Complete Genome Sequence of
            <i>Psychrobacillus</i>
            sp. Strain INOP01, a Phosphate-Solubilizing Bacterium Isolated from an Agricultural Soil in Germany

Chiba, Akane; Peine, Manuela; Kublik, Susanne; Baum, Christel; Schloter, Michael; Schulz, Stefanie

doi:10.1128/mra.00207-22

Cited by 5 publications

(2 citation statements)

References 9 publications

(9 reference statements)

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“…Nowadays, more and more species belonging to the genus Psycrobacillus are being studied for various peculiar characteristics, including the ability to degrade oils ( 16 ), produce bio-emulsifiers ( 17 ), and phosphate-solubilizing ability ( 18 ). These capabilities are also associated with the ubiquitous discovery of this genus, ranging from Egypt ( 19 ) to polar ices ( 17 , 20 ), from ancient findings ( 10 ) to cleanrooms of space observatories (as reported for the DSM 30,747 strain) or in clean-room environments of NASA (as reported in the bioproject PRJNA832800).…”

Section: Resultsmentioning

confidence: 99%

Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans ?

Colautti,

Comi,

Peterlunger

et al. 2023

Microbiol Spectr

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Thanks to the development of whole-genome sequencing technologies, nowadays researchers have access to rapid, effective, and precise resources for the genetic analysis of prokaryotes. The use of metrics that consider the entire DNA sequence, such as average nucleotide identity and digital DNA-DNA hybridization calculation, in fact, allows better results when compared to single-target gene analysis. However, it is increasingly important to employ reference databases containing correct information with high-quality sequences. The aim of this work is to taxonomically identify an unknown bacterial strain isolated from an ancient Roman amphora. However, it was necessary to resequence the genomes of the reference strains Paenisporosarcina quisquiliarum SK 55 and Psychrobacillus psychrodurans DSM 11713 to obtain correct and more reliable sequences than those available. It was, therefore, possible to uniquely identify the strain Aquil_B6 as Psy. psychrodurans . Also, to obtain further genetic information, given the low number of sequences available for this species, the genome of strain DSM 30747 was sequenced. Further characterization was made to identify the presence of possible genetic characteristic features such as CRISPR-Cas, prophages, resistance factors, and bacteriocins of this species, making a comparison between the available genomes of Paenisporosarcina quisquiliarum SK 55 and Psychrobacillus psychrodurans strains DSM 11713, DSM 30747, and Aquil_B6, to evaluate the impact of time on the evolution of the considered species. IMPORTANCE Since 1988, through the United States government’s founding, the National Center for Biotechnology Information (NCBI) has provided an invaluable service to scientific advancement. The universality and total freedom of use if on the one hand allow the use of this database on a global level by all researchers for their valuable work, on the other hand, it has the disadvantage of making it difficult to check the correctness of all the materials present. It is, therefore, of fundamental importance for the correctness and ethics of research to improve the databases at our disposal, identifying and amending the critical issues. This work aims to provide the scientific community with a new sequence for the type strain Paenisporosarcina quisquiliarum SK 55 and broaden the knowledge of the Psychrobacillus psychrodurans species, in particular, considering the ancient strain Aquil_B6 found in an ancient Roman amphora.

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Section: Resultsmentioning

confidence: 99%

Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans ?

Colautti,

Comi,

Peterlunger

et al. 2023

Microbiol Spectr

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“…For example, the specific genera in male and female algal bodies were still related to metabolism. The specific genera in male algal bodies included the alginate-degrading bacterium Brachybacterium , phosphorus-solubilizing bacterium Psychrobacillus (Chiba et al, 2022), carotenoid-producing bacterium Flavicella (Teramoto and Nishijima, 2015), and Rubricoccus (Nakajima et al, 2017), which contains rhodopsin-producing genes and plays an important role in energy conversion. Interestingly, there were also some gut metabolic bacteria present, such as Lentisphaera (related to pentose metabolism) and Dialister (Louis et al, 2014) (related to propionic acid production).…”

Section: The Differences In Endophytic Bacterial Communities Between ...mentioning

confidence: 99%

The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles

Zhao,

Sun,

et al. 2024

Front. Microbiol.

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Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

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How to adequately represent biological processes in modeling multifunctionality of arable soils

Vogel,

Amelung,

Baum

et al. 2024

Biol Fertil Soils

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Essential soil functions such as plant productivity, C storage, nutrient cycling and the storage and purification of water all depend on soil biological processes. Given this insight, it is remarkable that in modeling of these soil functions, the various biological actors usually do not play an explicit role. In this review and perspective paper we analyze the state of the art in modeling these soil functions and how biological processes could more adequately be accounted for. We do this for six different biologically driven processes clusters that are key for understanding soil functions, namely i) turnover of soil organic matter, ii) N cycling, iii) P dynamics, iv) biodegradation of contaminants v) plant disease control and vi) soil structure formation. A major conclusion is that the development of models to predict changes in soil functions at the scale of soil profiles (i.e. pedons) should be better rooted in the underlying biological processes that are known to a large extent. This is prerequisite to arrive at the predictive models that we urgently need under current conditions of Global Change.

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Complete Genome Sequence of Psychrobacillus sp. Strain INOP01, a Phosphate-Solubilizing Bacterium Isolated from an Agricultural Soil in Germany

Cited by 5 publications

References 9 publications

Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans ?

Ancient Roman bacterium against current issues: strain Aquil_B6, Paenisporosarcina quisquiliarum, or Psychrobacillus psychrodurans ?

The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles

How to adequately represent biological processes in modeling multifunctionality of arable soils

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