Application of in situ cultivation in marine microbial resource mining

Nonribosomal Peptide Synthetase Specific Genome Amplification Using Rolling Circle Amplification for Targeted Gene Sequencing

Next-generation sequencing has transformed the acquisition of vast amounts of genomic information, including the rapid identification of target gene sequences in metagenomic databases. However, dominant species can sometimes hinder the detection of rare bacterial species. Therefore, a highly sensitive amplification technique that can selectively amplify bacterial genomes containing target genes of interest was developed in this study. The rolling circle amplification (RCA) method can initiate amplification from a single locus using a specific single primer to amplify a specific whole genome. A mixed cell suspension was prepared using Pseudomonas fluorescens ATCC17400 (targeting nonribosomal peptide synthetase [NRPS]) and Escherichia coli (non-target), and a specific primer designed for the NRPS was used for the RCA reaction. The resulting RCA product (RCP) amplified only the Pseudomonas genome. The NRPS was successfully amplified using RCP as a template from even five cells, indicating that the single-priming RCA technique can specifically enrich the target genome using gene-specific primers. Ultimately, this specific genome RCA technique was applied to metagenomes extracted from sponge-associated bacteria, and NRPS sequences were successfully obtained from an unknown sponge-associated bacterium. Therefore, this method could be effective for accessing species-specific sequences of NRPS in unknown bacteria, including viable but non-culturable bacteria.

Searching for microbial contribution to micritization of shallow marine sediments

Micritization is an early diagenetic process that gradually alters primary carbonate sediment grains through cycles of dissolution and reprecipitation of microcrystalline calcite (micrite). Typically observed in modern shallow marine environments, micritic textures have been recognized as a vital component of storage and flow in hydrocarbon reservoirs, attracting scientific and economic interests. Due to their endolithic activity and the ability to promote nucleation and reprecipitation of carbonate crystals, microorganisms have progressively been shown to be key players in micritization, placing this process at the boundary between the geological and biological realms. However, published research is mainly based on geological and geochemical perspectives, overlooking the biological and ecological complexity of microbial communities of micritized sediments. In this paper, we summarize the state-of-the-art and research gaps in micritization from a microbial ecology perspective. Since a growing body of literature successfully applies in vitro and in situ 'fishing' strategies to unveil elusive microorganisms and expand our knowledge of microbial diversity, we encourage their application to the study of micritization. By employing these strategies in micritization research, we advocate promoting an interdisciplinary approach/perspective to identify and understand the overlooked/neglected microbial players and key pathways governing this phenomenon and their ecology/dynamics, reshaping our comprehension of this process.

Design of a multi-band Raman tweezers objective for in situ studies of deep-sea microorganisms

The investigation of deep-sea microorganisms holds immense significance and value in advancing the fields of life sciences, biotechnology, and environmental conservation. However, the current lack of specialized underwater objectives specifically designed for in situ studies of deep-sea microorganisms hampers progress in this area. To address this limitation, we present the design of a multi-band Raman tweezer objective tailored for deep-sea environments. The objective is integrated into a high-pressure chamber capable of withstanding depths up to 1.5 km, enabling in situ microscopic imaging, optical tweezer capture, and Raman detection of deep-sea microorganisms. Through meticulous structural optimization, meticulous material selection, and thorough mechanical analysis of the underwater optical window, the objective exhibits remarkable attributes such as multi-band functionality, extended working distance, and high numerical aperture. Our design yields image quality near the diffraction limit, successfully achieving flat-field and apochromatic performance in each respective wavelength bands. Moreover, the tolerance analysis demonstrates that the full-field root mean square (RMS) wave aberration approaches λ/14, effectively meeting the demands of manufacturing and practical applications. This objective lens constitutes a vital tool for the in situ exploration of deep-sea microorganisms.

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.

Microbial Interaction is Among the Key Factors for Isolation of Previous Uncultured Microbes

Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory conditions. The experience accumulated from advanced techniques such as in situ cultivation has identified that microbial interactions exist in natural habitats but are absent in laboratory cultures. These microbial interactions are likely one of the key factors in isolating previously uncultured microbes. The need for better knowledge of the mechanisms operating in microbial interactions has led to various experiments that have utilized microbial interactions in different approaches to microbial cultivation. These new attempts to understand microbial interactions not only present a new perspective on microbial uncultivability but also provide an opportunity to access uncultured phylogenetically novel microbes with their potential biotechnology applications. In this review, we focus on studies of the mechanisms of microbial interaction where the growth of other microbes is affected. Additionally, we review some successful applications of microbial interactions in cultivation methods, an approach that can play an important role in the bioprospecting of untapped microbial resources.

Global analysis of the biosynthetic chemical space of marine prokaryotes

BACKGROUND

Marine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize novel secondary metabolites. However, the exact biosynthetic chemical space encoded by the marine prokaryotes has yet to be systematically evaluated.

RESULTS

We first investigated the secondary metabolic potential of marine prokaryotes by analyzing the diversity and novelty of the biosynthetic gene clusters (BGCs) in 7541 prokaryotic genomes from cultivated and single cells, along with 26,363 newly assembled medium-to-high-quality genomes from marine environmental samples. To quantitatively evaluate the unexplored biosynthetic chemical space of marine prokaryotes, the clustering thresholds for constructing the biosynthetic gene cluster and molecular networks were optimized to reach a similar level of the chemical similarity between the gene cluster family (GCF)-encoded metabolites and molecular family (MF) scaffolds using the MIBiG database. The global genome mining analysis demonstrated that the predicted 70,011 BGCs were organized into 24,536 mostly new (99.5%) GCFs, while the reported marine prokaryotic natural products were only classified into 778 MFs at the optimized clustering thresholds. The number of MF scaffolds is only 3.2% of the number of GCF-encoded scaffolds, suggesting that at least 96.8% of the secondary metabolic potential in marine prokaryotes is untapped. The unexplored biosynthetic chemical space of marine prokaryotes was illustrated by the 88 potential novel antimicrobial peptides encoded by ribosomally synthesized and post-translationally modified peptide BGCs. Furthermore, a sea-water-derived Aquimarina strain was selected to illustrate the diverse biosynthetic chemical space through untargeted metabolomics and genomics approaches, which identified the potential biosynthetic pathways of a group of novel polyketides and two known compounds (didemnilactone B and macrolactin A 15-ketone).

CONCLUSIONS

The present bioinformatics and cheminformatics analyses highlight the promising potential to explore the biosynthetic chemical diversity of marine prokaryotes and provide valuable knowledge for the targeted discovery and biosynthesis of novel marine prokaryotic natural products. Video Abstract.

Modern Trends in Natural Antibiotic Discovery

Natural scaffolds remain an important basis for drug development. Therefore, approaches to natural bioactive compound discovery attract significant attention. In this account, we summarize modern and emerging trends in the screening and identification of natural antibiotics. The methods are divided into three large groups: approaches based on microbiology, chemistry, and molecular biology. The scientific potential of the methods is illustrated with the most prominent and recent results.

Use of modified ichip for the cultivation of thermo-tolerant microorganisms from the hot spring

BACKGROUND

Thermostable microorganisms are extremophiles. They have a special genetic background and metabolic pathway and can produce a variety of enzymes and other active substances with special functions. Most thermo-tolerant microorganisms from environmental samples have resisted cultivation on artificial growth media. Therefore, it is of great significance to isolate more thermo-tolerant microorganisms and study their characteristics to explore the origin of life and exploit more thermo-tolerant enzymes. Tengchong hot spring in Yunnan contains a lot of thermo-tolerant microbial resources because of its perennial high temperature. The ichip method was developed by D. Nichols in 2010 and can be used to isolate so-called "uncultivable" microorganisms from different environments. Here, we describe the first application of modified ichip to isolate thermo-tolerant bacteria from hot springs.

RESULTS

In this study, 133 strains of bacteria belonging to 19 genera were obtained. 107 strains of bacteria in 17 genera were isolated by modified ichip, and 26 strains of bacteria in 6 genera were isolated by direct plating methods. 25 strains are previously uncultured, 20 of which can only be cultivated after being domesticated by ichip. Two strains of previously unculturable Lysobacter sp., which can withstand 85 °C, were isolated for the first time. Alkalihalobacillus, Lysobacter and Agromyces genera were first found to have 85 °C tolerance.

CONCLUSION

Our results indicate that the modified ichip approach can be successfully applied in a hot spring environment.

Culturable Bacterial Diversity from the Basaltic Subsurface of the Young Volcanic Island of Surtsey, Iceland

The oceanic crust is the world's largest and least explored biosphere on Earth. The basaltic subsurface of Surtsey island in Iceland represents an analog of the warm and newly formed-oceanic crust and offers a great opportunity for discovering novel microorganisms. In this study, we collected borehole fluids, drill cores, and fumarole samples to evaluate the culturable bacterial diversity from the subsurface of the island. Enrichment cultures were performed using different conditions, media and temperatures. A total of 195 bacterial isolates were successfully cultivated, purified, and identified based on MALDI-TOF MS analysis and by 16S rRNA gene sequencing. Six different clades belonging to Firmicutes (40%), Gammaproteobacteria (28.7%), Actinobacteriota (22%), Bacteroidota (4.1%), Alphaproteobacteria (3%), and Deinococcota (2%) were identified. Bacillus (13.3%) was the major genus, followed by Geobacillus (12.33%), Enterobacter (9.23%), Pseudomonas (6.15%), and Halomonas (5.64%). More than 13% of the cultured strains potentially represent novel species based on partial 16S rRNA gene sequences. Phylogenetic analyses revealed that the isolated strains were closely related to species previously detected in soil, seawater, and hydrothermal active sites. The 16S rRNA gene sequences of the strains were aligned against Amplicon Sequence Variants (ASVs) from the previously published 16S rRNA gene amplicon sequence datasets obtained from the same samples. Compared with the culture-independent community composition, only 5 out of 49 phyla were cultivated. However, those five phyla accounted for more than 80% of the ASVs. Only 121 out of a total of 5642 distinct ASVs were culturable (≥98.65% sequence similarity), representing less than 2.15% of the ASVs detected in the amplicon dataset. Here, we support that the subsurface of Surtsey volcano hosts diverse and active microbial communities and that both culture-dependent and -independent methods are essential to improving our insight into such an extreme and complex volcanic environment.

Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting

Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.

The Eco-Evo Mandala: Simplifying Bacterioplankton Complexity into Ecohealth Signatures

The microbiome emits informative signals of biological organization and environmental pressure that aid ecosystem monitoring and prediction. Are the many signals reducible to a habitat-specific portfolio that characterizes ecosystem health? Does an optimally structured microbiome imply a resilient microbiome? To answer these questions, we applied our novel Eco-Evo Mandala to bacterioplankton data from four habitats within the Great Barrier Reef, to explore how patterns in community structure, function and genetics signal habitat-specific organization and departures from theoretical optimality. The Mandala revealed communities departing from optimality in habitat-specific ways, mostly along structural and functional traits related to bacterioplankton abundance and interaction distributions (reflected by ϵ and λ as power law and exponential distribution parameters), which are not linearly associated with each other. River and reef communities were similar in their relatively low abundance and interaction disorganization (low ϵ and λ) due to their protective structured habitats. On the contrary, lagoon and estuarine inshore reefs appeared the most disorganized due to the ocean temperature and biogeochemical stress. Phylogenetic distances (D) were minimally informative in characterizing bacterioplankton organization. However, dominant populations, such as Proteobacteria, Bacteroidetes, and Cyanobacteria, were largely responsible for community patterns, being generalists with a large functional gene repertoire (high D) that increases resilience. The relative balance of these populations was found to be habitat-specific and likely related to systemic environmental stress. The position on the Mandala along the three fundamental traits, as well as fluctuations in this ecological state, conveys information about the microbiome's health (and likely ecosystem health considering bacteria-based multitrophic dependencies) as divergence from the expected relative optimality. The Eco-Evo Mandala emphasizes how habitat and the microbiome's interaction network topology are first- and second-order factors for ecosystem health evaluation over taxonomic species richness. Unhealthy microbiome communities and unbalanced microbes are identified not by macroecological indicators but by mapping their impact on the collective proportion and distribution of interactions, which regulates the microbiome's ecosystem function.