Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Simple Summary

The study of a microbial community nowadays mostly relies on environmental DNA (eDNA)-based amplicon sequencing. However, some studies report that this method is not able to capture all bacterial taxa in the community. This study presents an enrichment culture-based amplicon sequencing method to estimate the proportion of culturable bacteria in soil. A bacterial community derived from this method was compared with those derived from culture-independent methods (eDNA-based amplicon sequencing). This study revealed that the majority of cultured bacteria were rare or completely absent in the community detected by the culture-independent method. Nevertheless, the dominant bacterial Operational Taxonomic Units (OTUs) were also observed, as 8 out of the 30 most frequently detected bacteria from eDNA were found in the enrichment cultures. The method proposed in this study could extend bacterial community’s information derived from the culture-independent method. Furthermore, the enrichment culture-based amplicon sequencing method could be a promising tool for quick screening of a culturable bacterial community and its associated function for various applications.

Abstract

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Antimicrobial and Antioxidant Effects of a Forest Actinobacterium V002 as New Producer of Spectinabilin, Undecylprodigiosin and Metacycloprodigiosin

The aim of the study is the research and identification of a Streptomyces strain as a new producer of spectinabilin, undecylprodigiosin and metacycloprodigiosin. Among 54 actinomycete isolates isolated from El-Ogbane forest soils in Algeria, only one isolate, designated V₀₀₂, was selected for its ability to produce prodigiosins. The selected strain was analysed for its ability to produce three different secondary metabolites as well as their biological activities. V₀₀₂ belongs to the Streptomyces genus and has significant antimicrobial and antioxidant activities. The taxonomic position of V₀₀₂ by 16S rRNA sequence analysis showed a similarity of 99.93% with Streptomyces lasiicapitis DSM 103124^T and 98.96% with Streptomyces spectabilis DSM 40512^T. Fractionation of crude secondary metabolites produced by the strain using HPLC-MS revealed the presence of spectinabilin, undecylprodigiosin and metacycloprodigiosin, which demonstrated significant activity. Strain V₀₀₂ is considered a new producer of spectinabilin, undecylprodigiosin and metacycloprodigiosin with significant antimicrobial and antioxidant activity.

Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro

A new bacterial strain, designated HM134^T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134^T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134^T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105^T, M. wenchangensis CCTCC AA 2012002^T and M. mangrovi 2803GPT1-18^T. The ANI values between strain HM134^T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134^T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134^T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134^T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134^T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134^T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC₅₀ value of 38.4 μg/mL.

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Micromonospora sonneratiae sp. nov., isolated from a root of Sonneratia apetala

A novel endophytic actinomycete, strain 274745(T), was isolated from a root of Sonneratia apetala collected in a mangrove forest in Sanya, Hainan province, China. The 16S rRNA gene sequence of strain 274745(T) showed the greatest similarity to Micromonospora pattaloongensis TJ2-2(T) (98.3 %). Phylogenetic analysis based on the gyrB gene also supported the close relationship of these two strains. The predominant menaquinone was MK-10(H8) and the major fatty acids were iso-C15 : 0, C17 : 0 and anteiso-C15 : 0. The characteristic whole-cell sugars were xylose and mannose. The cell wall contained meso-diaminopimelic acid and glycine. The polar lipid profile mainly comprised phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The DNA G+C content was 71.6 mol%. Furthermore, a combination of DNA-DNA relatedness and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 274745(T) represents a novel species of the genus Micromonospora, for which the name Micromonospora sonneratiae sp. nov. is proposed. The type strain is 274745(T) ( = CCTCC AA 2012003(T) = DSM 45704(T)).

Micromonospora yangpuensis sp. nov., isolated from a sponge

An actinomycete, strain FXJ6.011T, was isolated from a cup-shaped sponge collected at Dachan reef, Yangpu in the South China Sea. The strain had morphological characteristics of members of the family Micromonosporaceae. Phylogenetic analysis of the 16S rRNA gene sequence of strain FXJ6.011T indicated the highest similarity (98.7 %) to Micromonospora auratinigra JCM 12357T, Micromonospora chaiyaphumensis JCM 12873T and Micromonospora echinofusca JCM 3327T. Analysis of the gyrB gene sequence also showed that strain FXJ6.011T should be assigned to the genus Micromonospora. It contained dd-diaminopimelic acid as the major cell-wall diamino acid and MK-10(H2) as predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidyl mannosides and phosphatidylinositol dimannoside. The major cellular fatty acids were iso-C16 : 0, C17 : 1ω8c and C16 : 0. Physiological and biochemical data and low DNA–DNA relatedness values enabled the strain to be differentiated from members of closely related species. Based on phenotypic and genotypic data, strain FXJ6.011T represents a novel Micromonospora species, for which the name Micromonospora yangpuensis sp. nov. is proposed; the type strain is FXJ6.011T ( = CGMCC 4.5736T = NBRC 107727T).