scholarly journals Dormancy dampens the microbial distance-decay relationship

2019 ◽  
Author(s):  
KJ Locey ◽  
ME Muscarella ◽  
ML Larsen ◽  
SR Bray ◽  
SE Jones ◽  
...  
Keyword(s):  
Environmental Filtering ◽  
Distance Decay ◽  
Regional Survey ◽  
Geographical Patterns ◽  
Local Diversity ◽  
Theoretical Predictions ◽  
Active Portion ◽  
Total Community ◽  
Total Dna ◽  
New Habitats

ABSTRACTMuch of Earth’s biodiversity has the capacity to engage in dormancy whereby individuals enter a reversible state of reduced metabolic activity. By increasing resilience to unfavorable conditions, dormancy leads to the accumulation of “seed banks” that should diminish the influence of environmental filtering, while allowing passive dispersers to colonize new habitats. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biodiversity and biogeography is lacking. We constructed geographical and environmental distance-decay relationships (DDRs) using 16S rRNA sequencing to characterize the total (DNA) and the active (RNA) bacterial communities in a regional survey of 49 forested ponds. As expected, the total community harbored greater diversity and exhibited weaker DDRs than the active portion of the community. These empirical observations were robust to different measures of community similarity and random resampling tests. Furthermore, findings from the field survey were reproduced by models that included aspects of dormancy along with the geographical coordinates and environmental characteristics of our study system. In addition to maintaining local diversity, our results support recent theoretical predictions that dormancy shapes geographical patterns of biodiversity.

scholarly journals Dormancy dampens the microbial distance–decay relationship

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190243 ◽  
Author(s):  
K. J. Locey ◽  
M. E. Muscarella ◽  
M. L. Larsen ◽  
S. R. Bray ◽  
S. E. Jones ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Regional Scale ◽  
Environmental Filtering ◽  
Model Performance ◽  
Seed Banks ◽  
Distance Decay ◽  
Biogeographic Patterns ◽  
Microbial Community Ecology ◽  
Theoretical Predictions ◽  
Total Dna

Much of Earth's biodiversity has the capacity to engage in dormancy, a reversible state of reduced metabolic activity. By increasing resilience to unfavourable conditions, dormancy leads to the accumulation of ‘seed banks’. These reservoirs of genetic and phenotypic diversity should diminish the strength of environmental filtering and increase rates of dispersal. Although prevalent among single-celled organisms, evidence that dormancy influences patterns of microbial biogeography is lacking. We constructed geographical and environmental distance–decay relationships (DDRs) for the total (DNA) and active (RNA) portions of bacterial communities in a regional-scale 16S rRNA survey of forested ponds in Indiana, USA. As predicted, total communities harboured greater diversity and exhibited weaker DDRs than active communities. These observations were robust to random resampling and different community metrics. To evaluate the processes underlying the biogeographic patterns, we developed a platform of mechanistic models that used the geographical coordinates and environmental characteristics of our study system. Based on more than 10 6 simulations, our models approximated the empirical DDRs when there was strong environmental filtering along with the presence of long-lived seed banks. By contrast, the inclusion of dispersal generally decreased model performance. Together, our findings support recent theoretical predictions that seed banks can influence the biogeographic patterns of microbial communities. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves

2011 ◽  
Vol 279 (1735) ◽  
pp. 1993-2002 ◽  
Author(s):  
Craig R. McClain ◽  
James C. Stegen ◽  
Allen H. Hurlbert
Keyword(s):  
Deep Sea ◽  
Environmental Filtering ◽  
Dispersal Limitation ◽  
Environmental Variable ◽  
Distance Decay ◽  
Spatial Distance ◽  
Explanatory Variables ◽  
Faunal Turnover ◽  
Theoretical Predictions ◽  
Rates Of Decay

Patterns of beta-diversity or distance decay at oceanic scales are completely unknown for deep-sea communities. Even when appropriate data exist, methodological problems have made it difficult to discern the relative roles of environmental filtering and dispersal limitation for generating faunal turnover patterns. Here, we combine a spatially extensive dataset on deep-sea bivalves with a model incorporating ecological dynamics and shared evolutionary history to quantify the effects of environmental filtering and dispersal limitation. Both the model and empirical data are used to relate functional, taxonomic and phylogenetic similarity between communities to environmental and spatial distances separating them for 270 sites across the Atlantic Ocean. This study represents the first ocean-wide analysis examining distance decay as a function of a broad suite of explanatory variables. We find that both strong environmental filtering and dispersal limitation drive turnover in taxonomic, functional and phylogenetic composition in deep-sea bivalves, explaining 26 per cent, 34 per cent and 9 per cent of the variation, respectively. This contrasts with previous suggestions that dispersal is not limiting in broad-scale biogeographic and biodiversity patterning in marine systems. However, rates of decay in similarity with environmental distance were eightfold to 44-fold steeper than with spatial distance. Energy availability is the most influential environmental variable evaluated, accounting for 3.9 per cent, 9.4 per cent and 22.3 per cent of the variation in functional, phylogenetic and taxonomic similarity, respectively. Comparing empirical patterns with process-based theoretical predictions provided quantitative estimates of dispersal limitation and niche breadth, indicating that 95 per cent of deep-sea bivalve propagules will be able to persist in environments that deviate from their optimum by up to 2.1 g m −2 yr −1 and typically disperse 749 km from their natal site.

scholarly journals An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

2016 ◽  
Vol 113 (49) ◽  
pp. E7927-E7936 ◽  
Author(s):  
Maggie C. Y. Lau ◽  
Thomas L. Kieft ◽  
Olukayode Kuloyo ◽  
Borja Linage-Alvarez ◽  
Esta van Heerden ◽  
...  
Keyword(s):  
Deep Subsurface ◽  
Sulfate Reducers ◽  
Paradoxical Situation ◽  
Gain Energy ◽  
Total Community ◽  
Diverse Community ◽  
Sulfur Oxidizing ◽  
Total Dna ◽  
Microbial Groups ◽  
Energy Processes

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H2. Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH4to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H2oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.

Mass Effects

Ecology ◽  
2021 ◽  
Author(s):  
Jani Heino ◽  
Luis Mauricio Bini
Keyword(s):  
Environmental Filtering ◽  
Biotic Interactions ◽  
Alpha Diversity ◽  
Suitable Habitat ◽  
Habitat Patches ◽  
Mass Effects ◽  
Local Diversity ◽  
Complex Interactions ◽  
High Dispersal ◽  
Local And Regional Processes

In the last two decades, community ecology has matured to consider biotic communities as a product of both local and regional processes. Therefore, local communities are currently thought to be connected by the dispersal of organisms, thereby forming a metacommunity. A metacommunity is organized by multiple processes, including environmental filtering, biotic interactions, dispersal, and ecological drift. Thus, spatial variations in local diversity (i.e., alpha diversity) and community composition (i.e., beta diversity) result from the relative roles of these major processes. In turn, these processes are mediated by organisms’ characteristics, environmental heterogeneity, and the connectivity between localities in a metacommunity. For a given environmental gradient, the role of environmental filtering is likely to be dependent on the dispersal rates shown by organisms. Unsuitable habitat patches (i.e., sinks), in terms of biotic and abiotic characteristics, may be occupied by different species due to high dispersal rates from suitable habitat patches (i.e., sources). Thus, mass effects occur when species are established at localities where their populations cannot be self-maintained. Even though it may be difficult to prove the action of mass effects per se, given the complex interactions between different mechanisms shaping biotic communities, there is some empirical evidence supporting their importance in nature. In addition, high dispersal rates that lead to mass effects may have important implications for biomonitoring and biodiversity conservation. This is because species occurring at sites beyond their niche requirements may provide false information about a site’s ecological quality or result in misleading plans to conserve species at sites where they cannot persist in the absence of continuous influx of propagules.

scholarly journals On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations

2019 ◽  
Author(s):  
David Murray-Stoker
Keyword(s):  
Temporal Variability ◽  
Restoration Ecology ◽  
Headwater Streams ◽  
Statistical Tests ◽  
Secondary Analysis ◽  
Environmental Filtering ◽  
Taxonomic Richness ◽  
Stream Network ◽  
Differential Effects ◽  
Local Diversity

ABSTRACTSwan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, meta-community, and restoration ecology. Swan and Brown (2017, 2018) evaluated the effect of restoration on sites receiving various combinations of in-channel manipulation and riparian reforestation treatments. Given the difference in the relative importance of environmental filtering and dispersal between headwaters and mainstems and the structure of river networks, I contend that different restoration treatments have differential effects between headwaters and mainstems. I hypothesized in-channel manipulations would have more consistent effects between headwaters and mainstems compared to riparian reforestation, and I used this hypothesis to guide site selection in the re-analysis. I then compared results from the re-analysis to those presented by Swan and Brown (2017, 2018). I did not find any effects of restoration on local diversity, spatial dissimilarity, or temporal variability, let alone differential effects of restoration between headwaters and mainstems; these results are contrary Swan and Brown (2017, 2018), who reported that restoration increased taxonomic richness, increased spatial dissimilarity, and decreased temporal variability in restored headwater streams. I demonstrate further that the statistical tests conducted by Swan and Brown (2017, 2018) were invalid and, therefore, recommend the use of the results presented here. More broadly, I suggest, in agreement with Swan and Brown (2017, 2018) and a growing body of research, that river and stream restoration will likely have greater success if a regional approach is taken to designing and implementing restoration projects.

scholarly journals Taxa–area and distance–decay relationships of unicellular eukaryotes along an elevation gradient of mountainous freshwater ecosystems

2019 ◽  
Vol 41 (6) ◽  
pp. 821-834
Author(s):  
Sofia C Macingo ◽  
Konstantinos A Kormas ◽  
Andreas Oikonomou ◽  
Hera Karayanni
Keyword(s):  
High Throughput Sequencing ◽  
Gene Diversity ◽  
Elevation Gradient ◽  
Environmental Filtering ◽  
18S Rrna Gene ◽  
Freshwater Ecosystems ◽  
Distance Decay ◽  
Unicellular Eukaryote ◽  
Rrna Gene ◽  
Unicellular Eukaryotes

Abstract Unicellular eukaryotes have pivotal ecological roles in aquatic ecosystems by participating in biogeochemical processes and structuring microbial food webs. However, revealing their biogeographical patterns remains challenging, as it is reflected in the rather limited available knowledge. In this study, two central patterns, the taxa–area and the distance–decay relationships, were tested for freshwater unicellular eukaryotes. Sampling was performed in 31 mountainous freshwater ecosystems in Thessaly (Greece). Sampling sites had different geohydromorphological characteristics (altitude, 124–704 m; depth, 0.3–1 m; surface area, 188–123 000 m2; geographical distances, 0.03–48.4 km). Unicellular eukaryote diversity was assessed by 18S rRNA gene diversity with high-throughput sequencing. Five supergroups (Stramenopiles, Alveolata, Rhizaria, Archaeplastida and Opisthokonta) were found with the most abundant taxa being Stramenopiles and Alveolata. Aquatic unicellular eukaryotes showed statistically significant but weak DDR and TAR. This can be attributed to the large proportion of specialists (91.9% of operational taxonomic units according to Levin’s index). These results indicate that although mountainous pools and ponds can host high diversity of unicellular eukaryotes, the shaping of their communities is mainly regulated by niche-specific processes and environmental filtering and to a lesser extent by species dispersion processes.

Microcalorimeters for X-Ray Spectroscopy

1988 ◽  
Vol 102 ◽  
pp. 41
Author(s):  
E. Silver ◽  
C. Hailey ◽  
S. Labov ◽  
N. Madden ◽  
D. Landis ◽  
...  
Keyword(s):  
High Resolution ◽  
High Efficiency ◽  
Thermal Response ◽  
Low Noise ◽  
High Resolution Spectroscopy ◽  
Superconducting Transition ◽  
Sapphire Substrates ◽  
Laboratory Plasmas ◽  
Adiabatic Demagnetization ◽  
Theoretical Predictions

The merits of microcalorimetry below 1°K for high resolution spectroscopy has become widely recognized on theoretical grounds. By combining the high efficiency, broadband spectral sensitivity of traditional photoelectric detectors with the high resolution capabilities characteristic of dispersive spectrometers, the microcalorimeter could potentially revolutionize spectroscopic measurements of astrophysical and laboratory plasmas. In actuality, however, the performance of prototype instruments has fallen short of theoretical predictions and practical detectors are still unavailable for use as laboratory and space-based instruments. These issues are currently being addressed by the new collaborative initiative between LLNL, LBL, U.C.I., U.C.B., and U.C.D.. Microcalorimeters of various types are being developed and tested at temperatures of 1.4, 0.3, and 0.1°K. These include monolithic devices made from NTD Germanium and composite configurations using sapphire substrates with temperature sensors fabricated from NTD Germanium, evaporative films of Germanium-Gold alloy, or material with superconducting transition edges. A new approache to low noise pulse counting electronics has been developed that allows the ultimate speed of the device to be determined solely by the detector thermal response and geometry. Our laboratory studies of the thermal and resistive properties of these and other candidate materials should enable us to characterize the pulse shape and subsequently predict the ultimate performance. We are building a compact adiabatic demagnetization refrigerator for conveniently reaching 0.1°K in the laboratory and for use in future satellite-borne missions. A description of this instrument together with results from our most recent experiments will be presented.

A crystallographic analysis of the CoSi/Si(111) interface using Transmission Electron Microscopy

1990 ◽  
Vol 48 (4) ◽  
pp. 574-575
Author(s):  
A.C. Daykin ◽  
C.J. Kiely ◽  
R.C. Pond ◽  
J.L. Batstone
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Defect Structure ◽  
Room Temperature ◽  
Theoretical Method ◽  
Crystallographic Analysis ◽  
Si Substrate ◽  
Transmission Electron ◽  
Theoretical Predictions

When CoSi2 is grown onto a Si(111) surface it can form in two distinct orientations. A-type CoSi2 has the same orientation as the Si substrate and B-type is rotated by 180° degrees about the [111] surface normal.One method of producing epitaxial CoSi2 is to deposit Co at room temperature and anneal to 650°C.If greater than 10Å of Co is deposited then both A and B-type CoSi2 form via a number of intermediate silicides .The literature suggests that the co-existence of A and B-type CoSi2 is in some way linked to these intermediate silicides analogous to the NiSi2/Si(111) system. The phase which forms prior to complete CoSi2 formation is CoSi. This paper is a crystallographic analysis of the CoSi2/Si(l11) bicrystal using a theoretical method developed by Pond. Transmission electron microscopy (TEM) has been used to verify the theoretical predictions and to characterise the defect structure at the interface.

Combining Defaults and Transparency Information to Increase Policy Compliance

2020 ◽  
Vol 51 (5) ◽  
pp. 354-359 ◽  
Author(s):  
Yavor Paunov ◽  
Michaela Wänke ◽  
Tobias Vogel
Keyword(s):  
Independent Effect ◽  
Online Experiment ◽  
Policy Compliance ◽  
Empirical Question ◽  
Theoretical Predictions

Abstract. Combining the strengths of defaults and transparency information is a potentially powerful way to induce policy compliance. Despite negative theoretical predictions, a recent line of research revealed that default nudges may become more effective if people are informed why they should exhibit the targeted behavior. Yet, it is an open empirical question whether the increase in compliance came from setting a default and consequently disclosing it, or the provided information was sufficient to deliver the effect on its own. Results from an online experiment indicate that both defaulting and transparency information exert a statistically independent effect on compliance, with highest compliance rates observed in the combined condition. Practical and theoretical implications are discussed.

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