activity areas. © 2018 John Wiley & Sons Ltd.

Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra.

PubMed

Liang, Junyi; Xia, Jiangyang; Shi, Zheng; Jiang, Lifen; Ma, Shuang; Lu, Xingjie; Mauritz, Marguerite; Natali, Susan M; Pegoraro, Elaine; Penton, C Ryan; Plaza, César; Salmon, Verity G; Celis, Gerardo; Cole, James R; Konstantinidis, Konstantinos T; Tiedje, James M; Zhou, Jizhong; Schuur, Edward A G; Luo, Yiqi

2018-05-26

Climate warming can result in both abiotic (e.g., permafrost thaw) and biotic (e.g., microbial functional genes) changes in Arctic tundra. Recent research has incorporated dynamic permafrost thaw in Earth system models (ESMs) and indicates that Arctic tundra could be a significant future carbon (C) source due to the enhanced decomposition of thawed deep soil C. However, warming-induced biotic changes may influence biologically related parameters and the consequent projections in ESMs. How model parameters associated with biotic responses will change under warming and to what extent these changes affect projected C budgets have not been carefully examined. In this study, we synthesized six data sets over five years from a soil warming experiment at the Eight Mile Lake, Alaska, into the Terrestrial ECOsystem (TECO) model with a probabilistic inversion approach. The TECO model used multiple soil layers to track dynamics of thawed soil under different treatments. Our results show that warming increased light use efficiency of vegetation photosynthesis but decreased baseline (i.e., environment-corrected) turnover rates of SOC in both the fast and slow pools in comparison with those under control. Moreover, the parameter changes generally amplified over time, suggesting processes of gradual physiological acclimation and functional gene shifts of both plants and microbes. The TECO model predicted that field warming from 2009 to 2013 resulted in cumulative C losses of 224 or 87 g m -2 , respectively, without or with changes in those parameters. Thus, warming-induced parameter changes reduced predicted soil C loss by 61%. Our study suggests that it is critical to incorporate biotic changes in ESMs to improve the model performance in predicting C dynamics in permafrost regions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Spatial variability of biotic and abiotic tree establishment constraints across a treeline ecotone in the Alaska range.

PubMed

Stueve, Kirk M; Isaacs, Rachel E; Tyrrell, Lucy E; Densmore, Roseann V

2011-02-01

Throughout interior Alaska (U.S.A.), a gradual warming trend in mean monthly temperatures occurred over the last few decades (approximatlely 2-4 degrees C). The accompanying increases in woody vegetation at many alpine treeline (hereafter treeline) locations provided an opportunity to examine how biotic and abiotic local site conditions interact to control tree establishment patterns during warming. We devised a landscape ecological approach to investigate these relationships at an undisturbed treeline in the Alaska Range. We identified treeline changes between 1953 (aerial photography) and 2005 (satellite imagery) in a geographic information system (GIS) and linked them with corresponding local site conditions derived from digital terrain data, ancillary climate data, and distance to 1953 trees. Logistic regressions enabled us to rank the importance of local site conditions in controlling tree establishment. We discovered a spatial transition in the importance of tree establishment controls. The biotic variable (proximity to 1953 trees) was the most important tree establishment predictor below the upper tree limit, providing evidence of response lags with the abiotic setting and suggesting that tree establishment is rarely in equilibrium with the physical environment or responding directly to warming. Elevation and winter sun exposure were important predictors of tree establishment at the upper tree limit, but proximity to trees persisted as an important tertiary predictor, indicating that tree establishment may achieve equilibrium with the physical environment. However, even here, influences from the biotic variable may obscure unequivocal correlations with the abiotic setting (including temperature). Future treeline expansion will likely be patchy and challenging to predict without considering the spatial variability of influences from biotic and abiotic local site conditions.

The Geographic Distribution of a Tropical Montane Bird Is Limited by a Tree: Acorn Woodpeckers (Melanerpes formicivorus) and Colombian Oaks (Quercus humboldtii) in the Northern Andes

PubMed Central

2015-01-01

Species distributions are limited by a complex array of abiotic and biotic factors. In general, abiotic (climatic) factors are thought to explain species’ broad geographic distributions, while biotic factors regulate species’ abundance patterns at local scales. We used species distribution models to test the hypothesis that a biotic interaction with a tree, the Colombian oak (Quercus humboldtii), limits the broad-scale distribution of the Acorn Woodpecker (Melanerpes formicivorus) in the Northern Andes of South America. North American populations of Acorn Woodpeckers consume acorns from Quercus oaks and are limited by the presence of Quercus oaks. However, Acorn Woodpeckers in the Northern Andes seldom consume Colombian oak acorns (though may regularly drink sap from oak trees) and have been observed at sites without Colombian oaks, the sole species of Quercus found in South America. We found that climate-only models overpredicted Acorn Woodpecker distribution, suggesting that suitable abiotic conditions (e.g. in northern Ecuador) exist beyond the woodpecker’s southern range margin. In contrast, models that incorporate Colombian oak presence outperformed climate-only models and more accurately predicted the location of the Acorn Woodpecker’s southern range margin in southern Colombia. These findings support the hypothesis that a biotic interaction with Colombian oaks sets Acorn Woodpecker’s broad-scale geographic limit in South America, probably because Acorn Woodpeckers rely on Colombian oaks as a food resource (possibly for the oak’s sap rather than for acorns). Although empirical examples of particular plants limiting tropical birds’ distributions are scarce, we predict that similar biotic interactions may play an important role in structuring the geographic distributions of many species of tropical montane birds with specialized foraging behavior. PMID:26083262

The WRKY transcription factors in the diploid woodland strawberry Fragaria vesca: Identification and expression analysis under biotic and abiotic stresses.

PubMed

Wei, Wei; Hu, Yang; Han, Yong-Tao; Zhang, Kai; Zhao, Feng-Li; Feng, Jia-Yue

2016-08-01

WRKY proteins comprise a large family of transcription factors that play important roles in response to biotic and abiotic stresses and in plant growth and development. To date, little is known about the WRKY gene family in strawberry. In this study, we identified 62 WRKY genes (FvWRKYs) in the wild diploid woodland strawberry (Fragaria vesca, 2n = 2x = 14) accession Heilongjiang-3. According to the phylogenetic analysis and structural features, these identified strawberry FvWRKY genes were classified into three main groups. In addition, eight FvWRKY-GFP fusion proteins showed distinct subcellular localizations in Arabidopsis mesophyll protoplasts. Furthermore, we examined the expression of the 62 FvWRKY genes in 'Heilongjiang-3' under various conditions, including biotic stress (Podosphaera aphanis), abiotic stresses (drought, salt, cold, and heat), and hormone treatments (abscisic acid, ethephon, methyl jasmonate, and salicylic acid). The expression levels of 33 FvWRKY genes were upregulated, while 12 FvWRKY genes were downregulated during powdery mildew infection. FvWRKY genes responded to drought and salt treatment to a greater extent than to temperature stress. Expression profiles derived from quantitative real-time PCR suggested that 11 FvWRKY genes responded dramatically to various stimuli at the transcriptional level, indicating versatile roles in responses to biotic and abiotic stresses. Interaction networks revealed that the crucial pathways controlled by WRKY proteins may be involved in the differential response to biotic stress. Taken together, the present work may provide the basis for future studies of the genetic modification of WRKY genes for pathogen resistance and stress tolerance in strawberry. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Assessment of derelict soil quality: Abiotic, biotic and functional approaches.

PubMed

Vincent, Quentin; Auclerc, Apolline; Beguiristain, Thierry; Leyval, Corinne

2018-02-01

The intensification and subsequent closing down of industrial activities during the last century has left behind large surfaces of derelict lands. Derelict soils have low fertility, can be contaminated, and many of them remain unused. However, with the increasing demand of soil surfaces, they might be considered as a resource, for example for non-food biomass production. The study of their physico-chemical properties and of their biodiversity and biological activity may provide indications for their potential re-use. The objective of our study was to investigate the quality of six derelict soils, considering abiotic, biotic, and functional parameters. We studied (i) the soil bacteria, fungi, meso- and macro-fauna and plant communities of six different derelict soils (two from coking plants, one from a settling pond, two constructed ones made from different substrates and remediated soil, and an inert waste storage one), and (ii) their decomposition function based on the decomposer trophic network, enzyme activities, mineralization activity, and organic pollutant degradation. Biodiversity levels in these soils were high, but all biotic parameters, except the mycorrhizal colonization level, discriminated them. Multivariate analysis showed that biotic parameters co-varied more with fertility proxies than with soil contamination parameters. Similarly, functional parameters significantly co-varied with abiotic parameters. Among functional parameters, macro-decomposer proportion, enzyme activity, average mineralization capacity, and microbial polycyclic aromatic hydrocarbon degraders were useful to discriminate the soils. We assessed their quality by combining abiotic, biotic, and functional parameters: the compost-amended constructed soil displayed the highest quality, while the settling pond soil and the contaminated constructed soil displayed the lowest. Although differences among the soils were highlighted, this study shows that derelict soils may provide a biodiversity ecosystem service and are functional for decomposition. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatial variability of biotic and abiotic tree establishment constraints across a treeline ecotone in the Alaska Range

USGS Publications Warehouse

Stueve, K.M.; Isaacs, R.E.; Tyrrell, L.E.; Densmore, R.V.

2011-01-01

Throughout interior Alaska (USA), a gradual warming trend in mean monthly temperatures occurred over the last few decades (;2-48C). The accompanying increases in woody vegetation at many alpine treeline (hereafter treeline) locations provided an opportunity to examine how biotic and abiotic local site conditions interact to control tree establishment patterns during warming. We devised a landscape ecological approach to investigate these relationships at an undisturbed treeline in the Alaska Range. We identified treeline changes between 1953 (aerial photography) and 2005 (satellite imagery) in a geographic information system (GIS) and linked them with corresponding local site conditions derived from digital terrain data, ancillary climate data, and distance to 1953 trees. Logistic regressions enabled us to rank the importance of local site conditions in controlling tree establishment. We discovered a spatial transition in the importance of tree establishment controls. The biotic variable (proximity to 1953 trees) was the most important tree establishment predictor below the upper tree limit, providing evidence of response lags with the abiotic setting and suggesting that tree establishment is rarely in equilibrium with the physical environment or responding directly to warming. Elevation and winter sun exposure were important predictors of tree establishment at the upper tree limit, but proximity to trees persisted as an important tertiary predictor, indicating that tree establishment may achieve equilibrium with the physical environment. However, even here, influences from the biotic variable may obscure unequivocal correlations with the abiotic setting (including temperature). Future treeline expansion will likely be patchy and challenging to predict without considering the spatial variability of influences from biotic and abiotic local site conditions. ?? 2011 by the Ecological Society of America.

Geomicrobiological perspective on the pattern and causes of the 5-million-year Permo/Triassic biotic crisis

NASA Astrophysics Data System (ADS)

Xie, Shucheng; Wang, Yongbiao

2011-03-01

The pattern and causes of Permo/Triassic biotic crisis were mainly documented by faunal and terrestrial plant records. We reviewed herein the geomicrobiological perspective on this issue based on the reported cyanobacterial record. Two episodic cyanobacterial blooms were observed to couple with carbon isotope excursions and faunal mass extinction at Meishan section, suggestive of the presence of at least two episodic biotic crises across the Permian-Triassic boundary (PTB). The two episodes of cyanobacterial blooms, carbon isotope excursions and faunal mass extinction were, respectively, identified in several sections of the world, inferring the presence of two global changes across the PTB. Close associations among the three records (cyanobacterial bloom, shift in carbon isotope composition, and faunal extinction) were subsequently observed in three intervals in the Early Triassic, the protracted recovery period as previously thought, inferring the occurrence of more episodes of global changes. Spatiotemporal association of cyanobacterial blooms with volcanic materials in South China, and probably in South-east Asia, infers their causal relationship. Volcanism is believed to trigger the biotic crisis in several ways and to cause the close association among microbial blooms, the carbon isotope excursions and faunal mass extinctions in four intervals from the latest Permian to the Early Triassic. The major episodes of the well-known Siberian flood eruption are proposed to be responsible for the extinctions in the Early Triassic, but their synchronicity with the end-Permian extinction awaits more precise dating data to confirm. Geomicrobial records are thus suggestive of a long-term episodic biotic crisis (at least four episodes) lasting from the latest Permian to the end of the Early Triassic, induced by the global volcanic eruptions and sea level changes during Pangea formation.

Internalization of Escherichia coli O157:H7 gfp+ in rocket and Swiss chard baby leaves as affected by abiotic and biotic damage.

PubMed

Hartmann, R; Fricke, A; Stützel, H; Mansourian, S; Dekker, T; Wohanka, W; Alsanius, B

2017-07-01

Internalization of human pathogens in edible parts of vegetables eaten raw is a major concern, since once internalized they are protected from sanitizing treatments. In this study, we examined the invasion of gfp-labelled Escherichia coli O157:H7 into intact and biotically (infection with Xanthomonas campestris/Pseudomonas syringae) and abiotically (grating with silicon carbide) damaged leaves of wild rocket (Diplotaxis tenuifolia) and Swiss chard (Beta vulgaris subsp. cicla) using laser scanning confocal microscopy. Bacterial cells were found in internal locations of the tissue, irrespective of tissue health status. Contaminated leaf sections of biotically and abiotically damaged wild rocket leaves showed higher susceptibility to microbial invasion, while the pathogen was internalized in greater numbers into intact Swiss chard leaf sections when abiotically, but not biotically, damaged. The greatest differences were observed between the plant species; after surface sanitization, E. coli O157:H7 was still detected in wild rocket leaves, but not in Swiss chard leaves. Contamination of leafy vegetables with Escherichia coli O157:H7 is a growing problem, as reported outbreaks are increasing. However, establishment of this human pathogen in the phyllosphere is not completely understood. Using laser scanning confocal microscopy, we demonstrated that E. coli O157:H7gfp+ can invade plant tissue of Swiss chard and wild rocket leaves and that the bacterium is more sensitive to surface sanitization of Swiss chard leaves. Damage to leaf tissue promoted leaf invasion, but the nature of the damage (abiotic or biotic) and plant species had an impact. © 2017 The Society for Applied Microbiology.

Abiotic versus biotic iron mineral transformation studied by a miniaturized backscattering Mössbauer spectrometer (MIMOS II), X-ray diffraction and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Markovski, C.; Byrne, J. M.; Lalla, E.; Lozano-Gorrín, A. D.; Klingelhöfer, G.; Rull, F.; Kappler, A.; Hoffmann, T.; Schröder, C.

2017-11-01

Searching for biomarkers or signatures of microbial transformations of minerals is a critical aspect for determining how life evolved on Earth, and whether or not life may have existed in other planets, including Mars. In order to solve such questions, several missions to Mars have sought to determine the geochemistry and mineralogy on the Martian surface. This research includes the two miniaturized Mössbauer spectrometers (MIMOS II) on board the Mars Exploration Rovers Spirit and Opportunity, which have detected a variety of iron minerals on Mars, including magnetite (Fe2+Fe3+2O4) and goethite (α-FeO(OH)). On Earth, both minerals can derive from microbiological activity (e.g. through dissimilatory iron reduction of ferrihydrite by Fe(III)-reducing bacteria). Here we used a lab based MIMOS II to characterize the mineral products of biogenic transformations of ferrihydrite to magnetite by the Fe(III)-reducing bacteria Geobacter sulfurreducens. In combination with Raman spectroscopy and X-ray diffraction (XRD), we observed the formation of magnetite, goethite and siderite. We compared the material produced by biogenic transformations to abiotic samples in order to distinguish abiotic and biotic iron minerals by techniques that are or will be available onboard Martian based laboratories. The results showed the possibility to distinguish the abiotic and biotic origin of the minerals. Mossbauer was able to distinguish the biotic/abiotic magnetite with the interpretation of the geological context (Fe content mineral assemblages and accompanying minerals) and the estimation of the particle size in a non-destructive way. The Raman was able to confirm the biotic/abiotic principal peaks of the magnetite, as well as the organic principal vibration bands attributed to the bacteria. Finally, the XRD confirmed the particle size and mineralogy.

Effects of Abiotic and Biotic Stresses on the Internalization and Dissemination of Human Norovirus Surrogates in Growing Romaine Lettuce.

PubMed

DiCaprio, Erin; Purgianto, Anastasia; Li, Jianrong

2015-07-01

Human norovirus (NoV) is the major causative agent of fresh-produce-related outbreaks of gastroenteritis; however, the ecology and persistence of human NoV in produce systems are poorly understood. In this study, the effects of abiotic and biotic stresses on the internalization and dissemination of two human NoV surrogates (murine norovirus 1 [MNV-1] and Tulane virus [TV]) in romaine lettuce were determined. To induce abiotic stress, romaine lettuce was grown under drought and flood conditions that mimic extreme weather events, followed by inoculation of soil with MNV-1 or TV. Independently, lettuce plants were infected with lettuce mosaic virus (LMV) to induce biotic stress, followed by inoculation with TV. Plants were grown for 14 days, and viral titers in harvested tissues were determined by plaque assays. It was found that drought stress significantly decreased the rates of both MNV-1 and TV internalization and dissemination. In contrast, neither flood stress nor biotic stress significantly impacted viral internalization or dissemination. Additionally, the rates of TV internalization and dissemination in soil-grown lettuce were significantly higher than those for MNV-1. Collectively, these results demonstrated that (i) human NoV surrogates can be internalized via roots and disseminated to shoots and leaves of romaine lettuce grown in soil, (ii) abiotic stress (drought) but not biotic stress (LMV infection) affects the rates of viral internalization and dissemination, and (iii) the type of virus affects the efficiency of internalization and dissemination. This study also highlights the need to develop effective measures to eliminate internalized viruses in fresh produce. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Effects of biotic disturbances on forest carbon cycling in the United States and Canada

USGS Publications Warehouse

Vogelmann, James E.; Allen, Craig D.; Hicke, Jeffrey A.; Desai, Ankur R.; Dietze, Michael C.; Hall, Ronald J.; ,

2012-01-01

Forest insects and pathogens are major disturbance agents that have affected millions of hectares in North America in recent decades, implying significant impacts to the carbon (C) cycle. Here, we review and synthesize published studies of the effects of biotic disturbances on forest C cycling in the United States and Canada. Primary productivity in stands was reduced, sometimes considerably, immediately following insect or pathogen attack. After repeated growth reductions caused by some insects or pathogens or a single infestation by some bark beetle species, tree mortality occurred, altering productivity and decomposition. In the years following disturbance, primary productivity in some cases increased rapidly as a result of enhanced growth by surviving vegetation, and in other cases increased slowly because of lower forest regrowth. In the decades following tree mortality, decomposition increased as a result of the large amount of dead organic matter. Net ecosystem productivity decreased immediately following attack, with some studies reporting a switch to a C source to the atmosphere, and increased afterward as the forest regrew and dead organic matter decomposed. Large variability in C cycle responses arose from several factors, including type of insect or pathogen, time since disturbance, number of trees affected, and capacity of remaining vegetation to increase growth rates following outbreak. We identified significant knowledge gaps, including limited understanding of carbon cycle impacts among different biotic disturbance types (particularly pathogens), their impacts at landscape and regional scales, and limited capacity to predict disturbance events and their consequences for carbon cycling. We conclude that biotic disturbances can have major impacts on forest C stocks and fluxes and can be large enough to affect regional C cycling. However, additional research is needed to reduce the uncertainties associated with quantifying biotic disturbance effects on the North American C budget.

The effects of salinity, pH, and dissolved organic matter on acute copper toxicity to the rotifer, Brachionus plicatilis ("L" strain).

PubMed

Arnold, W R; Diamond, R L; Smith, D S

2010-08-01

This paper presents data from original research for use in the development of a marine biotic ligand model and, ultimately, copper criteria for the protection of estuarine and marine organisms and their uses. Ten 48-h static acute (unfed) copper toxicity tests using the euryhaline rotifer Brachionus plicatilis ("L" strain) were performed to assess the effects of salinity, pH, and dissolved organic matter (measured as dissolved organic carbon; DOC) on median lethal dissolved copper concentrations (LC50). Reconstituted and natural saltwater samples were tested at seven salinities (6, 11, 13, 15, 20, 24, and 29 g/L), over a pH range of 6.8-8.6 and a range of dissolved organic carbon of <0.5-4.1 mg C/L. Water chemistry analyses (alkalinity, calcium, chloride, DOC, hardness, magnesium, potassium, sodium, salinity, and temperature) are presented for input parameters to the biotic ligand model. In stepwise multiple regression analysis of experimental results where salinity, pH, and DOC concentrations varied, copper toxicity was significantly related only to the dissolved organic matter content (pH and salinity not statistically retained; alpha=0.05). The relationship of the 48-h dissolved copper LC50 values and dissolved organic carbon concentrations was LC50 (microg Cu/L)=27.1xDOC (mg C/L)1.25; r2=0.94.

Effects of biotic and abiotic factors on the oxygen content of green sea turtle nests during embryogenesis.

PubMed

Chen, Chiu-Lin; Wang, Chun-Chun; Cheng, I-Jiunn

2010-10-01

Several biotic and abiotic factors can influence nest oxygen content during embryogenesis. Several of these factors were determined during each developmental stage of green sea turtle embryos on Wan-an Island, Penghu Archipelago, Taiwan. We examined oxygen content in 7 nests in 2007 and 11 in 2008. Oxygen in the adjacent sand, total and viable clutch sizes, air, sand and nest temperatures, and sand characters of each nest were also determined. Oxygen content was lower in late stages than in the early and middle stages. It was also lower in the middle layer than in the upper and bottom layers. Nest temperature showed opposite trends, reaching its maximum value in late stages of development. Nest oxygen content was influenced by fraction of viable eggs, total clutch sizes, sand temperatures, maximum nest temperature and maximum change in the nest temperature during incubation. Clutch size during embryogenesis was the most influential factor overall. However, the major influential factors were different for different developmental stages. In the first half of the incubation, the development rate was low, and the change in the nest oxygen content was influenced mainly by the clutch size. During the second half, the rapid embryonic development rate became the dominant factor, and hatchling activities caused even greater oxygen consumption during the last stage of development.

Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro-ecosystems

PubMed Central

Thrall, Peter H; Oakeshott, John G; Fitt, Gary; Southerton, Simon; Burdon, Jeremy J; Sheppard, Andy; Russell, Robyn J; Zalucki, Myron; Heino, Mikko; Ford Denison, R

2011-01-01

Anthropogenic impacts increasingly drive ecological and evolutionary processes at many spatio-temporal scales, demanding greater capacity to predict and manage their consequences. This is particularly true for agro-ecosystems, which not only comprise a significant proportion of land use, but which also involve conflicting imperatives to expand or intensify production while simultaneously reducing environmental impacts. These imperatives reinforce the likelihood of further major changes in agriculture over the next 30–40 years. Key transformations include genetic technologies as well as changes in land use. The use of evolutionary principles is not new in agriculture (e.g. crop breeding, domestication of animals, management of selection for pest resistance), but given land-use trends and other transformative processes in production landscapes, ecological and evolutionary research in agro-ecosystems must consider such issues in a broader systems context. Here, we focus on biotic interactions involving pests and pathogens as exemplars of situations where integration of agronomic, ecological and evolutionary perspectives has practical value. Although their presence in agro-ecosystems may be new, many traits involved in these associations evolved in natural settings. We advocate the use of predictive frameworks based on evolutionary models as pre-emptive management tools and identify some specific research opportunities to facilitate this. We conclude with a brief discussion of multidisciplinary approaches in applied evolutionary problems. PMID:25567968

Effects of preconditioning the rhizosphere of different plant species on biotic methane oxidation kinetics.

PubMed

Ndanga, Éliane M; Lopera, Carolina B; Bradley, Robert L; Cabral, Alexandre R

2016-09-01

The rhizosphere is known as the most active biogeochemical layer of the soil. Therefore, it could be a beneficial environment for biotic methane oxidation. The aim of this study was to document - by means of batch incubation tests - the kinetics of CH4 oxidation in rhizosphere soils that were previously exposed to methane. Soils from three pre-exposure to CH4 zones were sampled: the never-before pre-exposed (NEX), the moderately pre-exposed (MEX) and the very pre-exposed (VEX). For each pre-exposure zone, the rhizosphere of several plant species was collected, pre-incubated, placed in glass vials and submitted to CH4 concentrations varying from 0.5% to 10%. The time to the beginning of CH4 consumption and the CH4 oxidation rate were recorded. The results showed that the fastest CH4 consumption occurred for the very pre-exposed rhizosphere. Specifically, a statistically significant difference in CH4 oxidation half-life was found between the rhizosphere of the VEX vegetated with a mixture of different plants and the NEX vegetated with ryegrass. This difference was attributed to the combined effect of the preconditioning level and plant species as well as to the organic matter content. Regardless of the preconditioning level, the oxidation rate values obtained in this study were comparable to those reported in the reviewed literature for mature compost. Copyright © 2016 Elsevier Ltd. All rights reserved.

Critical soil conditions for oxygen stress to plant roots: Substituting the Feddes-function by a process-based model

NASA Astrophysics Data System (ADS)

Bartholomeus, Ruud P.; Witte, Jan-Philip M.; van Bodegom, Peter M.; van Dam, Jos C.; Aerts, Rien

2008-10-01

SummaryEffects of insufficient soil aeration on the functioning of plants form an important field of research. A well-known and frequently used utility to express oxygen stress experienced by plants is the Feddes-function. This function reduces root water uptake linearly between two constant pressure heads, representing threshold values for minimum and maximum oxygen deficiency. However, the correctness of this expression has never been evaluated and constant critical values for oxygen stress are likely to be inappropriate. On theoretical grounds it is expected that oxygen stress depends on various abiotic and biotic factors. In this paper, we propose a fundamentally different approach to assess oxygen stress: we built a plant physiological and soil physical process-based model to calculate the minimum gas filled porosity of the soil ( ϕgas_min) at which oxygen stress occurs. First, we calculated the minimum oxygen concentration in the gas phase of the soil needed to sustain the roots through (micro-scale) diffusion with just enough oxygen to respire. Subsequently, ϕgas_min that corresponds to this minimum oxygen concentration was calculated from diffusion from the atmosphere through the soil (macro-scale). We analyzed the validity of constant critical values to represent oxygen stress in terms of ϕgas_min, based on model simulations in which we distinguished different soil types and in which we varied temperature, organic matter content, soil depth and plant characteristics. Furthermore, in order to compare our model results with the Feddes-function, we linked root oxygen stress to root water uptake (through the sink term variable F, which is the ratio of actual and potential uptake). The simulations showed that ϕgas_min is especially sensitive to soil temperature, plant characteristics (root dry weight and maintenance respiration coefficient) and soil depth but hardly to soil organic matter content. Moreover, ϕgas_min varied considerably between soil types and was larger in sandy soils than in clayey soils. We demonstrated that F of the Feddes-function indeed decreases approximately linearly, but that actual oxygen stress already starts at drier conditions than according to the Feddes-function. How much drier is depended on the factors indicated above. Thus, the Feddes-function might cause large errors in the prediction of transpiration reduction and growth reduction through oxygen stress. We made our method easily accessible to others by implementing it in SWAP, a user-friendly soil water model that is coupled to plant growth. Since constant values for ϕgas_min in plant and hydrological modeling appeared to be inappropriate, an integrated approach, including both physiological and physical processes, should be used instead. Therefore, we advocate using our method in all situations where oxygen stress could occur.

A Biotic Game Design Project for Integrated Life Science and Engineering Education

PubMed Central

Denisin, Aleksandra K.; Rensi, Stefano; Sanchez, Gabriel N.; Quake, Stephen R.; Riedel-Kruse, Ingmar H.

2015-01-01

Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games. PMID:25807212

A biotic game design project for integrated life science and engineering education.

PubMed

Cira, Nate J; Chung, Alice M; Denisin, Aleksandra K; Rensi, Stefano; Sanchez, Gabriel N; Quake, Stephen R; Riedel-Kruse, Ingmar H

2015-03-01

Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

Using forest inventory and analysis data to understand biotic resistance to plant invasions across the Eastern United States

Treesearch

Basil V. III Iannone; Kevin M. Potter; Hao Zhang; Christopher M. Guo Oswalt; Christopher W. Woodall; Songlin Fei

2015-01-01

Biological invasions and their impacts are likely to increase with the expansion of global commerce, making the need to identify key drivers and regulators of invasion perhaps greater than ever. One of the most enduring, and tested, hypotheses for explaining invasions is the “biotic resistance hypothesis.” Broadly, this hypothesis states that communities having greater...

Biotic and abiotic factors regulating forest floor CO2 flux across a range of forest age classes in the southern Appalachians

Treesearch

James M. Vose; Paul V. Bolstad

2007-01-01

We measured forest floor CO2 flux in three age classes of forest in the southern Appalachians: 20-year-old, 85-year-old, and old-growth. Our objectives were to quantify differences in forest floor CO2 flux among age classes, and determine the relative importance of abiotic and biotic driving variables. Forest floor CO

Area and percent of forest affected by biotic agents beyond reference conditions

Treesearch

Jeffrey A. Mai

2012-01-01

Criterion 3, Indicator 15, of the Montréal Process identifies the impact that biotic processes and agents have on forests (Montréal Process Working Group 2007). Where change due to these agents and processes occurs beyond a critical threshold, forest ecosystem health and vitality may be significantly altered and a forest’s ability to recover could be reduced or lost....

Forests in decline: yellow-cedar research yields prototype for climate change adaptation planning

Treesearch

Marie Oliver; Paul Hennon; David D' Amore

2013-01-01

Yellow-cedar has been dying across 600 miles of North Pacific coastal rain forest—from Alaska to British Columbia—since about 1880. Thirty years ago, a small group of pathologists began investigating possible biotic causes of the decline. When no biotic cause could be found, the scope broadened into a research program that eventually encompassed the fields of ecology,...

Function of ABA in Stomatal Defense against Biotic and Drought Stresses

PubMed Central

Lim, Chae Woo; Baek, Woonhee; Jung, Jangho; Kim, Jung-Hyun; Lee, Sung Chul

2015-01-01

The plant hormone abscisic acid (ABA) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. Under stress conditions, plants synthesize ABA in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression of defense-related genes conferring resistance to environmental stresses. The regulation of stomatal opening and closure is important to pathogen defense and control of transpirational water loss. Recent studies using a combination of approaches, including genetics, physiology, and molecular biology, have contributed considerably to our understanding of ABA signal transduction. A number of proteins associated with ABA signaling and responses—especially ABA receptors—have been identified. ABA signal transduction initiates signal perception by ABA receptors and transfer via downstream proteins, including protein kinases and phosphatases. In the present review, we focus on the function of ABA in stomatal defense against biotic and abiotic stresses, through analysis of each ABA signal component and the relationships of these components in the complex network of interactions. In particular, two ABA signal pathway models in response to biotic and abiotic stress were proposed, from stress signaling to stomatal closure, involving the pyrabactin resistance (PYR)/PYR-like (PYL) or regulatory component of ABA receptor (RCAR) family proteins, 2C-type protein phosphatases, and SnRK2-type protein kinases. PMID:26154766

Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles.

PubMed

Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C

2016-04-01

High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

Quantitative XRD analysis of {110} twin density in biotic aragonites.

PubMed

Suzuki, Michio; Kim, Hyejin; Mukai, Hiroki; Nagasawa, Hiromichi; Kogure, Toshihiro

2012-12-01

{110} Twin densities in biotic aragonite have been estimated quantitatively from the peak widths of specific reflections in powder X-ray diffraction (XRD) patterns, as well as direct confirmation of the twins using transmission electron microscopy (TEM). Influence of the twin density on the peak widths in the XRD pattern was simulated using DIFFaX program, regarding (110) twin as interstratification of two types of aragonite unit layers with mirrored relationship. The simulation suggested that the twin density can be estimated from the difference of the peak widths between 111 and 021, or between 221 and 211 reflections. Biotic aragonite in the crossed-lamellar microstructure (three species) and nacreous microstructure (four species) of molluscan shells, fish otoliths (two species), and a coral were investigated. The XRD analyses indicated that aragonite crystals in the crossed-lamellar microstructure of the three species contain high density of the twins, which is consistent with the TEM examination. On the other hand, aragonite in the nacre of the four species showed almost no difference of the peak widths between the paired reflections, indicating low twin densities. The results for the fish otoliths were varied between the species. Such variation of the twin density in biotic aragonites may reflect different schemes of crystal growth in biomineralization. Copyright © 2012 Elsevier Inc. All rights reserved.

Ictalurids in Iowa’s streams and rivers: Status, distribution, and relationships with biotic integrity

USGS Publications Warehouse

Sindt, Anthony R.; Fischer, Jesse R.; Quist, Michael C.; Pierce, Clay

2011-01-01

Anthropogenic alterations to Iowa’s landscape have greatly altered lotic systems with consequent effects on the biodiversity of freshwater fauna. Ictalurids are a diverse group of fishes and play an important ecological role in aquatic ecosystems. However, little is known about their distribution and status in lotic systems throughout Iowa. The purpose of this study was to describe the distribution of ictalurids in Iowa and examine their relationship with ecological integrity of streams and rivers. Historical data (i.e., 1884–2002) compiled for the Iowa Aquatic Gap Analysis Project (IAGAP) were used to detect declines in the distribution of ictalurids in Iowa streams and rivers at stream segment and watershed scales. Eight variables characterizing ictalurid assemblages were used to evaluate relationships with index of biotic integrity (IBI) ratings. Comparisons of recent and historic data from the IAGAP database indicated that 9 of Iowa’s 10 ictalurid species experienced distribution declines at one or more spatial scales. Analysis of variance indicated that ictalurid assemblages differed among samples with different IBI ratings. Specifically, total ictalurid, sensitive ictalurid, and Noturus spp. richness increased as IBI ratings increased. Results indicate declining ictalurid species distributions and biotic integrity are related, and management strategies aimed to improve habitat and increase biotic integrity will benefit ictalurid species.

The application of biotic elicitor on Artemisia annua L. to increase artemisinin content

NASA Astrophysics Data System (ADS)

Darwati, I.; Manohara, D.; Rohimatun; Nurhayati, H.

2018-01-01

Artemisinin-based Combination Therapy (ACT) has been recommended by WHO as an alternative to treat malaria overcoming drug resistance. The secondary metabolic products in plants, including artemisinin, can be increased by utilizing biotic elicitor from fungi. The research was conducted in Gunung Putri Research Installation, Cipanas, West Java from 2010 to 2011. Phytophthora sp. from eggplant and Colletotrichum sp. from Artemisia annua were applied as biotic elicitor. The types of biotic elicitor applied to the plants were 1) the medium of potato dextrose broth were inoculated with fungi and harvested after 10 days (filtrate), 2) powdery mycelium of both fungi. There were 16 treatments: control negative, control positive (uninoculated medium) 1%, 2%, 3% (v/v)], Phytophthora sp. filtrate [1, 2% and 3% (v/v)], Colletotrichum sp. filtrate [1, 2% and 3% (v/v)], Phytophthora sp. mycelium [1%, 2% and 3% (w/v)], Colletotrichum sp mycelium [1%, 2% and 3% (w/v)]. The elicitor application increased plant production by 26.21% and artemisinin yield by 72% compared to control. Furthermore, the artemisinin production of the plants treated with medium inoculated with 2% filtrate of Phytophthora sp (FP2) (25.19 kg/ha) and 1% powdery mycelium of Colletotrichum sp (MC1) (26.42 kg/ha) were higher than control (K) (11.17 kg/ha).

Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

PubMed Central

Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C.

2016-01-01

High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments. PMID:27032533

Emerging horizons for tick-borne pathogens: from the ‘one pathogen–one disease’ vision to the pathobiome paradigm

PubMed Central

Vayssier-Taussat, Muriel; Kazimirova, Maria; Hubalek, Zdenek; Hornok, Sándor; Farkas, Robert; Cosson, Jean-François; Bonnet, Sarah; Vourch, Gwenaël; Gasqui, Patrick; Mihalca, Andrei Daniel; Plantard, Olivier; Silaghi, Cornelia; Cutler, Sally; Rizzoli, Annapaola

2015-01-01

Ticks, as vectors of several notorious zoonotic pathogens, represent an important and increasing threat for human and animal health in Europe. Recent applications of new technology revealed the complexity of the tick microbiome, which may affect its vectorial capacity. Appreciation of these complex systems is expanding our understanding of tick-borne pathogens, leading us to evolve a more integrated view that embraces the ‘pathobiome’; the pathogenic agent integrated within its abiotic and biotic environments. In this review, we will explore how this new vision will revolutionize our understanding of tick-borne diseases. We will discuss the implications in terms of future research approaches that will enable us to efficiently prevent and control the threat posed by ticks. PMID:26610021

Ca, Sr, Mo and U isotopes evidence ocean acidification and deoxygenation during the Late Permian mass extinction

NASA Astrophysics Data System (ADS)

Silva-Tamayo, Juan Carlos; Payne, Jon; Wignall, Paul; Newton, Rob; Eisenhauer, Anton; Weyer, Stenfan; Neubert, Nadja; Lau, Kim; Maher, Kate; Paytan, Adina; Lehrmann, Dan; Altiner, Demir; Yu, Meiyi

2014-05-01

The most catastrophic extinction event in the history of animal life occurred at the end of the Permian Period, ca. 252 Mya. Ocean acidification and global oceanic euxinia have each been proposed as causes of this biotic crisis, but the magnitude and timing of change in global ocean chemistry remains poorly constrained. Here we use multiple isotope systems - Ca, Sr, Mo and U - measured from well dated Upper Permian- Lower Triassic sedimentary sections to better constrain the magnitude and timing of change in ocean chemistry and the effects of ocean acidification and de-oxygenation through this interval. All the investigated carbonate successions (Turkey, Italy and China) exhibit decreasing δ44/40Ca compositions, from ~-1.4‰ to -2.0‰ in the interval preceding the main extinction. These values remain low during most of the Griesbachian, to finally return to -1.4‰ in the middle Dienerian. The limestone succession from southern Turkey also displays a major decrease in the δ88/86Sr values from 0.45‰ to 0.3‰ before the extinction. These values remain low during the Griesbachian and finally increase to 0.55‰ by the middle Dienerian. The paired negative anomalies on the carbonate δ44/40Ca and δ88/86Sr suggest a decrease in the carbonate precipitation and thus an episode of ocean acidification coincident with the major biotic crisis. The Mo and U isotope records also exhibit significant rapid negative anomalies at the onset of the main extinction interval, suggesting rapid expansion of anoxic and euxinic marine bottom waters during the extinction interval. The rapidity of the isotope excursions in Mo and U suggests substantially reduced residence times of these elements in seawater relative to the modern, consistent with expectations for a time of widespread anoxia. The large C-isotope variability within Lower Triassic rocks, which is similar to that of the Lower-Middle Cambrian, may reflect biologically controlled perturbations of the oceanic carbon cycle. These findings strengthen the evidence for a global ocean acidification event coupled with rapid expansion of anoxic zones as drivers of end-Permian extinction in the oceans.

Euryhaline ecology of early tetrapods revealed by stable isotopes.

PubMed

Goedert, Jean; Lécuyer, Christophe; Amiot, Romain; Arnaud-Godet, Florent; Wang, Xu; Cui, Linlin; Cuny, Gilles; Douay, Guillaume; Fourel, François; Panczer, Gérard; Simon, Laurent; Steyer, J-Sébastien; Zhu, Min

2018-06-01

The fish-to-tetrapod transition-followed later by terrestrialization-represented a major step in vertebrate evolution that gave rise to a successful clade that today contains more than 30,000 tetrapod species. The early tetrapod Ichthyostega was discovered in 1929 in the Devonian Old Red Sandstone sediments of East Greenland (dated to approximately 365 million years ago). Since then, our understanding of the fish-to-tetrapod transition has increased considerably, owing to the discovery of additional Devonian taxa that represent early tetrapods or groups evolutionarily close to them. However, the aquatic environment of early tetrapods and the vertebrate fauna associated with them has remained elusive and highly debated. Here we use a multi-stable isotope approach (δ 13 C, δ 18 O and δ 34 S) to show that some Devonian vertebrates, including early tetrapods, were euryhaline and inhabited transitional aquatic environments subject to high-magnitude, rapid changes in salinity, such as estuaries or deltas. Euryhalinity may have predisposed the early tetrapod clade to be able to survive Late Devonian biotic crises and then successfully colonize terrestrial environments.

Ecogeomorphic feedbacks in regrowth of travertine step-pool morphology after dam decommissioning, Fossil Creek, Arizona

NASA Astrophysics Data System (ADS)

Fuller, Brian M.; Sklar, Leonard S.; Compson, Zacchaeus G.; Adams, Kenneth J.; Marks, Jane C.; Wilcox, Andrew C.

2011-03-01

The linkages between fluvial geomorphology and aquatic ecosystems are commonly conceptualized as a one-way causal chain in which geomorphic processes create the physical template for ecological dynamics. In streams with a travertine step-pool morphology, however, biotic processes strongly influence the formation and growth of travertine dams, creating the potential for numerous feedbacks. Here we take advantage of the decommissioning of a hydroelectric project on Fossil Creek, Arizona, where restoration of CaCO 3-rich baseflow has triggered rapid regrowth of travertine dams, to explore the interactions between biotic and abiotic factors in travertine morphodynamics. We consider three conceptual frameworks, where biotic factors independently modulate the rate of physical and chemical processes that produce travertine dams; combine with abiotic factors in a set of feedback loops; and work in opposition to abiotic processes, such that the travertine step-pool morphology reflects a dynamic balance between dominantly-biotic constructive processes and dominantly-abiotic destructive processes. We consider separately three phases of an idealized life cycle of travertine dams: dam formation, growth, and destruction by erosive floods. Dam formation is catalyzed by abiotic factors (e.g. channel constrictions, and bedrock steps) and biotic factors (e.g. woody debris, and emergent vegetation). From measurements of changes over time in travertine thickness on a bedrock step, we find evidence for a positive feedback between flow hydraulics and travertine accrual. Measurements of organic content in travertine samples from this step show that algal growth contributes substantially to travertine accumulation and suggest that growth is most rapid during seasonal algal blooms. To document vertical growth of travertine dams, we embedded 252 magnets into nascent travertine dams, along a 10 km stretch of river. Growth rates are calculated from changes over time in the magnetic field intensity at the dam surface. At each magnet we record a range of hydraulic and travertine composition variables to characterize the dominant mechanism of growth: abiotic precipitation, algal growth, trapping of organic material, or in situ plant growth. We find: (1) rapid growth of travertine dams following flow restoration, averaging more than 2 cm/year; (2) growth rates decline downstream, consistent with loss of dissolved constituents because of upstream travertine deposition, but also parallel to a decline in organic content in dam surface material and a downstream shift in dominant biotic mechanism; (3) biotic mechanisms are associated with faster growth rates; and (4) correlations between hydraulic attributes and growth rates are more consistent with biotic than abiotic controls. We conclude that the strong influence of living organisms on rates of travertine growth, coupled with the beneficial effects of travertine on ecosystem dynamics, demonstrate a positive feedback between biology and geomorphology. During our two-year study period, erosive flood flows occurred causing widespread removal of travertine. The temporal distribution of travertine growth and erosion over the study period is consistent with a bimodal magnitude-frequency relation in which growth dominates except when large, infrequent storms occur. This model may be useful in other systems where biology exerts strong controls on geomorphic processes.

Statistical physics of self-replication.

PubMed

England, Jeremy L

2013-09-28

Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.

Bioconcentration of lipophilic compounds by some aquatic organisms

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

Hawker, D.W.; Connell, D.W.

1986-04-01

With nondegradable, lipophilic compounds having log P values ranging from 2 to 6, direct linear relationships have been found between the logarithms of the equilibrium bioconcentration factors, and also reciprocal clearance rate constants, with log P for daphnids and molluscs. These relationships permit calculation of the times required for equilibrium and significant bioconcentration of lipophilic chemicals. Compared with fish, these time periods are successively shorter for molluscs, then daphnids. The equilibrium biotic concentration was found to decrease with increasing chemical hydrophobicity for both molluscs and daphnids. Also, new linear relationships between the logarithm of the bioconcentration factor and log Pmore » were found for compounds not attaining equilibrium within finite exposure times.« less

[Life cycle strategies: a synthesis of empirical and theoretical approaches].

PubMed

Romanovskiĭ, Iu E

1998-01-01

A scheme of relationships among life-history characters is developed on assumptions of determinate growth and dependence of juvenile mortality on the specific growth rate. It is shown that constraints on the relative neonate size, (W0/W infinity), and minimum value of the biotic potential, (rmax), lead to "triangular" shape of life history set on the plain defined by juvenile and adult mortality. This completely coincides with the Ramenskiĭ++--Grime (C-S-R) classification of life-history strategies. Phylogenetic constraints can reduce this set to a relatively narŕow r/K-continuum specifically oriented for a certain taxon. Similar restrictions generate models of life history optimization which predict interspecific allometries between life-history traits.

Use of the Biotic Ligand Model to predict metal toxicity to aquatic biota in areas of differing geology

USGS Publications Warehouse

Smith, Kathleen S.

2005-01-01

This work evaluates the use of the biotic ligand model (BLM), an aquatic toxicity model, to predict toxic effects of metals on aquatic biota in areas underlain by different rock types. The chemical composition of water, soil, and sediment is largely derived from the composition of the underlying rock. Geologic source materials control key attributes of water chemistry that affect metal toxicity to aquatic biota, including: 1) potentially toxic elements, 2) alkalinity, 3) total dissolved solids, and 4) soluble major elements, such as Ca and Mg, which contribute to water hardness. Miller (2002) compiled chemical data for water samples collected in watersheds underlain by ten different rock types, and in a mineralized area in western Colorado. He found that each rock type has a unique range of water chemistry. In this study, the ten rock types were grouped into two general categories, igneous and sedimentary. Water collected in watersheds underlain by sedimentary rock has higher mean pH, alkalinity, and calcium concentrations than water collected in watersheds underlain by igneous rock. Water collected in the mineralized area had elevated concentrations of calcium and sulfate in addition to other chemical constituents. Miller's water-chemistry data were used in the BLM (computer program) to determine copper and zinc toxicity to Daphnia magna. Modeling results show that waters from watersheds underlain by different rock types have characteristic ranges of predicted LC 50 values (a measurement of aquatic toxicity) for copper and zinc, with watersheds underlain by igneous rock having lower predicted LC 50 values than watersheds underlain by sedimentary rock. Lower predicted LC 50 values suggest that aquatic biota in watersheds underlain by igneous rock may be more vulnerable to copper and zinc inputs than aquatic biota in watersheds underlain by sedimentary rock. For both copper and zinc, there is a trend of increasing predicted LC 50 values with increasing dissolved organic carbon (DOC) concentrations. Predicted copper LC 50 values are extremely sensitive to DOC concentrations, whereas alkalinity appears to have an influence on zinc toxicity at alkalinities in excess of about 100 mg/L CaCO 3 . These findings show promise for coupling the BLM (computer program) with measured water-chemistry data to predict metal toxicity to aquatic biota in different geologic settings and under different scenarios. This approach may ultimately be a useful tool for mine-site planning, mitigation and remediation strategies, and ecological risk assessment.

Mineralogical and isotopic record of biotic and abiotic diagenesis of the Callovian-Oxfordian clayey formation of Bure (France)

NASA Astrophysics Data System (ADS)

Lerouge, C.; Grangeon, S.; Gaucher, E. C.; Tournassat, C.; Agrinier, P.; Guerrot, C.; Widory, D.; Fléhoc, C.; Wille, G.; Ramboz, C.; Vinsot, A.; Buschaert, S.

2011-05-01

The Callovian-Oxfordian (COx) clayey unit is being studied in the Eastern part of the Paris Basin at depths between 400 and 500 m depth to assess of its suitability for nuclear waste disposal. The present study combines new mineralogical and isotopic data to describe the sedimentary history of the COx unit. Petrologic study provided evidence of the following diagenetic mineral sequence: (1) framboidal pyrite and micritic calcite, (2) iron-rich euhedral carbonates (ankerite, sideroplesite) and glauconite (3) limpid calcite and dolomite and celestite infilling residual porosity in bioclasts and cracks, (4) chalcedony, (5) quartz/calcite. Pyrite in bioturbations shows a wide range of δ 34S (-38‰ to +34.5‰), providing evidence of bacterial sulphate reduction processes in changing sedimentation conditions. The most negative values (-38‰ to -22‰), measured in the lower part of the COx unit indicate precipitation of pyrite in a marine environment with a continuous sulphate supply. The most positive pyrite δ 34S values (-14‰ up to +34.5‰) in the upper part of the COx unit indicate pyrite precipitation in a closed system. Celestite δ 34S values reflect the last evolutionary stage of the system when bacterial activity ended; however its deposition cannot be possible without sulphate supply due to carbonate bioclast dissolution. The 87Sr/ 86Sr ratio of celestite (0.706872-0.707040) is consistent with deposition from Jurassic marine-derived waters. Carbon and oxygen isotopic compositions of bulk calcite and dolomite are consistent with marine carbonates. Siderite, only present in the maximum clay zone, has chemical composition and δ 18O consistent with a marine environment. Its δ 13C is however lower than those of marine carbonates, suggesting a contribution of 13C-depleted carbon from degradation of organic matter. δ 18O values of diagenetic chalcedony range between +27‰ and +31‰, suggesting precipitation from marine-derived pore waters. Late calcite crosscutting a vein filled with chalcedony and celestite, and late euhedral quartz in a limestone from the top of the formation have lower δ 18O values (˜+19‰), suggesting that they precipitated from meteoric fluids, isotopically close to present-day pore waters of the formation. Finally, the study illustrates the transition from very active, biotic diagenesis to abiotic diagenesis. This transition appears to be driven by compaction of the sediment, which inhibited movement of bacterial cells by reduction of porosity and pore sizes, rather than a lack of inorganic carbon or sulphates.

Geochemical and iron isotopic insights into hydrothermal iron oxyhydroxide deposit formation at Loihi Seamount

NASA Astrophysics Data System (ADS)

Rouxel, Olivier; Toner, Brandy; Germain, Yoan; Glazer, Brian

2018-01-01

Low-temperature hydrothermal vents, such as those encountered at Loihi Seamount, harbor abundant microbial communities and provide ideal systems to test hypotheses on biotic versus abiotic formation of hydrous ferric oxide (FeOx) deposits at the seafloor. Hydrothermal activity at Loihi Seamount produces abundant microbial mats associated with rust-colored FeOx deposits and variably encrusted with Mn-oxyhydroxides. Here, we applied Fe isotope systematics together with major and trace element geochemistry to study the formation mechanisms and preservation of such mineralized microbial mats. Iron isotope composition of warm (<60 °C), Fe-rich and H2S-depleted hydrothermal fluids yielded δ56Fe values near +0.1‰, indistinguishable from basalt values. Suspended particles in the vent fluids and FeOx deposits recovered nearby active vents yielded systematically positive δ56Fe values. The enrichment in heavy Fe isotopes between +1.05‰ and +1.43‰ relative to Fe(II) in vent fluids suggest partial oxidation of Fe(II) during mixing of the hydrothermal fluid with seawater. By comparing the results with experimentally determined Fe isotope fractionation factors, we determined that less than 20% of Fe(II) is oxidized within active microbial mats, although this number may reach 80% in aged or less active deposits. These results are consistent with Fe(II) oxidation mediated by microbial processes considering the expected slow kinetics of abiotic Fe oxidation in low oxygen bottom water at Loihi Seamount. In contrast, FeOx deposits recovered at extinct sites have distinctly negative Fe-isotope values down to -1.77‰ together with significant enrichment in Mn and occurrence of negative Ce anomalies. These results are best explained by the near-complete oxidation of an isotopically light Fe(II) source produced during the waning stage of hydrothermal activity under more oxidizing conditions. Light Fe isotope values of FeOx are therefore generated by subsurface precipitation of isotopically heavy Fe-oxides rather than by the activity of dissimilatory Fe reduction in the subsurface. Overall, Fe-isotope compositions of microbial mats at Loihi Seamount display a remarkable range between -1.2‰ and +1.6‰ which indicate that Fe isotope compositions of hydrothermal Fe-oxide precipitates are particularly sensitive to local environmental conditions where they form, and are less sensitive to abiotic versus biotic origins. It follows that FeOx deposits at Loihi Seamount provides important modern analogues for ancient seafloor Fe-rich deposits allowing for testing hypotheses about the biogeochemical cycling of Fe isotopes on early Earth.

Relationships between biotic and abiotic factors and regeneration of chestnut oak, white oak, and northern red oak

Treesearch

Songlin Fei; Kim C. Steiner; James C. Finley; Marc E. McDill

2003-01-01

A series of substantial field surveys of 38 mixed-oak stands in central Pennsylvania were carried out during 1996-2000. All the stands were surveyed 1 year prior to harvest, and 16 stands have been surveyed 1 year after harvest. Three abiotic factors at stand scale, four abiotic factors at plot scale, and two biotic factors and one abiotic factor at subplot scale was...

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing.

PubMed

Pereira-Leal, José B; Abreu, Isabel A; Alabaça, Cláudia S; Almeida, Maria Helena; Almeida, Paulo; Almeida, Tânia; Amorim, Maria Isabel; Araújo, Susana; Azevedo, Herlânder; Badia, Aleix; Batista, Dora; Bohn, Andreas; Capote, Tiago; Carrasquinho, Isabel; Chaves, Inês; Coelho, Ana Cristina; Costa, Maria Manuela Ribeiro; Costa, Rita; Cravador, Alfredo; Egas, Conceição; Faro, Carlos; Fortes, Ana M; Fortunato, Ana S; Gaspar, Maria João; Gonçalves, Sónia; Graça, José; Horta, Marília; Inácio, Vera; Leitão, José M; Lino-Neto, Teresa; Marum, Liliana; Matos, José; Mendonça, Diogo; Miguel, Andreia; Miguel, Célia M; Morais-Cecílio, Leonor; Neves, Isabel; Nóbrega, Filomena; Oliveira, Maria Margarida; Oliveira, Rute; Pais, Maria Salomé; Paiva, Jorge A; Paulo, Octávio S; Pinheiro, Miguel; Raimundo, João A P; Ramalho, José C; Ribeiro, Ana I; Ribeiro, Teresa; Rocheta, Margarida; Rodrigues, Ana Isabel; Rodrigues, José C; Saibo, Nelson J M; Santo, Tatiana E; Santos, Ana Margarida; Sá-Pereira, Paula; Sebastiana, Mónica; Simões, Fernanda; Sobral, Rómulo S; Tavares, Rui; Teixeira, Rita; Varela, Carolina; Veloso, Maria Manuela; Ricardo, Cândido P P

2014-05-15

Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

A spatial framework for representing nearshore ecosystems

NASA Astrophysics Data System (ADS)

Gregr, Edward J.; Lessard, Joanne; Harper, John

2013-08-01

The shallow, coastal regions of the world's oceans are highly productive ecosystems providing important habitat for commercial, forage, endangered, and iconic species. Given the diversity of ecosystem services produced or supported by this ecosystem, a better understanding of its structure and function is central to developing an ecosystem-based approach to management. However this region - termed the ‘white strip' by marine geologists because of the general lack of high-resolution bathymetric data - is dynamic, highly variable, and difficult to access making data collection challenging and expensive. Since substrate is a key indicator of habitat in this important ecosystem, our objective was to create a continuous substrate map from the best available bottom type data. Such data are critical to assessments of species distributions and anthropogenic risk. Using the Strait of Georgia in coastal British Columbia, Canada, as a case study, we demonstrate how such a map can be created from a diversity of sources. Our approach is simple, quantitative, and transparent making it amenable to iterative improvement as data quality and availability improve. We evaluated the ecological performance of our bottom patches using observed shellfish distributions. We found that observations of geoduck clam, an infaunal species, and red urchins, a species preferentially associated with hard bottom, were strongly and significantly associated with our soft and hard patches respectively. Our description of bottom patches also corresponded well with a more traditional, morphological classification of a portion of the study area. To provide subsequent analyses (such as habitat models) with some confidence in the defined bottom type values, we developed a corresponding confidence surface based on the agreement of, and distance between observations. Our continuous map of nearshore bottom patches thus provides a spatial framework to which other types of data, both abiotic (e.g., energy) and biotic, can be attached. As more data are associated with the bottom patches, we anticipate they will become increasingly useful for representing and developing species-habitat relationships, ultimately leading to a comprehensive representation of the nearshore ecosystem.

Chromatin modification and remodelling: a regulatory landscape for the control of Arabidopsis defence responses upon pathogen attack.

PubMed

Berr, Alexandre; Ménard, Rozenn; Heitz, Thierry; Shen, Wen-Hui

2012-06-01

Due to their sessile lifestyle, plants have to cope with an ever-changing environment and to defend themselves against a multitude of biotic aggressors that compromise their development and reproduction. Responses to various biotic stresses largely depend on the plant's capacity to modulate rapidly and specifically its transcriptome. In a stress type-dependent manner, external signals are translocated into the nucleus to activate transcription factors, resulting in the increased expression of particular sets of defence-related genes. Among mechanisms of transcriptional regulation, chromatin remodelling accomplished through the activity of histone-modifying enzymes and ATP-dependent chromatin-remodelling complexes is emerging as a key process in the orchestration of plant biotic stress responses. In this review, we summarize and discuss roles that chromatin-remodelling mechanisms may play in regulating Arabidopsis defence responses. © 2012 Blackwell Publishing Ltd.

Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

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

O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

2015-02-27

In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less

Structure and functioning of dryland ecosystems in a changing world.

PubMed

Maestre, Fernando T; Eldridge, David J; Soliveres, Santiago; Kéfi, Sonia; Delgado-Baquerizo, Manuel; Bowker, Matthew A; García-Palacios, Pablo; Gaitán, Juan; Gallardo, Antonio; Lázaro, Roberto; Berdugo, Miguel

2016-11-01

Understanding how drylands respond to ongoing environmental change is extremely important for global sustainability. Here we review how biotic attributes, climate, grazing pressure, land cover change and nitrogen deposition affect the functioning of drylands at multiple spatial scales. Our synthesis highlights the importance of biotic attributes (e.g. species richness) in maintaining fundamental ecosystem processes such as primary productivity, illustrate how N deposition and grazing pressure are impacting ecosystem functioning in drylands worldwide, and highlight the importance of the traits of woody species as drivers of their expansion in former grasslands. We also emphasize the role of attributes such as species richness and abundance in controlling the responses of ecosystem functioning to climate change. This knowledge is essential to guide conservation and restoration efforts in drylands, as biotic attributes can be actively managed at the local scale to increase ecosystem resilience to global change.

Structure and functioning of dryland ecosystems in a changing world

PubMed Central

Maestre, Fernando T.; Eldridge, David J.; Soliveres, Santiago; Kéfi, Sonia; Delgado-Baquerizo, Manuel; Bowker, Matthew A.; García-Palacios, Pablo; Gaitán, Juan; Gallardo, Antonio; Lázaro, Roberto; Berdugo, Miguel

2017-01-01

Understanding how drylands respond to ongoing environmental change is extremely important for global sustainability. Here we review how biotic attributes, climate, grazing pressure, land cover change and nitrogen deposition affect the functioning of drylands at multiple spatial scales. Our synthesis highlights the importance of biotic attributes (e.g. species richness) in maintaining fundamental ecosystem processes such as primary productivity, illustrate how N deposition and grazing pressure are impacting ecosystem functioning in drylands worldwide, and highlight the importance of the traits of woody species as drivers of their expansion in former grasslands. We also emphasize the role of attributes such as species richness and abundance in controlling the responses of ecosystem functioning to climate change. This knowledge is essential to guide conservation and restoration efforts in drylands, as biotic attributes can be actively managed at the local scale to increase ecosystem resilience to global change. PMID:28239303

Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains

PubMed Central

Jordan, Heather R.; Tomberlin, Jeffery K.

2017-01-01

A number of abiotic and biotic factors are known to regulate arthropod attraction, colonization, and utilization of decomposing vertebrate remains. Such information is critical when assessing arthropod evidence associated with said remains in terms of forensic relevance. Interactions are not limited to just between the resource and arthropods. There is another biotic factor that has been historically overlooked; however, with the advent of high-throughput sequencing, and other molecular techniques, the curtain has been pulled back to reveal a microscopic world that is playing a major role with regards to carrion decomposition patterns in association with arthropods. The objective of this publication is to review many of these factors and draw attention to their impact on microbial, specifically bacteria, activity associated with these remains as it is our contention that microbes serve as a primary mechanism regulating associated arthropod behavior. PMID:28538664

Testing the extended biotic index in Slovakia: consistency, advantages, and limitations versus the saprobic assessment method of water quality.

PubMed

Pennelli, Bruno; Nagel, Karl-Otto; Crivellaro, Giuseppe; Fabiani, Claudio; Vancova, Alexandra; Mancini, Laura

2006-04-01

The European Union Water Framework Directive requires the achievement of environmental objectives for the ecological quality of water bodies. A comparable implementation of the Directive throughout member countries of the European Union is necessary to verify equal protection of surface waters. The Directive specifies that member states determine ecological quality by means of biological indices. To improve comparability of water quality assessment, this research carried out an intercalibration trial between the Slovak Saprobic Index and the Italian protocol of the Extended Biotic Index, as part of a cooperative program between Italy and the Slovak Republic. When assessing streams with no or low pollution, statistics showed similar results for both methods. In contrast, the comparison of indices was not accurate in the case of severely affected waters. Reliable conversion formulas are feasible to transform the Italian Extended Biotic Index into the Slovak Saprobic Index, and not vice versa.

Geomorphic field experiment to quantify grain size and biotic influence on riverbed sedimentation dynamics in a dry-season reservoir, Russian River, CA

NASA Astrophysics Data System (ADS)

Florsheim, J. L.; Ulrich, C.; Hubbard, S. S.; Borglin, S. E.; Rosenberry, D. O.

2013-12-01

An important problem in geomorphology is to differentiate between abiotic and biotic fine sediment deposition on coarse gravel river beds because of the potential for fine sediment to infiltrate and clog the pore space between gravel clasts. Infiltration of fines into gravel substrate is significant because it may reduce permeability; therefore, differentiation of abiotic vs. biotic sediment helps in understanding the causes of such changes. We conducted a geomorphic field experiment during May to November 2012 in the Russian River near Wohler, CA, to quantify biotic influence on riverbed sedimentation in a small temporary reservoir. The reservoir is formed upstream of a small dam inflated during the dry season to enhance water supply pumping from the aquifer below the channel; however, some flow is maintained in the reservoir to facilitate fish outmigration. In the Russian River field area, sediment transport dynamics during storm flows prior to dam inflation created an alternate bar-riffle complex with a coarser gravel surface layer over the relatively finer gravel subsurface. The objective of our work was to link grain size distribution and topographic variation to biotic and abiotic sediment deposition dynamics in this field setting where the summertime dam annually increases flow depth and inundates the bar surfaces. The field experiment investigated fine sediment deposition over the coarser surface sediment on two impounded bars upstream of the reservoir during an approximately five month period when the temporary dam was inflated. The approach included high resolution field surveys of topography, grain size sampling and sediment traps on channel bars, and laboratory analyses of grain size distributions and loss on ignition (LOI) to determine biotic content. Sediment traps were installed at six sites on bars to measure sediment deposited during the period of impoundment. Preliminary results show that fine sediment deposition occurred at all of the sample sites, and is spatially variable--likely influenced by topographic differences that moderate flow over the bars. Traps initially filled with coarse gravel from the bar's surface trapped more fine sediment than traps initially filled with material from the bar's subsurface sediment, suggesting that a gravel bar's armor layer may enhance the source of material available to infiltrate into the channel substrate. LOI analysis indicates that both surface and subsurface samples have organic content ranging between 2 and 4%, following winter storm flows prior to impoundment. In contrast, samples collected after the 5-month impoundment have higher organic content ranging between 5 and 11%. This work aids in differentiating between abiotic and biotic fine sediment deposition in order to understand their relative potential for clogging gravel substrate.

22 CFR 23.4 - Representative value in exchange.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Representative value in exchange. 23.4 Section 23.4 Foreign Relations DEPARTMENT OF STATE FEES AND FUNDS FINANCE AND ACCOUNTING § 23.4 Representative value in exchange. Representative value in exchange for the collection of a fee means foreign...

Temporal effects of prescribed burning on terpene production in Mediterranean pines.

PubMed

Valor, Teresa; Ormeño, Elena; Casals, Pere

2017-12-01

Prescribed burning is used to reduce fuel hazard but underburning can damage standing trees. The effect of burning on needle terpene storage, a proxy for secondary metabolism, in fire-damaged pines is poorly understood despite the protection terpenes confer against biotic and abiotic stressors. We investigated variation in needle terpene storage after burning in three Mediterranean pine species featuring different adaptations to fire regimes. In two pure-stands of Pinus halepensis Mill. and two mixed-stands of Pinus sylvestris L. and Pinus nigra ssp. salzmanni (Dunal) Franco, we compared 24 h and 1 year post-burning concentrations with pre-burning concentrations in 20 trees per species, and evaluated the relative contribution of tree fire severity and physiological condition (δ13C and N concentration) on temporal terpene dynamics (for mono- sesqui- and diterpenes). Twenty-four hours post-burning, monoterpene concentrations were slightly higher in P. halepensis than at pre-burning, while values were similar in P. sylvestris. Differently, in the more fire-resistant P. nigra monoterpene concentrations were lower at 24 h, compared with pre-burning. One year post-burning, concentrations were always lower compared with pre- or 24 h post-burning, regardless of the terpene group. Mono- and sesquiterpene variations were negatively related to pre-burning δ13C, while diterpene variations were associated with fire-induced changes in needle δ13C and N concentration. At both post-burning times, mono- and diterpene concentrations increased significantly with crown scorch volume in all species. Differences in post-burning terpene contents as a function of the pine species' sensitivity to fire suggest that terpenic metabolites could have adaptive importance in fire-prone ecosystems in terms of flammability or defence against biotic agents post-burning. One year post-burning, our results suggest that in a context of fire-induced resource availability, pines likely prioritize primary rather than secondary metabolism. Overall, this study contributes to the assessment of the direct and indirect effects of fire on pine terpene storage, providing valuable information about their vulnerability to biotic and abiotic stressors throughout time. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Common bean proteomics: Present status and future strategies.

PubMed

Zargar, Sajad Majeed; Mahajan, Reetika; Nazir, Muslima; Nagar, Preeti; Kim, Sun Tae; Rai, Vandna; Masi, Antonio; Ahmad, Syed Mudasir; Shah, Riaz Ahmad; Ganai, Nazir Ahmad; Agrawal, Ganesh K; Rakwal, Randeep

2017-10-03

Common bean (Phaseolus vulgaris L.) is a legume of appreciable importance and usefulness worldwide to the human population providing food and feed. It is rich in high-quality protein, energy, fiber and micronutrients especially iron, zinc, and pro-vitamin A; and possesses potentially disease-preventing and health-promoting compounds. The recently published genome sequence of common bean is an important landmark in common bean research, opening new avenues for understanding its genetics in depth. This legume crop is affected by diverse biotic and abiotic stresses severely limiting its productivity. Looking at the trend of increasing world population and the need for food crops best suited to the health of humankind, the legumes will be in great demand, including the common bean mostly for its nutritive values. Hence the need for new research in understanding the biology of this crop brings us to utilize and apply high-throughput omics approaches. In this mini-review our focus will be on the need for proteomics studies in common bean, potential of proteomics for understanding genetic regulation under abiotic and biotic stresses and how proteogenomics will lead to nutritional improvement. We will also discuss future proteomics-based strategies that must be adopted to mine new genomic resources by identifying molecular switches regulating various biological processes. Common bean is regarded as "grain of hope" for the poor, being rich in high-quality protein, energy, fiber and micronutrients (iron, zinc, pro-vitamin A); and possesses potentially disease-preventing and health-promoting compounds. Increasing world population and the need for food crops best suited to the health of humankind, puts legumes into great demand, which includes the common bean mostly. An important landmark in common bean research was the recent publication of its genome sequence, opening new avenues for understanding its genetics in depth. This legume crop is affected by diverse biotic and abiotic stresses severely limiting its productivity. Therefore, the need for new research in understanding the biology of this crop brings us to utilize and apply high-throughput omics approaches. Proteomics can be used to track all the candidate proteins/genes responsible for a biological process under specific conditions in a particular tissue. The potential of proteomics will not only help in determining the functions of a large number of genes in a single experiment but will also be a useful tool to mine new genes that can provide solution to various problems (abiotic stress, biotic stress, nutritional improvement, etc). We believe that a combined approach including breeding along with omics tools will lead towards attaining sustainability in legumes, including common bean. Copyright © 2017 Elsevier B.V. All rights reserved.

Integrated ecological and chemical food web accumulation modeling explains PAH temporal trends during regime shifts in a shallow lake.

PubMed

Kong, Xiangzhen; He, Wei; Qin, Ning; Liu, Wenxiu; Yang, Bin; Yang, Chen; Xu, Fuliu; Mooij, Wolf M; Koelmans, Albert A

2017-08-01

Shallow lakes can switch suddenly from a turbid situation with high concentrations of phytoplankton and other suspended solids to a vegetated state with clear water, and vice versa. These alternative stable states may have a substantial impact on the fate of hydrophobic organic compounds (HOCs). Models that are fit to simulate impacts from these complex interactions are scarce. We developed a contaminant fate model which is linked to an ecosystem model (PCLake) for shallow lakes. This integrated model was successful in simulating long-term dynamics (1953-2012) of representative polycyclic aromatic hydrocarbons (PAHs) in the main biotic and abiotic components in a large shallow lake (Chaohu in China), which has undergone regime shifts in this period. Historical records from sediment cores were used to evaluate the model. The model revealed that regime shifts in shallow lakes had a strong impact on the fate of less hydrophobic compounds due to the large storage capacity of macrophytes, which accumulated up to 55.6% of phenanthrene in the clear state. The abrupt disappearance of macrophytes after the regime shift resulted in a sudden change in phenanthrene distribution, as the sediment became the major sink. For more hydrophobic compounds such as benzo(a)pyrene, the modeled impact of the regime shift was negligible for the whole environment, yet large for biotic compartments. This study is the first to provide a full mechanistic analysis of the impact of regime shifts on the fate of PAHs in a real lake ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.