Unique microbial signatures of the alien Hawaiian marine sponge Suberites zeteki

Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations

Sterane molecular fossils are broadly interpreted as eukaryotic biomarkers, although diverse bacteria also produce sterols. Steranes with side-chain methylations can act as more specific biomarkers if their sterol precursors are limited to particular eukaryotes and are absent in bacteria. One such sterane, 24-isopropylcholestane, has been attributed to demosponges and potentially represents the earliest evidence for animals on Earth, but enzymes that methylate sterols to give the 24-isopropyl side-chain remain undiscovered. Here, we show that sterol methyltransferases from both sponges and yet-uncultured bacteria function in vitro and identify three methyltransferases from symbiotic bacteria each capable of sequential methylations resulting in the 24-isopropyl sterol side-chain. We demonstrate that bacteria have the genomic capacity to synthesize side-chain alkylated sterols, and that bacterial symbionts may contribute to 24-isopropyl sterol biosynthesis in demosponges. Together, our results suggest bacteria should not be dismissed as potential contributing sources of side-chain alkylated sterane biomarkers in the rock record.

Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.

Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation

Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host–microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.

Host-specific symbioses and the microbial prey of a pelagic tunicate (Pyrosoma atlanticum)

Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. This is the first study of the marine microorganisms associated with pyrosomes undertaken to improve the understanding of pyrosome biology, the impact of pyrosome blooms on marine microbial systems, and microbial symbioses with marine animals. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry. We found that pyrosomes harbor a microbiome distinct from the surrounding seawater, which was dominated by a few novel taxa. In addition to the dominant taxa, numerous more rare pyrosome-specific microbial taxa were recovered. Multiple bioluminescent taxa were present in pyrosomes, which may be a source of the iconic pyrosome luminescence. We also discovered free-living marine microorganisms in association with pyrosomes, suggesting that pyrosome feeding impacts all microbial size classes but preferentially removes larger eukaryotic taxa. This study demonstrates that microbial symbionts and microbial prey are central to pyrosome biology. In addition to pyrosome impacts on higher trophic level marine food webs, the work suggests that pyrosomes also alter marine food webs at the microbial level through feeding and seeding of the marine microbial communities with their symbionts. Future efforts to predict pyrosome blooms, and account for their ecosystem impacts, should consider pyrosome interactions with marine microbial communities.

Cultivable yeasts associated with marine sponges in the Gulf of Thailand, South China Sea

Marine sponges harbor numerous microorganisms, among which sponge-associated yeasts are the least explored. To gain greater knowledge of sponge-associated yeasts, an investigation was therefore performed on marine sponges in Sattahip Bay, Gulf of Thailand, South China Sea. Seventy-one (71) marine sponge samples were collected at sites near Samae-san, Mu, and Khram islands, and were subsequently identified as 17 sponge species in 14 genera. Eighty-seven (87) yeast strains were isolated from 42 samples. The identification of yeasts by similarity analysis of the D1/D2 domain sequences of the large subunit rRNA gene revealed that 64% of the yeast strains obtained belonged to the phylum Basidiomycota, while the remaining strains belonged to the phylum Ascomycota. The strains that belonged to Ascomycota comprised 11 known yeast species in five genera (Candida, Kodamaea, Magnusiomyces, Meyerozyma, and Pichia). The strains belonging to the phylum Basidiomycota comprised 14 known yeast species in eight genera (Cutaneotrichosporon, Cystobasidium, Naganishia, Papiliotrema, Rhodosporidiobolus, Rhodotorula, Trichosporon, and Vishniacozyma). In addition, three strains represented a potential novel species closest to Cys. slooffiae; one strain represented a potential novel species closest to R. toruloides; and one strain represented a potential novel species closest to V. foliicola. The species with the highest occurrence was Rhodotorula mucilaginosa. No marked difference was found in the principal coordinates analysis of the ordinations of yeast communities from the three sampling sites. The estimation using EstimateS software showed that the expected species richness was higher than the observed species richness. As the marine sponge-yeast association remains unclear, more systematic investigations should be carried out.

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.

Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.

Distribution of Toxigenic Halomicronema spp. in Adjacent Environments on the Island of Ischia: Comparison of Strains from Thermal Waters and Free Living in Posidonia Oceanica Meadows

Organisms adaptable to extreme conditions share the ability to establish protective biofilms or secrete defence toxins. The extracellular substances that are secreted may contain monosaccharides and other toxic compounds, but environmental conditions influence biofilm characteristics. Microorganisms that are present in the same environment achieve similar compositions, regardless of their phylogenetic relationships. Alternatively, cyanobacteria phylogenetically related may live in different environments, but we ignore if their physiological answers may be similar. To test this hypothesis, two strains of cyanobacteria that were both ascribed to the genus Halomicronema were isolated. H. metazoicum was isolated in marine waters off the island of Ischia (Bay of Naples, Italy), free living on leaves of Posidonia oceanica. Halomicronema sp. was isolated in adjacent thermal waters. Thus, two congeneric species adapted to different environments but diffused in the same area were polyphasically characterized by microscopy, molecular, and toxicity analyses. A variable pattern of toxicity was exhibited, in accordance with the constraints imposed by the host environments. Cyanobacteria adapted to extreme environments of thermal waters face a few competitors and exhibit a low toxicity; in contrast, congeneric strains that have adapted to stable and complex environments as seagrass meadows compete with several organisms for space and resources, and they produce toxic compounds that are constitutively secreted in the surrounding waters.

First evidence of Halomicronema metazoicum (Cyanobacteria) free-living on Posidonia oceanica leaves

Cyanobacteria contribute to the ecology of various marine environments, also for their symbioses, since some of them are common hosts of sponges and ascidians. They are also emerging as an important source of novel bioactive secondary metabolites in pharmacological (as anticancer drugs) and biotechnological applications. In the present work we isolated a cyanobacteria in a free-living state from leaves of the seagrass Posidonia oceanica leaves. This newly collected strain was then cultivated under two laboratory conditions, and then characterized by combining morphological observation and molecular studies based on 16S rRNA gene sequences analysis. The strain showed 99% pairwise sequence identity with Halomicronema metazoicum ITAC101, never isolated before as a free-living organisms, but firstly described as an endosymbiont of the Mediterranean marine spongae Petrosia ficiformis, under the form of a filamentous strain. Further studies will investigate the actual role of this cyanobacterium in the leaf stratum of P. oceanica leaves, given its demonstrated ability to influence the vitality and the life cycle of other organisms. In fact, its newly demonstrated free-living stage, described in this study, indicate that Phormidium-like cyanobacteria could play important roles in the ecology of benthic and planktonic communities.

Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification

Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

Characteristics of chlamydia-like organisms pathogenic to fish

Bacteria from the Chlamydiales order have been long known, especially as pathogenic bacteria to humans and many animal species, principally including birds and mammals. But for slightly over 20 years, they have been identified in the aquatic environment as endosymbionts of amoebas and sea worms. For several years, they have also been recorded as a cause of diseases among fish, causing respiratory system infections in the form of epitheliocystis of the gill. At present, 11 chlamydia-like organisms pathogenic to fish have been described, including nine new ones, classified into six families, four of which are already known (Parachlamydiaceae, Rhabdochlamydiaceae, Candidatus Parilichlamydiaceae, Candidatus Clavichlamydiaceae) and two newly created families, namely Candidatus Actinochlamydiaceae and Candidatus Parilichlamydiaceae. This paper characterises 11 chlamydia-like organisms, as well as seven isolates not classified into families, which are pathogenic to fish, presenting their genetical properties allowing for their classification, as well as morphological properties and diseases caused.

Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns

Sponges are ancient metazoans that host diverse and complex microbial communities. Sponge-associated microbial diversity has been studied from wide oceans across the globe, particularly in subtidal regions, but the microbial communities from intertidal sponges have remained mostly unexplored. Here we used pyrosequencing to characterize the microbial communities in 12 different co-occurring intertidal marine sponge species sampled from the Atlantic coast, revealing a total of 686 operational taxonomic units (OTUs) at 97% sequence similarity. Taxonomic assignment of 16S ribosomal RNA tag sequences estimated altogether 26 microbial groups, represented by bacterial (75.5%) and archaeal (22%) domains. Proteobacteria (43.4%) and Crenarchaeota (20.6%) were the most dominant microbial groups detected in all the 12 marine sponge species and ambient seawater. The Crenarchaeota microbes detected in three Atlantic Ocean sponges had a close similarity with Crenarchaeota from geographically separated subtidal Red Sea sponges. Our study showed that most of the microbial communities observed in sponges (73%) were also found in the surrounding ambient seawater suggesting possible environmental acquisition and/or horizontal transfer of microbes. Beyond the microbial diversity and community structure assessments (NMDS, ADONIS, ANOSIM), we explored the interactions between the microbial communities coexisting in sponges using the checkerboard score (C-score). Analyses of the microbial association pattern (co-occurrence) among intertidal sympatric sponges revealed the random association of microbes, favoring the hypothesis that the sponge-inhabiting microbes are recruited from the habitat mostly by chance or influenced by environmental factors to benefit the hosts.

Two distinct microbial communities revealed in the sponge Cinachyrella

Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.

Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products

Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.

Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis

Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.

Planctomycetes and macroalgae, a striking association

Planctomycetes are part of the complex microbial biofilm community of a wide range of macroalgae. Recently, some studies began to unveil the great diversity of Planctomycetes present in this microenvironment and the interactions between the two organisms. Culture dependent and independent methods revealed the existence of a great number of species but, so far, only less than 10 species have been isolated. Planctomycetes comprise the genera Rhodopirellula, Blastopirellula, and Planctomyces, Phycisphaera and the uncultured class OM190 and some other taxa have only been found in this association. Several factors favor the colonization of macroalgal surfaces by planctomycetes. Many species possess holdfasts for attachment. The macroalgae secrete various sulfated polysaccharides that are the substrate for the abundant sulfatases produced by planctomycetes. Specificity between planctomycetes and macroalgae seem to exist which may be related to the chemical nature of the polysaccharides produced by each macroalga. Furthermore, the peptidoglycan-free cell wall of planctomycetes allows them to resist the action of several antimicrobial compounds produced by the macroalgae or other bacteria in the biofilm community that are effective against biofouling by other microorganisms. Despite the increase in our knowledge on the successful planctomycetes-macroalgae association, a great effort to fully understand this interaction is needed.

Community composition of the Planctomycetes associated with different macroalgae

Insights into the diversity of marine natural microbial biofilms, as for example those developing at the surface of marine macroalgae, can be obtained by using molecular techniques based on 16S rRNA genes. We applied denaturing gradient gel electrophoresis (DGGE) with 16S rRNA genes-specific primers for Planctomycetes to compare the communities of these organisms developing on six different macroalgae (Chondrus crispus, Fucus spiralis, Mastocarpus stellatus, Porphyra dioica, Sargassum muticum, and Ulva sp.) sampled in spring 2012 in two rocky beaches in the north of Portugal. Planctomycetes can be one of the dominant organisms found in the epibacterial community of macroalgae, and we wanted to determine the degree of specificity and the spatial variation of these group. Shannon diversity indexes obtained from the comparison of DGGE profiles were similar in all the macroalgae, and in both sites, F. spiralis was the algae presenting lower Planctomycetes diversity, while M. stellatus and P. dioica from Porto showed the highest diversity. The analysis of DGGE profiles, including anosim statistics, indicate the existence of a specific Planctomycetes community associated with the algal host, likely independent of geographical variation. Sequencing of DGGE bands indicated that Planctomycetes communities were highly diverse, and some Operational Taxonomic Units seemed to be specifically associated with each macroalgae.

Induction of lipids and resultant FAME profiles of microalgae from coastal waters of Pearl River Delta

This article presents a study on identification, cultivation and characterisation of microalgal strains from the coastal waters of the Pearl River Delta in Guangdong, China. Thirty-seven identified strains belong to the families: Chlorellaceae, Scotiellocystoidaceae, Scenedesmaceae,Selenastraceae,Micractiniaceae, Coccomyxaceae, Trebouxiaceae and Chlorococcaceae. Of isolated strains, Hindakia PKUAC 169 was selected for lipid induction using two methods: nitrogen starvation and salt stress. After derivatisation of algal lipids through in situ transesterification, lipid profiles of the alga under the two methods were analysed. The results have shown that both lipid yield and fatty acid profiles vary with the methods. Of the two tested methods of inducing lipid production, salt stress yielded three-fold higher lipid productivity than nitrogen starvation. The lipids are predominantly composed of C14-C18 fatty acids, which are favourable for biodiesel production. Moreover, the content of polyunsaturated fatty acids was below the limit of 12% set by EN14214 biodiesel standard.

First insights into the microbiome of a carnivorous sponge

Using 454 pyrosequencing, we characterized for the first time the associated microbial community of the deep-sea carnivorous Demosponge Asbestopluma hypogea (Cladorhizidae). Targeting the 16S rRNA gene V3 and V6 hypervariable regions, we compared the diversity and composition of associated microbes of two individual sponges of A. hypogea freshly collected in the cave with surrounding seawater and with one sponge sample maintained 1 year in an aquarium after collection. With more than 22 961 high quality sequences from sponge samples, representing c. 800 operational taxonomic units per sponge sample at 97% sequence similarities, the phylogenetic affiliation of A. hypogea-associated microbes was assigned to 20 bacterial and two archaeal phyla, distributed into 45 classes and 95 orders. Several differences between the sponge and seawater microbes were observed, highlighting a specific and stable A. hypogea microbial community dominated by Proteobacteria and Bacteroidetes and Thaumarchaeota phyla. A high relative abundance of ammonia-oxidizing archaea and a dominance of sulfate oxidizing/reducing bacteria were observed. Our findings shed lights on the potential roles of associated microbial community in the lifestyle of A. hypogea.

Subtilomycin: a new lantibiotic from Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans

Bacteriocins are attracting increased attention as an alternative to classic antibiotics in the fight against infectious disease and multidrug resistant pathogens. Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans displays a broad spectrum antimicrobial activity, which includes Gram-positive and Gram-negative pathogens, as well as several pathogenic Candida species. This activity is in part associated with a newly identified lantibiotic, herein named as subtilomycin. The proposed biosynthetic cluster is composed of six genes, including protein-coding genes for LanB-like dehydratase and LanC-like cyclase modification enzymes, characteristic of the class I lantibiotics. The subtilomycin biosynthetic cluster in B. subtilis strain MMA7 is found in place of the sporulation killing factor (skf) operon, reported in many B. subtilis isolates and involved in a bacterial cannibalistic behaviour intended to delay sporulation. The presence of the subtilomycin biosynthetic cluster appears to be widespread amongst B. subtilis strains isolated from different shallow and deep water marine sponges. Subtilomycin possesses several desirable industrial and pharmaceutical physicochemical properties, including activity over a wide pH range, thermal resistance and water solubility. Additionally, the production of the lantibiotic subtilomycin could be a desirable property should B. subtilis strain MMA7 be employed as a probiotic in aquaculture applications.

The ecological perspective of microbial communities in two pairs of competitive Hawaiian native and invasive macroalgae

Marine macroalgae are known to harbor large populations of microbial symbionts, and yet, microbe symbiosis in invasive macroalgae remains largely unknown. In this study, we applied molecular methods to study microbial communities associated with two invasive algae Acanthophora spicifera and Gracilaria salicornia and the two native algae Gracilaria coronopifolia and Laurencia nidifica at spatial and temporal scales in Hawaiian coral reef ecosystems. Bacterial communities of both the invasive and native macroalgae displayed little spatial and temporal variations, suggesting consistent and stable bacterial associations with these macroalgae. Results of this study identified three types of bacterial populations: nonspecific (present in both algal and water samples); algae-specific (found in all algal species); and species-specific (only found in individual species). The bacterial diversity of invasive algae was lower than that of their native counterparts at phylum and species levels. Notably, the vast majority (71 %) of bacterial communities associated with the invasive algae G. salicornia were representatives of Cyanobacteria, suggesting a potential ecological significance of symbiotic Cyanobacteria.

Diversity and biosynthetic potential of culturable actinomycetes associated with marine sponges in the China Seas

The diversity and secondary metabolite potential of culturable actinomycetes associated with eight different marine sponges collected from the South China Sea and the Yellow sea were investigated. A total of 327 strains were isolated and 108 representative isolates were selected for phylogenetic analysis. Ten families and 13 genera of Actinomycetales were detected, among which five genera represent first records isolated from marine sponges. Oligotrophic medium M5 (water agar) proved to be efficient for selective isolation, and “Micromonospora–Streptomyces” was proposed as the major distribution group of sponge-associated actinomycetes from the China Seas. Ten isolates are likely to represent novel species. Sponge Hymeniacidon perleve was found to contain the highest genus diversity (seven genera) of actinomycetes. Housekeeping gene phylogenetic analyses of the isolates indicated one ubiquitous Micromonospora species, one unique Streptomyces species and one unique Verrucosispora phylogroup. Of the isolates, 27.5% displayed antimicrobial activity, and 91% contained polyketide synthase and/or nonribosomal peptide synthetase genes, indicating that these isolates had a high potential to produce secondary metabolites. The isolates from sponge Axinella sp. contained the highest presence of both antimicrobial activity and NRPS genes, while those from isolation medium DNBA showed the highest presence of antimicrobial activity and PKS I genes.

Candidatus Renichlamydia lutjani, a Gram-negative bacterium in internal organs of blue-striped snapper Lutjanus kasmira from Hawaii

The blue-striped snapper Lutjanus kasmira (Perciformes, Lutjanidae) are cosmopolitan in the Indo-Pacific but were introduced into Oahu, Hawaii, USA, in the 1950s and have since colonized most of the archipelago. Studies of microparasites in blue-striped snappers from Hawaii revealed chlamydia-like organisms (CLO) infecting the spleen and kidney, characterized by intracellular basophilic granular inclusions containing Gram-negative and Gimenez-positive bacteria similar in appearance to epitheliocysts when seen under light microscopy. We provide molecular evidence that CLO are a new member of Chlamydiae, i.e. Candidatus Renichlamydia lutjani, that represents the first reported case of chlamydial infection in organs other than the gill in fishes.

Metaproteogenomic analysis of a community of sponge symbionts

Sponges harbour complex communities of diverse microorganisms, which have been postulated to form intimate symbiotic relationships with their host. Here we unravel some of these interactions by characterising the functional features of the microbial community of the sponge Cymbastela concentrica through a combined metagenomic and metaproteomic approach. We discover the expression of specific transport functions for typical sponge metabolites (for example, halogenated aromatics, dipeptides), which indicates metabolic interactions between the community and the host. We also uncover the simultaneous performance of aerobic nitrification and anaerobic denitrification, which would aid to remove ammonium secreted by the sponge. Our analysis also highlights the requirement for the microbial community to respond to variable environmental conditions and hence express an array of stress protection proteins. Molecular interactions between symbionts and their host might also be mediated by a set of expressed eukaryotic-like proteins and cell-cell mediators. Finally, some sponge-associated bacteria (for example, a Phyllobacteriaceae phylotype) appear to undergo an evolutionary adaptation process to the sponge environment as evidenced by active mobile genetic elements. Our data clearly show that a combined metaproteogenomic approach can provide novel information on the activities, physiology and interactions of sponge-associated microbial communities.

Diversity and bioactive potential of endospore-forming bacteria cultured from the marine sponge Haliclona simulans

AIMS

Despite the frequent isolation of endospore-formers from marine sponges, little is known about the diversity and characterization of individual isolates. The main aims of this study were to isolate and characterize the spore-forming bacteria from the marine sponge Haliclona simulans and to examine their potential as a source for bioactive compounds.

METHODS AND RESULTS

A bank of presumptive aerobic spore-forming bacteria was isolated from the marine sponge H. simulans. These represented c. 1% of the total culturable bacterial population. A subgroup of thirty isolates was characterized using morphological, phenotypical and phylogenetic analysis. A large diversity of endospore-forming bacteria was present, with the thirty isolates being distributed through a variety of Bacillus and Paenibacillus species. These included ubiquitous species, such as B. subtilis, B. pumilus, B. licheniformis and B. cereus group, as well as species that are typically associated with marine habitats, such as B. aquimaris, B. algicola and B. hwajinpoensis. Two strains carried the aiiA gene that encodes a lactonase known to be able to disrupt quorum-sensing mechanisms, and various isolates demonstrated protease activity and antimicrobial activity against different pathogenic indicator strains, including Clostridium perfringens, Bacillus cereus and Listeria monocytogenes.

CONCLUSIONS

The marine sponge H. simulans harbours a diverse collection of endospore-forming bacteria, which produce proteases and antibiotics. This diversity appears to be overlooked by culture-dependent and culture-independent methods that do not specifically target sporeformers.

SIGNIFICANCE AND IMPACT OF STUDY

Marine sponges are an as yet largely untapped and poorly understood source of endospore-forming bacterial diversity with potential biotechnological, biopharmaceutical and probiotic applications. These results also indicate the importance of combining different methodologies for the comprehensive characterization of complex microbial populations such as those found in marine sponges.

Phylogenetic diversity of bacteria associated with the marine sponge Gelliodes carnosa collected from the Hainan Island coastal waters of the South China Sea

Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges.

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp

Three methods were examined to cultivate bacteria associated with the marine sponge Haliclona (gellius) sp.: agar plate cultures, liquid cultures, and floating filter cultures. A variety of oligotrophic media were employed, including media with aqueous and organic sponge extracts, bacterial signal molecules, and siderophores. More than 3,900 isolates were analyzed, and 205 operational taxonomic units (OTUs) were identified. Media containing low concentrations of mucin or a mixture of peptone and starch were most successful for the isolation of diversity, while the commonly used marine broth did not result in a high diversity among isolates. The addition of antibiotics generally led to a reduced diversity on plates but yielded different bacteria than other media. In addition, diversity patterns of isolates from agar plates, liquid cultures, and floating filters were significantly different. Almost 89% of all isolates were Alphaproteobacteria; however, members of phyla that are less commonly encountered in cultivation studies, such as Planctomycetes, Verrucomicrobia, and Deltaproteobacteria, were isolated as well. The sponge-associated bacteria were categorized into three different groups. The first group represented OTUs that were also obtained in a clone library from previously analyzed sponge tissue (group 1). Furthermore, we distinguished OTUs that were obtained from sponge tissue (in a previous study) but not from sponge isolates (group 2), and there were also OTUs that were not obtained from sponge tissue but were obtained from sponge isolates (group 3). The 17 OTUs categorized into group 1 represented 10 to 14% of all bacterial OTUs that were present in a large clone library previously generated from Haliclona (gellius) sp. sponge tissue, which is higher than previously reported cultivability scores for sponge-associated bacteria. Six of these 17 OTUs were not obtained from agar plates, which underlines that the use of multiple cultivation methods is worthwhile to increase the diversity of the cultivable microorganisms from sponges.

Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica

Marine sponges are ancient, sessile, filter-feeding metazoans, which represent a significant component of the benthic communities throughout the world. Sponges harbor a remarkable diversity of bacteria, however, little is known about the functional properties of such bacterial symbionts. In this study, we present the genomic and functional characterization of an uncultured δ-proteobacterium associated with the sponge Cymbastela concentrica. We show that this organism represents a novel phylogenetic clade and propose that it lives in association with a cyanobacterium. We also provide an overview of the predicted functional and ecological properties of this δ-proteobacterium, and discuss its complex interactions with surrounding cells and milieu, including traits of cell attachment, nutrient transport and protein-protein interactions.

Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250 000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described ‘sponge-specific’ clusters that were detected in this study, 48% were found exclusively in adults and larvae – implying vertical transmission of these groups. The remaining taxa, including ‘Poribacteria’, were also found at very low abundance among the 135 000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought.

Physiological traits of the symbiotic bacterium Teredinibacter turnerae isolated from the mangrove shipworm Neoteredo reynei

Nutrition in the Teredinidae family of wood-boring mollusks is sustained by cellulolytic/nitrogen fixing symbiotic bacteria of the Teredinibacter clade. The mangrove Teredinidae Neoteredo reynei is popularly used in the treatment of infectious diseases in the north of Brazil. In the present work, the symbionts of N. reynei, which are strictly confined to the host's gills, were conclusively identified as Teredinibacter turnerae. Symbiont variants obtained in vitro were able to grow using casein as the sole carbon/nitrogen source and under reduced concentrations of NaCl. Furthermore, cellulose consumption in T. turnerae was clearly reduced under low salt concentrations. As a point of interest, we hereby report first hand that T. turnerae in fact exerts antibiotic activity. Furthermore, this activity was also affected by NaCl concentration. Finally, T. turnerae was able to inhibit the growth of Gram-negative and Gram-positive bacteria, this including strains of Sphingomonas sp., Stenotrophomonas maltophilia, Bacillus cereus and Staphylococcus sciuri. Our findings introduce new points of view on the ecology of T. turnerae, and suggest new biotechnological applications for this marine bacterium.

Detection of Chlamydiae from freshwater environments by PCR, amoeba coculture and mixed coculture

Water systems have been shown to be a potential source of Chlamydiae, intracellular symbionts of eukaryotes. However, their diversity is likely underestimated, and natural hosts remain undetermined in many cases. In this study, we combined PCR-based and cultivation approaches to search for chlamydiae in different freshwaters, including natural ponds, garden pots and fountains. From a total of 40 samples, we recovered 16 phylotypes, clustered into nine species-level taxa belonging to the Parachlamydiaceae, Simkaniaceae, Rhabdochlamydiaceae, cvE6 lineage and a novel lineage. Parachlamydiaceae (four species) were recovered by amoeba coculture, while the other chlamydiae were maintained in mixed eukaryotic cultures. This study confirms the widespread occurrence of novel chlamydiae in the environment and enlarges our knowledge of their biodiversity in freshwater habitats.

Microbial communities associated with the invasive Hawaiian sponge Mycale armata

Microbial symbionts are fundamentally important to their host ecology, but microbial communities of invasive marine species remain largely unexplored. Clone libraries and Denaturing gradient gel electrophoresis analyses revealed diverse microbial phylotypes in the invasive marine sponge Mycale armata. Phylotypes were related to eight phyla: Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Acidobacteria, Chloroflexi, Crenarchaeota and Firmicutes, with predominant alphaproteobacterial sequences (>58%). Three Bacterial Phylotype Groups (BPG1--associated only with sequence from marine sponges; BPG2--associated with sponges and other marine organisms and BPG3--potential new phylotypes) were identified in M. armata. The operational taxonomic units (OTU) of cluster BPG2-B, belonging to Rhodobacteraceae, are dominant sequences of two clone libraries of M. armata, but constitute only a small fraction of sequences from the non-invasive sponge Dysidea sp. Six OTUs from M. armata were potential new phylotypes because of their low sequence identity with their reference sequences. Our results suggest that M. armata harbors both sponge-specific phylotypes and bacterial phylotypes from other marine organisms.

Molecular detection of fungal communities in the Hawaiian marine sponges Suberites zeteki and Mycale armata

Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (< or =98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into "marine fungus clades" with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.