scholarly journals Interactive Effects of Scion and Rootstock Genotypes on the Root Microbiome of Grapevines (Vitis spp. L.)

2021 ◽  
Vol 11 (4) ◽  
pp. 1615
Author(s):  
Stefanie Nicoline Vink ◽  
Francisco Dini-Andreote ◽  
Rebecca Höfle ◽  
Anna Kicherer ◽  
Joana Falcão Salles
Keyword(s):  
Community Structure ◽  
Community Diversity ◽  
Interactive Effects ◽  
Plant Performance ◽  
Cultivar Differences ◽  
Β Diversity ◽  
Bacterial Indicator ◽  
Α Diversity ◽  
Functional Implications ◽  
Rhizosphere Community

Diversity and community structure of soil microorganisms are increasingly recognized as important contributors to sustainable agriculture and plant health. In viticulture, grapevine scion cultivars are grafted onto rootstocks to reduce the incidence of the grapevine pest phylloxera. However, it is unknown to what extent this practice influences root-associated microbial communities. A field survey of bacteria in soil surrounding the roots (rhizosphere) of 4 cultivars × 4 rootstock combinations was conducted to determine whether rootstock and cultivar genotypes are important drivers of rhizosphere community diversity and composition. Differences in α-diversity was highly dependent on rootstock–cultivar combinations, while bacterial community structure primarily clustered according to cultivar differences, followed by differences in rootstocks. Twenty-four bacterial indicator genera were significantly more abundant in one or more cultivars, while only thirteen were found to be specifically associated with one or more rootstock genotypes, but there was little overlap between cultivar and rootstock indicator genera. Bacterial diversity in grafted grapevines was affected by both cultivar and rootstock identity, but this effect was dependent on which diversity measure was being examined (i.e., α- or β-diversity) and specific rootstock–cultivar combinations. These findings could have functional implications, for instance, if specific combinations varied in their ability to attract beneficial microbial taxa which can control pathogens and/or assist plant performance.

scholarly journals The plant circadian clock influences rhizosphere community structure and function

2017 ◽  
Author(s):  
Charley J. Hubbard ◽  
Marcus T. Brock ◽  
Linda T.A. van Diepen ◽  
Loïs Maignien ◽  
Brent E. Ewers ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Circadian Clock ◽  
Structure And Function ◽  
Plant Performance ◽  
Wild Type ◽  
Night Time ◽  
History Of ◽  
And Function ◽  
Rhizosphere Community

AbstractPlants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S rRNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs. clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison to clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.

scholarly journals The Influence of Climate Warming and Humidity on Plant Diversity and Soil Bacteria and Fungi Diversity in Desert Grassland

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2580
Author(s):  
Yi Zhang ◽  
Yingzhong Xie ◽  
Hongbin Ma ◽  
Juan Zhang ◽  
Le Jing ◽  
...  
Keyword(s):  
Plant Diversity ◽  
Soil Bacteria ◽  
Interactive Effects ◽  
Desert Grassland ◽  
Plant Soil ◽  
Β Diversity ◽  
Temperature And Precipitation ◽  
Α Diversity ◽  
Soil Bacteria And Fungi ◽  
Bacteria And Fungi

Our study, which was conducted in the desert grassland of Ningxia in China (E 107.285, N 37.763), involved an experiment with five levels of annual precipitation 33% (R33), 66% (R66), 100% (CK), 133% (R133), 166% (R166) and two temperature levels (inside Open-Top Chamber (OTC) and outside OTC). Our objective was to determine how plant, soil bacteria, and fungi diversity respond to climate change. Our study suggested that plant α-diversity in CK and TCK were significantly higher than that of other treatments. Increased precipitation promoted root biomass (RB) growth more than aboveground living biomass (ALB). R166 promoted the biomass of Agropyron mongolicum the most. In the fungi communities, temperature and precipitation interaction promoted α-diversity. In the fungi communities, the combination of increased temperature and natural precipitation (TCK) promoted β-diversity the most, whose distance was determined to be 25,124 according to PCA. In the bacteria communities, β-diversity in CK was significantly higher than in other treatments, and the distance was determined to be 3010 according to PCA. Soil bacteria and fungi α- and β-diversity, and ALB promoted plant diversity the most. The interactive effects of temperature and precipitation on C, N, and P contents of plants were larger than their independent effects.

scholarly journals The Influence of Maternal Unhealthy Diet On Maturation of Offspring Gut Microbiota in Rat

2021 ◽  
Author(s):  
Kyoko Hasebe ◽  
Michael D Kendig ◽  
Nadeem O Kaakoush ◽  
Aynaz Tajaddini ◽  
R Frederick Westbrook ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Maternal Diet ◽  
Female Offspring ◽  
Developmental Trajectory ◽  
The Other ◽  
Interactive Effects ◽  
Female Rats ◽  
Microbial Composition ◽  
Β Diversity ◽  
Α Diversity

Abstract Background: Despite well-known effects of diet on gut microbiota diversity, relatively little is known about how maternal diet quality shapes the longitudinal maturation of gut microbiota in offspring. To investigate, we fed female rats standard chow (Chow) or a western-style, high-choice cafeteria diet (Caf) prior to and during mating, gestation and lactation. At weaning (3 weeks), male and female offspring were either maintained on their mother’s diet (ChowChow, CafCaf groups) or switched to the other diet (ChowCaf, CafChow). Fecal microbial composition was assessed in dams and longitudinally in offspring at 3, 7 and 14 weeks of age.Results: The effect of maternal diet on maturation of offspring gut microbiota was assessed by α- and β-diversities, Deseq2/LEfSe, and SourceTracker analyses. Weanling gut microbiota composition was characterised by reduced α- and β-diversity profiles that clustered away from dams and older siblings. After weaning, offspring gut microbiota came to resemble an adult-like gut microbiota, with increased α-diversity and reduced dissimilarity of β-diversity. Similarly, Deseq2/LEfSe analyses found fewer numbers of altered operational taxonomic units (OTUs) between groups from weaning to adulthood. SourceTracker analyses indicated a greater overall contribution of Caf mothers’ microbial community (up to 20%) to that of their offspring than the contribution of Chow mothers (up to 8%). Groups maintained on the maternal diet (ChowChow, CafCaf), versus those switched to the other diet (ChowCaf, CafChow) post-weaning significantly differed from each other at 14 weeks (Permutational Multivariate Analysis of Variance), indicating interactive effects of maternal and post-weaning diet on offspring gut microbiota maturation. Nevertheless, this developmental trajectory was unaffected by sex and appeared consistent between ChowChow, CafCaf, ChowCaf and CafChow groups. Conclusions: Introducing solid food at weaning triggered the maturation of offspring gut microbiota to an adult-like profile in rats, in line with previous human studies. Postweaning Caf diet exposure had the largest impact on offspring gut microbiome, but this was modulated by maternal diet history. An unhealthy maternal Caf diet did not alter the developmental trajectory of offspring gut microbiota towards an adult-like profile, insofar as it did not prevent the age-associated increase in α-diversity and reduction in β-diversity dissimilarity.

scholarly journals Partitioning of diversity: the "within communities" component

Web Ecology ◽  
2014 ◽  
Vol 14 (1) ◽  
pp. 51-60 ◽  
Author(s):  
H.-R. Gregorius
Keyword(s):  
Diversity Indices ◽  
Community Diversity ◽  
Crucial Point ◽  
Β Diversity ◽  
Diversity Measures ◽  
Α Diversity ◽  
Straightforward Generalization ◽  
The Common ◽  
Additional Level ◽  
Total Diversity

Abstract. It is routinely understood that the total diversity within a metacommunity (γ-diversity) can be partitioned into one component summarizing the diversity within communities (α-diversity) and a second component representing the contribution of diversity (or differences) between communities (β-diversity). The underlying thought is that merging differentiated communities should raise the total diversity above the average level of diversity within the communities. The crucial point in this partitioning criterion is set by the notion of "diversity within communities" (DWC) and its relation to the total diversity. The common approach to summarizing DWC is in terms of averages. Yet there are many different ways to average diversity, and not all of these averages stay below the total diversity for every measure of diversity, corrupting the partitioning criterion. This raises the question of whether conceptual properties of diversity measures exist, the fulfillment of which implies that all measures of DWC obey the partitioning criterion. It is shown that the straightforward generalization of the plain counting of types (richness) leads to a generic diversity measure that has the desired properties and, together with its effective numbers, fulfills the partitioning criterion for virtually all of the relevant diversity measures in use. It turns out that the classical focus on DWC (α) and its complement (β as derived from α and γ) in the partitioning of total diversity captures only the apportionment perspective of the distribution of trait diversity over communities (which implies monomorphism within communities at the extreme). The other perspective, differentiation, cannot be assessed appropriately unless an additional level of diversity is introduced that accounts for differences between communities (such as the joint "type-community diversity"). Indices of apportionment IA (among which is GST and specially normalized versions of β) and differentiation ID are inferred, and it is demonstrated that conclusions derived from IA depend considerably on the measure of diversity to which it is applied, and that in most cases an assessment of the distribution of diversity over communities requires additional computation of ID.

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.

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.

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.

An inter-dependence of flood and drought: disentangling amphibian beta diversity in seasonal floodplains

2017 ◽  
Vol 68 (11) ◽  
pp. 2115 ◽  
Author(s):  
Leonardo F. B. Moreira ◽  
Tainá F. Dorado-Rodrigues ◽  
Vanda L. Ferreira ◽  
Christine Strüssmann
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Quantitative Data ◽  
Explanatory Variable ◽  
Biotic Interactions ◽  
Ecological Role ◽  
Β Diversity ◽  
Amphibian Community ◽  
Dry Seasons

Species composition in floodplains is often affected by different structuring factors. Although floods play a key ecological role, habitat selection in the dry periods may blur patterns of biodiversity distribution. Here, we employed a partitioning framework to investigate the contribution of turnover and nestedness to β-diversity patterns in non-arboreal amphibians from southern Pantanal ecoregion. We investigated whether components of β-diversity change by spatial and environmental factors. We sampled grasslands and dense arboreal savannas distributed in 12 sampling sites across rainy and dry seasons, and analysed species dissimilarities using quantitative data. In the savannas, both turnover and nestedness contributed similarly to β diversity. However, we found that β diversity is driven essentially by turnover, in the grasslands. In the rainy season, balanced variation in abundance was more related to altitude and factors that induce spatial patterns, whereas dissimilarities were not related to any explanatory variable during dry season. In the Pantanal ecoregion, amphibian assemblages are influenced by a variety of seasonal constraints on terrestrial movements and biotic interactions. Our findings highlighted the role of guild-specific patterns and indicated that mass effects are important mechanisms creating amphibian community structure in the Pantanal.

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.

scholarly journals Interaction between typical sulfonamides and bacterial diversity in drinking water

2018 ◽  
Vol 16 (6) ◽  
pp. 914-920 ◽  
Author(s):  
Qing Wu ◽  
Shuqun Li ◽  
Xiaofei Zhao ◽  
Xinhua Zhao
Keyword(s):  
Drinking Water ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Microbial Community Structure ◽  
Antibiotic Use ◽  
Community Diversity ◽  
Wide Range ◽  
Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

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