scholarly journals Strain-level diversity drives alternative community types in millimeter scale granular biofilms

2018 ◽  
Author(s):  
Gabriel E. Leventhal ◽  
Carles Boix ◽  
Urs Kuechler ◽  
Tim N. Enke ◽  
Elzbieta Sliwerska ◽  
...  
Keyword(s):  
Environmental Parameters ◽  
Granular Sludge ◽  
Strain Level ◽  
Coarse Grained ◽  
Extrinsic Factors ◽  
Community Types ◽  
Demographic Fluctuations ◽  
Close Relatives ◽  
Lineage Structure ◽  
Alternative Community

Microbial communities are often highly diverse in their composition, both at the level of coarse-grained taxa such as genera as well as at the level of strains within species. This variability can be driven by both extrinsic factors like temperature, pH, etc., as well as by intrinsic ones, such as demographic fluctuations or ecological interactions. The relative contributions of these factors and the taxonomic level at which they influence community structure remain poorly understood, in part because of the difficulty of identifying true community replicates assembled under the same environmental parameters. Here, we address this problem using an activated granular sludge reactor in which millimeter scale biofilm granules represent true community replicates whose differences in composition are expected to be driven primarily by biotic factors. Using 142 shotgun metagenomes of single biofilm granules we found that, at the commonly used genuslevel resolution, community replicates varied much more in their composition than would be expected from neutral assembly processes. This variation, however, did not translate into any clear partitioning into discrete community types, i.e. the equivalent of enterotypes in the human gut. However, a strong partition into community types did emerge at the strain level for the most abundant organism: strains of Candidatus Accumulibacter that coexisted in the metacommunity--i.e. the reactor--excluded each other within community replicates. Single-granule communities maintained a significant lineage structure, whereby the strain phylogeny of Accumulibacter correlated with the overall species composition of the community, indicating high potential for co-diversification among species and communities. Our results suggest that due to the high functional redundancy and competition between close relatives, alternative community types are most likely observed at the level of recently differentiated genotypes but not higher orders of genetic resolution.

scholarly journals Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

2018 ◽  
Vol 3 (11) ◽  
pp. 1295-1303 ◽  
Author(s):  
Gabriel E. Leventhal ◽  
Carles Boix ◽  
Urs Kuechler ◽  
Tim N. Enke ◽  
Elzbieta Sliwerska ◽  
...  
Keyword(s):  
Strain Level ◽  
Community Types ◽  
Alternative Community

scholarly journals Spatial distribution and functional significance of leaf lamina shape in Amazonian forest trees

2009 ◽  
Vol 6 (1) ◽  
pp. 1837-1874 ◽  
Author(s):  
A. C. M. Malhado ◽  
R. J. Whittaker ◽  
Y. Malhi ◽  
R. J. Ladle ◽  
H. ter Steege ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Leaf Shape ◽  
Environmental Parameters ◽  
Complex Problem ◽  
Permanent Plots ◽  
Mean Annual Temperature ◽  
Leaf Lamina ◽  
Extrinsic Factors ◽  
Regional Patterns ◽  
Dry Conditions

Abstract. Leaves in tropical forests come in an enormous variety of sizes and shapes, each of which can be ultimately viewed as an adaptation to the complex problem of optimising the capture of light for photosynthesis. However, the fact that many different shape "strategies" coexist within a habitat demonstrate that there are many other intrinsic and extrinsic factors involved, such as the differential investment in support tissues required for different leaf lamina shapes. Here, we take a macrogeographic approach to understanding the function of different lamina shape categories. Specifically, we use 106 permanent plots spread across the Amazon rainforest basin to: (1) describe the geographic distribution of some simple metrics of lamina shape in plots from across Amazonia, and; (2) identify and quantify relationships between key environmental parameters and lamina shape in tropical forests. Because the plots are not randomly distributed across the study area, achieving this latter objective requires the use of statistics that can account for spatial auto-correlation. We found that between 60–70% of the 2791 species and 83 908 individual trees in the dataset could be classified as elliptic (=the widest part of a leaf is on an axis in the middle fifth of the long axis of the leaf). Furthermore, the average Amazonian tree leaf is 2.5 times longer than it is wide and has an entire margin. Contrary to theoretical expectations we found little support for the hypothesis that narrow leaves are an adaptation to dry conditions and low nutrient soils. However, we did find strong regional patterns in leaf lamina length-width ratios and several significant correlations with precipitation variables suggesting that water availability may be exerting an as yet unrecognised selective pressure on leaf shape of rainforest trees. Furthermore, we found a strong correlation between the proportion of trees with non-entire laminas (dissected, toothed, etc.) and mean annual temperature once again supporting the well documented association that provides a basis for reconstructing past temperature regimes.

scholarly journals Palaeophytogeographical Patterns Across the Permian–Triassic Boundary

2020 ◽  
Vol 8 ◽  
Author(s):  
Hendrik Nowak ◽  
Christian Vérard ◽  
Evelyn Kustatscher
Keyword(s):  
Environmental Parameters ◽  
Land Plant ◽  
Time Interval ◽  
Triassic Boundary ◽  
Unequal Distribution ◽  
Population Turnover ◽  
Community Types ◽  
Permian Mass Extinction ◽  
Permian Triassic Boundary ◽  
The Impact

It has long been recognized that terrestrial floras underwent major and long-lasting changes during the Permian and Triassic, some of which have been attributed to the end-Permian mass extinction. However, these changes are still poorly understood with regard to the late Permian and Early Triassic. In particular, the impact that ecological disturbances around the Permian–Triassic boundary had on the composition and palaeogeographical distribution of land plant communities needs to be scrutinized. We analyse this impact based on fossil floras from across the world, covering the Wuchiapingian to Ladinian time interval. The plant assemblages are assigned to biomes representing particular environmentally controlled community types. Variations in the distribution of biomes between stages indicate shifts in the environmental parameters affecting terrestrial floras, and provide insights into population turnover dynamics. A substantial shift towards increasing seasonality and a reduction of biome diversity occurs in the earliest Triassic and stabilised throughout the Middle Triassic. However, results also show that the stratigraphically and (palaeo-) geographically unequal distribution of sampled localities constitutes an important limitation for this kind of analysis.

Organic and ammonium nitrogen and oxygen in relation to granular sludge growth in lab-scale UASB reactors

1994 ◽  
Vol 30 (12) ◽  
pp. 43-53 ◽  
Author(s):  
J. Thaveesri ◽  
K. Gernaey ◽  
B. Kaonga ◽  
G. Boucneau ◽  
W. Verstraete
Keyword(s):  
Environmental Parameters ◽  
Granular Sludge ◽  
Ammonium Nitrogen ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Negative Effects ◽  
A Minor ◽  
Anaerobic Sludge Blanket ◽  
Uasb Reactors ◽  
Oxygen Ratio

Laboratory studies of in-reactor granular-sludge yield (Ygran) were carried out to investigate the effect of substrates rich in proteins. Both lab-scale upflow anaerobic sludge blanket (UASB) and shake-flask systems were used to monitor the behaviour of the sludge. Influent based on molasses with a COD to N ratio of 100:2.5-3.0 gave good Ygran; increasing substitution of the carbohydrate COD by protein COD resulted in a deterioration of the sludge characteristics. The negative effects appear to be related to the protein rather than to the NH4+ formed. Of the various environmental parameters examined, the surface tension of the mixed liquor was the main deviating factor. At a proper range of oxygenation i.e., by means of monitoring of both the input COD to oxygen ratio (gCOD gO2−1) and the daily oxygen loading rate (mgO2 gVSS−1.d−1), the UASB reactors treating the nitrogen-rich wastewater showed enhanced Ygran with only a minor reduction in methanogenesis. A range of working conditions in which this principle can be applied to decrease fluffy growth to the advantage of granular increase is proposed.

The relationship between sedimentary facies and faunal associations in the Llandovery siliciclastic Ross Brook Formation, Arisaig, Nova Scotia

1986 ◽  
Vol 23 (5) ◽  
pp. 705-726 ◽  
Author(s):  
J. M. Hurst ◽  
R. K. Pickerill
Keyword(s):  
Nova Scotia ◽  
Environmental Parameters ◽  
Sedimentary Facies ◽  
Great Distance ◽  
Thin Layers ◽  
Coarse Grained ◽  
Individual Species ◽  
Silty Mudstone ◽  
Evolutionary Pattern ◽  
Fine Grained

The Llandovery siliciclastic Ross Brook Formation of Arisaig, Nova Scotia, comprises three broadly defined sedimentary facies. These are a mottled silty mudstone facies (facies A), a laminated shale facies (facies B), and a laminated siltstone facies (facies C). Facies A consists of variably bioturbated silty mudstones, muddy siltstones, and fissile shales. It developed in relatively shallow water conditions; mudstones were presumably deposited from suspension, and siltstone laminae and thin layers were formed by increased wave and current activity. Mottling resulted from bioturbation by epifaunal and, particularly, infaunal benthic organisms. Within facies A, two subfacies are recognized: A(i) is mudstone dominated, and A(ii) is fine-grained siltstone dominated. Facies B consists of alternating laminae of undisturbed mudstone and fine-grained siltstone probably produced as a result of deposition from suspension during a temporary upward expansion of the oxygen-minimum layer. Facies C consists of 0.5–30 cm thick fine- to coarse-grained siltstones, which occur in lenses or layers of single, composite, or amalgamated units. Internally they are extremely variable, but all are interpreted as a result of deposition from storm-generated currents.The Ross Brook Formation formed on a shallow-marine, storm-influenced, subtidal inner–mid muddy shelf and is dominated by extensive but stratigraphically variable developments of facies A and facies C. Absolute water depth per se is difficult to assess, and although fluctuations occurred, much of the sequence is believed to have accumulated at or in the immediate vicinity of fair-weather wave base in water depths estimated to have been between 30 and 60 m. Silt supply was generally low, possibly reflecting great distance from source or the presence of a mud-dominated shoreline.Five brachiopod-dominated associations, which are stratigraphically the Eocoelia hemisphaerica, the Eocoelia intermedia – Eocoelia curtisi, the Visbyella nana, the "Camarotoechia" rossonia, and the Eocoelia sulcata associations, occur through the sequence. Associations change where die sum of the facies characteristics change, suggesting that the major physical controlling factor was substrate type and related environmental parameters. The development of discrete but intergrading associations is viewed as a consequence of the long-term persistence of a set of conservative animal–sediment relationships, superimposed on which is the evolutionary pattern of immigration and extinction of individual species.

scholarly journals Spatial distribution and functional significance of leaf lamina shape in Amazonian forest trees

2009 ◽  
Vol 6 (8) ◽  
pp. 1577-1590 ◽  
Author(s):  
A. C. M. Malhado ◽  
R. J. Whittaker ◽  
Y. Malhi ◽  
R. J. Ladle ◽  
H. ter Steege ◽  
...  
Keyword(s):  
Tropical Forests ◽  
Leaf Shape ◽  
Environmental Parameters ◽  
Complex Problem ◽  
Permanent Plots ◽  
Mean Annual Temperature ◽  
Leaf Lamina ◽  
Extrinsic Factors ◽  
Regional Patterns ◽  
Dry Conditions

Abstract. Leaves in tropical forests come in an enormous variety of sizes and shapes, each of which can be ultimately viewed as an adaptation to the complex problem of optimising the capture of light for photosynthesis. However, the fact that many different shape "strategies" coexist within a habitat demonstrate that there are many other intrinsic and extrinsic factors involved, such as the differential investment in support tissues required for different leaf lamina shapes. Here, we take a macrogeographic approach to understanding the function of different lamina shape categories. Specifically, we use 106 permanent plots spread across the Amazon rainforest basin to: 1) describe the geographic distribution of some simple metrics of lamina shape in plots from across Amazonia, and; 2) identify and quantify relationships between key environmental parameters and lamina shape in tropical forests. Because the plots are not randomly distributed across the study area, achieving this latter objective requires the use of statistics that can account for spatial auto-correlation. We found that between 60–70% of the 2791 species and 83 908 individual trees in the dataset could be classified as having elliptic leaves (= the widest part of the leaf is on an axis in the middle fifth of the long axis of the leaf). Furthermore, the average Amazonian tree leaf is 2.5 times longer than it is wide and has an entire margin. Contrary to theoretical expectations we found little support for the hypothesis that narrow leaves are an adaptation to dry conditions. However, we did find strong regional patterns in leaf lamina length-width ratios and several significant correlations with precipitation variables suggesting that water availability may be exerting an as yet unrecognised selective pressure on leaf shape of rainforest trees. Some support was found for the hypothesis that narrow leaves are an adaptation to low nutrient soils. Furthermore, we found a strong correlation between the proportion of trees with non-entire laminas (dissected, toothed, etc.) and mean annual temperature once again supporting the well documented association that provides a basis for reconstructing past temperature regimes.

Simulation of dissociation of DNA duplexes attached to the surface

Open Physics ◽  
2010 ◽  
Vol 8 (6) ◽  
Author(s):  
Vladimir Zhdanov ◽  
Anders Gunnarsson ◽  
Fredrik Höök
Keyword(s):  
Surface Heterogeneity ◽  
Bound State ◽  
Coarse Grained ◽  
Dna Duplexes ◽  
Extrinsic Factors ◽  
Coarse Grained Model ◽  
Dna Base ◽  
Dna Base Pair ◽  
Complete Dissociation ◽  
And Diffusion

AbstractWe present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

Variation in the components of Benthic community structure in a Coastal Lagoon as a function of Spatial Scale

1989 ◽  
Vol 40 (1) ◽  
pp. 79 ◽  
Author(s):  
A Hatcher
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
Coastal Lagoon ◽  
Benthic Community ◽  
Spatial Scales ◽  
Small Scale ◽  
Benthic Community Structure ◽  
Extrinsic Factors ◽  
Sessile Invertebrates ◽  
Community Types

The perception of community structure is strongly related to the spatial resolution of data collection. To quantify variation in community structure at several spatial scales, the benthos was examined on the limestone substratum in a nearshore coastal lagoon. Community structure was described using a form of pattern analysis called correspondence analysis. Variance at three spatial scales was measured. These scales were described as: (I) between offshore and nearshore reefs (kilometres); (2) among areas on the nearshore reef-line (< 1 km); and (3) between community types on the nearshore reef-line (tens of metres and less). Organisms were classified according to higher taxa/functional classes. Parameters which varied between reef-lines included: (i) community composition determined using multivariate ordination, (ii) cover by calcareous and filamentous algae and (iii) abundance of seagrass and juvenile kelp (Ecklonia radiata). Among the areas on the nearshore reef-line, variance in community composition was due to the distribution of animals. There was a south to north gradient of increasing cover by encrusting animals and abundance of ascidians. Within the areas on the nearshore reef-line, there were two distinct community types characterized by macrophytic plants or sessile invertebrates. The major potential controls of the variation in benthic community structure were different at each of the spatial scales examined. The strong relationships between extrinsic factors and components of the communities suggested that the major potential controls were: (a) exposure to swell at the large scale (between reef-lines), (b) availability of food at the medium scale (within areas on the nearshore reef-line) and (c) biological interactions or responses to microtopography and light climate at the small scale (between and within communities on the nearshore reef-line).

scholarly journals A geomechanics classification for the rating of railroad subgrade performance

2021 ◽  
Author(s):  
António Gomes Correia ◽  
Ana Ramos
Keyword(s):  
Environmental Changes ◽  
Resilient Modulus ◽  
Deformation Behaviour ◽  
Permanent Deformation ◽  
Environmental Parameters ◽  
Coarse Grained ◽  
Track Structure ◽  
Train Speed ◽  
Loading Tests ◽  
Geomechanical Classification

AbstractThe type of subgrade of a railroad foundation is vital to the overall performance of the track structure. With the train speed and tonnage increase, as well as environmental changes, the evaluation and influence of subgrade are even more paramount in the railroad track structure performance. A geomechanics classification for subgrade is proposed coupling the stiffness (resilient modulus) and permanent deformation behaviour evaluated by means of repeated triaxial loading tests. This classification covers from fine- to coarse-grained soils, grouped by UIC and ASTM. For this achievement, we first summarize the main models for estimating resilient modulus and permanent deformation, including the evaluation of their robustness and their sensitivity to mechanical and environmental parameters. This is followed by the procedure required to arrive at the geomechanical classification and rating, as well as a discussion of the influence of environmental factors. This work is the first attempt to obtain a new geomechanical classification that can be a useful tool in the evaluation and modelling of the foundation of railway structures.

Factors Influencing Plankton Community Structure and Production in Freshwater Lakes

1987 ◽  
Vol 44 (3) ◽  
pp. 650-657 ◽  
Author(s):  
J. E. Paloheimo ◽  
R. R. Fulthorpe
Keyword(s):  
Turnover Rate ◽  
Environmental Parameters ◽  
Plankton Community ◽  
Structured Data ◽  
Predator Prey ◽  
Plankton Production ◽  
Community Types ◽  
Value Sets ◽  
Plankton Community Structure ◽  
Kjeldahl Nitrogen

Relationships among biomasses and levels of production of nannoplankton, netplankton, herbivorous zooplankton, and carnivorous zooplankton, as well their dependence on environmental parameters, were studied in 26 central Ontario lakes. Planktonic biomasses were only weakly correlated with each other. Correlations were improved by converting biomasses to production estimates using size-specific turnover rate corrections on size-structured data. Further use of size-structured data was of limited value. Sets of environmental parameters, particularly the water chemistry data, were better predictors of planktonic biomasses and productions than other biotic (predator/prey) data. Total Kjeldahl nitrogen was a better predictor of total plankton production estimates than total phosphorus. Lakes could not be clustered into stable community types due to the large year-to-year fluctuations in the data.

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