Engineering temporal dynamics in microbial communities

2022 ◽  
Vol 65 ◽  
pp. 47-55
Author(s):  
Carlotta Ronda ◽  
Harris H Wang
2021 ◽  
Author(s):  
Juliana Almario ◽  
Maryam Mahmoudi ◽  
Samuel Kroll ◽  
Matthew Agler ◽  
Aleksandra Placzek ◽  
...  

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.


2020 ◽  
Author(s):  
Haitao Wang ◽  
Micha Weil ◽  
Dominik Zak ◽  
Diana Münch ◽  
Anke Günther ◽  
...  

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.


mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland‐Moritz ◽  
Tess E. Brewer ◽  
...  

ABSTRACT Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.


2017 ◽  
Vol 8 ◽  
Author(s):  
Florine Degrune ◽  
Nicolas Theodorakopoulos ◽  
Gilles Colinet ◽  
Marie-Pierre Hiel ◽  
Bernard Bodson ◽  
...  

2021 ◽  
Vol 5 ◽  
Author(s):  
Sire Diedhiou-Sall ◽  
Komi B. Assigbetsee ◽  
Aminata N. Badiane ◽  
Ibrahima Diedhiou ◽  
M. Khouma ◽  
...  

The Sahel is an ecologically vulnerable region where increasing populations with a concurrent increase in agricultural intensity has degraded soils. Agroforestry offers an approach to remediate these landscapes. A largely unrecognized agroforestry resource in the Sahel are the native shrubs, Piliostigma reticulatum, and Guiera senegalensis that to varying degrees already coexist with row crops. These shrubs improve soil quality, redistribute water from the deep soil to the surface (hydraulic lift), and can improve crop growth. However, little information is available on whether these shrubs affect spatial and temporal dynamics of microbial communities. Therefore, the objective of this study was to determine microbial composition and activity in the wet and dry seasons of soil in the: shrub rhizosphere (RhizS), inter-root zone (IntrS), and outside the influence of shrub soil (OutS) for both G. senegalensis and P. reticulatum in Senegal. A 3 × 2 factorial field experiment was imposed at two locations (490 and 700 mm annual rainfall with G. senegalensis and P. reticulatum, respectively), that had the soil sampling treatments of three locations (RhizS, IntrS, and OutS) and two seasons (wet and dry). Soils were analyzed for: microbial diversity (DGGE with bacterial 16S or fungal 28S rRNA gene sequences phospholipids fatty acid, PLFA); enzyme activities; microbial biomass carbon (MBC); and nitrogen (N) mineralization potential. For the DGGE profiling, the bacterial community responded more to the rhizosphere effect, whereas, the fungal community was more sensitive to season. PLFA, MBC, enzyme activities and inorganic N were significantly higher in both seasons for the RhizS. The presence of shrubs maintained rhizosphere microbial communities and activity during the dry season. This represents a paradigm shift for semi-arid environments where logically it would be expected to have no microbial activity in the extended dry season. In contrast this study has shown this is not the case that rather the presence of shrub roots maintained the microbial community in the dry season most likely due to hydraulic lift and root exudates. This has implications when these shrubs are in cropped fields in that decomposition and mineralization of nutrients can proceed in the dry season. Thus, enabling accumulation of plant available nutrients during the dry season for uptake by crops in the rainy season.


2020 ◽  
Vol 84 ◽  
pp. 205-216
Author(s):  
P Salgado ◽  
A Machado ◽  
AA Bordalo

Understanding the spatial and seasonal dynamics of nitrogen (N)-cycle microbial communities is pivotal for the knowledge of N biogeochemistry. The present study addressed the spatial-temporal variability of nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, and nosZI) key genes, as well as of non-denitrifying nitrous oxide (N2O) reducers (nosZII), coupled with key environmental variables, in an estuarine ecosystem (Douro, NW Portugal). Samples were collected on a monthly basis over 1 yr, key physical-chemical parameters were measured, and specific functional gene abundances were assayed. The results revealed a clear seasonality for nirS, nosZII, and bacterial and archaeal amoA abundance, with an increase during the winter/spring seasons. This period was especially characterized by high levels of dissolved oxygen, low temperature, low salinity, and increased turbidity. Indeed, turbidity emerged as the key factor controlling the distribution of nirS, nosZII bacterial, and archaeal amoA abundance. In contrast, the abundance of nosZI increased during the summer, while nirK abundance was enhanced from the fall to late spring. Additionally, the availability of dissolved inorganic nitrogen nutrients had no commensurable effect on N-cycle functional genes. This study of the annual variation of N-cycle functional genes in a temperate Atlantic estuary provides a major contribution to the understanding of how environmental factors potentially influence the distribution and abundance of N-cycle microbial communities.


2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Alacia Armstrong ◽  
Angel Valverde ◽  
Jean-Baptiste Ramond ◽  
Thulani P. Makhalanyane ◽  
Janet K. Jansson ◽  
...  

2012 ◽  
Vol 103 (3) ◽  
pp. 589-601 ◽  
Author(s):  
Simone Raposo Cotta ◽  
Armando Cavalcante Franco Dias ◽  
Ivanildo Evódio Marriel ◽  
Eliane Aparecida Gomes ◽  
Jan Dirk van Elsas ◽  
...  

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