Phylogenomic analysis reveals a two‐stage process of the evolutionary transition of <i>Shewanella</i> from the upper ocean to the hadal zone

Tang, Xixiang; Yu, Libo; Yi, Yi; Wang, Jiahua; Wang, Siyuan; Meng, Canxing; Liu, Shunzhang; Hao, Yali; Zhang, Yue; Cao, Xiangyu; Jian, Huahua; Xiao, Xiang

doi:10.1111/1462-2920.15162

Cited by 20 publications

(12 citation statements)

References 70 publications

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“…These indexes can reflect the nutrient availabilities in the environment, as the comparison studies between epipelagic and mesopelagic Marinimicrobia genomic modalities [73]. Only a reduced use of carbon in the AA sequences was found in the NES-AT clade genomes, indicating that carbon-limited conditions in polar regions are likely an important factor influencing the evolution of Nesterenkonia [74]. Harsh conditions often limit plant growth, which provides a primary source of organic carbon.…”

Section: Genomic Feature Comparison Between Nes-at Isolates and Other...mentioning

confidence: 99%

Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments

et al. 2022

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The members of the Nesterenkonia genus have been isolated from various habitats, like saline soil, salt lake, sponge-associated and the human gut, some of which are even located in polar areas. To identify their stress resistance mechanisms and draw a genomic profile across this genus, we isolated four Nesterenkonia strains from the lakes in the Tibetan Plateau, referred to as the third pole, and compared them with all other 30 high-quality Nesterenkonia genomes that are deposited in NCBI. The Heaps’ law model estimated that the pan-genome of this genus is open and the number of core, shell, cloud, and singleton genes were 993 (6.61%), 2782 (18.52%), 4117 (27.40%), and 7132 (47.47%), respectively. Phylogenomic and ANI/AAI analysis indicated that all genomes can be divided into three main clades, named NES-1, NES-2, and NES-3. The strains isolated from lakes in the Tibetan Plateau were clustered with four strains from different sources in the Antarctic and formed a subclade within NES-2, described as NES-AT. Genome features of this subclade, including GC (guanine + cytosine) content, tRNA number, carbon/nitrogen atoms per residue side chain (C/N-ARSC), and amino acid composition, in NES-AT individuals were significantly different from other strains, indicating genomic adaptation to cold, nutrient-limited, osmotic, and ultraviolet conditions in polar areas. Functional analysis revealed the enrichment of specific genes involved in bacteriorhodopsin synthesis, biofilm formation, and more diverse nutrient substance metabolism genes in the NES-AT clade, suggesting potential adaptation strategies for energy metabolism in polar environments. This study provides a comprehensive profile of the genomic features of the Nesterenkonia genus and reveals the possible mechanism for the survival of Nesterenkonia isolates in polar areas.

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Section: Genomic Feature Comparison Between Nes-at Isolates and Other...mentioning

confidence: 99%

Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments

et al. 2022

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“…It would be useful to construct a "grammar of interactions" among microbiotic particles, which should consider not only the identification of classic taxa, but the local ecotypes that help stabilize the diversification of the species to preserve the same functions despite environmental changes (García-García et al, 2019). Indeed that is influenced by the of particle's connectivity, depending on dynamics of the different ecological subcompartments; as an example, evolution (diversification) of Shewanella differs in the upper ocean to the abyssal zones (Tang et al, 2021).…”

Section: Interactions Among Microbiotic Particles In Soil-water Environments: Bacterial Coalescence and Dispersalmentioning

confidence: 99%

Microbiotic particles in water and soil, water-soil microbiota coalescences, and antimicrobial resistance

Baquero¹,

Coque²,

Guerra-Pinto³

et al. 2021

Preprint

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Bacterial organisms like surfaces. Water and soil contain a multiplicity of particulated material where bacterial populations and communities might attach. Microbiotic particles refers to any type of small particles (less than 2 mm) where bacteria (and other microbes) might attach, resulting in medium- long-term colonization. In this work, the interactions of bacterial organisms with microbiotic particles of the soil and water are reviewed. These particles include bacteria-bacteria aggregates, and aggregates with particles of fungi (particularly in the rhizosphere), protozoa, phytoplankton, zooplankton, biodetritus resulting from animal and vegetal decomposition, humus, mineral particles (clay, carbonates, silicates), and anthropogenic particles (including wastewater particles or microplastics). At they turn, these particles might interact and coalesce (as in the marine snow). Natural phenomena (from river flows to tides, tsunamis, currents, or heavy winds) and anthropogenic activity (such as agriculture, waste-water management, mining, soil-mass movement) favors interaction and merging between all these soil and water particles, and consequently coalescence of their bacterial-associated populations and communities, resulting in an enhancement of mixed-recombinant communities capable of genetic exchange, including antimicrobial resistance genes, particularly in antimicrobial-polluted environments. Particles also favor compartmentalization of bacterial populations favoring diversification and acquisition of mutational resistance by random drift. In general, microbial evolution is accelerated by the aggregation of microbiotic particles. We propose that the world spread of antimicrobial resistance might relate with the environmental dynamics of microbiotic particles, and discuss possible methods to reduce this problem influencing One Health and Planetary Health.

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“…WP2 represents a distinct clade that is distant from two other Group 1 Shewanella strains that have been represented using Genome-scale models (GEMs): Shewanella loihica PV-4 and S. piezotolerans WP3 (34,36). An analysis of the complete genome of WP2 revealed an expansion of transposable elements, motility genes, and chemotaxis genes compared to other deep-sea Shewanella (37).…”

Section: Introductionmentioning

confidence: 99%

Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations

Dufault‐Thompson

Nie

Jian

et al. 2022

Preprint

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Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in non-mesophilic organisms, however, is currently missing. In this study, thermodynamically-constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (ΔrG′), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to the lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and the electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures.

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Phylogenomic analysis reveals a two‐stage process of the evolutionary transition of Shewanella from the upper ocean to the hadal zone

Cited by 20 publications

References 70 publications

Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments

Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments

Microbiotic particles in water and soil, water-soil microbiota coalescences, and antimicrobial resistance

Reconstruction and analysis of thermodynamically-constrained models reveal metabolic responses of a deep-sea bacterium to temperature perturbations

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