Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis

AbstractAlthough the Mediterranean Sea covers approximately a 0.7% of the world’s ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and “Porto Paone”, “Secca delle fumose”, “Punta San Pancrazio” in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.

Download Full-text

Biotechnological Potential of Marine Sponges and their Associated Bacteria as Producers of New Pharmaceuticals (Part I)

Journal of International Biotechnology Law ◽

10.1515/jibl.2005.2.5.217 ◽

2005 ◽

Vol 2 (5) ◽

Cited By ~ 3

Author(s):

Carsten Thoms ◽

Peter Schupp

Keyword(s):

Natural Products ◽

Large Scale ◽

Marine Sponges ◽

Sponge Tissue ◽

Associated Bacteria ◽

Biotechnological Potential ◽

Highly Active ◽

Medicinal Treatment ◽

Microbial Infections ◽

Sponge Associated Bacteria

AbstractThroughout human history natural products have provided the basis for medicinal treatment. About 60 years ago the advent of SCUBA diving techniques granted access to a thitherto untapped source of pharmacologically highly active natural products: the marine environment. In the oceans not plants but sessile animals, particularly sponges, have proven to be the most fruitful organisms in this context. Sponges have evolved a vast arsenal of chemical weapons to defend themselves against various threats from their environment. These molecules remarkably often show potent activities in pharmaceutical assays. Several sponge-derived compounds are already in clinical trials as agents against cancer, microbial infections, inflammation and other diseases. However, in many cases drug development is severely hampered by the limited supply of the respective compounds, as they are often present only in minute amounts in the sponge tissue. Big hope to circumvent this obstacle lies on the supposition that sponge-associated bacteria and not the sponges themselves are in many cases the true producers of the pharmaceutically relevant agents. Once these microorganisms are determined and cultivated outside the sponge tissue, they could be fermented for large-scale compound production. This in future could substantially increase the number of powerful sponge-derived drugs on the market.

Download Full-text

Diversity of tryptophan halogenases in sponges of the genus Aplysina

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz108 ◽

2019 ◽

Vol 95 (8) ◽

Cited By ~ 3

Author(s):

Johanna Gutleben ◽

Jasper J Koehorst ◽

Kyle McPherson ◽

Shirley Pomponi ◽

René H Wijffels ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Bacterial Community Composition ◽

Protein Sequences ◽

Operational Taxonomic Unit ◽

Marine Sponges ◽

Biotechnological Potential ◽

Polymerase Chain ◽

The Mediterranean ◽

Aplysina Aerophoba

ABSTRACT Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.

Download Full-text

A Metataxonomic Approach Reveals Diversified Bacterial Communities in Antarctic Sponges

Marine Drugs ◽

10.3390/md19030173 ◽

2021 ◽

Vol 19 (3) ◽

pp. 173

Author(s):

Nadia Ruocco ◽

Roberta Esposito ◽

Marco Bertolino ◽

Gianluca Zazo ◽

Michele Sonnessa ◽

...

Keyword(s):

Secondary Metabolites ◽

Morphological Analysis ◽

Marine Sponges ◽

Bioactive Metabolites ◽

Associated Bacteria ◽

Sponge Associated Bacteria ◽

Antarctic Research ◽

Pharmacologically Active ◽

Pharmacologically Active Compounds ◽

Antarctic Sponges

Marine sponges commonly host a repertoire of bacterial-associated organisms, which significantly contribute to their health and survival by producing several anti-predatory molecules. Many of these compounds are produced by sponge-associated bacteria and represent an incredible source of novel bioactive metabolites with biotechnological relevance. Although most investigations are focused on tropical and temperate species, to date, few studies have described the composition of microbiota hosted by Antarctic sponges and the secondary metabolites that they produce. The investigation was conducted on four sponges collected from two different sites in the framework of the XXXIV Italian National Antarctic Research Program (PNRA) in November–December 2018. Collected species were characterized as Mycale (Oxymycale) acerata, Haliclona (Rhizoniera) dancoi, Hemigellius pilosus and Microxina sarai by morphological analysis of spicules and amplification of four molecular markers. Metataxonomic analysis of these four Antarctic sponges revealed a considerable abundance of Amplicon Sequence Variants (ASVs) belonging to the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia. In particular, M. (Oxymycale) acerata, displayed several genera of great interest, such as Endozoicomonas, Rubritalea, Ulvibacter, Fulvivirga and Colwellia. On the other hand, the sponges H. pilosus and H. (Rhizoniera) dancoi hosted bacteria belonging to the genera Pseudhongella, Roseobacter and Bdellovibrio, whereas M. sarai was the sole species showing some strains affiliated to the genus Polaribacter. Considering that most of the bacteria identified in the present study are known to produce valuable secondary metabolites, the four Antarctic sponges could be proposed as potential tools for the discovery of novel pharmacologically active compounds.

Download Full-text

Ecology and Biotechnological Potential of Bacteria Belonging to the GenusPseudovibrio

Applied and Environmental Microbiology ◽

10.1128/aem.02516-17 ◽

2018 ◽

Vol 84 (8) ◽

Cited By ~ 5

Author(s):

Stefano Romano

Keyword(s):

Marine Invertebrates ◽

Marine Sponges ◽

Nutrient Cycles ◽

Free Living ◽

Associated Bacteria ◽

Biotechnological Potential ◽

Content Type ◽

Tropical Regions ◽

Marine Systems ◽

Major Nutrient

ABSTRACTMembers of the genusPseudovibriohave been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally,Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities ofPseudovibriospp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.

Download Full-text

PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

Journal of Animal Science ◽

10.1093/jas/skaa278.729 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 418-419

Author(s):

Gercino F Virgínio Júnior ◽

Milaine Poczynek ◽

Ana Paula Silva ◽

Ariany Toledo ◽

Amanda Cezar ◽

...

Keyword(s):

Illumina Miseq ◽

Diversity Indices ◽

Dairy Calves ◽

Rrna Gene ◽

Gastrointestinal Microbiome ◽

Fecal Microbiome ◽

Miseq Platform ◽

Holstein Calves ◽

Ad Libitum ◽

Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

Download Full-text

The Culturable Mycobiome of Mesophotic Agelas oroides: Constituents and Changes Following Sponge Transplantation to Shallow Water

Journal of Fungi ◽

10.3390/jof7070567 ◽

2021 ◽

Vol 7 (7) ◽

pp. 567

Author(s):

Eyal Ben-Dor Cohen ◽

Micha Ilan ◽

Oded Yarden

Keyword(s):

Microbial Community ◽

Shallow Water ◽

Mediterranean Sea ◽

Hyphal Growth ◽

Marine Sponges ◽

The Core ◽

The Mediterranean ◽

Dynamic Components ◽

In Vitro Interactions

Marine sponges harbor a diverse array of microorganisms and the composition of the microbial community has been suggested to be linked to holo-biont health. Most of the attention concerning sponge mycobiomes has been given to sponges present in shallow depths. Here, we describe the presence of 146 culturable mycobiome taxa isolated from mesophotic niche (100 m depth)-inhabiting samples of Agelas oroides, in the Mediterranean Sea. We identify some potential in vitro interactions between several A. oroides-associated fungi and show that sponge meso-hyl extract, but not its predominantly collagen-rich part, is sufficient to support hyphal growth. We demonstrate that changes in the diversity of culturable mycobiome constituents occur following sponge transplantation from its original mesophotic habitat to shallow (10 m) waters, where historically (60 years ago) this species was found. We conclude that among the 30 fungal genera identified as associated with A. oroides, Aspergillus, Penicillium and Trichoderma constitute the core mycobiome of A. oroides, and that they persist even when the sponge is transplanted to a suboptimal environment, indicative of the presence of constant, as well as dynamic, components of the sponge mycobiome. Other genera seemed more depth-related and appeared or disappeared upon host’s transfer from 100 to 10 m.

Download Full-text

A Rapid Bacteriophage DNA Extraction Method

Methods and Protocols ◽

10.3390/mps1030027 ◽

2018 ◽

Vol 1 (3) ◽

pp. 27 ◽

Cited By ~ 2

Author(s):

Džiuginta Jakočiūnė ◽

Arshnee Moodley

Keyword(s):

Dna Extraction ◽

Illumina Miseq ◽

Extraction Methods ◽

Resistant Bacteria ◽

Simple Method ◽

Antibiotic Resistant ◽

Phage Dna ◽

Specialized Equipment ◽

Miseq Platform ◽

Dna Extraction Methods

Bacteriophages (phages) are intensely investigated as non-antibiotic alternatives to circumvent antibiotic resistance development as well as last resort therapeutic options against antibiotic resistant bacteria. As part of gaining a better understanding of phages and to determine if phages harbor putative virulence factors, whole genome sequencing is used, for which good quality phage DNA is needed. Traditional phage DNA extraction methods are tedious and time consuming, requiring specialized equipment e.g., an ultra-centrifuge. Here, we describe a quick and simple method (under four hours) to extract DNA from double stranded DNA (dsDNA) phages at titers above 1.0 × 1010 plaque-forming units (PFU)/mL. This DNA was suitable for library preparation using the Nextera XT kit and sequencing on the Illumina MiSeq platform.

Download Full-text

A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2017.0395 ◽

2018 ◽

Vol 374 (1763) ◽

pp. 20170395 ◽

Cited By ~ 9

Author(s):

Barnabas H. Daru ◽

Elizabeth A. Bowman ◽

Donald H. Pfister ◽

A. Elizabeth Arnold

Keyword(s):

Species Interactions ◽

Fungal Endophytes ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Herbarium Specimens ◽

Proof Of Concept ◽

Ledum Palustre ◽

Surface Contaminants ◽

Symptomless Plant ◽

Miseq Platform

Herbarium specimens represent important records of morphological and genetic diversity of plants that inform questions relevant to global change, including species distributions, phenology and functional traits. It is increasingly appreciated that plant microbiomes can influence these aspects of plant biology, but little is known regarding the historic distribution of microbes associated with plants collected in the pre-molecular age. If microbiomes can be observed reliably in herbarium specimens, researchers will gain a new lens with which to examine microbial ecology, evolution, species interactions. Here, we describe a method for accessing historical plant microbiomes from preserved herbarium specimens, providing a proof of concept using two plant taxa from the imperiled boreal biome ( Andromeda polifolia and Ledum palustre subsp . groenlandicum, Ericaceae). We focus on fungal endophytes, which occur within symptomless plant tissues such as leaves. Through a three-part approach (i.e. culturing, cloning and next-generation amplicon sequencing via the Illumina MiSeq platform, with extensive controls), we examined endophyte communities in dried, pressed leaves that had been processed as regular herbarium specimens and stored at room temperature in a herbarium for four years . We retrieved only one endophyte in culture, but cloning and especially the MiSeq analysis revealed a rich community of foliar endophytes. The phylogenetic distribution and diversity of endophyte assemblages, especially among the Ascomycota, resemble endophyte communities from fresh plants collected in the boreal biome. We could distinguish communities of endophytes in each plant species and differentiate likely endophytes from fungi that could be surface contaminants. Taxa found by cloning were observed in the larger MiSeq dataset, but species richness was greater when subsets of the same tissues were evaluated with the MiSeq approach. Our findings provide a proof of concept for capturing endophyte DNA from herbarium specimens, supporting the importance of herbarium records as roadmaps for understanding the dynamics of plant-associated microbial biodiversity in the Anthropocene. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

Download Full-text

Detection and monitoring of insect traces in bioaerosols

PeerJ ◽

10.7717/peerj.10862 ◽

2021 ◽

Vol 9 ◽

pp. e10862

Author(s):

Panyapon Pumkaeo ◽

Junko Takahashi ◽

Hitoshi Iwahashi

Keyword(s):

Aerosol Particles ◽

Illumina Miseq ◽

Identification Accuracy ◽

Insect Community ◽

Cytochrome C Oxidase I ◽

True Bugs ◽

Illumina Miseq Platform ◽

Miseq Platform ◽

Pm2.5 And Pm10 ◽

First Time

Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.

Download Full-text

Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

Microorganisms ◽

10.3390/microorganisms8091363 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1363

Author(s):

Julia Hankel ◽

Amr Abd El-Wahab ◽

Richard Grone ◽

Birgit Keller ◽

Eric Galvez ◽

...

Keyword(s):

Intestinal Microbiota ◽

Hypervariable Region ◽

Illumina Miseq ◽

Vegetarian Diet ◽

Rrna Gene ◽

Feather Meal ◽

Illumina Miseq Platform ◽

Faecal Samples ◽

Miseq Platform ◽

Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

Download Full-text