scholarly journals Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a dessicated Namib Desert soil

2018 ◽  
Author(s):  
Carlos León-Sobrino ◽  
Jean-Baptiste Ramond ◽  
Gillian Maggs-Kölling ◽  
Don A Cowan
Keyword(s):  
Stress Response ◽  
Carbon Fixation ◽  
Nutrient Acquisition ◽  
Desert Soil ◽  
Namib Desert ◽  
Community Function ◽  
Network Analyses ◽  
Diel Cycles ◽  
Functional Profiling ◽  
Acquisition Processes

AbstractHot desert surface soils are characterised by extremely low water activities for large parts of any annual cycle. It is widely assumed that microbial processes in such soils are very limited. Here we present the first metatranscriptomic survey of microbial community function in a low water activity hyperarid desert soil. Sequencing of total mRNA revealed a diverse and active community, dominated byActinobacteria. Metatranscriptomic analysis of samples taken at different times over three days indicated that most functions did not fluctuate on a diel basis, except for a eukaryotic subpopulation which was induced during the cooler night hours. High levels of transcription of chemoautotrophic carbon fixation genes contrasted with limited expression of photosynthetic genes, indicating that chemoautotrophy is an important alternative to photosynthesis for carbon cycling in desiccated desert soils. Analysis of the transcriptional levels of key N-cycling genes provided strong evidence that soil nitrate was the dominant nitrogen input source. Transcriptional network analyses and taxon-resolved functional profiling suggested that nutrient acquisition processes, and not diurnal environmental variation, were the main drivers of community activity in hyperarid Namib Desert soil. While we also observed significant levels of expression of common stress response genes, these genes were not dominant hubs in the co-occurrence network.

scholarly journals Namib Desert Soil Microbial Community Diversity, Assembly, and Function Along a Natural Xeric Gradient

2017 ◽  
Vol 75 (1) ◽  
pp. 193-203 ◽  
Author(s):  
Vincent Scola ◽  
Jean-Baptiste Ramond ◽  
Aline Frossard ◽  
Olivier Zablocki ◽  
Evelien M. Adriaenssens ◽  
...  
Keyword(s):  
Microbial Community ◽  
Soil Microbial Community ◽  
Desert Soil ◽  
Community Diversity ◽  
Namib Desert ◽  
Microbial Community Diversity ◽  
Soil Microbial ◽  
And Function

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 BrphyB is critical for rapid recovery to darkness in mature Brassica rapa leaves

2020 ◽  
Author(s):  
Andrej A. Arsovski ◽  
Joseph E. Zemke ◽  
Morgan Hamm ◽  
Lauren Houston ◽  
Andrés Romanowski ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Carbon Fixation ◽  
Light Response ◽  
Nutrient Acquisition ◽  
Similar Response ◽  
Growth Responses ◽  
Wild Type ◽  
Transcriptomic Response ◽  
Transcriptional Dynamics ◽  
Optimal Resource

ABSTRACTCrop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the phytochrome (phy) class of photoreceptors signal and re-deploy carbon resources to alter growth, plant architecture, and reproductive timing. Brassica rapa has been used as a crop model to test for conservation of the phytochrome–carbon network. B. rapa phyB mutants have significantly decreased or absent CO2-stimulated growth responses in seedlings, and adult plants have reduced chlorophyll levels, photosynthetic rate, stomatal index, and seed yield. Here, we examine the transcriptomic response of adult wild-type and BrphyB leaves to darkening and recovery in light. Three days of darkness was sufficient to elicit a response in wild type leaves suggesting a shift from carbon fixation and nutrient acquisition to active redistribution of cellular resources. Upon a return to light, wild-type leaves appeared to transcriptionally return to a pre-darkness state restoring a focus on nutrient acquisition. Overall, BrphyB mutant plants have a similar response with key differences in genes involved in photosynthesis and light response which deviate from the wild type transcriptional dynamics. Genes targeted to the chloroplast are especially affected. Adult BrphyB mutant plants had fewer, larger chloroplasts, further linking phytochromes, chloroplast development, photosynthetic deficiencies and optimal resource allocation.

scholarly journals Network Analysis of Local Gene Regulators in Arabidopsis thaliana under Spaceflight Stress

Computers ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 18
Author(s):  
Vidya Manian ◽  
Harshini Gangapuram ◽  
Jairo Orozco ◽  
Heeralal Janwa ◽  
Carlos Agrinsoni
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Response ◽  
Network Analysis ◽  
Target Genes ◽  
Carbon Fixation ◽  
Reduction Process ◽  
Centrality Measures ◽  
Lasso Regression ◽  
Gene Expressions ◽  
Stress Response Genes

Spaceflight microgravity affects normal plant growth in several ways. The transcriptional dataset of the plant model organism Arabidopsis thaliana grown in the international space station is mined using graph-theoretic network analysis approaches to identify significant gene transcriptions in microgravity essential for the plant’s survival and growth in altered environments. The photosynthesis process is critical for the survival of the plants in spaceflight under different environmentally stressful conditions such as lower levels of gravity, lesser oxygen availability, low atmospheric pressure, and the presence of cosmic radiation. Lasso regression method is used for gene regulatory network inferencing from gene expressions of four different ecotypes of Arabidopsis in spaceflight microgravity related to the photosynthetic process. The individual behavior of hub-genes and stress response genes in the photosynthetic process and their impact on the whole network is analyzed. Logistic regression on centrality measures computed from the networks, including average shortest path, betweenness centrality, closeness centrality, and eccentricity, and the HITS algorithm is used to rank genes and identify interactor or target genes from the networks. Through the hub and authority gene interactions, several biological processes associated with photosynthesis and carbon fixation genes are identified. The altered conditions in spaceflight have made all the ecotypes of Arabidopsis sensitive to dehydration-and-salt stress. The oxidative and heat-shock stress-response genes regulate the photosynthesis genes that are involved in the oxidation-reduction process in spaceflight microgravity, enabling the plant to adapt successfully to the spaceflight environment.

scholarly journals MOLECULAR EVOLUTION OF GPCRS: CRH/CRH receptors

2014 ◽  
Vol 52 (3) ◽  
pp. T43-T60 ◽  
Author(s):  
David A Lovejoy ◽  
Belinda S W Chang ◽  
Nathan R Lovejoy ◽  
Jon del Castillo
Keyword(s):  
Stress Response ◽  
Molecular System ◽  
Peptide Hormone ◽  
Nutrient Acquisition ◽  
Energy Usage ◽  
Receptor System ◽  
Genome Duplications ◽  
Complex Forms ◽  
Multicellular Organisms ◽  
Crh Receptors

Corticotrophin-releasing hormone (CRH) is the pivotal neuroendocrine peptide hormone associated with the regulation of the stress response in vertebrates. However, CRH-like peptides are also found in a number of invertebrate species. The origin of this peptide can be traced to a common ancestor of lineages leading to chordates and to arthropods, postulated to occur some 500 million years ago. Evidence indicates the presence of a single CRH-like receptor and a soluble binding protein system that acted to transduce and regulate the actions of the early CRH peptide. In vertebrates, genome duplications led to the divergence of CRH receptors into CRH1 and CRH2 forms in tandem with the development of four paralogous ligand lineages that included CRH; urotensin I/urocortin (Ucn), Ucn2 and Ucn3. In addition, taxon-specific genome duplications led to further local divergences in CRH ligands and receptors. Functionally, the CRH ligand–receptor system evolved initially as a molecular system to integrate early diuresis and nutrient acquisition. As multicellular organisms evolved into more complex forms, this ligand–receptor system became integrated with the organismal stress response to coordinate homoeostatic challenges with internal energy usage. In vertebrates, CRH and the CRH1 receptor became associated with the hypothalamo-pituitary–adrenal/interrenal axis and the initial stress response, whereas the CRH2 receptor was selected to play a greater role in diuresis, nutrient acquisition and the latter aspects of the stress response.

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