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

Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments

Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.

Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding

Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.

Effects of sponge-to-sponge contact on the microbiomes of three spatially competing Caribbean coral reef species

Sponges perform important ecosystem functions, host diverse microbial symbiont communities (microbiomes), and have been increasing in density on Caribbean coral reefs over the last decade. Sponges compete for space in coral reef communities through both morphological and allelopathic strategies, but no studies of microbiome impacts during these interactions have been conducted. Microbiome alterations mediate spatial competition in other coral reef invertebrates and may similarly impact competitive outcomes for sponges. In this study, we characterized the microbiomes of three common Caribbean sponges (Agelas tubulata, Iotrochota birotulata, and Xestospongia muta) observed to naturally interact spatially in Key Largo, Florida (USA). For each species, replicate samples were collected from sponges in contact with neighbors at the site of contact (contact) and distant from the site of contact (no contact), and from sponges spatially isolated from neighbors (control). Next-generation amplicon sequencing (V4 region of 16S rRNA) revealed significant differences in microbial community structure and diversity among sponge species, but no significant effects were observed within sponge species across all contact states and competitor pairings, indicating no large community shifts in response to direct contact. At a finer scale, particular symbiont taxa (operational taxonomic units at 97% sequence identity, OTUs) were shown to decrease significantly in some interaction pairings, suggesting localized effects for specific sponge competitors. Overall, these results revealed that direct contact during spatial competition does not significantly alter microbial community composition or structure of interacting sponges, suggesting that allelopathic interactions and competitive outcomes are not mediated by microbiome damage or destabilization.

Adding functions to marine infrastructure: Pollutant accumulation, physiological and microbiome changes in sponges attached to floating pontoons inside marinas

The rate of introduction of man-made habitats in coastal environments is growing at an unprecedented pace, as a consequence of the expansion of urban areas. Floating installations, due to their unique hydrodynamic features, are able to provide great opportunities for enhancing water detoxification through the use of sessile, filtering organisms. We assessed whether the application of sponges to floating pontoons could function as a tool for biomonitoring organic and inorganic pollutants and for improving water quality inside a moderately contaminated marina in the NW Mediterranean. Fragments of two common Mediterranean sponges (Petrosia (Petrosia) ficiformis and Ircinia oros) were fixed to either suspended natural fibre nets beneath a floating pontoon or to metal frames deployed on the sea bottom. We assessed the accumulation of organic and inorganic contaminants in sponge fragments and, in order to provide an insight into their health status, we examined changes in their metabolic and oxidative stress responses and associated microbiomes. Fragments of both sponge species filtered out pollutants from seawater on both support types, but generally showed a better physiological and metabolic status when fixed to nets underneath the pontoon than to bottom frames. P. (P) ficiformis maintained a more efficient metabolism and exhibited a lower physiological stress levels and higher stability of the associated microbiome in comparison with I. oros. Our study suggests that the application of sponges to floating pontoon represents a promising nature-based solution to improve the ecological value of urban environments.

Identification of Sponge-Associated Bacteria From the Coast of Kuwait and Their Potential Biotechnological Applications

Sponges are among the most ancient animals harboring complex microbial communities with potential applications in biotechnology. The Arabian Gulf is a thermally stressed enclosed body of water located in an arid region where sponges and their halobionts are understudied. This study combined 16S rRNA next-generation gene amplicon sequencing and cultivation techniques to explore the abundance and diversity of sponge-associated bacteria. Culture-independent techniques showed the associations of more than 25 bacterial phyla with Amphimedon sp., Chondrilla australiensis, Haliclona sp., and Niphates spp. Regarding cultivable bacteria, 315 bacterial isolates associated with the sponge Haliclona sp. were cultivated; these isolates were affiliated with the phyla Proteobacteria and Firmicutes and were distributed among six bacterial genera. Selected strains of Bacillus, Ferrimonas, Pseudovibrio, Shewanella, Spongiobacter, and Vibrio were tested for antimicrobial activity against indicator microorganisms and protease enzyme production. Seven Bacillus strains exhibited weak to moderate growth inhibition against Bacillus subtilis, Staphylococcus aureus, and Candida albicans. Furthermore, 29 different strains of Bacillus, Ferrimonas, Shewanella, and Vibrio exhibited different degrees of positive protease activity. In addition, cultivated strains of Bacillus, Shewanella, Pseudovibrio, and Vibrio were tested for their biomineralization abilities. Herein we report for the first time the isolation of biomineralizing bacteria from sponge tissue where eleven bacterial isolates produced different shapes of calcium carbonate crystals on agar. Our observations shed light on the diversity and biotechnological potentials of sponges-associated bacteria inhabiting one of the world’s hottest seas.

Recent Advances of Marine Sponge-Associated Microorganisms as a Source of Commercially Viable Natural Products

Many industrially significant compounds have been derived from natural products in the environment. Research efforts so far have contributed to the discovery of beneficial natural products that have improved the quality of life on Earth. As one of the sources of natural products, marine sponges have been progressively recognised as microbial hotspots with reports of the sponges harbouring diverse microbial assemblages, genetic material, and metabolites with multiple industrial applications. Therefore, this paper aims at reviewing the recent literature (primarily published between 2016 and 2022) on the types and functions of natural products synthesised by sponge-associated microorganisms, thereby helping to bridge the gap between research and industrial applications. The metabolites that have been derived from sponge-associated microorganisms, mostly bacteria, fungi, and algae, have shown application prospects especially in medicine, cosmeceutical, environmental protection, and manufacturing industries. Sponge bacteria-derived natural products with medical properties harboured anticancer, antibacterial, antifungal, and antiviral functions. Efforts in re-identifying the origin of known and future sponge-sourced natural products would further clarify the roles and significance of microbes within marine sponges.

Marine biofilms: diversity, interactions and biofouling

Marine biofilms are ubiquitous in the marine environment. These complex microbial communities rapidly respond to environmental changes and encompass hugely diverse microbial structures, functions and metabolisms. Nevertheless, knowledge is limited on the microbial community structures and functions of natural marine biofilms and their influence on global geochemical cycles. Microbial cues, including secondary metabolites and microbial structures, regulate interactions between microorganisms, with their environment and with other benthic organisms, which affects their community succession and metamorphosis. Furthermore, marine biofilms are key mediators of marine biofouling, which greatly affect marine industries. In this Review, we discuss marine biofilm dynamics, including their diversity, abundance and functions. We also highlight knowledge gaps, areas for future research and potential biotechnological applications of marine biofilms.

Depth effect on the prokaryotic community assemblage associated with sponges from different rocky reefs

Background

Sponge microbiomes are essential for the function and survival of their host and produce biologically active metabolites, therefore, they are ideal candidates for ecological, pharmacologic and clinical research. Next-generation sequencing (NGS) has revealed that many factors, including the environment and host, determine the composition and structure of these symbiotic communities but the controls of this variation are not well described. This study assessed the microbial communities associated with two marine sponges of the genera Aplysina (Nardo, 1834) and Ircinia (Nardo, 1833) in rocky reefs from Punta Arena de la Ventana (Gulf of California) and Pichilingue (La Paz Bay) in the coast of Baja California Sur, México to determine the relative importance of environment and host in structuring the microbiome of sponges.

Methods

Specimens of Aplysina sp were collected by scuba diving at 10 m and 2 m; Ircinia sp samples were collected at 2 m. DNA of sponge-associated prokaryotes was extracted from 1 cm³ of tissue, purified and sent for 16S amplicon sequencing. Primer trimmed pair-ended microbial 16S rDNA gene sequences were merged using Ribosomal Database Project (RDP) Paired-end Reads Assembler. Chao1, Shannon and Simpson (alpha) biodiversity indices were estimated, as well permutational analysis of variance (PERMANOVA), and Bray-Curtis distances.

Results

The most abundant phyla differed between hosts. Those phyla were: Proteobacteria, Acidobacteria, Cyanobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes. In Ircinia sp the dominant phylum was Acidobacteria. Depth was the main factor influencing the microbial community, as analysis of similarities (ANOSIM) showed a significant difference between the microbial communities from different depths.

Conclusion

Microbial diversity analysis showed that depth was more important than host in structuring the Aplysina sp and Ircinia sp microbiome. This observation contrast with previous reports that the sponge microbiome is highly host specific.

Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra

Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.

Factors affecting the isolation and diversity of marine sponge-associated bacteria

Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges. KEY POINTS: Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels. Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing. At least 70% of culturable genera were not revealed by NGS methods.

Marine sponges maintain stable bacterial communities between reef sites with different coral to algae cover ratios

Marine sponges play a major ecological role in recycling resources on coral reef ecosystems. The cycling of resources may largely depend on the stability of the host-microbiome interactions and their susceptibility to altered environmental conditions. Given the current coral to algal phase shift on coral reefs, we investigated whether the sponge-associated bacterial communities of four sponge species, with either high or low microbial abundances (HMA and LMA), remain stable at two reefs sites with different coral to algae cover ratios. Additionally, we assessed the bacterial community composition of two of these sponge species before and after a reciprocal transplantation experiment between the sites. An overall stable bacterial community composition was maintained across the two sites in all sponge species, with a high degree of host-specificity. Furthermore, the core bacterial communities of the sponges remained stable also after a 21-day transplantation period, although a minor shift was observed in less abundant taxa (< 1%). Our findings support the conclusion that host identity and HMA-LMA status are stronger traits in shaping bacterial community composition than habitat. Nevertheless, long-term microbial monitoring of sponges along with benthic biomass and water quality assessments are needed for identifying ecosystem tolerance ranges and tipping points in ongoing coral reef phase shifts.

Untapped sponge microbiomes: structure specificity at host order and family levels

Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.

Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals

Bats (order Chiroptera) are one of the most diverse and widely distributed group of mammals with a close relationship to humans. Over the past few decades, a number of studies have been performed on bat viruses; in contrast, bacterial pathogens carried by bats were largely neglected. As more bacterial pathogens are being identified from bats, the need to study their natural microbiota is becoming urgent. In the current study, fecal samples of four bat species from different locations of China were analyzed for their microbiota composition. Together with the results of others, we concluded that bat microbiota is most commonly dominated by Firmicutes and Proteobacteria; the strict anaerobic phylum Bacteroidetes, which is dominant in other terrestrial mammals, especially humans and mice, is relatively rare in bats. This phenomenon was interpreted as a result of a highly specified gastrointestinal tract in adaptation to the flying lifestyle of bats. Further comparative study implied that bat microbiota resemble those of the order Carnivora. To discover potential bacterial pathogens, a database was generated containing the 16S rRNA gene sequences of known bacterial pathogens. Potential bacterial pathogens belonging to 12 genera were detected such as Salmonella, Shigella, and Yersinia, among which some have been previously reported in bats. This study demonstrated high resolution and repeatability in detecting organisms of rare existence, and the results could be used as guidance for future bacterial pathogen isolation.

Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida)

In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.

Geographical location and habitat predict variation in prokaryotic community composition of Suberites diversicolor

Purpose

Marine lakes are unique habitats that house diverse assemblages of benthic and planktonic organisms including endemic species. In this study, we aimed to assess to what extent geographical location (Berau versus Papua) and the degree of marine lake connectivity (relatively open versus closed) to the surrounding marine environment structures the prokaryotic community composition of the sponge species Suberites diversicolor.

Methods

Sponge specimens were sampled in five marine lakes in Borneo and Papua and one open sea habitat in Taiwan.

Result

Prokaryotic communities of S. diversicolor were dominated by members assigned to the Proteobacteria (particularly Alphaproteobacteria and Gammaproteobacteria) and Cyanobacteria, which together made up from 78 to 87% of sequences in all samples. The dominant operational taxonomic units (OTUs) in most samples, OTUs 1 and 3, were both assigned to the alphaproteobacterial order Rhodospirillales with OTU-1 dominant in the marine lakes of Berau and Papua and OTU-3 in Taiwan. OTU-3 was also largely absent from Papuan samples but present in all Berau samples. Compositionally, S. diversicolor samples clustered according to geographical location with the main axis of variation separating marine lake samples collected in Berau from those collected in Papua and the second axis of variation separating open sea samples collected in Taiwan from all marine lake samples. In addition, our results suggest that the degree of lake connectivity to the open sea also influences prokaryotic composition.

Conclusion

Although previous studies have shown that sponge-associated microbial communities tend to be stable across different geographical and environmental gradients, in the present study, both geography and local environmental conditions were significant predictors of variation in prokaryotic community composition of S. diversicolor.

Antarctic sponges from the Terra Nova Bay (Ross Sea) host a diversified bacterial community

Sponges represent important habitats for a community of associated (micro)organisms. Even if sponges dominate vast areas of the Antarctic shelves, few investigations have been performed on Antarctic sponge-associated bacteria. Using a culture-dependent approach, the composition of the bacterial communities associated with 14 Antarctic sponge species from different sites within the Terra Nova Bay (Ross Sea) area was analyzed. Overall, isolates were mainly affiliated to Gammaproteobacteria, followed by Actinobacteria and CF group of Bacteroidetes, being the genera Pseudoalteromonas, Arthrobacter and Gillisia predominant, respectively. Alphaproteobacteria and Firmicutes were less represented. Cluster analyses highlighted similarities/differences among the sponge-associated bacterial communities, also in relation to the sampling site. The gammaproteobacterial Pseudoalteromonas sp. SER45, Psychrobacter sp. SER48, and Shewanella sp. SER50, and the actinobacterial Arthrobacter sp. SER44 phylotypes occurred in association with almost all the analyzed sponge species. However, except for SER50, these phylotypes were retrieved also in seawater, indicating that they may be transient within the sponge body. The differences encountered within the bacterial communities may depend on the different sites of origin, highlighting the importance of the habitat in structuring the composition of the associated bacterial assemblages. Our data support the hypothesis of specific ecological interactions between bacteria and Porifera.

Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges

BACKGROUND

Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO₄, NO_x, NH₄) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart).

RESULTS

Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO₄, and NO_x flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH₄ flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH₄ flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum.

CONCLUSIONS

Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.

In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench

The low temperature and elevated hydrostatic pressure in hadal trenches at water depths below 6000 m render sample collection difficult. Here, in situ hadal water microbial samples were collected from the Mariana Trench and analysed. The hadal microbial communities at different depths were revealed to be consistent and were dominated by heterotrophic Marinimicrobia. Thirty high-quality metagenome-assembled genomes (MAGs) were retrieved to represent the major hadal microbes affiliated with 12 prokaryotic phyla. Most of the MAGs were newly reported and probably derived from novel hadal inhabitants as exemplified by a potentially new candidate archaeal phylum in the DPANN superphylum. Metabolic reconstruction indicated that a great number of the MAGs participated in nitrogen and sulfur cycling, in which the nitrification process was driven sequentially by Thaumarchaeota and Nitrospirae and sulfur oxidization by Rhodospirillales in the Alphaproteobacteria class. Moreover, several groups of hadal microbes were revealed to be potential carbon monoxide oxidizers. Metatranscriptomic result highlighted the contribution of Chloroflexi in degrading recalcitrant dissolved organic matter and Marinimicrobia in extracellular protein decomposition. The present work provides an in-depth view on the hadal microbial communities regarding their endemism and element cycles.

Disentangling the complex microbial community of coral reefs using standardized Autonomous Reef Monitoring Structures (ARMS)

Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to describe eukaryotic cryptic reef fauna. Conversely, bacterial communities, which are critical components of coral reef ecosystem functioning, remain largely overlooked. Here we deployed 56 ARMS across the 2,000-km spread of the Red Sea to assay biodiversity, composition and inferred underlying functions of coral reef-associated bacterial communities via 16S rRNA gene sequencing. We found that bacterial community structure and diversity aligned with environmental differences. Indeed, sea surface temperature and macroalgae cover were key in explaining bacterial relative abundance. Importantly, taxonomic and functional alpha diversity decreased under more extreme environmental conditions (e.g., higher temperatures) in the southern Red Sea. This may imply a link between bacterial community diversity and functional capabilities, with implications for conservation management. Our study demonstrates the utility of ARMS to investigate the response of coral reef-associated bacterial communities to environmental change.

Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea, Saudi Arabia

Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.

The sponge microbiome within the greater coral reef microbial metacommunity

Much recent marine microbial research has focused on sponges, but very little is known about how the sponge microbiome fits in the greater coral reef microbial metacommunity. Here, we present an extensive survey of the prokaryote communities of a wide range of biotopes from Indo-Pacific coral reef environments. We find a large variation in operational taxonomic unit (OTU) richness, with algae, chitons, stony corals and sea cucumbers housing the most diverse prokaryote communities. These biotopes share a higher percentage and number of OTUs with sediment and are particularly enriched in members of the phylum Planctomycetes. Despite having lower OTU richness, sponges share the greatest percentage (>90%) of OTUs with >100 sequences with the environment (sediment and/or seawater) although there is considerable variation among sponge species. Our results, furthermore, highlight that prokaryote microorganisms are shared among multiple coral reef biotopes, and that, although compositionally distinct, the sponge prokaryote community does not appear to be as sponge-specific as previously thought.

Jellyfish-Associated Microbiome in the Marine Environment: Exploring Its Biotechnological Potential

Despite accumulating evidence of the importance of the jellyfish-associated microbiome to jellyfish, its potential relevance to blue biotechnology has only recently been recognized. In this review, we emphasize the biotechnological potential of host⁻microorganism systems and focus on gelatinous zooplankton as a host for the microbiome with biotechnological potential. The basic characteristics of jellyfish-associated microbial communities, the mechanisms underlying the jellyfish-microbe relationship, and the role/function of the jellyfish-associated microbiome and its biotechnological potential are reviewed. It appears that the jellyfish-associated microbiome is discrete from the microbial community in the ambient seawater, exhibiting a certain degree of specialization with some preferences for specific jellyfish taxa and for specific jellyfish populations, life stages, and body parts. In addition, different sampling approaches and methodologies to study the phylogenetic diversity of the jellyfish-associated microbiome are described and discussed. Finally, some general conclusions are drawn from the existing literature and future research directions are highlighted on the jellyfish-associated microbiome.

Vertical Stratification of Sediment Microbial Communities Along Geochemical Gradients of a Subterranean Estuary Located at the Gloucester Beach of Virginia, United States

Subterranean estuaries (STEs) have been recognized as important ecosystems for the exchange of materials between the land and sea, but the microbial players of biogeochemical processes have not been well examined. In this study, we investigated the bacterial and archaeal communities within 10 cm depth intervals of a permeable sediment core (100 cm in length) collected from a STE located at Gloucester Point (GP-STE), VA, United States. High throughput sequencing of 16S rRNA genes and subsequent bioinformatics analyses were conducted to examine the composition, diversity, and potential functions of the sediment communities. The community composition varied significantly from the surface to a depth of 100 cm with up to 13,000 operational taxonomic units (OTUs) based on 97% sequence identities. More than 95% of the sequences consisted of bacterial OTUs, while the relative abundances of archaea, dominated by Crenarchaea, gradually increased with sediment core depth. Along the redox gradients of GP-STE, differential distribution of ammonia- and methane-oxidizing, denitrifying, and sulfate reducing bacteria was observed as well as methanogenic archaea based on predicted microbial functions. The aerobic-anaerobic transition zone (AATZ) had the highest diversity and abundance of microorganisms, matching with the predicted functional diversity. This indicates the AATZ as a hotspot of biogeochemical processes of STEs. The physical and geochemical gradients in different depths have attributed to vertical stratification of microbial community composition and function in the GP-STE.

Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida)

Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.

Showcasing the role of seawater in bacteria recruitment and microbiome stability in sponges

We studied the core bacterial communities of 19 sponge species from Nha Trang Bay (Central Vietnam), with particular emphasis on the contribution of planktonic seawater bacteria to the sponge core microbiomes. To ensure consistent sponge-microbe associations and accurate identification of planktonic bacteria transmitted from seawater, we were very restrictive with the definition of the sponge core microbiomes (present in all the replicates), and with the identification of valid biological 16S rRNA gene sequences (100% sequence identity) that belonged to potentially different bacterial taxa. We found a high overlap (>50% relative abundance) between the sponge species core microbiome and the seawater bacterial core in ca. a half of the studied species, including representatives of both, HMA and LMA sponges. From our restrictive analysis, we point to horizontal transmission as a relevant way of symbiont acquisition in sponges. Some species-specific recognition mechanisms may act in sponges to enrich specific seawater bacteria in their tissues. These mechanisms would allow the maintenance of bacterial communities in a species across geographical ranges. Moreover, besides contrasting preferences in bacteria selection from seawater, divergent physiological traits may also account for the different microbiomes in species of HMA and LMA sponges.

Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities

The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.

First Record of Microbiomes of Sponges Collected From the Persian Gulf, Using Tag Pyrosequencing

The Persian Gulf is a special habitat of marine sponges whose bacterial communities are under-investigated. Recently, next-generation sequencing technology has comprehensively improved the knowledge of marine sponge-associated bacteria. For the first time, this study aimed to evaluate the diversity of the Persian Gulf sponge-associated bacteria using tag pyrosequencing in Iran. In this study, 10 sponge samples from 6 different taxonomic orders were collected from the Persian Gulf using SCUBA diving. The diversity of the bacteria associated with the marine sponges was investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. A total of 68,628 high-quality sequences were obtained and clustered at a 97% similarity into 724 unique operational taxonomic units (OTUs), representing 17 bacterial phyla. Cyanobacteria was the most abundant phylum in the sponges, followed by Proteobacteria, Chloroflexi, Acidobacteria, and Actinobacteria. Other phyla were detected as minor groups of bacteria. Bacterial community richness, Shannon, and Simpson indices revealed the highest diversity in sponge S11 (Dictyoceratida sp.) compared to other sponges. This study showed a diverse structure of bacterial communities associated with the Persian Gulf sponges. The dominance of Cyanobacteria may suggest an ecological importance of this phylum in the Persian Gulf sponges.

Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam

Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.

Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges

Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few "variable/core" fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord

The blue mussel Mytilus is a popular food source with high economical value. Species of the M. edulis complex (M. edulis, M. galloprovincialis and M. trossulus) hybridise whenever their geographic ranges overlap posing difficulties to species discrimination, which is important for blue mussel aquaculture. The aim of this study was to determine the genetic structure of farmed blue mussels in Kiel Fjord. Microbial and metabolic profile patterns were studied to investigate a possible dependency on the genotype of the bivalves. Genotyping confirmed the complex genetic structure of the Baltic Sea hybrid zone and revealed an unexpected dominance of M. trossulus alleles being in contrast to the predominance of M. edulis alleles described for wild Baltic blue mussels. Culture-dependent and -independent microbial community analyses indicated the presence of a diverse Mytilus-associated microbiota, while an LC-MS/MS-based metabolome study identified 76 major compounds dominated by pigments, alkaloids and polyketides in the whole tissue extracts. Analysis of mussel microbiota and metabolome did not indicate genotypic dependence, but demonstrated high intraspecific variability of farmed mussel individuals. We hypothesise that individual differences in microbial and metabolite patterns may be caused by high individual plasticity and might be enhanced by e.g. nutritional condition, age and gender.

Sympatric kelp species share a large portion of their surface bacterial communities

Kelp forest ecosystems are biodiversity hotspots, providing habitat for dense assemblages of marine organisms and nutrients for marine and terrestrial food webs. The surfaces of kelps support diverse microbial communities that facilitate the transfer of carbon from algal primary production to higher trophic levels. We quantified the diversity of bacteria on the surfaces of eight sympatric kelp species from four sites in British Columbia. Kelp-associated bacterial communities are significantly different from their environment, even though 86% of their bacterial taxa are shared with seawater and 97% are shared with rocky substrate. This differentiation is driven by differences in relative abundance of the bacterial taxa present. Similarly, a large portion of bacterial taxa (37%) is shared among all eight kelp species, yet differential abundance of bacterial taxa underlies differences in community structure among species. Kelp-associated bacterial diversity does not track host phylogeny; instead bacterial community composition is correlated with the life-history strategy of the host, with annual and perennial kelps supporting divergent bacterial communities. These data provide the first community-scale investigation of kelp forest-associated bacterial diversity. More broadly, this study provides insight into mechanisms that may structure bacterial communities among closely related sympatric host species.

Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor

Marine sponges have been shown to harbor diverse microbial symbiont communities that play key roles in host functioning, yet little is known about how anthropogenic disturbances impact sponge-microbe interactions. The Mediterranean sponge Crambe crambe is known to accumulate heavy metals in polluted harbors. In this study, we investigated whether the microbiome of C. crambe differed between sponges inhabiting a polluted harbor in Blanes (Spain) and a nearby (<1 km) natural environment. Triplicate sponge and ambient seawater samples were collected from each site and the microbial composition of each sample was determined by 16S rRNA gene sequence analysis (Illumina Hi-Seq platform). No significant differences in the diversity or structure of microbial communities in C. crambe were detected between habitats, while a significant difference in community structure was observed in ambient seawater inside and outside of the polluted harbor. The microbiome of C. crambe was clearly differentiated from free-living seawater microbes and dominated by Proteobacteria, specifically a single betaproteobacterium that accounted for >86% of all sequence reads. These results indicate that sponge microbiomes exhibit greater stability and pollution tolerance than their free-living microbial counterparts, potentially mitigating the effects of pollutants on coastal marine communities.

Bacillus amyloliquefaciens L-S60 Reforms the Rhizosphere Bacterial Community and Improves Growth Conditions in Cucumber Plug Seedling

Vegetable plug seedling has become the most important way to produce vegetable seedlings in China. This seedling method can significantly improve the quality and yield of vegetables compared to conventional methods. In the process of plug seedling, chemical fertilizers or pesticides are often used to improve the yield of the seedlings albeit with increasing concerns. Meanwhile, little is known about the impact of beneficial bacteria on the rhizosphere microbiota and the growth conditions of vegetables during plug seedling. In this study, we applied a culture-independent next-generation sequencing-based approach and investigated the impact of a plant beneficial bacterium, Bacillus amyloliquefaciens L-S60, on the composition and dynamics of rhizosphere microbiota and the growth conditions of cucumbers during plug seedling. Our results showed that application of L-S60 significantly altered the structure of the bacterial community associated with the cucumber seedling; presence of beneficial rhizosphere species such as Bacillus, Rhodanobacter, Paenibacillus, Pseudomonas, Nonomuraea, and Agrobacterium was higher upon L-S60 treatment than in the control group. We also measured the impact of L-S60 application on the physiological properties of the cucumber seedlings as well as the availability of main mineral elements in the seedling at different time points during the plug seedling. Results from those measurements indicated that L-S60 application promoted growth conditions of cucumber seedlings and that more available mineral elements were detected in the cucumber seedlings from the L-S60 treated group than from the control group. The findings in this study provided evidence for the beneficial effects of plant growth-promoting rhizosphere bacteria on the bacterial community composition and growth conditions of the vegetables during plug seedling.

Fight Fungi with Fungi: Antifungal Properties of the Amphibian Mycobiome

Emerging infectious diseases caused by fungal taxa are increasing and are placing a substantial burden on economies and ecosystems worldwide. Of the emerging fungal diseases, chytridomycosis caused by the fungus Batrachochytrium dendrobatidis (hereafter Bd) is linked to global amphibian declines. Amphibians have innate immunity, as well as additional resistance through cutaneous microbial communities. Despite the targeting of bacteria as potential probiotics, the role of fungi in the protection against Bd infection in unknown. We used a four-part approach, including high-throughput sequencing of bacterial and fungal communities, cultivation of fungi, Bd challenge assays, and experimental additions of probiotic to Midwife Toads (Altyes obstetricans), to examine the overlapping roles of bacterial and fungal microbiota in pathogen defense in captive bred poison arrow frogs (Dendrobates sp.). Our results revealed that cutaneous fungal taxa differed from environmental microbiota across three species and a subspecies of Dendrobates spp. frogs. Cultivation of host-associated and environmental fungi realved numerous taxa with the ability to inhibit or facilitate the growth of Bd. The abundance of cutaneous fungi contributed more to Bd defense (~45% of the fungal community), than did bacteria (~10%) and frog species harbored distinct inhibitory communities that were distinct from the environment. Further, we demonstrated that a fungal probiotic therapy did not induce an endocrine-immune reaction, in contrast to bacterial probiotics that stressed amphibian hosts and suppressed antimicrobial peptide responses, limiting their long-term colonization potential. Our results suggest that probiotic strategies against amphibian fungal pathogens should, in addition to bacterial probiotics, focus on host-associated and environmental fungi such as Penicillium and members of the families Chaetomiaceae and Lasiosphaeriaceae.

Soil microbial communities of three grassland ecosystems in the Bayinbuluke, China

The microbial community plays an important role in soil nutrient cycles and energy transformations in alpine grassland. In this study, we investigated the composition of the soil microbial community collected from alpine cold swamp meadow (ASM), alpine cold meadow (AM), and alpine cold desert steppe (ADS) within the Bayinbuluke alpine grassland, China, using Illumina amplicon sequencing. Of the 147 271 sequences obtained, 36 microbial phyla or groups were detected. The results showed that the ADS had lower microbial diversity than the ASM and AM, as estimated by the Shannon index. The Verrucomicrobia, Chloroflexi, Planctomycetes, Proteobacteria, and Actinobacteria were the predominant phyla in all 3 ecosystems. Particularly, Thaumarchaeota was only abundant in ASM, Bacteroidetes in AM, and Acidobacteria in ADS. Additionally, the predominant genus also differed with each ecosystem. Candidatus Nitrososphaera was predominant in ADS, the Pir4 lineage in ASM, and Sphingomonas in AM. Our results indicated that the soil microbial community structure was different for each grassland ecosystem in the Bayinbuluke.

Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa

Montastraea cavernosa is a common coral in the Caribbean basin found in several color morphs. To investigate the causes for brown and orange morphs we undertook a genomics approach on corals collected at the same time and depth in the Bahamas. The coral holobiont includes the host, symbiotic dinoflagellates (Symbiodinium spp.), and a diverse microbiome. While the coral host showed significant genetic differentiation between color morphs both the composition of the Symbiodinium spp. communities and the prokaryotic communities did not. Both targeted and global gene expression differences in the transcriptome of the host show no difference in fluorescent proteins while the metatranscriptome of the microbiome shows that pigments such as phycoerythrin and orange carotenoid protein of cyanobacterial origin are significantly greater in orange morphs, which is also consistent with the significantly greater number of cyanobacteria quantified by 16S rRNA reads and flow cytometry. The microbiome of orange color morphs expressed significantly more nitrogenase (nifH) transcripts consistent with their known ability to fix nitrogen. Both coral and Symbiodinium spp. transcriptomes from orange morphs had significantly increased expression of genes related to immune response and apoptosis, which may potentially be involved in maintaining and regulating the unique symbiont population in orange morphs.

Recovery of Previously Uncultured Bacterial Genera from Three Mediterranean Sponges

Sponges often harbour a dense and diverse microbial community. Presently, a large discrepancy exists between the cultivable bacterial fraction from sponges and the community in its natural environment. Here, we aimed to acquire additional insights into cultivability of (previously uncultured) bacteria from three sponge species, namely Aplysina aerophoba, Corticium candelabrum and Petrosia ficiformis, by studying bacterial growth on five media in the form of 60 communities scraped from plates without antibiotics, as well as in the form of individual isolates that were grown on these media supplemented with antibiotics. We applied (double-)barcoded 16S ribosomal RNA (rRNA) gene amplicon sequencing for species identification. We show that previously uncultured bacteria can be cultivated using conventional plating and that application of antibiotics in the media can serve to capture a greater bacterial diversity. Moreover, we present criteria to address an important caveat of the plate scraping method whereby bacteria may be detected that did not actually grow. Fourteen out of 27 cultivated novel taxa (<95% identity of the 16S rRNA gene amplicon to reported species) belong to Actinobacteria, which indicates the presence of a large untapped reservoir of bioactive compounds. Three Flavobacteriaceae spp. were isolated that potentially constitute two new genera and one new species.

The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights

The South China Sea is a special reservoir of sponges of which prokaryotic communities are less studied. Here, a new record of the sponge Dactylospongia elegans is reported near the coast of Jinqing Island in the South China Sea, and its prokaryotic community is comprehensively investigated. Sponge specimens displayed lower microbial diversity compared with surrounding seawater. At the phylum level, prokaryotic communities were consistently dominated by Proteobacteria, followed by Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Poribacteria. Operational taxonomic unit (OTU) analysis alternatively showed that the most abundant symbiont was the sponge-specific cyanobacterial species “Candidatus Synechococcus spongiarum,” followed by OTUs belonging to the unidentified Chloroflexi and Acidobacteria. Phylogenetic tree based on 16S-23S internal transcribed spacer regions indicated that the dominated cyanobacterial OTU represented a new clade of “Ca. Synechococcus spongiarum.” More reliable metagenomic data further revealed that poribacterial symbionts were highly abundant and only secondary to the cyanobacterial symbiont. One draft genome for each of the Cyanobacteria, Chloroflexi and Acidobacteria and three poribacterial genomes were extracted from the metagenomes. Among them, genomes affiliated with the Chloroflexi and Acidobacteria were reported for the first time in sponge symbionts. Eukaryotic-like domains were found in all the binned genomes, indicating their potential symbiotic roles with the sponge host. The high quality of the six recovered genomes of sponge symbionts from the sponge D. elegans makes it possible to understand their symbiotic roles and interactions with the sponge host as well as among one another.

Microbial community analysis of simultaneous ammonium removal and Fe3+ reduction at different influent ammonium concentrations

This study investigates the impacts of influent ammonium concentrations on the microbial community in immobilized heterotrophic ammonium removal system. Klebsiella sp. FC61, the immobilized species, has the ability to perform simultaneous ammonium removal and Fe³⁺ reduction. It was found that average ammonium removal rate decreased from 0.308 to 0.157 mg/L/h, as the influent NH₄⁺-N was reduced from 20 to 10 mg/L. Meanwhile, at a total Fe³⁺ concentration of 20 mg/L, the average Fe³⁺ reduction removal efficiency and rate decreased from 44.61% and 0.18 mg/L/h, to 27.10% and 0.11 mg/L/h, respectively. High-throughput sequencing was used to observe microbial communities in bioreactor Samples B1, B2, and B3, after exposure to different influent NH₄⁺-N conditions. Results show that higher influent NH₄⁺-N concentrations increased microbial richness and diversity and that Klebsiella sp. FC61 play a functional role in the simultaneous removal of NH₄⁺-N and Fe³⁺ reduction in bioreactor systems.

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

Characterization of lignocellulolytic activities from fungi isolated from the deep-sea sponge Stelletta normani

Extreme habitats have usually been regarded as a source of microorganisms that possess robust proteins that help enable them to survive in such harsh conditions. The deep sea can be considered an extreme habitat due to low temperatures (<5°C) and high pressure, however marine sponges survive in these habitats. While bacteria derived from deep-sea marine sponges have been studied, much less information is available on fungal biodiversity associated with these sponges. Following screening of fourteen fungi isolated from the deep-sea sponge Stelletta normani sampled at a depth of 751 metres, three halotolerant strains (TS2, TS11 and TS12) were identified which displayed high CMCase and xylanase activities. Molecular based taxonomic approaches identified these strains as Cadophora sp. TS2, Emericellopsis sp. TS11 and Pseudogymnoascus sp. TS 12. These three fungi displayed psychrotolerance and halotolerant growth on CMC and xylan as sole carbon sources, with optimal growth rates at 20°C. They produced CMCase and xylanase activities, which displayed optimal temperature and pH values of between 50-70°C and pH 5-8 respectively, together with good thermostability and halotolerance. In solid-state fermentations TS2, TS11 and TS12 produced CMCases, xylanases and peroxidase/phenol oxidases when grown on corn stover and wheat straw. This is the first time that CMCase, xylanase and peroxidase/phenol oxidase activities have been reported in these three fungal genera isolated from a marine sponge. Given the biochemical characteristics of these ligninolytic enzymes it is likely that they may prove useful in future biomass conversion strategies involving lignocellulosic materials.

Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments.

As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a new deep-sea SOB group. Microscopic observations suggest that Gsub is probably an extracellular symbiont. Gsub has complete sulfide oxidation and carbon fixation pathways, suggesting a chemoautotrophic lifestyle. Comparative genomics with other sponge-associated SOB and free-living SOB revealed significant genome reduction in Gsub, characterized by the loss of genes for carbohydrate metabolism, motility, DNA repair, and osmotic stress response. Intriguingly, this scenario of genome reduction is highly similar to those of the endosymbionts in deep-sea clams. However, Gsub has retained genes for phage defense and protein secretion, with the latter potentially playing a role in interactions with the sponge host. In addition, we recovered the genome of an ammonia-oxidizing archaeon (AOA), which may carry out ammonia oxidation and carbon fixation within the sponge body.

IMPORTANCE Sponges and their symbionts are important players in the biogeochemical cycles of marine environments. As a unique habitat within marine ecosystems, cold seeps have received considerable interest in recent years. This study explores the lifestyle of a new symbiotic SOB in a cold seep sponge. The results demonstrate that both this sponge symbiont and endosymbionts in deep-sea clams employ similar strategies of genome reduction. However, this bacterium has retained unique functions for immunity and defense. Thus, the functional features are determined by both the symbiotic relationship and host type. Moreover, analyses of the genome of an AOA suggest that microbes play different roles in biochemical cycles in the sponge body. Our findings provide new insights into invertebrate-associated bacteria in cold seep environments.