scholarly journals Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Alacia Armstrong ◽  
Angel Valverde ◽  
Jean-Baptiste Ramond ◽  
Thulani P. Makhalanyane ◽  
Janet K. Jansson ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Temporal Dynamics ◽  
Functional Responses

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 Temporal dynamics of microbial transcription in wetted hyperarid desert soils

2021 ◽  
Author(s):  
Carlos León-Sobrino ◽  
Jean-Baptiste Ramond ◽  
Clément Coclet ◽  
Ritha-Meriam Kapitango ◽  
Gillian Maggs-Kölling ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Carbon Fixation ◽  
Temporal Dynamics ◽  
Time Frame ◽  
Water Addition ◽  
Functional Responses ◽  
Desert Soils ◽  
Biological Responses ◽  
Acquisition Processes ◽  
Alpha Proteobacteria

Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses which are considered to be essential for the long-term maintenance of biodiversity. In such environments, microbial communities have major roles in nutrient cycling, but their functional responses to short-lived resource opportunities are poorly understood. We used whole community metatranscriptomic data to demonstrate structured and sequential functional responses in desiccated desert soils to a simulated rainfall event over a seven-day time frame. Rapid transcriptional activation of Actinobacteria, Alpha-proteobacteria and phage transcripts was followed by a marked increase in protist and myxobacterial activity, before returning to the original state. In functional terms, motility systems were activated in the early phases, whereas competition-toxicity systems increased in parallel to the activity from predators and the drying of soils. The dispersal-predation dynamic was identified as a central driver of microbial community responses to watering. Carbon fixation mechanisms that were active under dry condition were rapidly down-regulated in wetted soils, and only reactivated on a return to a near-dry state, suggesting a reciprocal balance between carbon fixation and fixed-carbon acquisition processes. Water addition induced a general reduction in the transcription of stress response genes, most prominently HSP20, indicating that this chaperone is particularly important for life in desiccated ecosystems. Based on these data, we propose a rainfall response model for desert soil microbiomes.

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.

scholarly journals Territorial landscapes: incorporating density-dependence into wolf habitat selection studies

2019 ◽  
Vol 6 (11) ◽  
pp. 190282 ◽  
Author(s):  
Shawn T. O'Neil ◽  
Dean E. Beyer ◽  
Joseph K. Bump
Keyword(s):  
Habitat Selection ◽  
Density Dependence ◽  
Temporal Dynamics ◽  
Wildlife Habitat ◽  
Population Increase ◽  
Habitat Availability ◽  
Functional Responses ◽  
Model Framework ◽  
Selection Probability ◽  
Density Dependent

Habitat selection is a process that spans space, time and individual life histories. Ecological analyses of animal distributions and preferences are most accurate when they account for inherent dynamics of the habitat selection process. Strong territoriality can constrain perception of habitat availability by individual animals or groups attempting to colonize or establish new territory. Because habitat selection is a function of habitat availability, broad-scale changes in habitat availability or occupancy can drive density-dependent habitat functional responses. We investigated density-dependent habitat selection over a 19-year period of grey wolf ( Canis lupus ) recovery in Michigan, USA, using a generalized linear mixed model framework to develop a resource selection probability function (RSPF) with habitat coefficients conditioned on random effects for wolf packs and random year intercepts. In addition, we allowed habitat coefficients to vary as interactions with increasing wolf density over space and time. Results indicated that pack presence was driven by factors representing topography, human development, winter prey availability, forest structure, roads, streams and snow. Importantly, responses to many of these predictors were density-dependent. Spatio-temporal dynamics and population changes can cause considerable variation in wildlife–habitat relationships, possibly confounding interpretation of conventional habitat selection models. By incorporating territoriality into an RSPF analysis, we determined that wolves' habitat use in Michigan shifted over time, for example, exhibiting declining responses to winter prey indices and switching from positive to negative responses with respect to stream densities. We consider this an important example of a habitat functional response in wolves, driven by colonization, density-dependence and changes in occupancy during a time period of range expansion and population increase.

scholarly journals Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul Carini ◽  
Manuel Delgado-Baquerizo ◽  
Eve-Lyn S. Hinckley ◽  
Hannah Holland‐Moritz ◽  
Tess E. Brewer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Variability ◽  
Spatial Heterogeneity ◽  
Microbial Communities ◽  
Temporal Variability ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Preferences ◽  
Soil Microbial

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.

Molecular and functional responses of soil microbial communities under grassland restoration

2008 ◽  
Vol 127 (3-4) ◽  
pp. 286-293 ◽  
Author(s):  
Pierre Plassart ◽  
Marthe Akpa Vinceslas ◽  
Christophe Gangneux ◽  
Anne Mercier ◽  
Sylvie Barray ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Grassland Restoration ◽  
Functional Responses ◽  
Soil Microbial

scholarly journals Temporal Dynamics of Soil Microbial Communities below the Seedbed under Two Contrasting Tillage Regimes

2017 ◽  
Vol 8 ◽  
Author(s):  
Florine Degrune ◽  
Nicolas Theodorakopoulos ◽  
Gilles Colinet ◽  
Marie-Pierre Hiel ◽  
Bernard Bodson ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Temporal Dynamics ◽  
Soil Microbial Communities ◽  
Soil Microbial

scholarly journals Functional Responses of Salt Marsh Microbial Communities to Long-Term Nutrient Enrichment

2016 ◽  
Vol 82 (9) ◽  
pp. 2862-2871 ◽  
Author(s):  
Christopher J. Graves ◽  
Elizabeth J. Makrides ◽  
Victor T. Schmidt ◽  
Anne E. Giblin ◽  
Zoe G. Cardon ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Nutrient Enrichment ◽  
Nutrient Loading ◽  
Whole Genome ◽  
Sewage Effluent ◽  
Fine Scale ◽  
Functional Responses

ABSTRACTEnvironmental nutrient enrichment from human agricultural and waste runoff could cause changes to microbial communities that allow them to capitalize on newly available resources. Currently, the response of microbial communities to nutrient enrichment remains poorly understood, and, while some studies have shown no clear changes in community composition in response to heavy nutrient loading, others targeting specific genes have demonstrated clear impacts. In this study, we compared functional metagenomic profiles from sediment samples taken along two salt marsh creeks, one of which was exposed for more than 40 years to treated sewage effluent at its head. We identified strong and consistent increases in the relative abundance of microbial genes related to each of the biochemical steps in the denitrification pathway at enriched sites. Despite fine-scale local increases in the abundance of denitrification-related genes, the overall community structures based on broadly defined functional groups and taxonomic annotations were similar and varied with other environmental factors, such as salinity, which were common to both creeks. Homology-based taxonomic assignments of nitrous oxide reductase sequences in our data show that increases are spread over a broad taxonomic range, thus limiting detection from taxonomic data alone. Together, these results illustrate a functionally targeted yet taxonomically broad response of microbial communities to anthropogenic nutrient loading, indicating some resolution to the apparently conflicting results of existing studies on the impacts of nutrient loading in sediment communities.IMPORTANCEIn this study, we used environmental metagenomics to assess the response of microbial communities in estuarine sediments to long-term, nutrient-rich sewage effluent exposure. Unlike previous studies, which have mainly characterized communities based on taxonomic data or primer-based amplification of specific target genes, our whole-genome metagenomics approach allowed an unbiased assessment of the abundance of denitrification-related genes across the entire community. We identified strong and consistent increases in the relative abundance of gene sequences related to denitrification pathways across a broad phylogenetic range at sites exposed to long-term nutrient addition. While further work is needed to determine the consequences of these community responses in regulating environmental nutrient cycles, the increased abundance of bacteria harboring denitrification genes suggests that such processes may be locally upregulated. In addition, our results illustrate how whole-genome metagenomics combined with targeted hypothesis testing can reveal fine-scale responses of microbial communities to environmental disturbance.

scholarly journals Spatial and Temporal Distribution of Soil Microbial Properties in Two Shrub Intercrop Systems of the Sahel

2021 ◽  
Vol 5 ◽  
Author(s):  
Sire Diedhiou-Sall ◽  
Komi B. Assigbetsee ◽  
Aminata N. Badiane ◽  
Ibrahima Diedhiou ◽  
M. Khouma ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Enzyme Activities ◽  
Temporal Dynamics ◽  
Dry Season ◽  
Hydraulic Lift ◽  
Annual Rainfall ◽  
Rrna Gene ◽  
28S Rrna ◽  
Microbial Composition ◽  
Row Crops

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.

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