Occurrence, Diversity, and Genomes of “
            <i>Candidatus</i>
            Patescibacteria” along the Early Diagenesis of Marine Sediments

Zhao, Rui; Farag, Ibrahim; Jørgensen, Steffen Leth; Biddle, Jennifer F.

doi:10.1128/aem.01409-22

Cited by 11 publications

(3 citation statements)

References 100 publications

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“…The phylum Patescibacteria is considered a superphylum composed of a diverse set of bacteria [45,46]. Bacteria within this phylum are often found in aquatic environments [46][47][48][49]. Thus, it is likely that the abundance of this bacterial phylum on the skin increases with prolonged exposure to an aquatic environment (i.e., seawater) and therefore is found in higher abundance on the skin of nesting females.…”

Section: Comparisons Across Life-stage Classesmentioning

confidence: 99%

Baseline Skin Microbiota of the Leatherback Sea Turtle

Kuschke,

Wyneken,

Miller

2024

Microorganisms

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The integumentary system of the leatherback sea turtle (Dermochelys coriacea) is the most visible and defining difference of the species, with its smooth and waxy carapace and finely scaled skin, distinguishing it from the other six sea turtle species. The skin is the body’s largest organ and serves as a primary defense against the outside world and is thus essential to health. To date, we have begun to understand that the microorganisms located on the skin aid in these functions. However, many host–microbial interactions are not yet fully defined or understood. Prior to uncovering these crucial host–microbial interactions, we must first understand the communities of microorganisms present and how they differ through life-stage classes and across the body. Here, we present a comprehensive bacterial microbial profile on the skin of leatherbacks. Using next-generation sequencing (NGS), we identified the major groups of bacteria on the skin of neonates at emergence, neonates at 3–4 weeks of age (i.e., post-hatchlings), and nesting females. These data show that the predominant bacteria on the skin of the leatherback are different at each life-stage class sampled. This suggests that there is a shift in the microbial communities of the skin associated with life-stage class or even possibly age. We also found that different sample locations on the nesting female (i.e., carapace and front appendages = flipper) have significantly different communities of bacteria present. This is likely due to differences in the microhabitats of these anatomic locations and future studies should explore if this variation also holds true for neonates. These data define baseline skin microbiota on the leatherback and can serve as a foundation for additional work to broaden our understanding of the leatherbacks’ host–microbial interactions, the impacts of environmental changes or stressors over time, and even the pathogenicity of disease processes.

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Section: Comparisons Across Life-stage Classesmentioning

confidence: 99%

Baseline Skin Microbiota of the Leatherback Sea Turtle

Kuschke,

Wyneken,

Miller

2024

Microorganisms

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“…Finally, Acidobacteria, Chloroflexi phyla, which were abundant in the barcode diversity, Patescibacteria, Spirochaetes, Armatimonadetes, Verrucomicrobia and Nitrospirae, which were less abundant, and finally the scarce phyla Fusobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, WSP-2 and Epsilonbacteraeota were completely missing (Fig 8). With the exception of the Patescibacteria, Fusobacteria, Latescibacteria, Rokubacteria and WSP-2 phyla, which are currently candidate phyla lacking cultured representatives [103][104][105][106][107], viable isolates could be obtained for other mentioned phyla. For example, the culture conditions for isolating bacteria from Acidobacteria, Verrucomicrobia [108][109][110] and Spirochaetes phyla [111,112] have been described.…”

Section: Plos Onementioning

confidence: 99%

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Sondo,

Wonni,

Koïta

et al. 2023

PLoS ONE

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Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity, to assess the diversity of the obtained isolates based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both cultivars, while five others were effective on only one cultivar. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the in vitro and in planta PGP capacities description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

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“…Within the Actinobacteria phylum, which was not well represented in our collection (Fig 7), several orders were missing, with the most important being Micromonosporales, Acidimicrobiales and Kineosporiales, and within the Bacteroidetes phylum the missing orders were Bacteroidales, Flavobacteriales and Cytophagales.Finally, Acidobacteria, Chloroflexi phyla, which were abundant in the barcode diversity, Patescibacteria, Spirochaetes, Armatimonadetes, Verrucomicrobia and Nitrospirae, which were less abundant, and finally the scarce phyla Fusobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, WSP-2 and Epsilonbacteraeota were completely missing (Fig 7). With the exception of the Patescibacteria, Fusobacteria, Latescibacteria, Rokubacteria and WSP-2 phyla, which are currently candidate phyla lacking cultured representatives(99)(100)(101)(102)(103), viable isolates could be obtained for other mentioned phyla. For example, the culture conditions for isolating bacteria from Acidobacteria, Verrucomicrobia(104)(105)(106) and Spirochaetes phyla (107,108) have been described.…”

mentioning

confidence: 99%

Culturable approach to rice-root associated bacteria in Burkina Faso: diversity, plant growth-promoting rhizobacteria properties and cross-comparison with metabarcoding data

Sondo

Wonni

Koïta

et al. 2023

Preprint

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Plant-associated bacteria are essential partners in plant health and development. In addition to taking advantage of the rapid advances recently achieved in high-throughput sequencing approaches, studies on plant-microbiome interactions require experiments with culturable bacteria. A study on the rice root microbiome was recently initiated in Burkina Faso. As a follow up, the aim of the present study was to develop a collection of corresponding rice root-associated bacteria covering maximum diversity so as, to be able to assess the diversity of the collection based on the culture medium used, and to describe the taxonomy, phenotype and abundance of selected isolates in the rice microbiome. More than 3,000 isolates were obtained using five culture media (TSA, NGN, NFb, PCAT, Baz). The 16S rRNA fragment sequencing of 1,013 selected working collection isolates showed that our working collection covered four bacterial phyla (Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes) and represented 33% of the previously described diversity of the rice root microbiome at the order level. Phenotypic in vitro analysis of the plant growth promoting capacity of the isolates revealed an overall ammonium production and auxin biosynthesis capacity, while siderophore production and phosphate solubilisation were enriched in Burkholderia, Ralstonia, Acinetobacter and Pseudomonas species. Of 45 representative isolates screened for growth promotion on seedlings of two rice cultivars, five showed an ability to improve the growth of both varieties, while five others were effective on only one variety. The best results were obtained with Pseudomonas taiwanensis ABIP 2315 and Azorhizobium caulinodans ABIP 1219, which increased seedling growth by 158% and 47%, respectively. Among the 14 best performing isolates, eight appeared to be abundant in the rice root microbiome dataset from previous study. The findings of this research contribute to the functional description of rice root-associated bacteria and their potential importance for plants by providing, for the first time, insight into their prevalence in the rice root microbiome.

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Occurrence, Diversity, and Genomes of “ Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments

Cited by 11 publications

References 100 publications

Baseline Skin Microbiota of the Leatherback Sea Turtle

Baseline Skin Microbiota of the Leatherback Sea Turtle

Diversity and plant growth promoting ability of rice root-associated bacteria in Burkina-Faso and cross-comparison with metabarcoding data

Culturable approach to rice-root associated bacteria in Burkina Faso: diversity, plant growth-promoting rhizobacteria properties and cross-comparison with metabarcoding data

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