scholarly journals Life on leaves : uncovering temporal dynamics in Arabidopsis' leaf microbiota

2021 ◽  
Author(s):  
Juliana Almario ◽  
Maryam Mahmoudi ◽  
Samuel Kroll ◽  
Matthew Agler ◽  
Aleksandra Placzek ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Photosynthetic Activity ◽  
Temporal Dynamics ◽  
Growing Season ◽  
High Turnover ◽  
Microbial Network ◽  
Stabilization Phase ◽  
Time Patterns ◽  
Microbe Interactions ◽  
Compositional Changes

Leaves are primarily responsible for the plant′s photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plant′s lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plant′s growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plant′s growing season. Despite a high turnover in these communities, we identified 19 "core" taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network "hubs" and "hubs" alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.

scholarly journals The Leaf Microbiota of Arabidopsis Displays Reproducible Dynamics And Patterns Throughout The Growing Season

2021 ◽  
Author(s):  
Juliana Almario ◽  
Maryam Mahmudi ◽  
Samuel Kroll ◽  
Mathew Agler ◽  
Aleksandra Placzek ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Microbial Communities ◽  
Photosynthetic Activity ◽  
Temporal Dynamics ◽  
Growing Season ◽  
Plant Fitness ◽  
High Turnover ◽  
Microbial Network ◽  
Stabilization Phase ◽  
Microbe Interactions

Abstract Background: Leaves are primarily responsible for the plant's photosynthetic activity. Thus, changes in the leaf microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. Identifying the processes and microorganisms that drive these changes over a plant’s lifetime is, therefore, crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating changes in both, composition and microbe-microbe interactions via the study of microbial networks.Results: Field-grown Arabidopsis were used to monitor leaf bacterial, fungal and oomycete communities throughout the plant’s growing season (extending from November to March) over three consecutive years. Our results revealed the existence of conserved temporal patterns, with microbial communities and networks going through a stabilization phase of decreased diversity and variability at the beginning of the plant’s growing season. Despite a high turnover in these communities, we identified 19 'core' taxa persisting on Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network 'hubs' and 'hubs' alternate with time. Conclusions: Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting the possibility of predicting those patterns to drive microbial communities towards desired states.

Temporal fluctuations of microbial communities within the crop growing season

Geoderma ◽  
2021 ◽  
Vol 391 ◽  
pp. 114951
Author(s):  
Zachery R. Leitner ◽  
Aaron Lee M. Daigh ◽  
Jodi DeJong-Hughes
Keyword(s):  
Microbial Communities ◽  
Growing Season ◽  
Temporal Fluctuations

scholarly journals Differences in the Concentration and Composition of Human Milk Components Are Related to Variation in Milk and Infant Fecal Microbiomes

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1056-1056
Author(s):  
Ryan Pace ◽  
Janet Williams ◽  
Kimberly Lackey ◽  
Mark McGuire ◽  
Michelle McGuire ◽  
...  
Keyword(s):  
Human Milk ◽  
Microbial Communities ◽  
Infant Health ◽  
Hypervariable Region ◽  
Fecal Microbiota ◽  
National Institutes Of Health ◽  
Funding Sources ◽  
Infant Feces ◽  
Microbe Interactions ◽  
Foundation Award

Abstract Objectives Profiles of human milk oligosaccharides (HMO) and milk/infant fecal microbiota vary globally. However, associations between and among HMO, other milk-borne factors (e.g., lactose, protein), and milk/infant fecal microbiomes have not been well-investigated. Here we tested the hypothesis that variations in milk lactose, protein, and HMO concentrations are associated with variations in the structure of milk and infant fecal microbial communities. Methods Milk/infant fecal samples from 357 maternal-infant dyads collected as part of the INSPIRE study from 11 geographically/culturally diverse sites located in eight countries (Ethiopia, The Gambia, Ghana, Kenya, Peru, Spain, Sweden, and USA) were analyzed. DNA was extracted and bacterial 16S rRNA V1V3 hypervariable region amplified/sequenced for microbiome analysis. HMO, lactose, and protein profiles were generated from HPLC and spectrophotometric assays. Results Milk and infant feces share many of the same abundant bacterial genera, while also containing unique bacterial communities. Community states type (CST) analyses indicate both sample types group into a relatively small number of discrete communities characterized by enrichment of specific taxa (e.g., Streptococcus, Bifidobacterium). Concentrations of milk lactose and protein varied by population/CST. Additionally, variation in the microbial community structure of milk and infant feces was associated with concentrations of total/individual HMO, lactose, and protein. Conclusions Similar to HMO concentrations, milk lactose and protein vary globally. Variations in milk and infant fecal microbial communities are associated with those of milk lactose, protein, and HMO concentrations. Given these results, as well as prior data on the influence of other environmental variables (e.g., pumped vs. direct breastfeeding), additional longitudinal studies are needed to better understand this complex network of maternal-infant-microbe interactions with respect to environmental factors and how differences impact postnatal maternal-infant health. Funding Sources National Science Foundation (award 1,344,288), National Institutes of Health (R01 HD092297), and USDA.

scholarly journals A Microbial Perspective on the Grand Challenges in Comparative Animal Physiology

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Kevin D. Kohl
Keyword(s):  
Microbial Communities ◽  
Vertical Integration ◽  
Temporal Integration ◽  
Data Sets ◽  
Grand Challenges ◽  
Animal Physiology ◽  
Physiological Processes ◽  
Microbe Interactions ◽  
Animal Hosts ◽  
Host Microbe Interactions

ABSTRACTInteractions with microbial communities can have profound influences on animal physiology, thereby impacting animal performance and fitness. Therefore, it is important to understand the diversity and nature of host-microbe interactions in various animal groups (invertebrates, fish, amphibians, reptiles, birds, and mammals). In this perspective, I discuss how the field of host-microbe interactions can be used to address topics that have been identified as grand challenges in comparative animal physiology: (i) horizontal integration of physiological processes across organisms, (ii) vertical integration of physiological processes across organizational levels within organisms, and (iii) temporal integration of physiological processes during evolutionary change. Addressing these challenges will require the use of a variety of animal models and the development of systems approaches that can integrate large, multiomic data sets from both microbial communities and animal hosts. Integrating host-microbe interactions into the established field of comparative physiology represents an exciting frontier for both fields.

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Pei Wang ◽  
Xiao Kong ◽  
Hongsong Chen ◽  
Youlun Xiao ◽  
Huijun Liu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Rice Cultivars ◽  
Rice Varieties ◽  
Microbial Network ◽  
Β Diversity ◽  
Group I ◽  
Α Diversity ◽  
Microbe Interactions ◽  
Endophytic Bacterial Community ◽  
Group Ii

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

scholarly journals Photosynthetic activity and productivity of potato plants when using foliar dressings with complex micronutrients and humate

2021 ◽  
Vol 285 ◽  
pp. 02028
Author(s):  
Olga Savina ◽  
Svetlana Afinogenova ◽  
Valentina Krishtafovich ◽  
Bakhytkul Baikhozhaeva
Keyword(s):  
Leaf Area ◽  
Photosynthetic Activity ◽  
Growing Season ◽  
Treatment Control ◽  
Potato Plants ◽  
Photosynthetic Potential

The article presents the results of many years of research on the effect of foliar dressing with complex fertilizers and humate on photosynthetic activity and productivity of potato plants of Gala and Latona varieties. The following options have been studied: 1) without treatment (control); 2) dressing with Ekorost humate at a dose of 0.2-0.4 l/ha; 3) dressing with micronutrient Strada N at a dose of 3-5 l/ha; 4) dressing with micronutrient Strada R at a dose of 3-5 l/ha. The treatment was carried out twice during the growing season: when full shoots appeared and 14 days after the first one. Determination of the leaf area and calculation of the photosynthetic potential were carried out according to the VNIIKH method (1967) three times during the growing season in the following phases: budding, flowering, and the beginning of withering away of lower leaves. The crop was harvested by the method of continuous harvesting of the accounting area of the plots with weighing. The effectiveness of the studied agrotechnical methods has been proved. The best variant of the investigated ones is the use of Strada R. The plants of this variant formed a more powerful assimilation apparatus and had the highest photosynthetic potential, which ultimately affected the yield of tubers. The increase in the yield of two varieties of potatoes was 21.8-23.1 % in relation to the control. Gala variety turned out to be more responsive to the action of vegetative treatments in comparison with Latona variety.

scholarly journals Temporal and spatial dynamics of peat microbiomes in drained and rewetted soils of three temperate peatlands

2020 ◽  
Author(s):  
Haitao Wang ◽  
Micha Weil ◽  
Dominik Zak ◽  
Diana Münch ◽  
Anke Günther ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Greenhouse Gas Emissions ◽  
Greenhouse Gas ◽  
Community Composition ◽  
Structural Equation ◽  
Structural Equation Models ◽  
Temporal Dynamics ◽  
Salt Water ◽  
Microbial Community Composition ◽  
Gas Emissions

AbstractBackgroundDrainage of high-organic peatlands for agricultural purposes has led to increased greenhouse gas emissions and loss of biodiversity. In the last decades, rewetting of peatlands is on the rise worldwide, to mitigate these negative impacts. However, it remains still questionable how rewetting would influence peat microbiota as important drivers of nutrient cycles and ecosystem restoration. Here, we investigate the spatial and temporal dynamics of the diversity, community composition and network interactions of prokaryotes and eukaryotes, and the influence of rewetting on these microbial features in formerly long-term drained and agriculturally used fens. Peat-soils were sampled seasonally from three drained and three rewetted sites representing the dominating fen peatland types of glacial landscapes in Northern Germany, namely alder forest, costal fen and percolation fen.ResultsCostal fens as salt-water impacted systems showed a lower microbial diversity and their microbial community composition showed the strongest distinction from the other two peatland types. Prokaryotic and eukaryotic community compositions showed a congruent pattern which was mostly driven by peatland type and rewetting. Rewetting decreased the abundances of fungi and prokaryotic decomposers, while the abundance of potential methanogens was significantly higher in the rewetted sites. Rewetting also influenced the abundance of ecological clusters in the microbial communities identified from the co-occurrence network. The microbial communities changed only slightly with depth and over time. According to structural equation models rewetted conditions affected the microbial communities through different mechanisms across the three studied peatland types.ConclusionsOur results suggest that rewetting strongly impacts the structure of microbial communities and, thus, important biogeochemical processes, which may explain the high variation in greenhouse gas emissions upon rewetting of peatlands. The improved understanding of functional mechanisms of rewetting in different peatland types lays the foundation for securing best practices to fulfil multiple restoration goals including those targeting on climate, water, and species protection.

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