The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors.

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.

Lessons from Digestive-Tract Symbioses Between Bacteria and Invertebrates.

In most animals, digestive tracts harbor the greatest number of bacteria in the animal that contribute to its health: by aiding in the digestion of nutrients, provisioning essential nutrients and protecting against colonization by pathogens. Invertebrates have been used to enhance our understanding of metabolic processes and microbe-host interactions owing to experimental advantages. This review describes how advances in DNA sequencing technologies have dramatically altered how researchers investigate microbe-host interactions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies. Advantages and challenges of each of these approaches are described herein. Hypotheses generated through omics studies can be directly tested using site-directed mutagenesis, and findings from transposon studies and site-directed experiments are presented. Finally, unique structural aspects of invertebrate digestive tracts that contribute to symbiont specificity are presented. The combination of omics approaches with genetics and microscopy allows researchers to move beyond correlations to identify conserved mechanisms of microbe-host interactions.

Zophobihabitans entericus gen. nov., sp. nov., a new member of the family Orbaceae isolated from the gut of a superworm Zophobas morio.

A novel bacterial strain, designated IPMB12T, isolated from the gut of the superworm Zophobas morio in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, facultatively anaerobic, non-motile, coccoid or rod-shaped and formed translucent colonies. Optimal growth occurred at 25-37 °C, pH 9-10, and with 0-2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain IPMB12T is affiliated with genus in the the family Orbaceae in the class Gammaproteobacteria. Strain IPMB12T was most closely related to Gilliamella mensalis LMG 29880T with a 94.6 % 16S rRNA gene sequence similarity. Strain IPMB12T showed less than 71.6 % average nucleotide identity, less than 71.5 % average amino acid identity and less than 21.2 % digital DNA-DNA hybridization identity compared to the strains of related genera within the family Orbaceae. The major fatty acids of strain IPMB12T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized phosphoaminoglycolipid and one uncharacterized aminophospholipid. The major isoprenoid quinone was Q-8. Genomic DNA G+C content of strain IPMB12T was 39.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain IPMB12T represents a novel species of a new genus in the family Orbaceae, for which the name Zophobihabitans entericus gen. nov., sp. nov. is proposed. The type strain is IPMB12T (=BCRC 80908T =LMG 32079T=KCTC 82347T=KACC 22323T).

Utilization of Agro-Industrial Byproducts for Bacteriocin Production Using Enterococcus spp. Strains Isolated from Patagonian Marine Invertebrates.

This work's objective was to determine the antagonist activity of 11 Enterococcus spp. using industrial food wastes as a culture medium. The strains were isolated from invertebrates collected on the Argentinian Patagonia coast and selected by their high antibacterial activity. Phenotypic and genotypic techniques allowed identifying five E. hirae strains, five E. faecium strains, and one E. mundtii strain. The cell-free supernatants displayed inhibitory activity against most of the Gram-positive bacteria tested and Vibrio anguilarum. PCR amplification techniques detected the encoding genes of enterocin P in ten strains, mundtiicin KS in seven strains, enterocin B in six strains, hiracin JM79 in five strains, and enterocin A in three strains. The strains did not show gelatinase or hemolytic activities and were sensitive to gentamicin, kanamycin, streptomycin, tylosine, tetracycline, chloramphenicol and vancomycin. Cheese whey and hot trub derived from beer brewing were used alone or in combination to assay enterocin production. In all cases, the highest inhibitory activities were achieved when mixtures of both byproducts were used as growth medium. The results suggest that the selected strains can produce high levels of enterocins in a low-cost media composed of a mix of cheese whey and hot trub without additional supplementation with carbon or nitrogen sources.

Lethal and sub-lethal activity of Brevibacillus laterosporus on the mosquito Aedes albopictus and side effects on non-target water-dwelling invertebrates.

The biocidal potential of Brevibacillus laterosporus against mosquitoes of major medical importance has been widely documented, but its effects on non-target invertebrates are still poorly known. In this study, we determined the lethal and sub-lethal effects of B. laterosporus strain UNISS 18, an entomopathogenic bacterium known for its effectiveness against synanthropic Diptera, on the larvae of the Asian tiger mosquito Aedes albopictus, a vector of several pathogens to humans. Moreover, we compared the larvicidal activity with the lethal action on the invasive snail Physella acuta and on two non-target water-dwelling species: the mayfly Cloeon dipterum, and the harlequin fly Chironomus riparius. B. laterosporus exhibited significant lethal effects on all the tested species with a concentration-dependent activity. However, the susceptibility varied among species, with a higher susceptibility of Ae. albopictus (LC50 = 0.16 × 107 spores mL-1) than the other species (LC50 = 0.31, 0.33, and 0.30 × 107 spores mL-1 for C. dipterum, C. riparius, and P. acuta, respectively). While 1st instar mosquito larvae were very susceptible to the bacterial infection, no effects on preimaginal development stages and adult emergence were observed at sub-lethal spores' concentrations. Even if the efficacy of B. laterosporus against Ae. albopictus and the invasive freshwater snail P. acuta is promising for their control, the susceptibility of non-target beneficial aquatic insects, highlights the need of accurate evaluations before applying B. laterosporus for pest management in water environments.

Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content.

In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.

The Microbial Community of Tetrodotoxin-Bearing and Non-Tetrodotoxin-Bearing Ribbon Worms (Nemertea) from the Sea of Japan.

A potent marine toxin, tetrodotoxin (TTX), found in a great variety of marine and some terrestrial species, leaves intriguing questions about its origin and distribution in marine ecosystems. TTX-producing bacteria were found in the cultivable microflora of many TTX-bearing hosts, thereby providing strong support for the hypothesis that the toxin is of bacterial origin in these species. However, metagenomic studies of TTX-bearing animals addressing the whole microbial composition and estimating the contribution of TTX-producing bacteria to the overall toxicity of the host were not conducted. The present study is the first to characterize and compare the 16S rRNA gene data obtained from four TTX-bearing and four non-TTX-bearing species of marine ribbon worms. The statistical analysis showed that different nemertean species harbor distinct bacterial communities, while members of the same species mostly share more similar microbiomes. The bacterial species historically associated with TTX production were found in all studied samples but predominated in TTX-bearing nemertean species. This suggests that deeper knowledge of the microbiome of TTX-bearing animals is a key to understanding the origin of TTX in marine ecosystems.

Degradation Mechanism of 2,4-Dichlorophenol by Fungi Isolated from Marine Invertebrates.

2,4-Dichlorophenol (2,4-DCP) is a ubiquitous environmental pollutant categorized as a priority pollutant by the United States (US) Environmental Protection Agency, posing adverse health effects on humans and wildlife. Bioremediation is proposed as an eco-friendly, cost-effective alternative to traditional physicochemical remediation techniques. In the present study, fungal strains were isolated from marine invertebrates and tested for their ability to biotransform 2,4-DCP at a concentration of 1 mM. The most competent strains were studied further for the expression of catechol dioxygenase activities and the produced metabolites. One strain, identified as Tritirachium sp., expressed high levels of extracellular catechol 1,2-dioxygenase activity. The same strain also produced a dechlorinated cleavage product of the starting compound, indicating the assimilation of the xenobiotic by the fungus. This work also enriches the knowledge about the mechanisms employed by marine-derived fungi in order to defend themselves against chlorinated xenobiotics.

Microbes and macro-invertebrates show parallel ß-diversity but contrasting α-diversity patterns in a marine natural experiment.

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of ß-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of ß-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Unraveling the Detoxification Mechanism of 2,4-Dichlorophenol by Marine-Derived Mesophotic Symbiotic Fungi Isolated from Marine Invertebrates.

Chlorophenols (CPs) are environmental pollutants that are produced through various anthropogenic activities and introduced in the environment. Living organisms, including humans, are exposed to these toxic xenobiotics and suffer from adverse health effects. More specifically, 2,4-dichlorophenol (2,4-DCP) is released in high amounts in the environment and has been listed as a priority pollutant by the US Environmental Protection Agency. Bioremediation has been proposed as a sustainable alternative to conventional remediation methods for the detoxification of phenolic compounds. In this work, we studied the potential of fungal strains isolated as symbionts of marine invertebrates from the underexplored mesophotic coral ecosystems. Hence, the unspecific metabolic pathways of these fungal strains are being explored in the present study, using the powerful analytical capabilities of a UHPLC-HRMS/MS. The newly identified 2,4-DCP metabolites add significantly to the knowledge of the transformation of such pollutants by fungi, since such reports are scarce.

A Microsporidian Infection in Phoronids (Phylum Phoronida): Microsporidium phoronidi n. sp. from a Phoronis embryolabi.

Microsporidia-like spores (2.0-3.0 × 1.3-1.5 µm) were discovered upon examination of histological sections taken from Phoronis embryolabi Temereva, Chichvarkhin 2017 found inhabiting burrows of shrimps Nihonotrypeae japonica (Decapoda, Callianassidae) from the Sea of Japan, Russia. Ultrastructural examination of spores revealed one nucleus and a uniform polar filament of 7-11 coils. Representatives of the phylum Phoronida have never been recorded as hosts of microsporidia. Parasites developed in vasoperitoneal tissue and caused formation of multinucleate syncytia. Basing on unique host and fine morphology, we assign the novel finding to Microsporidium phoronidi n. sp. and place provisionally in the collective genus Microsporidium.

The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates.

Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity.

New Invasive Nemertean Species (Cephalothrix Simula) in England with High Levels of Tetrodotoxin and a Microbiome Linked to Toxin Metabolism.

The marine nemertean Cephalothrix simula originates from the Pacific Ocean but in recent years has been discovered in northern Europe. The species has been associated with high levels of the marine neurotoxin Tetrodotoxin, traditionally associated with Pufferfish Poisoning. This study reports the first discovery of two organisms of C. simula in the UK, showing the geographical extent of this species is wider than originally described. Species identification was initially conducted morphologically, with confirmation by Cox 1 DNA sequencing. 16S gene sequencing enabled the taxonomic assignment of the microbiome, showing the prevalence of a large number of bacterial genera previously associated with TTX production including Alteromonas, Vibrio and Pseudomonas. LC-MS/MS analysis of the nemertean tissue revealed the presence of multiple analogues of TTX, dominated by the parent TTX, with a total toxin concentration quantified at 54 µg TTX per g of tissue. Pseudomonas luteola isolated from C. simula, together with Vibrio alginolyticus from the native nemertean Tubulanus annulatus, were cultured at low temperature and both found to contain TTX. Overall, this paper confirms the high toxicity of a newly discovered invasive nemertean species with links to toxin-producing marine bacteria and the potential risk to human safety. Further work is required to assess the geographical extent and toxicity range of C. simula along the UK coast in order to properly gauge the potential impacts on the environment and human safety.

Bioprospecting from cultivable bacterial communities of marine sediment and invertebrates from the underexplored Ubatuba region of Brazil.

Shrimp fisheries along the Brazilian coast have significant environmental impact due to high by-catch rates (21 kg per kilogram of shrimp). Typically discarded, by-catch contains many invertebrates that may host a great variety of bacterial genera, some of which may produce bioactive natural products with biotechnological applications. Therefore, to utilize by-catch that is usually discarded we explored the biotechnological potential of culturable bacteria of two abundant by-catch invertebrate species, the snail Olivancillaria urceus and the sea star Luidia senegalensis. Sediment from the collection area was also investigated. Utilizing multiple isolation approaches, 134 isolates were obtained from the invertebrates and sediment. Small-subunit rRNA (16S) gene sequencing revealed that the isolates belonged to Proteobacteria, Firmicutes and Actinobacteria phyla and were distributed among 28 genera. Several genera known for their capacity to produce bioactive natural products (Micromonospora, Streptomyces, Serinicoccus and Verrucosispora) were retrieved from the invertebrate samples. To query the bacterial isolates for their ability to produce bioactive metabolites, all strains were fermented and fermentation extracts profiled by UP LC-HRMS and tested for antimicrobial activity. Four strains exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus warneri.

Pharmacological Potential of Phylogenetically Diverse Actinobacteria Isolated from Deep-Sea Coral Ecosystems of the Submarine Avilés Canyon in the Cantabrian Sea.

Marine Actinobacteria are emerging as an unexplored source for natural product discovery. Eighty-seven deep-sea coral reef invertebrates were collected during an oceanographic expedition at the submarine Avilés Canyon (Asturias, Spain) in a range of 1500 to 4700 m depth. From these, 18 cultivable bioactive Actinobacteria were isolated, mainly from corals, phylum Cnidaria, and some specimens of phyla Echinodermata, Porifera, Annelida, Arthropoda, Mollusca and Sipuncula. As determined by 16S rRNA sequencing and phylogenetic analyses, all isolates belong to the phylum Actinobacteria, mainly to the Streptomyces genus and also to Micromonospora, Pseudonocardia and Myceligenerans. Production of bioactive compounds of pharmacological interest was investigated by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) techniques and subsequent database comparison. Results reveal that deep-sea isolated Actinobacteria display a wide repertoire of secondary metabolite production with a high chemical diversity. Most identified products (both diffusible and volatiles) are known by their contrasted antibiotic or antitumor activities. Bioassays with ethyl acetate extracts from isolates displayed strong antibiotic activities against a panel of important resistant clinical pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi, all of them isolated at two main hospitals (HUCA and Cabueñes) from the same geographical region. The identity of the active extracts components of these producing Actinobacteria is currently being investigated, given its potential for the discovery of pharmaceuticals and other products of biotechnological interest.

Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals?

The active role of gastrointestinal microbiota in mercury (Hg) methylation has been investigated in different terrestrial organisms from insects or annelids to rats and mammals, including the human beings. Some findings reveal the animal digestive tracts as new potential niches for Hg methylation especially in terrestrial invertebrates. However, contradictory results have been reported so far and there is still a long way to fully understand how important the MeHg production in this habitat could be, as well as its implications on the toxicity and biomagnification of MeHg within terrestrial food chains. It is important to know what has been studied in the past and discuss the previous results according to the new perspectives opened in this field. Therefore, the aim of this work is to review the present state of knowledge about the potential capability of gastrointestinal microbiota in Hg methylation with special emphasis in terrestrial animals and to propose new approaches profiting the new and powerful molecular and analytical tools.

Are There Any Other Compounds Isolated From Dermacoccus spp at All?

Microbial-derived natural products have functional and structural diversity and complexity. For several decades, they have provided the basic foundation for most drugs available to modern medicine. Microbial-derived natural products have wide-ranging applications, especially as chemotherapeutics for various diseases and disorders. By exploring distinct microorganisms in different environments, small novel bioactive molecules with unique functionalities and biological or biomedical significance can be identified. Aquatic environments, such as oceans or seas, are considered to be sources of abundant novel bioactive compounds. Studies on marine microorganisms have revealed that several bioactive compounds extracted from marine algae and invertebrates are eventually generated by their associated bacteria. These findings have prompted intense research interest in discovering novel compounds from marine microorganisms. Natural products derived from Dermacoccus exhibit antibacterial, antitumor, antifungal, antioxidant, antiviral, antiparasitic, and eventually immunosuppressive bioactivities. In this review, we discussed the diversity of secondary metabolites generated by genus Dermacoccus with respect to their chemical structure, biological activity, and origin. This brief review highlights and showcases the pivotal importance of Dermacoccus-derived natural products and sheds light on the potential venues of discovery of new bioactive compounds from marine microorganisms.

Foreign DNA acquisition by invertebrate genomes.

Recent studies have highlighted that the accidental acquisition of DNA from other species by invertebrate genomes is much more common than originally thought. The transferred DNAs are of bacterial or eukaryote origin and in both cases the receiver species may end up utilising the transferred genes for its own benefit. Frequent contact with prokaryotic DNA from symbiotic endocellular bacteria may predispose invertebrates to incorporate this genetic material into their genomes. Increasing evidence also points to viruses as major players in transferring genes and mobile elements between the species they infect. Unexpectedly a gene flux between Hymenoptera and Lepidoptera mediated by endogenous viruses of parasitic wasps has been recently unravelled, suggesting we are probably just seeing the tip of the iceberg concerning horizontal gene transfers in invertebrates. In the context of insect for feed and food, if the new technology of insect genome editing (such as Crisper/Cas9) were used to modify the genome of reared insects it is important to take into account the risk that an introduced gene can be transferred. More generally, although insects are traditionally consumed in Asia and Africa, knowledge on insect viruses is still limited rendering it difficult to predict the impact they might have in the context of insect rearing at an industrial scale.

Miniaturized Cultivation of Microbiota for Antimalarial Drug Discovery.

The ongoing search for effective antiplasmodial agents remains essential in the fight against malaria worldwide. Emerging parasitic drug resistance places an urgent need to explore chemotherapies with novel structures and mechanisms of action. Natural products have historically provided effective antimalarial drug scaffolds. In an effort to search nature's chemical potential for antiplasmodial agents, unconventionally sourced organisms coupled with innovative cultivation techniques were utilized. Approximately 60,000 niche microbes from various habitats (slow-growing terrestrial fungi, Antarctic microbes, and mangrove endophytes) were cultivated on a small-scale, extracted, and used in high-throughput screening to determine antimalarial activity. About 1% of crude extracts were considered active and 6% partially active (≥ 67% inhibition at 5 and 50 µg/mL, respectively). Active extracts (685) were cultivated on a large-scale, fractionated, and screened for both antimalarial activity and cytotoxicity. High interest fractions (397) with an IC50 < 1.11 µg/mL were identified and subjected to chromatographic separation for compound characterization and dereplication. Identifying active compounds with nanomolar antimalarial activity coupled with a selectivity index tenfold higher was accomplished with two of the 52 compounds isolated. This microscale, high-throughput screening project for antiplasmodial agents is discussed in the context of current natural product drug discovery efforts.

Gut microbiota-generated metabolites in animal health and disease.

Gut microbiota is found in virtually any metazoan, from invertebrates to vertebrates. It has long been believed that gut microbiota, more specifically, the activity of the microbiome and its metabolic products, directly influence a variety of aspects in metazoan physiology. However, the exact molecular relationship among microbe-derived gut metabolites, host signaling pathways, and host physiology remains to be elucidated. Here we review recent discoveries regarding the molecular links between gut metabolites and host physiology in different invertebrate and vertebrate animal models. We describe the different roles of gut microbiome activity and their metabolites in regulating distinct host physiology and the molecular mechanisms by which gut metabolites cause physiological homeostasis via regulating specific host signaling pathways. Future studies in this direction using different animal models will provide the key concepts to understanding the evolutionarily conserved chemical dialogues between gut microbiota and metazoan cells and also human diseases associated with gut microbiota and metabolites.