Actinospica durhamensis sp. nov., isolated from a spruce forest soil

Temporary establishment of bacteria from indoor plant leaves and soil on human skin

BACKGROUND

Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing.

RESULTS

Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing.

CONCLUSIONS

This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.

Actinospica acidithermotolerans sp. nov., a novel actinomycete isolated from sediment from an Indonesian hot spring

A polyphasic study was designed to resolve the taxonomic position of isolate MGRD01-02^T which was recovered from an acidic hot spring in Indonesia and assigned to the genus Actinospica. Phylogenetic analyses based on 16S rRNA gene sequences show that the isolate is most closely related to the type strains of Actinospica acidiphila (98.5%), Actinospica robiniae (97.8%) and Actinospica durhamensis (96.8%). Morphological and chemotaxonomic data underpin the assignment of the isolate to the genus Actinospica as it forms an extensively branched substrate mycelium which carries tufts of white aerial hyphae that differentiate into straight to flexuous chains of cylindrical spores with faint rugose surfaces, contains 2,6-diamino-3-hydroxydiaminopimelic acid in the peptidoglycan, mixtures of hydrogenated menaquinones with nine isoprene units, iso-C _15:O and iso-C _16:O as major fatty acids and phosphatidylethanolamine as the diagnostic phospholipid. Whole-genome sequence analyses show that the isolate, A. durhamensis CSCA 57^T and Actinocrinis puniceicyclus DSM 45168^T have genome sizes of 7.9, 9.6 and 6.7 Mbp, respectively. A phylogenomic tree shows that they form distinct branches in a well-supported clade, a result supported by associated phenotypic data. Average nucleotide identity and digital DNA:DNA hybridization similarities are below the recommended thresholds for assigning strains to the same species; they also indicate that isolate MGRD01-02^T is most closely related to the A. durhamensis and A. robiniae strains. Corresponding amino acid identity and conserved protein data not only support these relationships but also confirm the taxonomic integrity of the genus Actinocrinis. Based on these results, it is proposed that isolate MGRD01-02^T (= CCMM B1308^T = ICEBB-09^T = NCIMB 15218^T) be classified in the genus Actinospica as Actinospica acidithermotolerans sp. nov. The draft genome of the isolate and its closest phylogenomic neighbours contain biosynthetic gene clusters with the potential to produce new natural products, notably antibiotics.

Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra

Two actinobacteria, strains NF3 and NH11^T, isolated from a pine forest soil, near Torun, Poland were examined for diverse chemotaxonomic and morphological properties that placed them in the genus Catenulispora. They produced an extensively branched stable mycelium, contained LL-diaminopimelic acid as the diamino acid of the peptidoglycan, arabinose as the diagnostic whole-organism sugar, tetra-, hexa- and octa-hydrogenated menaquinones with nine isoprenoid units as the predominant isoprenologues, iso-C_16:0 and anteiso-C_17:0 as major fatty acids, and formed a well supported clade within the Catenulispora 16S rRNA gene tree together with Catenulispora acidiphila DSM 44928^T and Catenulispora rubra DSM 44948^T sharing sequence similarities with the latter of 98.8 and 99.0%, respectively. The sizes of whole genome sequences generated for the isolates and the C. rubra strain ranged from 11.20 to 12.80 Mbp with corresponding in silico DNA G+C values of 69.9-70.0%. The isolates and the C. acidiphila and C. rubra strains formed a well supported branch in the actinobacterial phylogenomic tree. Isolates NF3 and NH11^T belong to the same species as they have identical 16S rRNA gene sequences, share many chemotaxonomic, cultural and phenotypic features and show very high average nucleotide identity (ANI) and digital DNA:DNA relatedness (dDDH) similarities. They can be distinguished from their closest phylogenomic neighbours by using a combination of chemotaxonomic and phenotypic properties and by ANI and dDDH values well below the thresholds of these metrics used to assign closely related strains to different species. Consequently, we propose that the isolates be classified as a new Catenulispora species, Catenulispora pinisilvae sp. nov., the type strain is NH11^T (=DSM 111109^T =PCM 3046^T). An emended description is given for C. rubra based on data acquired in the present study. Analyses of the draft genomes of the isolates and the C. acidiphila and C. rubra strains revealed the presence of many biosynthetic gene clusters with the potential to synthesize novel drug-like metabolites. In vitro screens showed that the isolates inhibited the growth of Gram-positive bacteria and wheat pathogens belonging to the genus Fusarium.

Community Structure of Endophytic Actinobacteria in a New Zealand Native Medicinal Plant Pseudowintera colorata (Horopito) and Their Influence on Plant Growth

The role of plant endophytic Actinobacteria remains poorly understood with no reports of these communities in New Zealand native plants. This first investigation of endophytic Actinobacteria in New Zealand targeted the culturally significant medicinal shrub Pseudowintera colorata (horopito) as a model plant. Community analysis in plant tissues collected from ten geographically distinct sites showed that tissue type had the strongest influence on diversity and richness of endophytic Actinobacteria. More denaturing gradient gel electrophoresis (DGGE) bands were obtained from stems (n = 18) compared to roots (n = 13). Sequencing analysis of the major bands (n = 20) identified them as uncultured bacteria, Streptomyces sp. and Angustibacter peucedani. Using two Actinobacteria-specific media, nine isolates were recovered from surface-sterilised P. colorata tissues. This was approximately 12% of the total taxa and correlated well with culturable numbers in international studies. In vitro analysis of the functionality of these strains showed that Streptomyces sp. PRY2RB2 inhibited all the tested phytopathogenic fungi (n = 4), Streptomyces sp. UKCW/B and Nocardia sp. TP1BA1B solubilised phosphate and produced siderophores. The functionality of the phosphate solubilising strains (n = 2) in vivo was investigated by inoculation of P. colorata seedlings. After 4 months, the mean shoot height of seedlings treated with Nocardia sp. TP1BA1B was 1.65× longer, had higher shoot dry weight (1.6×) and number of internodes (1.67×) compared to control. This study identified for the first time a key group of endophytic Actinobacteria that are likely to be important in the ecology of New Zealand flora.

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history.

Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.

Streptacidiphilus toruniensis sp. nov., isolated from a pine forest soil

Two acidophilic actinobacteria, isolates NA14 and NF37^T, were the subject of a polyphasic taxonomic study. Chemotaxonomic and morphological properties of the isolates were characteristic of the genus Streptacidiphilus. The isolates were shown to have identical 16S rRNA gene sequences and to be closely related to Streptacidiphilus neutrinimicus DSM 41755^T (>99.9 %). However, DNA:DNA relatedness between isolate NF37^T and the type strain of S. neutrinimicus was found to be low at 11.1 (±3.5) %. A broad range of phenotypic features were shown to distinguish the isolates from their close phylogenetic neighbours. These data shown that the isolates form a novel species of Streptacidiphilus for which the name Streptacidiphilus toruniensis sp. nov. is proposed. The type strain is NF37^T (= DSM 102291^T = NCIMB 15025^T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.