Metatranscriptomics of pastures under drought stress show a rhizospheric meta-organism reshape

Tartaglia, Maria Carmela; Ranauda, Maria Antonietta; Falzarano, Alessandra; Maisto, Maria; Postiglione, Alessia; Prigioniero, Antonello; Scarano, Pierpaolo; Zuzolo, Daniela; Sciarrillo, Rosaria; Guarino, Carmine

doi:10.1016/j.rhisph.2023.100687

Cited by 6 publications

(2 citation statements)

References 49 publications

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“…To our knowledge, the effect of drought was not previously studied on hypersaline stromatolite-like systems. Nevertheless, the reported stress response employed by the Solar Lake microbial mat community, evident in the ROS and salinity response gene enrichment, is similar to other environments such as vegetated mudflat ecosystems ( 90 ), paddy soil ( 24 ), grassland rhizosphere ( 91 ), and alkaline wetland ( 92 ).…”

Section: Discussionmentioning

confidence: 58%

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

Abdallah,

Elbehery,

Ahmed

et al. 2024

mSystems

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The Solar Lake in Taba, Egypt, encompasses one of the few modern-day microbial mats’ systems metabolically analogous to Precambrian stromatolites. Solar Lake benthic communities and their adaptation to the Lake’s unique limnological cycle have not been described for over two decades. In this study, we revisit the flat mat and describe the summer’s shallow water versus exposed microbial community; the latter occurs in response to the seasonal partial receding of water. We employed metagenomic NovaSeq-6000 shotgun sequencing and 16S rRNA, mcrA, and dsrB quantitative PCR. A total of 292 medium-to-high-quality metagenome-assembled genomes (MAGs) were reconstructed. At the structural level, Candidatus Aenigmatarchaeota, Micrarchaeota, and Omnitrophota MAGs were exclusively detected in the shallow-water mats, whereas Halobacteria and Myxococcota MAGs were specific to the exposed microbial mat. Functionally, genes involved in reactive oxygen species (ROS) detoxification and osmotic pressure were more abundant in the exposed than in the shallow-water microbial mats, whereas genes involved in sulfate reduction/oxidation and nitrogen fixation were ubiquitously detected. Genes involved in the utilization of methylated amines for methane production were predominant when compared with genes associated with alternative methanogenesis pathways. Solar Lake methanogen MAGs belonged to Methanosarcinia , Bathyarchaeia , Candidatus Methanofastidiosales , and Archaeoglobales . The latter had the genetic capacity for anaerobic methane oxidation. Moreover, Coleofasciculus chthonoplastes , previously reported to dominate the winter shallow-water flat mat, had a substantial presence in the summer. These findings reveal the taxonomic and biochemical microbial zonation of the exposed and shallow-water Solar Lake flat mat benthic community and their capacity to ecologically adapt to the summer water recession. IMPORTANCE Fifty-five years ago, the extremophilic “Solar Lake” was discovered on the Red Sea shores, garnering microbiologists’ interest worldwide from the 1970s to 1990s. Nevertheless, research on the lake paused at the turn of the millennium. In our study, we revisited the Solar Lake benthic community using a genome-centric approach and described the distinct microbial communities in the exposed versus shallow-water mat unveiling microbial zonation in the benthic communities surrounding the Solar Lake. Our findings highlighted the unique structural and functional adaptations employed by these microbial mat communities. Moreover, we report new methanogens and phototrophs, including an intriguing methanogen from the Archaeoglobales family. We describe how the Solar Lake’s flat mat microbial community adapts to stressors like oxygen intrusion and drought due to summer water level changes, which provides insights into the genomic strategies of microbial communities to cope with altered and extreme environmental conditions.

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Section: Discussionmentioning

confidence: 58%

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

Abdallah,

Elbehery,

Ahmed

et al. 2024

mSystems

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“…These authors demonstrated that certain transcripts were more abundant in the roots and rhizosphere under severe water stress, including heat shock proteins (HSPs), as well as carbohydrate and amino acid transport and metabolism-related transcripts. Another metatranscriptomic study reported that drought stress promoted the transcripts of Proteobacteria and Bacteroidetes, while reducing those of Actinobacteria and Acidobacteria (Tartaglia et al, 2023). This study also indicated an over-expression of universal stress proteins by Proteobacteria and Bacteroidetes in water-stressed treatment compared to the control.…”

Section: 3mentioning

confidence: 61%

Plant-microbiome interactions under drought—insights from the molecular machinist’s toolbox

Ait-El-Mokhtar,

Meddich,

Baslam

2023

Front. Sustain. Food Syst.

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Plants face numerous challenges in novel and harsh environments, including altered precipitation regimes, salinity, extreme temperatures, increased atmospheric CO2, nutrient deficiency, heavy metals, and oxygen. Drought remains a major constraint to crop productivity and meeting food demand, with the frequency, intensity, and duration of drought expected to raise in the coming century. The “cry for help” hypothesis proposes that timely recruiting of the microbiome by plants may confer benefits in stress alleviation, plant growth, fitness, and health. The root-associated microbiome harbors 10–100 times more functional genes than the host, which can significantly stimulate the metabolic and genetic potential of plant–microbiome assembly. However, cross-talk among drought and the root-associated microbes, and among the root-associated microbiome and the host-plant, is less well understood. Understanding the molecular aspect of multiple mechanisms by which microbes associate with plants during drought stress is of fundamental importance in plant biology and agriculture. In this review, we examine the progress in research on the response of plant and its microbiome assemblages and interactions to drought stress, including the impact of drought and root exudates on host resilience. We delve into the potential of ‘omics’ technologies to unravel the signaling networks underlying these interactions and the multiway interactions that occur among the host and its associated microbiome. We then discuss the shortfalls, challenges, and future research directions in this field. Overall, we argue that harnessing/manipulating the crop microbiome presents a promising strategy for improving agricultural systems in the face of global climate change.

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Metatranscriptomics, Metaproteomics, and Metabolomics Approaches for Microbiome Characterization

Mathuria,

Jain,

Saini

et al. 2024

Multi-Omics Analysis of the Human Microbiome

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Metatranscriptomics of pastures under drought stress show a rhizospheric meta-organism reshape

Cited by 6 publications

References 49 publications

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

Deciphering the functional and structural complexity of the Solar Lake flat mat microbial benthic communities

Plant-microbiome interactions under drought—insights from the molecular machinist’s toolbox

Metatranscriptomics, Metaproteomics, and Metabolomics Approaches for Microbiome Characterization

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