Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Bacteria on the foundational kelp in kelp forest ecosystems: Insights from culturing, whole genome sequencing and metabolic assays

In coastal marine ecosystems, kelp forests serve as a vital habitat for numerous species and significantly influence local nutrient cycles. Bull kelp, or Nereocystis luetkeana, is a foundational species in the iconic kelp forests of the northeast Pacific Ocean and harbours a complex microbial community with potential implications for kelp health. Here, we report the isolation and functional characterisation of 16 Nereocystis-associated bacterial species, comprising 13 Gammaproteobacteria, 2 Flavobacteriia and 1 Actinomycetia. Genome analyses of these isolates highlight metabolisms potentially beneficial to the host, such as B vitamin synthesis and nitrogen retention. Assays revealed that kelp-associated bacteria thrive on amino acids found in high concentrations in the ocean and in the kelp (glutamine and asparagine), generating ammonium that may facilitate host nitrogen acquisition. Multiple isolates have genes indicative of interactions with key elemental cycles in the ocean, including carbon, nitrogen and sulphur. We thus report a collection of kelp-associated microbial isolates that provide functional insight for the future study of kelp-microbe interactions.

Insights on biological phosphorus removal with partial nitrification in single sludge system via sidestream free ammonia and free nitrous acid dosing

The sidestream sludge treatment by free ammonium (FA)/free nitrous acid (FNA) dosing was frequently demonstrated to maintain the nitrite pathway for the partial nitrification (PN) process. Nevertheless, the inhibitory effect of FA and FNA would severely influence polyphosphate accumulating organisms (PAOs), destroying the microbe-based phosphorus (P) removal. Therefore, a strategic evaluation was proposed to successfully achieve biological P removal with a partial nitrification process in a single sludge system by sidestream FA and FNA dosing. Through the long-term operation of 500 days, excellent phosphorus, ammonium and total nitrogen removal performance were achieved at 97.5 ± 2.6 %, 99.1 ± 1.0 % and 75.5 ± 0.4 %, respectively. Stable partial nitrification with a nitrite accumulation ratio (NAR) of 94.1 ± 3.4 was attained. The batch tests also reported the robust aerobic phosphorus uptake based on FA and FNA adapted sludge after exposure of FA and FNA, respectively, suggesting the FA and FNA treatment strategy could potentially offer the opportunity for the selection of PAOs, which synchronously have the tolerance to FA and FNA. Microbial community analysis suggested that Accumulibacter, Tetrasphaera, and Comamonadaceae collectively contributed to the phosphorus removal in this system. Summarily, the proposed work presents a novel and feasible strategy to integrate enhanced biological phosphorus removal (EBPR) and short-cut nitrogen cycling and bring the combined mainstream phosphorus removal and partial nitrification process closer to practical application.

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts

BACKGROUND

Reef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont's homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification-warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control.

RESULTS

A, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects.

CONCLUSIONS

The metatranscriptome-based study indicates that acidification and/or warming might change coral's in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont's ability for acclimatization under future climate change.

Bacterial aerobic methane cycling by the marine sponge-associated microbiome

BACKGROUND

Methanotrophy by the sponge-hosted microbiome has been mainly reported in the ecological context of deep-sea hydrocarbon seep niches where methane is either produced geothermically or via anaerobic methanogenic archaea inhabiting the sulfate-depleted sediments. However, methane-oxidizing bacteria from the candidate phylum Binatota have recently been described and shown to be present in oxic shallow-water marine sponges, where sources of methane remain undescribed.

RESULTS

Here, using an integrative -omics approach, we provide evidence for sponge-hosted bacterial methane synthesis occurring in fully oxygenated shallow-water habitats. Specifically, we suggest methane generation occurs via at least two independent pathways involving methylamine and methylphosphonate transformations that, concomitantly to aerobic methane production, generate bioavailable nitrogen and phosphate, respectively. Methylphosphonate may be sourced from seawater continuously filtered by the sponge host. Methylamines may also be externally sourced or, alternatively, generated by a multi-step metabolic process where carnitine, derived from sponge cell debris, is transformed to methylamine by different sponge-hosted microbial lineages. Finally, methanotrophs specialized in pigment production, affiliated to the phylum Binatota, may provide a photoprotective function, closing a previously undescribed C₁-metabolic loop that involves both the sponge host and specific members of the associated microbial community.

CONCLUSION

Given the global distribution of this ancient animal lineage and their remarkable water filtration activity, sponge-hosted methane cycling may affect methane supersaturation in oxic coastal environments. Depending on the net balance between methane production and consumption, sponges may serve as marine sources or sinks of this potent greenhouse gas. Video Abstract.

Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta

Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.

Uptake of inorganic and organic phosphorus compounds by two marine sponges and their associated bacterial communities in aquaria

Marine sponges are abundant filter-feeders in benthic ecosystems and many host copious microorganisms. Sponges and their symbionts have emerged as major players within marine biogeochemical cycles, facilitating uptake and release of carbon, nitrogen, and sulfur. Sponge holobionts' role in transforming dissolved carbon and nitrogen is well established; however, the same depth of understanding has not yet been extended to phosphorus. In this aquaria-based study, ³² P-labelled orthophosphate and ATP were used to determine that two sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both take up ambient dissolved inorganic phosphate (DIP) and dissolved organic phosphorus (DOP). Subsequent genetic analyses and chemical extraction showed that sponge symbionts have the potential to synthesise polyphosphate (poly-P) and that this energy-rich form of stored phosphorus is present in both sponges. L. chondrodes, an oligotrophic sponge with a microbiome dominated by cyanobacteria, stores more phosphorus as poly-P (6%-8% of total phosphorus) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. DIP/DOP uptake, as well as poly-P storage, may be driven by two factors: cyanobacterial abundance and nutrient availability. Considering their prevalence in phosphorus-limited ecosystems and their ability to pump large amounts of seawater, sponge holobionts are likely to be key players within benthic phosphorus cycles.

Rapid Biotic and Abiotic Transformation of Toxins produced by Ostreopsis. cf. ovata

The dinoflagellate Ostreopsis cf. ovata produces several families of toxic polyketides. Despite only a few field measurements of these phycotoxins in seawater and aerosols, they are believed to be responsible for dermatitis and the toxic inhalations reported during blooms of this species. Therefore, the stability of these compounds in seawater is essential to understanding the causes of these symptoms, however, this has never been assessed. In the current study, the optimization of a solid phase extraction (SPE) procedure was first performed to ensure the most efficient extraction of all phycotoxins known to be produced by this strain, including the recently described liguriatoxins. The SPE cartridge SDBL® under non acidified conditions offered the best option. The stability of the ovatoxins and the liguriatoxins under biotic and abiotic stress was assessed by exposing the spent medium of a culture of Ostreopsis cf. ovata to its bacterial consortium and natural sunlight. A rapid biotic transformation was detected for both families of compounds. When exposed to bacteria, the half-lives of the ovatoxins were reached before 10 h and at 36 h, 97% of these toxins had been transformed. The half-lives of the liguriatoxins were 10 h under these conditions. Photolysis (abiotic degradation) of the ovatoxins (T1/2 < 36 h) was faster than for the liguriatoxins (T1/2 > 62 h). Although none of the catabolites of these phycotoxins were thoroughly identified, an untargeted metabolomics approach combined with molecular networking highlighted the presence of several compounds exhibiting structural similarities with the ovatoxins. Additional work should confirm the preliminary findings on these potential ovatoxins’ catabolites and their biological properties. The rapid transformation of O. cf. ovata’s phycotoxins introduces questions concerning their presence in seawater and their dispersion in the sea spray aerosols. The compounds involved in the toxic inhalations and dermatitis often experienced by beachgoers may stem from the catabolites of these toxins or even unrelated and as yet unidentified compounds.

Efficient removal of Imidacloprid and nutrients by algae-bacteria biofilm reactor (ABBR) in municipal wastewater: Performance, mechanisms and the importance of illumination

Neonicotinoids, such as Imidacloprid (IMI), are frequently detected in water and wastewater, posing a threat on both the environment and the health of living things. In this work, a novel algae-bacteria biofilm reactor (ABBR) was constructed to remove IMI and conventional nutrients from municipal wastewater, aiming to explore the removal effect and advantage of ABBR. Results showed that ABBR achieved 74.9% removal of IMI under 80 μmol m^-2·s^-1 light, higher than photobioreactor (PBR) without biofilm (61.2%) or ABBR under 40 μmol m^-2·s^-1 light (48.4%) after 16 days of operation. Moreover, it also showed that ABBR allowed a marked improvement on the removal of total dissolved nitrogen (TDN), total dissolved phosphorus (TDP) and soluble chemical oxygen demand (sCOD). ABBR showed different IMI removal efficiencies and bacterial communities under different light conditions, indicating that light played an important role in driving ABBR. The merits of ABBR are including (i) ABBR showed rapid pollutant removal in a short time, (ii) in ABBR, stable consortiums were formed and chlorophyll content in effluent was very low, (iii) compared with PBR, degradation products in ABBR showed lower biological toxicity. Our study highlights the benefits of ABBR on IMI removing from municipal wastewater and provides an effective and environment-friendly engineering application potential of IMI removal.

Harnessing solar power: photoautotrophy supplements the diet of a low-light dwelling sponge

The ability of organisms to combine autotrophy and heterotrophy gives rise to one of the most successful nutritional strategies on Earth: mixotrophy. Sponges are integral members of shallow-water ecosystems and many host photosynthetic symbionts, but studies on mixotrophic sponges have focused primarily on species residing in high-light environments. Here, we quantify the contribution of photoautotrophy to the respiratory demand and total carbon diet of the sponge Chondrilla caribensis, which hosts symbiotic cyanobacteria and lives in low-light environments. Although the sponge is net heterotrophic at 20 m water depth, photosynthetically fixed carbon potentially provides up to 52% of the holobiont’s respiratory demand. When considering the total mixotrophic diet, photoautotrophy contributed an estimated 7% to total daily carbon uptake. Visualization of inorganic ¹³C- and ¹⁵N-incorporation using nanoscale secondary ion mass spectrometry (NanoSIMS) at the single-cell level confirmed that a portion of nutrients assimilated by the prokaryotic community was translocated to host cells. Photoautotrophy can thus provide an important supplemental source of carbon for sponges, even in low-light habitats. This trophic plasticity may represent a widespread strategy for net heterotrophic sponges hosting photosymbionts, enabling the host to buffer against periods of nutritional stress.

Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths

In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30–60 m (upper mesophotic), and 60–90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.

High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata

Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.

A continuous-flow non-aerated microalgal-bacterial granular sludge process for aquaculture wastewater treatment under natural day-night conditions

This study developed a continuous-flow non-aerated microalgal-bacterial granular tubular reactor for aquaculture wastewater treatment under natural day-night conditions. Results showed that daytime was favorable for ammonia removal while nighttime for nitrate removal. Over 99% of nitrite-N could be removed over the day-night cycles at a hydraulic retention time of 6 h. However, the phosphorus removal was found to be sensitive to the weather condition, ranging from 35.0% to 96.6%. It was also observed that dissolved oxygen produced by microalgae in daytime was sufficient for creating a 6-h aerobic condition in nighttime for sustaining heterotrophic activity. Chlorella and Leptolyngbya were identified as the most abundant algae related to weather changes. Metagenomics analysis revealed that the high nitrite removal relied mainly on nitrite reduction. These experimental findings offer new insights into the non-aerated microalgal-bacterial granular sludge for environmentally sustainable aquaculture wastewater treatment.

Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts

The diversity and function of sponge-associated symbionts is now increasingly understood, however, we lack an understanding on how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here we performed a metatransciptomics analysis of three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidising Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidising archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our timeseries study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change. This article is protected by copyright. All rights reserved.

Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes

Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The "environment first" research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common "microbe first" research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.

Variability in Host Specificity and Functional Potential of Antarctic Sponge-Associated Bacterial Communities

Sponge-associated microorganisms are essential for sponge survival. They play an important role in recycling nutrients and, therefore, in the maintenance of the ecosystem. These microorganisms are diverse, species-specific, and different from those in the surrounding seawater. Bacterial sponge symbionts have been extensively studied in the tropics; however, little is known about these microorganisms in sponges from high-latitude environments. Sponges can cover up to 80% of the benthos in Antarctica and are crucial architects for the marine food web. In this study, we present analyses of the bacterial symbionts of three sponges: Haliclona (Rhizoniera) sp., Hymeniacidon torquata, and Isodictya kerguelenensis from the Western Antarctic Peninsula (WAP) with the aim to determine variations on the specificity of the bacteria–sponge interactions and potential signatures on their predicted functional profiles. We use high-throughput 16S rRNA gene sequencing of 30 sponge individuals inhabiting South Bay (Palmer Archipelago, WAP) to describe their microbiome taxonomy and diversity and predict potential functional profiles based on this marker gene. Our work shows similar bacterial community composition profiles among the same sponge species, although the symbiotic relationship is not equally conserved among the three Antarctic sponges. The number of species-specific core operational taxonomic units (OTUs) of these Antarctic sponges was low, with important differences between the total abundance accounted for these OTUs. Only eight OTUs were shared between the three sponge species. Analyses of the functional potential revealed that despite the high host–symbiont specificity, the inferred functions are conserved among these microbiomes, although with differences in the abundance of specific functions. H. torquata showed the highest level of intra-specificity and a higher potential of pathways related to energy metabolism, metabolisms of terpenoids and polyketides, and biosynthesis of other secondary metabolites. Overall, this work shows variations in the specificity of the sponge-associated bacterial communities, differences in how hosts and symbionts establish their relations, and in their potential functional capabilities.

Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review

The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.

Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts

The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia

Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge-microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment.

Did Cyclic Metaphosphates Have a Role in the Origin of Life?

How life began still eludes science life, the initial progenote in the context presented herein, being a chemical aggregate of primordial inorganic and organic molecules capable of self-replication and evolution into ever increasingly complex forms and functions.Presented is a hypothesis that a mineral scaffold generated by geological processes and containing polymerized phosphate units was present in primordial seas that provided the initiating factor responsible for the sequestration and organization of primordial life's constituents. Unlike previous hypotheses proposing phosphates as the essential initiating factor, the key phosphate described here is not a polynucleotide or just any condensed phosphate but a large (in the range of at least 1 kilo-phosphate subunits), water soluble, cyclic metaphosphate, which is a closed loop chain of polymerized inorganic phosphate residues containing only phosphate middle groups. The chain forms an intrinsic 4-phosphate helix analogous to its structure in Na Kurrol's salt, and as with DNA, very large metaphosphates may fold into hairpin structures. Using a Holliday-junction-like scrambling mechanism, also analogous to DNA, rings may be manipulated (increased, decreased, exchanged) easily with little to no need for additional energy, the reaction being essentially an isomerization.A literature review is presented describing findings that support the above hypothesis. Reviewed is condensed phosphate inorganic chemistry including its geological origins, biological occurrence, enzymes and their genetics through eukaryotes, polyphosphate functions, circular polynucleotides and the role of the Holliday junction, previous biogenesis hypotheses, and an Eoarchean Era timeline.

Temperature-effect on the performance of non-aerated microalgal-bacterial granular sludge process in municipal wastewater treatment

This paper investigated the performance of non-aerated microalgal-bacterial granular sludge (MBGS) process in municipal wastewater treatment at different temperatures. Results showed that the 70.5%, 81.9% and 86.1% of chemical oxygen demand (COD) could be removed at 15, 22 and 30 °C, respectively, indicating that a high temperature favored removal of organics due to promoted biomass growth. It was found that most of ammonia-N was removed via microbial assimilation by microalgae and bacteria in granules, with bacterial assimilation being dominant at the lower temperature. The phosphorus removal efficiency of 90.1% was achieved at 22 °C, with the presence of abundant Leptolyngbyales, a potential phosphorus accumulating alga. Chlorophyta grew much faster than Leptolyngbyales at 30 °C in microalgal-bacterial granules. It can be concluded that the contributions of microalgal and bacterial assimilations toward COD, ammonia and P removal appeared to be temperature-dependent, i.e. temperature could alter the symbiotic relationship between microalgae and bacteria. This study would contribute to the application of non-aerated MBGS process in municipal wastewater treatment with seasonal variation of temperature.

Critical Review of Polyphosphate and Polyphosphate Accumulating Organisms for Agricultural Water Quality Management

Despite ongoing management efforts, phosphorus (P) loading from agricultural landscapes continues to impair water quality. Wastewater treatment research has enhanced our knowledge of microbial mechanisms influencing P cycling, especially regarding microbes known as polyphosphate accumulating organisms (PAOs) that store P as polyphosphate (polyP) under oxic conditions and release P under anoxic conditions. However, there is limited application of PAO research to reduce agricultural P loading and improve water quality. Herein, we conducted a meta-analysis to identify articles in Web of Science on polyP and its use by PAOs across five disciplines (i.e., wastewater treatment, terrestrial, freshwater, marine, and agriculture). We also summarized research that provides preliminary support for PAO-mediated P cycling in natural habitats. Terrestrial, freshwater, marine, and agriculture disciplines had fewer polyP and PAO articles compared to wastewater treatment, with agriculture consistently having the least. Most meta-analysis articles did not overlap disciplines. We found preliminary support for PAOs in natural habitats and identified several knowledge gaps and research opportunities. There is an urgent need for interdisciplinary research linking PAOs, polyP, and oxygen availability with existing knowledge of P forms and cycling mechanisms in natural and agricultural environments to improve agricultural P management strategies and achieve water quality goals.

Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis

BACKGROUND

Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.

RESULTS

The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.

CONCLUSIONS

Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.

Filtering Activity and Nutrient Release by the Keratose Sponge Sarcotragus spinosulus Schmidt, 1862 (Porifera, Demospongiae) at the Laboratory Scale

Sponges are an important constituent of filter-feeder benthic communities, characterized by high ecological plasticity and abundance. Free bacteria constitute an important quota of their diet, making them excellent candidates in aquaculture microbial bioremediation, where bacteria can be a serious problem. Although there are studies on this topic, certain promising species are still under investigation. Here we report applied microbiological research on the filtering activity of Sarcotragus spinosulus on two different concentrations of the pathogenic bacterium Vibrio parahaemolyticus in a laboratory experiment. To evaluate the effects of the filtration on the surrounding nutrient load, the release of ammonium, nitrate, and phosphate was also measured. The results obtained showed the efficient filtration capability of S. spinosulus as able to reduce the Vibrio load with a maximum retention efficiency of 99.72% and 99.35% at higher and lower Vibrio concentrations, respectively, and remarkable values of clearance rates (average maximum value 45.0 ± 4.1 mL h−1 g DW−1) at the highest Vibrio concentration tested. The nutrient release measured showed low values for each considered nutrient category at less than 1 mg L−1 for ammonium and phosphate and less than 5 mg L−1 for nitrate. The filtering activity and nutrient release by S. spinosulus suggest that this species represents a promising candidate in microbial bioremediation, showing an efficient capability in removing V. parahaemolyticus from seawater with a contribution to the nutrient load.

Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges

Sponges are among the oldest metazoans and their success is partly due to their abundant and diverse microbial symbionts. They are one of the few animals that have Thaumarchaeota symbionts. Here we compare genomes of 11 Thaumarchaeota sponge symbionts, including three new genomes, to free-living ones. Like their free-living counterparts, sponge-associated Thaumarchaeota can oxidize ammonia, fix carbon, and produce several vitamins. Adaptions to life inside the sponge host include enrichment in transposases, toxin-antitoxin systems and restriction modifications systems, enrichments previously reported also from bacterial sponge symbionts. Most thaumarchaeal sponge symbionts lost the ability to synthesize rhamnose, which likely alters their cell surface and allows them to evade digestion by the host. All but one archaeal sponge symbiont encoded a high-affinity, branched-chain amino acid transporter system that was absent from the analyzed free-living thaumarchaeota suggesting a mixotrophic lifestyle for the sponge symbionts. Most of the other unique features found in sponge-associated Thaumarchaeota, were limited to only a few specific symbionts. These features included the presence of exopolyphosphatases and a glycine cleavage system found in the novel genomes. Thaumarchaeota have thus likely highly specific interactions with their sponge host, which is supported by the limited number of host sponge species to which each of these symbionts is restricted.

Morphogenetic (Mucin Expression) as Well as Potential Anti-Corona Viral Activity of the Marine Secondary Metabolite Polyphosphate on A549 Cells

The mucus layer of the nasopharynx and bronchial epithelium has a barrier function against inhaled pathogens such as the coronavirus SARS-CoV-2. We recently found that inorganic polyphosphate (polyP), a physiological, metabolic energy (ATP)-providing polymer released from blood platelets, blocks the binding of the receptor binding domain (RBD) to the cellular ACE2 receptor in vitro. PolyP is a marine natural product and is abundantly present in marine bacteria. Now, we have approached the in vivo situation by studying the effect of polyP on the human alveolar basal epithelial A549 cells in a mucus-like mucin environment. These cells express mucins as well as the ectoenzymes alkaline phosphatase (ALP) and adenylate kinase (ADK), which are involved in the extracellular production of ATP from polyP. Mucin, integrated into a collagen-based hydrogel, stimulated cell growth and attachment. The addition of polyP to the hydrogel significantly increased cell attachment and also the expression of the membrane-tethered mucin MUC1 and the secreted mucin MUC5AC. The increased synthesis of MUC1 was also confirmed by immunostaining. This morphogenetic effect of polyP was associated with a rise in extracellular ATP level. We conclude that the nontoxic and non-immunogenic polymer polyP could possibly also exert a protective effect against SARS-CoV-2-cell attachment; first, by stimulating the innate antiviral response by strengthening the mucin barrier with its antimicrobial proteins, and second, by inhibiting virus attachment to the cells, as deduced from the reduction in the strength of binding between the viral RBD and the cellular ACE2 receptor.

Phylogeny resolved, metabolism revealed: functional radiation within a widespread and divergent clade of sponge symbionts

The symbiosis between bacteria and sponges has arguably the longest evolutionary history for any extant metazoan lineage, yet little is known about bacterial evolution or adaptation in this process. An example of often dominant and widespread bacterial symbionts of sponges is a clade of uncultured and uncharacterised Proteobacteria. Here we set out to characterise this group using metagenomics, in-depth phylogenetic analyses, metatranscriptomics, and fluorescence in situ hybridisation microscopy. We obtained five metagenome-assembled-genomes (MAGs) from different sponge species that, together with a previously published MAG (AqS2), comprise two families within a new gammaproteobacterial order that we named ^UTethybacterales. Members of this order share a heterotrophic lifestyle but vary in their predicted ability to use various carbon, nitrogen and sulfur sources, including taurine, spermidine and dimethylsulfoniopropionate. The deep branching of the ^UTethybacterales within the Gammaproteobacteria and their almost exclusive presence in sponges suggests they have entered a symbiosis with their host relatively early in evolutionary time and have subsequently functionally radiated. This is reflected in quite distinct lifestyles of various species of ^UTethybacterales, most notably their diverse morphologies, predicted substrate preferences, and localisation within the sponge tissue. This study provides new insight into the evolution of metazoan-bacteria symbiosis.

Removal mechanisms of phosphorus in non-aerated microalgal-bacterial granular sludge process

Microalgal-bacterial granular sludge processes are attracting increasing research interest in fields of biological municipal wastewater treatment. However, these processes currently suffer from inefficient phosphorus removal and long hydraulic reaction time. As such, a self-sustaining synergetic microalgal-bacterial granular sludge process was explored for improving phosphorus removal. Results showed that about 86% of influent phosphorus could be removed within 6 h comprising 2-hr dark phase and 4-hr light phase. Slight phosphorus release was observed in dark phase, followed by a significant phosphorus uptake in light phase together with the accumulation of poly-phosphorus in microalgal cells. The analyses by PacBio's sequencing and fluorescence in situ hybridization revealed that microalgal genus of Pantanalinema were the major phosphorus-accumulating organisms. Based on these experimental observations, the removal mechanisms of phosphorus by microalgal-bacterial granular sludge process were identified. It is expected that this study may shed lights on the pathways of biological phosphorus removal in microalgal-bacterial granular sludge process.

A self-sustaining synergetic microalgal-bacterial granular sludge process towards energy-efficient and environmentally sustainable municipal wastewater treatment

Globally increasing concerns have been raised on the high energy consumption and greenhouse gas emissions in conventional municipal wastewater treatment processes over the past decades. In this study, a self-sustaining synergetic microalgal-bacterial granular sludge process was thus developed to address these challenges. The results showed that the microalgal-bacterial granular sludge process was capable of removing 92.69%, 96.84% and 87.16% of influent organics, ammonia and phosphorus under non-aeration conditions over a short time of 6 h. The effluent could meet the increasingly stringent discharge standards in many countries worldwide. A tight synergetic interrelationship effect between microalgae and bacteria in granules was essential for such excellent process performance. The stoichiometric and functional genes analyses further revealed that most of organic matter and nutrients were removed through microalgal and bacterial assimilations. Moreover, it was found that there existed a desirable distribution of functional species of microalgae and bacteria in microalgal-bacterial granules, which appeared to be essential for the self-sustaining synergetic reactions and stability of microalgal-bacterial granules. Consequently, this work may offer a promising engineering alternative with great potential to achieve energy-efficient and environmentally sustainable municipal wastewater treatment.

Polyphosphate: A Multifunctional Metabolite in Cyanobacteria and Algae

Polyphosphate (polyP), a polymer of orthophosphate (PO4 3-) of varying lengths, has been identified in all kingdoms of life. It can serve as a source of chemical bond energy (phosphoanhydride bond) that may have been used by biological systems prior to the evolution of ATP. Intracellular polyP is mainly stored as granules in specific vacuoles called acidocalcisomes, and its synthesis and accumulation appear to impact a myriad of cellular functions. It serves as a reservoir for inorganic PO4 3- and an energy source for fueling cellular metabolism, participates in maintaining adenylate and metal cation homeostasis, functions as a scaffold for sequestering cations, exhibits chaperone function, covalently binds to proteins to modify their activity, and enables normal acclimation of cells to stress conditions. PolyP also appears to have a role in symbiotic and parasitic associations, and in higher eukaryotes, low polyP levels seem to impact cancerous proliferation, apoptosis, procoagulant and proinflammatory responses and cause defects in TOR signaling. In this review, we discuss the metabolism, storage, and function of polyP in photosynthetic microbes, which mostly includes research on green algae and cyanobacteria. We focus on factors that impact polyP synthesis, specific enzymes required for its synthesis and degradation, sequestration of polyP in acidocalcisomes, its role in cellular energetics, acclimation processes, and metal homeostasis, and then transition to its potential applications for bioremediation and medical purposes.

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients

Sponge-associated bacteria possess biotechnologically interesting properties but as yet have largely evaded cultivation. Thus, "omics"-based information on the ecology and functional potential of sponge symbionts is awaiting its integration into the design of innovative cultivation approaches. To cultivate bacteria derived from the marine sponge Aplysina aerophoba, nine novel media formulations were created based on the predicted genomic potential of the prevalent sponge symbiont lineage Poribacteria. In addition, to maintain potential microbial metabolic interactions in vitro, a Liquid-Solid cultivation approach and a Winogradsky-column approach were applied. The vast majority of microorganisms in the inoculum appeared viable after cryopreservation of sponge specimen as determined by selective propidium monoazide DNA modification of membrane-compromised cells, however, only 2% of the initial prokaryotic diversity could be recovered through cultivation. In total, 256 OTUs encompassing seven prokaryotic phyla were cultivated. The diversity of the cultivated community was influenced by the addition of the antibiotic aeroplysinin-1 as well as by medium dilution, rather than carbon source. Furthermore, the Winogradsky-column approach reproducibly enriched distinct communities at different column depths, amongst which were numerous Clostridia and OTUs that could not be assigned to a known phylum. While some bacterial taxa such as Pseudovibrio and Ruegeria were recovered from nearly all applied cultivation conditions, others such as Bacteroidetes were specific to certain medium types. Predominant sponge-associated prokaryotic taxa remained uncultured, nonetheless, alternative cultivation approaches applied here enriched for previously uncultivated microbes.

Trait-Based Comparison of Coral and Sponge Microbiomes

Corals and sponges harbor diverse microbial communities that are integral to the functioning of the host. While the taxonomic diversity of their microbiomes has been well-established for corals and sponges, their functional roles are less well-understood. It is unclear if the similarities of symbiosis in an invertebrate host would result in functionally similar microbiomes, or if differences in host phylogeny and environmentally driven microhabitats within each host would shape functionally distinct communities. Here we addressed this question, using metatranscriptomic and 16S rRNA gene profiling techniques to compare the microbiomes of two host organisms from different phyla. Our results indicate functional similarity in carbon, nitrogen, and sulfur assimilation, and aerobic nitrogen cycling. Additionally, there were few statistical differences in pathway coverage or abundance between the two hosts. For example, we observed higher coverage of phosphonate and siderophore metabolic pathways in the star coral, Montastraea cavernosa, while there was higher coverage of chloroalkane metabolism in the giant barrel sponge, Xestospongia muta. Higher abundance of genes associated with carbon fixation pathways was also observed in M. cavernosa, while in X. muta there was higher abundance of fatty acid metabolic pathways. Metagenomic predictions based on 16S rRNA gene profiling analysis were similar, and there was high correlation between the metatranscriptome and metagenome predictions for both hosts. Our results highlight several metabolic pathways that exhibit functional similarity in these coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as well as potential specialization of some microbially based metabolism within each host.

Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach

Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO₂ fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.

The Emerging Ecological and Biogeochemical Importance of Sponges on Coral Reefs

With the decline of reef-building corals on tropical reefs, sponges have emerged as an important component of changing coral reef ecosystems. Seemingly simple, sponges are highly diverse taxonomically, morphologically, and in terms of their relationships with symbiotic microbes, and they are one of nature's richest sources of novel secondary metabolites. Unlike most other benthic organisms, sponges have the capacity to disrupt boundary flow as they pump large volumes of seawater into the water column. This seawater is chemically transformed as it passes through the sponge body as a consequence of sponge feeding, excretion, and the activities of microbial symbionts, with important effects on carbon and nutrient cycling and on the organisms in the water column and on the adjacent reef. In this review, we critically evaluate developments in the recently dynamic research area of sponge ecology on tropical reefs and provide a perspective for future studies.

Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas

Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP.

The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont

Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.

Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter⁻¹ polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter⁻¹ PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter⁻¹ PAH) and 1.6% (38 mg liter⁻¹ Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter⁻¹ PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants.

IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.

Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter

Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track ¹⁵N- and ¹³C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.

Cultivation of Sponge-Associated Bacteria from Agelas sventres and Xestospongia muta Collected from Different Depths

Sponge-associated bacteria have been mostly cultured from shallow water (≤30 m) sponges, whereas only few studies targeted specimens from below 30 m. This study assessed the cultivability of bacteria from two marine sponges Xestospongia muta and Agelas sventres collected from shallow (<30 m), upper mesophotic (30–60 m), and lower mesophotic (60–90 m) reefs. Sponge-associated bacteria were cultivated on six different media, and replicate plates were used to pick individual colonies or to recover the entire biomass. Prokaryotic community analysis was conducted using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 144 bacterial isolates were picked following a colony morphology coding scheme and subsequently identified by 16S rRNA gene sequence analysis. Sponge individuals at each depth-range harboured specific cultivable bacteria that were not retrieved from specimens collected at other depths. However, there were substantial differences in the number of colonies obtained for replicate sponges of the same species. In addition, source of inoculum and cultivation medium had more impact on the cultured prokaryotic community than sample collection depth. This suggests that the “plate count anomaly” is larger than differences in sponge-associated prokaryotic community composition related to depth.

Microbially mediated nutrient cycles in marine sponges

Efficient nutrient cycles mediated by symbiotic microorganisms with their hosts are vital to support the high productivity of coral reef ecosystems. In these ecosystems, marine sponges are important habitat-forming organisms in the benthic community and harbor abundant microbial symbionts. However, few studies have reviewed the critical microbially mediated nutrient cycling processes in marine sponges. To bridge this gap, in this review article, we summarize existing knowledge and recent advances in understanding microbially mediated carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles in sponges, propose a conceptual model that describes potential interactions and constraints in the major nutrient cycles, and suggest that shifting redox state induced by animal behavior like sponge pumping can exert great influence on the activities of symbiotic microbial communities. Constraints include the lack of knowledge on spatial and temporal variations and host behavior; more studies are needed in these areas. Sponge microbiomes may have a significant impact on the nutrient cycles in the world’s coral reef ecosystems.

Prokaryotic communities of Indo-Pacific giant barrel sponges are more strongly influenced by geography than host phylogeny

Sponges harbor complex communities of microorganisms that carry out essential roles for the functioning and survival of their hosts. In some cases, genetically related sponges from different geographic regions share microbes, while in other cases microbial communities are more similar in unrelated sponges collected from the same location. To better understand how geography and host phylogeny cause variation in the prokaryotic community of sponges, we compared the prokaryotic community of 44 giant barrel sponges (Xestospongia spp.). These sponges belonged to six reproductively isolated genetic groups from eight areas throughout the Indo-Pacific region. Using Illumina sequencing, we obtained 440 000 sequences of the 16S rRNA gene V3V4 variable region that were assigned to 3795 operational taxonomic units (OTUs). The prokaryotic community of giant barrel sponges was characterized by 71 core OTUs (i.e. OTUs present in each specimen) that represented 57.5% of the total number of sequences. The relative abundance of these core OTUs varied significantly among samples, and this variation was predominantly related to the geographic origin of the sample. These results show that in giant barrel sponges, the variation in the prokaryotic community is primarily associated with geography as opposed to phylogenetic relatedness.

In situ determination of Si, N, and P utilization by the demosponge Tethya citrina: A benthic-chamber approach

Sponges consume dissolved silicon (DSi) to build their skeletons. Few studies have attempted to quantify DSi utilization by these organisms and all available determinations come from laboratory measurements. Here we measured DSi consumption rates of the sponge Tethya citrina in its natural habitat, conducting 24h incubations in benthic chambers. Sponges consumed DSi at an average rate of 0.046 ± 0.018 μmol h^-1 mL^-1 when DSi availability in its habitat was 8.3 ± 1.8 μM. Such DSi consumption rates significantly matched the values predicted by a kinetic model elsewhere developed previously for this species through laboratory incubations. These results support the use of laboratory incubations as a suitable approach to learn about DSi consumption. During the field incubations, utilization of other dissolved inorganic nutrients by this low-microbial-abundance (LMA) sponge was also measured. The sponges were net sources of ammonium (-0.043 ± 0.031 μmol h^-1 mL^-1), nitrate (-0.063 ± 0.031 μmol h^-1 mL^-1), nitrite (-0.007 ± 0.003 μmol h^-1 mL^-1), and phosphate (-0.004 ± 0.005 μmol h^-1 mL^-1), in agreement with the general pattern in other LMA species. The detected effluxes were among the lowest reported for sponges, which agreed with the low respiration rates characterizing this species (0.35 ± 0.11 μmol-O₂ h^-1 mL^-1). Despite relatively low flux, the dense population of T. citrina modifies the availability of dissolved inorganic nutrients in the demersal water of its habitat, contributing up to 14% of nitrate and nitrite stocks. Through these effects, the bottom layer contacting the benthic communities where siliceous LMA sponges abound can be partially depleted in DSi, but can benefit from inputs of N and P dissolved inorganic nutrients that are critical to primary producers.

Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth

Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.

The Significance of Microbial Symbionts in Ecosystem Processes

It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained.

It is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained. Here, I explore the idea that, in some habitats, host-associated microbes may have an outsized role in ecosystem processes relative to functionally equivalent free-living microbes due to key aspects of the physiology, ecology, and evolution of symbiotic interactions. My research quantifying symbiont metabolism has shown that microbial symbionts have the potential to make a substantial impact on carbon and sulfur cycling. It is my perspective that direct measurement of symbiont activity and comparison to free-living counterparts will expand our understanding of the significance of microbial symbioses and, more broadly, the role of microbial processes in ecosystems.

Structure and dynamics of microbiomes associated with the marine sponge Tedania sp. during its life cycle

Tedania sp. is a dominant sponge that is ubiquitous along the southeast coast of China. High-throughput sequencing and transmission electron microscopy were used to describe a detailed profile of sponge-associated microbiomes at seven life stages: adult, embryo-containing spawning adult, embryo, pre-competent larva at 2 h and 4 h, competent larva at 8 h and post-larva within 1-2h after settlement, as well as the surrounding seawater. Among a total of 15098 operational taxonomic units (OTUs), 13 were present exclusively in all stages of the sponge life cycle and could thus be identified as sponge-specific bacteria. Many OTUs were shared between the sponge and seawater, though abundance differed. The relative abundance of β-Proteobacteria associated with sponges was much higher than found in seawater. The microbiomes from each life stage also exhibited a characteristic distribution. Synechococcales dominated in adults, and Enterobacteriaceae was prominent in larvae. The competent larva was notable, with sharp increases in the total OTUs, diversity indices, richness estimates and unique OTUs. Some bacterial groups that were rare in other sponge stages and seawater, such as Clostridia (5.6%), were markedly more abundant in competent larvae. In conclusion, this work greatly advances our understanding of the dynamics and persistence of the sponge-microbe association.

Biomimetic transformation of polyphosphate microparticles during restoration of damaged teeth

OBJECTIVE

In the present study, we investigated the fusion process between amorphous microparticles of the calcium salt of the physiological polymer comprising orthophosphate units, of inorganic polyphosphate (polyP), and enamel.

METHODS

This polymer was incorporated as an ingredient into toothpaste and the fusion process was studied by electron microscopy and by synchrotron-based X-ray tomography microscopy (SRXTM) techniques.

RESULTS

The data showed that toothpaste, supplemented with the amorphous Ca-polyP microparticles (aCa-polyP-MP), not only reseals tooth defects on enamel, like carious lesions, and dentin, including exposed dentinal tubules, but also has the potential to induce re-mineralization in the enamel and dentin regions. The formation of a regeneration mineralic zone on the tooth surface induced by aCa-polyP-MP was enhanced upon exposure to artificial saliva, as demonstrated by SRXTM. Energy dispersive X-ray analysis revealed an increase in the calcium/phosphorus atomic ratio of the enamel deposits to values characteristic for the particles during the treatment with polyP applied in the toothpaste, indicating a fusion of the particles with the tooth mineral.

SIGNIFICANCE

Our results suggest that toothpaste enriched with aCa-polyP-MP is a promising biomimetic material for accelerating enamel and dentin restoration.

Sponge-microbe partnerships are stable under eutrophication pressure from mariculture

Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.

Marine sponge microbial association: Towards disclosing unique symbiotic interactions

Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.