Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain)

Molina‐Menor, Esther; Gimeno-Valero, Helena; Pascual, Javier; Peretó, Juli; Porcar, Manuel

doi:10.3390/microorganisms8101547

Cited by 15 publications

(4 citation statements)

References 39 publications

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“…nov., and Kineococcus siccus sp. nov. ( Molina-Menor et al, 2020 ). Moreover, the isolates identified as Homoserinibacter and Ramlibacter , which were 10 and 7, respectively, were all potential new species, and one isolate in the collection showed an ID value lower than 95%, which is the threshold value for new genus description ( Chun et al, 2018 ).…”

Section: Resultsmentioning

confidence: 99%

“…This polysaccharide degradation has a crucial impact in the carbon sources reuse cycles (Yeager et al, 2017). Glucosidases, glycoside hydrolases, carbohydrate esterases, and other related enzymatic activities are abundant in the analyzed genomes of the three new Kineococcus strains described from Tabernas indeed (Molina-Menor et al, 2020). Actinobacterial species can play also an important role in bioremediation.…”

Section: Discussion the Tabernas Desert Soils Harbor A Wide Bacterialmentioning

confidence: 99%

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High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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One of the most diverse ecological niches for microbial bioprospecting is soil, including that of drylands. Drylands are one of the most abundant biomes on Earth, but extreme cases, such as deserts, are considered very rare in Europe. The so-called Tabernas Desert is one of the few examples of a desert area in continental Europe, and although some microbial studies have been performed on this region, a comprehensive strategy to maximize the isolation of environmental bacteria has not been conducted to date. We report here a culturomics approach to study the bacterial diversity of this dryland by using a simple strategy consisting of combining different media, using serial dilutions of the nutrients, and using extended incubation times. With this strategy, we were able to set a large (254 strains) collection of bacteria, the majority of which (93%) were identified through 16S ribosomal RNA (rRNA) gene amplification and sequencing. A significant fraction of the collection consisted of Actinobacteria and Proteobacteria, as well as Firmicutes strains. Among the 254 isolates, 37 different genera were represented, and a high number of possible new taxa were identified (31%), of which, three new Kineococcus species. Moreover, 5 out of the 13 genera represented by one isolate were also possible new species. Specifically, the sequences of 80 isolates held a percentage of identity below the 98.7% threshold considered for potentially new species. These strains belonged to 20 genera. Our results reveal a clear link between medium dilution and isolation of new species, highlight the unexploited bacterial biodiversity of the Tabernas Desert, and evidence the potential of simple strategies to yield surprisingly large numbers of diverse, previously unreported, bacterial strains and species.

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Section: Resultsmentioning

confidence: 99%

Section: Discussion the Tabernas Desert Soils Harbor A Wide Bacterialmentioning

confidence: 99%

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

et al. 2021

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“…Similarly, dominant genera within the class Actinobacteria, i.e., Modestobacter and Kineococcus, are known as phyllosphere colonizers [51,61]. Several type strains of these two actinobacterial genera were isolated from halophytic plants [67][68][69][70], desert [71,72], or saline environments [73]. Thus, members of these genera may be particularly well adapted to water-limiting conditions, likewise as reported for soil-dwelling Actinobacteria [74,75].…”

Section: Dominant Bacterial Classes and Genera Of T Landbeckii Plants...mentioning

confidence: 79%

Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment

Hakobyan,

Velte,

Sickel

et al. 2023

Microbiome

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Background The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. Results We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, “Candidatus Uzinura”) were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). Conclusions Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms.

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“…Our findings uncover that several widely recognized bacterial genera (namely Pseudomonas , Sphingomonas , and Bacillus ) have a notable impact on plant hormone production (Eshel et al, 2021). Moreover, certain bacterial species from the Kineosporiaceae families, such as Pseudokineococcus and Kineococcus , exhibit a remarkable tolerance to intense radiation when present on the leaf surface (Molina‐Menor et al, 2020). In root samples, many enriched genera were denoted as plant‐growth‐promoting rhizobacteria, including Actinophytocola , Promicromonospora , Streptomyces , Pseudonocardia , and Nocardioides within Actinobacteria (Qin et al, 2012), and Steroidobacter within Gammaproteobacteria (Wang et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Distinguishing the effects of micro‐ and macro‐habitats on plant‐associated microbiomes in the Qinghai‐Tibetan Qaidam Basin

Lai,

Liu,

Deng

et al. 2024

Land Degrad Dev

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Although microbiomes associated with plants and the environment are intricately intertwined, it remains unclear how various environmental scales affect these relationships differently. We employed high‐throughput amplicon sequencing to examine the plant‐associated bacterial and fungal communities across three different micro‐habitats (leaf, root, and root zone soil) in 16 shrubs distributed across a >500 km transect of the eastern Qinghai‐Tibetan Qaidam Basin. Among the three microhabitats, the diversity and composition of plant‐associated bacterial and fungal communities differed significantly. Although micro‐habitats play a crucial role in shaping plant‐associated microbial communities, geographic and climatic variables largely influenced the community compositions across the three micro‐habitats. Notably, the microbial communities in all three micro‐habitats showed significant distance‐decay patterns. Furthermore, fungi exhibited less variation across the three microenvironments, and were more sensitive to environmental changes than bacteria. Moreover, microbiome complexity and stochasticity gradually increased from soils to roots and finally to leaves. The microbial communities in soils and epiphytes (leaves and roots) were predominantly shaped by determinism and stochasticity, respectively. These results highlight that plant‐associated microbiomes are primarily shaped by the microenvironments associated with plants; however, their compositions, dynamics, and assembly are further influenced by geographic and climatic factors. Overall, our findings greatly increase our understanding of the intricate dynamics between plant‐associated microbiomes and their surrounding environment in drylands. This knowledge contributes to ongoing research on microbial ecology and provides substantial supports for the precise evaluation of desert ecosystem function. The findings are helpful for biodiversity conservation and sustainable management of desert shrublands.

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Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain)

Cited by 15 publications

References 39 publications

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

High Culturable Bacterial Diversity From a European Desert: The Tabernas Desert

Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment

Distinguishing the effects of micro‐ and macro‐habitats on plant‐associated microbiomes in the Qinghai‐Tibetan Qaidam Basin

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