scholarly journals Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities

2015 ◽  
Vol 282 (1809) ◽  
pp. 20142630 ◽  
Author(s):  
Jordan G. Okie ◽  
David J. Van Horn ◽  
David Storch ◽  
John E. Barrett ◽  
Michael N. Gooseff ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Negative Relationship ◽  
Low Complexity ◽  
Biodiversity Patterns ◽  
Soil Bacterial Communities ◽  
Β Diversity ◽  
Α Diversity ◽  
Magnitude Variation ◽  
Effects Of Temperature

The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.

scholarly journals Factors that drive zooplankton diversity in Neo-Tropical Savannah shallow lakes

2017 ◽  
Vol 29 (0) ◽  
Author(s):  
Claudia Padovesi-Fonseca ◽  
Renan de Souza Rezende
Keyword(s):  
Shallow Lakes ◽  
Environmental Gradients ◽  
Soluble Reactive Phosphorus ◽  
Zooplankton Community ◽  
Nitrogen And Phosphorus ◽  
System Productivity ◽  
Ecological Requirements ◽  
Β Diversity ◽  
Α Diversity ◽  
Lentic Systems

Abstract Zooplankton is an important community in aquatic ecosystems due to its linkage between primary producers and secondary consumers also playing a key role in cycling of organic materials. Aim: Therefore, our objective was to evaluate the effects of physicochemical variables of the water on the diversity of zooplankton community in seven tropical shallow lakes of Brazilian savannah. Methods Zooplankton samples were taken using a bucket and filtered 200 L by a 64 µm-mesh-plankton-net, and preserved for subsequent identification. Water temperature, dissolved oxygen, pH, electrical conductivity, turbidity, chlorophyll-a, ammonium, nitrate, nitrite, total phosphorus, and soluble reactive phosphorus were measured. Results The turbidity (decreases the temperature, luminosity and the system productivity) and ammonium (increases the toxicity) values were the major factors responsible for structuring the zooplankton community. On the other hand, also nitrogen and phosphorus (increase the productivity) are limiting in savannah lentic systems for the zooplankton. The higher α diversity was positively associated with aquatic macrophytes (increase of niches and refuge), whereas lakes with geographic proximity increase the similarity in species composition, decreasing the β diversity. Conclusions We conclude that the deterministic processes (niche theory), due to species have different ecological requirements, are different responses to environmental gradients and increase the diversity in heterogenic lentic systems.

scholarly journals Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2189
Author(s):  
Masaru Nakayasu ◽  
Shinichi Yamazaki ◽  
Yuichi Aoki ◽  
Kazufumi Yazaki ◽  
Akifumi Sugiyama
Keyword(s):  
Bacterial Communities ◽  
Steroidal Saponins ◽  
Specialized Metabolites ◽  
Soil Bacterial Communities ◽  
Β Diversity ◽  
Soil Zone ◽  
Α Diversity ◽  
Pure Compounds ◽  
Soil Bacterial ◽  
Microbiome Assembly

Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.

scholarly journals Turnover diversity drives large-scale biodiversity patterns in bathyal sediments of the Mediterranean Sea

2012 ◽  
Vol 9 (12) ◽  
pp. 17819-17853 ◽  
Author(s):  
S. Bianchelli ◽  
C. Gambi ◽  
M. Mea ◽  
A. Pusceddu ◽  
R. Danovaro
Keyword(s):  
Mediterranean Sea ◽  
Deep Sea ◽  
Large Scale ◽  
Spatial Scales ◽  
High Turnover ◽  
Trophic Conditions ◽  
Biodiversity Patterns ◽  
Β Diversity ◽  
Α Diversity ◽  
Nematode Diversity

Abstract. Understanding biodiversity patterns and how they are driven at different spatial scales is a crucial issue in ecological studies. This is particularly evident for the deep sea, the largest biome of the biosphere, where information on the scales of spatial variation is very scant. Here, we investigated deep-sea nematodes species richness, turnover and functional diversity, and life strategies at different spatial scales (from local to macro-regional) to identify the factors that shape regional (γ) and macro-regional (ϵ) deep-sea diversity. This study was conducted in several deep-sea habitats (canyons, open slopes, deep-water corals, and bathyal plains) over > 2000 km across the whole Mediterranean basin, at a fixed depth of ca. 1000 m. Our results indicate that the patterns of local (α) diversity across the deep Mediterranean follow the gradients of the trophic conditions, which decrease from the Western to the Eastern basins. For all of the sites and habitats, the α-diversity is generally low. Conversely, the turnover diversity changes significantly among habitats (β-diversity) and between regions (δ-diversity), showing values of dissimilarity (based on species presence/absence) between 59% and 90% for β-diversity and between 81% and 89% for δ-diversity. This suggests that patterns and values of regional (γ) and macro-regional (ϵ) diversity in the deep Mediterranean Sea are related to turnover diversity among habitats and between regions (β- and δ-diversity), rather than to the local biodiversity (α-diversity). These results indicate that the differences in β-diversity and δ-diversity are even more important than those for the α-diversity for the understanding of the drivers of biodiversity in the deep Mediterranean Sea. These data also allow us to conclude that habitat heterogeneity (and type) and gradients in environmental conditions, by promoting a high turnover diversity across the deep Mediterranean Sea, are crucial players for the nematode diversity levels.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

Drivers of diversity gradients of a highly mobile marine assemblage in a mesoscale seascape

2020 ◽  
Vol 638 ◽  
pp. 149-164
Author(s):  
GM Svendsen ◽  
M Ocampo Reinaldo ◽  
MA Romero ◽  
G Williams ◽  
A Magurran ◽  
...  
Keyword(s):  
Environmental Gradients ◽  
Regression Tree ◽  
Demersal Fish ◽  
Open Ocean ◽  
Shared Resources ◽  
Thermal Front ◽  
Boosted Regression Tree ◽  
Diversity Gradients ◽  
Α Diversity ◽  
Bottom Depth

With the unprecedented rate of biodiversity change in the world today, understanding how diversity gradients are maintained at mesoscales is a key challenge. Drawing on information provided by 3 comprehensive fishery surveys (conducted in different years but in the same season and with the same sampling design), we used boosted regression tree (BRT) models in order to relate spatial patterns of α-diversity in a demersal fish assemblage to environmental variables in the San Matias Gulf (Patagonia, Argentina). We found that, over a 4 yr period, persistent diversity gradients of species richness and probability of an interspecific encounter (PIE) were shaped by 3 main environmental gradients: bottom depth, connectivity with the open ocean, and proximity to a thermal front. The 2 main patterns we observed were: a monotonic increase in PIE with proximity to fronts, which had a stronger effect at greater depths; and an increase in PIE when closer to the open ocean (a ‘bay effect’ pattern). The originality of this work resides on the identification of high-resolution gradients in local, demersal assemblages driven by static and dynamic environmental gradients in a mesoscale seascape. The maintenance of environmental gradients, specifically those associated with shared resources and connectivity with an open system, may be key to understanding community stability.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

The species evenness of “prey” bacteria correlated with Bdellovibrio-and-like-organisms (BALOs) in the microbial network supports the biomass of BALOs in a paddy soil

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Hang Qian ◽  
Chunli Hou ◽  
Hao Liao ◽  
Li Wang ◽  
Shun Han ◽  
...  
Keyword(s):  
Soil Properties ◽  
Paddy Soil ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Negative Relationship ◽  
Sequencing Analysis ◽  
Nitrogen Use ◽  
Microbial Network ◽  
Α Diversity ◽  
Positive Effect

ABSTRACT To seek how soil biotic and abiotic factors which might shape the Bdellovibrio-and-like-organisms community, we sampled paddy soils under different fertilization treatments including fertilization without nitrogen (Control), the nitrogen use treatment (N) and the nitrogen overuse one (HNK) at three rice growing stages. The abundances of BALOs were impacted by the rice-growing stages but not the fertilization treatments. The abundances of Bdellovibrionaceae-like were positively associated with soil moisture, which showed a negative relationship with Bacteriovoracaceae-like bacteria. High-throughput sequencing analysis of the whole bacterial community revealed that the α-diversity of BALOs was not correlated with any soil properties data. Network analysis detected eight families directly linked to BALOs, namely, Pseudomonadaceae, Peptostreptococcaceae, Flavobacteriaceae, Sediment-4, Verrucomicrobiaceae, OM27, Solirubrobacteraceae and Roseiflexaceae. The richness and composition of OTUs in the eight families were correlated with different soil properties, while the evenness of them had a positive effect on the predicted BALO biomass. These results highlighted that the bottom-up control of BALOs in paddy soil at least partially relied on the changes of soil water content and the diversity of bacteria directly linked to BALOs in the microbial network.

scholarly journals Arthropod community structure in pastures of an island archipelago (Azores): looking for local–regional species richness patterns at fine-scales

2004 ◽  
Vol 94 (2) ◽  
pp. 111-121 ◽  
Author(s):  
P.A.V. Borges ◽  
V.K. Brown
Keyword(s):  
Species Richness ◽  
Regional Scale ◽  
Local Scale ◽  
Local Species Richness ◽  
Β Diversity ◽  
Arthropod Species ◽  
Α Diversity ◽  
Local Species ◽  
Richness Patterns

AbstractThe arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local–regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= α diversity) and regional species richness was estimated at the pasture level (= γ diversity) with the ‘first-order-Jackknife’ estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of α and β diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing β-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

A quantitative null model of additive diversity partitioning: examining the response of beta diversity to extinction

Paleobiology ◽  
2007 ◽  
Vol 33 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Karen M. Layou
Keyword(s):  
Null Model ◽  
Sampling Strategy ◽  
Diversity Partitioning ◽  
Opposite Pattern ◽  
Β Diversity ◽  
Α Diversity ◽  
Before And After ◽  
Four Levels ◽  
Total Diversity ◽  
Selective Extinction

Paleobiological diversity is often expressed as α (within-sample), β (among-sample), and γ (total) diversities. However, when studying the effects of extinction on diversity patterns, only variations in α and γ diversities are typically addressed. A null model that examines changes in β diversity as a function of percent extinction is presented here.The model examines diversity in the context of a hierarchical sampling strategy that allows for the additive partitioning of γ diversity into mean α and β diversities at varying scales. Here, the sampling hierarchy has four levels: samples, beds, facies, and region; thus, there are four levels of α diversity (α1, α2, α3, α4) and three levels of β diversity (β1, β2, and β3). Taxa are randomly assigned to samples within the hierarchy according to probability of occurrence, and initial mean α and β values are calculated. A regional extinction is imposed, and the hierarchy is resampled from the remaining extant taxa. Post-extinction mean α and β values are then calculated.Both non-selective and selective extinctions with respect to taxon abundance yield decreases in α, β, and γ diversities. Non-selective extinction with respect to taxon abundance shows little effect on diversity partitioning except at the highest extinction magnitudes (above 75% extinction), where the contribution of α1 to total γ increases at the expense of β3, with β1 and β2 varying little with increasing extinction magnitude. The pre-extinction contribution of α1 to total diversity increases with increased probabilities of taxon occurrence and the number of shared taxa between facies. Both β1 and β2 contribute equally to total diversity at low occurrence probabilities, but β2 is negligible at high probabilities, because individual samples preserve all the taxonomic variation present within a facies. Selective extinction with respect to rare taxa indicates a constant increase in α1 and constant decrease in β3 with increasing extinction magnitudes, whereas selective extinction with respect to abundant taxa yields the opposite pattern of an initial decrease in α1 and increase in β3. Both β1 and β2 remain constant with increasing extinction for both cases of selectivity. By comparing diversity partitioning before and after an extinction event, it may be possible to determine whether the extinction was selective with respect to taxon abundances, and if so, whether that selectivity was against rare or abundant taxa.Field data were collected across a Late Ordovician regional extinction in the Nashville Dome of Tennessee, with sampling hierarchy similar to that of the model. These data agree with the abundant-selective model, showing declines in α, β, and γ diversities, and a decrease in α1 and increase in β3, which suggests this extinction may have targeted abundant taxa.

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