Microbiome and virome on indoor surfaces of an Antarctic research ship.

BACKGROUND: Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS: We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS: Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS: This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

Collapse of scallop Nodipecten nodosus production in the tropical Southeast Brazil as a possible consequence of global warming and water pollution.

Mollusc rearing is a relevant global socioeconomic activity. However, this activity has faced severe problems in the last years in southeast Brazil. The mariculture scallop production dropped from 51,2 tons in 2016 to 10,2 tons in 2022 in the Baia da Ilha Grande (BIG; Rio de Janeiro). However, the possible causes of this collapse are unknown. This study aimed to analyze decadal trends of water quality in Nodipecten nodosus spat and adult production in BIG. We also performed physical-chemical and biological water quality analyses of three scallop farms and two nearby locations at BIG in 2022 to evaluate possible environmental stressors and risks. Scallop spat production dropped drastically in the last five years (2018-2022: mean ± stdev: 0.47 ± 0.45 million). Spat production was higher in colder waters and during peaks of Chlorophyll a in the last 13 years. Reduction of Chlorophyll a coincided with decreasing spat production in the last five years. Warmer periods (>27 °C) of the year may hamper scallop development. Counts of potentially pathogenic bacteria (Vibrios) and Escherichia coli were significantly higher in warmer periods which may further reduce scallop productivity. Shotgun metagenomics of seawater samples from the five studied corroborated these culture-based counts. Vibrios and fecal indicator bacteria metagenomic sequences were abundant across the entire study area throughout 2022. The results of this study suggest the collapse of scallop mariculture is the result of a synergistic negative effect of global warming and poor seawater quality.

Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.

The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.

Microbiome and virome on indoor surfaces of an Antarctic research ship

BACKGROUND Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods. OBJECTIVES AND METHODS We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity. FINDINGS Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae. MAIN CONCLUSIONS This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.

Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020.

Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA(+) viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.

Virome in roof-harvested rainwater of a densely urbanized low-income region.

Rainwater harvesting has been considered an affordable practice to supplement the conventional sources of water supply for potable and non-potable uses worldwide. This study characterizes the viral community found in roof-harvested rainwater (RHRW) samples obtained under different rain volumes in a densely urbanized low-income region in Rio de Janeiro, Brazil. Three pilot-scale standardized metal-sheet roofs (same catchment area, material age, and slope - 3%) were installed in the study area aiming at obtaining more reliable and representative samples. Fifty-four samples were collected from six rainfall events from January to April 2019 and concentrated by the skimmed-milk flocculation method. Pools of different rainfall volumes were submitted to high throughput sequencing using the shotgun metagenomic approach. Sequencing was performed on NextSeq platform. Genomic analysis of the virus community revealed that most are RNA non-human viruses, including two main families: Dicistroviridae and Iflaviridae, recognized for infecting arthropods. Bacteriophages were also relatively abundant, with a predominance of DNA phages belonging to Microviridae and Siphoviridae families, showing percentages from 5.3 and 3.7% of the total viral hits present in these samples, respectively. Viral genomic RNA viruses (77%) predominated over DNA viruses (23%). Concerning number of viral species identified, a higher percentage was observed for plant viruses (12 families, 58%). Hepatitis A virus and human klassevirus 1 were detected among the established human pathogens, suggesting the need for RHRW treatment before it is considered for human consumption. Australian bat lyssavirus was also detected, emphasizing the importance of environmental monitoring facing emerging viruses. The results corroborate the influence of the surrounding area on the rainwater quality.

Glacial-interglacial transitions in microbiomes recorded in deep-sea sediments from the western equatorial Atlantic.

In the late Quaternary, glacial-interglacial transitions are marked by major environmental changes. Glacial periods in the western equatorial Atlantic (WEA) are characterized by high continental terrigenous input, which increases the proportion of terrestrial organic matter (e.g. lignin, alkanes), nutrients (e.g. iron and sulphur), and lower primary productivity. On the other hand, interglacials are characterized by lower continental contribution and maxima in primary productivity. Microbes can serve as biosensors of past conditions, but scarce information is available on deep-sea sediments in the WEA. The hypothesis put forward in this study is that past changes in climate conditions modulated the taxonomic/functional composition of microbes from deep sediment layers. To address this hypothesis, we collected samples from a marine sediment core located in the WEA, which covered the last 130 kyr. This region is influenced by the presence of the Amazon River plume, which outputs dissolved and particulate nutrients in vast oceanic regions, as well as the Parnaiba river plume. Core GL-1248 was analysed by shotgun metagenomics and geochemical analyses (alkane, lignin, perylene, sulphur). Two clusters (glacial and interglacial-deglacial) were found based on taxonomic and functional profiles of metagenomes. The interglacial period had a higher abundance of genes belonging to several sub-systems (e.g. DNA, RNA metabolism, cell division, chemotaxis, and respiration) that are consistent with a past environment with enhanced primary productivity. On the other hand, the abundance of Alcanivorax, Marinobacter, Kangiella and aromatic compounds that may serve as energy sources for these bacteria were higher in the glacial. The glacial period was enriched in genes for the metabolism of aromatic compounds, lipids, isoprenoids, iron, and Sulphur, consistent with enhanced fluvial input during the last glacial period. In contrast, interglacials have increased contents of more labile materials originating from phytoplankton (e.g. Prochlorococcus). This study provides new insights into the microbiome as climatic archives at geological timescales.

New bacterial and archaeal lineages discovered in organic rich sediments of a large tropical Bay.

The nutrient and oxygen gradient present in marine sediments promotes high levels of microbial diversity. We applied metagenomics and biogeochemical tools to analyze microbial communities in different sediment depths (0-4 m below sea floor, mbsf) from Guanabara Bay, Brazil, a brackish tropical ecosystem with a history of massive anthropogenic impacts, and a largely unknown sediment microbial diversity. Methanogens (e.g. Methanosarcinales, Methanomicrobiales) were more abundant at 1 mbsf, while sulphate-reducing microbes (Desulfurococcales, Thermoprotales, and Sulfolobales) were more abundant at deeper layers (4 mbsf; corresponding to 3 K Radiocarbon years before present, Holocene Epoch). Taxonomic analyzes and functional gene identification associated with anaerobic methane oxidation (e.g. monomethylamine methyltransferase (mtmB), trimethylamine methyltransferase (mttB) and CO dehydrogenase/acetyl-CoA synthase delta subunit) and sulfate reduction indicated the dominance of Campylobacteria (Sulfurimonas) at deeper sediment layers. Gene sequences related to assimilation of inorganic sulfur increased with depth, while organic sulfur related sequences decrease, accompanying the clear reduction in the concentration of sulfur, organic carbon and chla torwards deeper layers. Analyzes of metagenome assembled genomes also led to the discovery of a novel order within the phylum Acidobacteriota, named Guanabacteria. This novel order had several in silico phenotyping features that differentiate it from closely related phylogenetic neighbors (e.g. Acidobacteria, Aminicenantes, and Thermoanaerobaculum), including several genes (carbon monoxide dehydrogenase, CO dehydrogenase/CO-methylating acetyl-CoA synthase complex subunit beta, heterodisulfide reductase, sulfite exporter TauE/SafE family protein, sulfurtransferase) that relevant for the S and C cycles. Furthermore, the recovered Bathyarchaeota genome SS9 illustrates the methanogenic potential in deeper sediment layer.

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia.

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

Genome sequence of Shewanella corallii strain A687 isolated from pufferfish (Sphoeroides spengleri).

We present here the genome sequence of Shewanella corallii strain A687 isolated from pufferfish Sphoeroides spengleri (Family Tetraodontidae). The assembly consists of 5,215,037 bp and contains 284 contigs, with a G+C content of 50.3%.

Enterovibrio baiacu sp. nov.

We report here the novel species to encompass the isolate A649T (=CBAS 716T = CBRVS P1061T) obtained from viscera of the healthy pufferfish Sphoeroides spengleri (Family Tetraodontidae). Genomic taxonomy analysis demonstrates that the novel strain A649T had < 95% average amino acid identity/average nucleotide identity (AAI/ANI) and < 70% similarity of genome-to-genome distance (GGDH) towards its closest neighbors which places A649T into a new Enterovibrio species (Enterovibrio baiacu sp nov.). In silico phenotyping disclosed several features that may be used to differentiate related Enterovibrio species. The nearly complete genome assembly of strain A649T consisted of 5.4 Mbp and 4826 coding genes.

Metagenomics sheds light on the metabolic repertoire of oil-biodegrading microbes of the South Atlantic Ocean.

Unplanned oil spills during offshore oil production are a serious problem for the industry and the marine environment. Here we assess the biodegradation potential of marine microorganisms from three water depths in the Campos Basin (South Atlantic Ocean): (i) 5 m (surface), (ii) ∼80 m (chlorophyll maximum layer), and (iii) ∼1200 m (near the bottom). After incubating seawater samples with or without crude oil for 52 days, we used metagenomics and classic microbiology techniques to analyze microbial abundance and diversity, and measured physical-chemical parameters to better understand biodegradation processes. We observed increased microbial abundance and concomitant decreases in dissolved oxygen and hydrocarbon concentrations, indicating oil biodegradation in the three water depths treatments within approximately 27 days. An increase in metagenomic sequences of oil-degrading archaea, fungi, and bacteria (Alcanivorax, Alteromonas, Colwellia, Marinobacter, and Pseudomonas) accompanied by a significant increase in metagenomic sequences involved in the degradation of aromatic compounds indicate that crude oil promotes the growth of microorganisms with oil degradation potential. The abundance of genes involved in biodegrading benzene, toluene, ethylbenzene, xylene, alkanes, and poly-aromatic hydrocarbons peaked approximately 3 days after oil addition. All 12 novel metagenome-assembled genomes contained genes involved in hydrocarbon degradation, indicating the oil-degrading potential of planktonic microbes in the Campos Basin.

Insights on the freshwater microbiomes metabolic changes associated with the world's largest mining disaster.

To evaluate the impacts of the Fundão tailings dam failure (Minas Gerais, Brazil) on water quality of the Doce River, we analyzed metagenomics and physicochemical parameters during the month of the disaster and again 6 and 10 months after the disaster. To compare dam conditions before and after the failure, we performed a meta-analysis of physicochemical data from a public database. Immediately after the failure, suspended particulate matter (SPM) in the Doce River was 225-1877 mg L-1. Turbidity and dissolved aluminum and iron concentrations were extremely high, whereas dissolved oxygen was below Brazilian legislation norm (<5 mg L-1) in several locations. Six months later, physicochemical values were below thresholds set by Brazilian guidelines (e.g., SPM = 8-166 mg L-1). Short-term impacts on microbial communities included an increase in Actinobacteria and Bacteroidetes and gene sequences related to microbial virulence, motility, respiration, membrane transport, iron and nitrogen metabolism, suggesting changes in microbial metabolic profiles. The 11 recovered partial genomes from metagenomes (MAGs) had genes related to Fe cycle and metal resistance.

Emergence of the East-Central-South-African genotype of Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection.

Brazil, which is hyperendemic for dengue virus (DENV), has had recent Zika (ZIKV) and (CHIKV) Chikungunya virus outbreaks. Since March 2016, CHIKV is the arbovirus infection most frequently diagnosed in Rio de Janeiro. In the analysis of 1835 syndromic patients, screened by real time RT-PCR, 56.4% of the cases were attributed to CHIKV, 29.6% to ZIKV, and 14.1% to DENV-4. Sequence analyses of CHIKV from sixteen samples revealed that the East-Central-South-African (ECSA) genotype of CHIKV has been circulating in Brazil since 2013 [95% bayesian credible interval (BCI): 03/2012-10/2013], almost a year before it was detected by arbovirus surveillance program. Brazilian cases are related to Central African Republic sequences from 1980's. To the best of our knowledge, given the available sequence published here and elsewhere, the ECSA genotype was likely introduced to Rio de Janeiro early on 2014 (02/2014; BCI: 07/2013-08/2014) through a single event, after primary circulation in the Bahia state at the Northestern Brazil in the previous year. The observation that the ECSA genotype of CHIKV was circulating undetected underscores the need for improvements in molecular methods for viral surveillance.

Genome Sequences of Vibrio maerlii sp. nov. and Vibrio rhodolitus sp. nov., Isolated from Rhodoliths.

We report here the genome sequences of the novel isolates G62T and G98T from rhodoliths. The nearly complete genomes consisted of 4.7 Mbp (4,233 coding sequences [CDS]) for G62T and 4.5 Mbp (4,085 CDS) for G98T. Genomic taxonomy places these new genomes into 2 new species.

Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.

Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 µM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.

Environmental conditions affect activity and associated microorganisms of marine sponges.

Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.

An observational clinical case of Zika virus-associated neurological disease is associated with primary IgG response and enhanced TNF levels.

Descriptive clinical data help to reveal factors that may provoke Zika virus (ZIKV) neuropathology. The case of a 24-year-old female with a ZIKV-associated severe acute neurological disorder was studied. The levels of ZIKV in the cerebrospinal fluid (CSF) were 50 times higher than the levels in other compartments. An acute anti-flavivirus IgG, together with enhanced TNF-alpha levels, may have contributed to ZIKV invasion in the CSF, whereas the unbiased genome sequencing [obtained by next-generation sequencing (NGS)] of the CSF revealed that no virus mutations were associated with the anatomic compartments (CSF, serum, saliva and urine).

Occurrence of Harmful Cyanobacteria in Drinking Water from a Severely Drought-Impacted Semi-arid Region.

Harmful cyanobacterial blooms have become increasingly common in freshwater ecosystems in recent decades, mainly due to eutrophication and climate change. Water becomes unreliable for human consumption. Here, we report a comprehensive study carried out to investigate the water quality of several Campina Grande reservoirs. Our approach included metagenomics, microbial abundance quantification, ELISA test for three cyanotoxins (microcystin, nodularins, and cylindrospermopsin), and in vivo ecotoxicological tests with zebrafish embryos. Cytometry analysis showed high cyanobacterial abundance, while metagenomics identified an average of 10.6% of cyanobacterial sequences, and demonstrated the presence of Microcystis, Cylindrospermopsis, and toxin coding genes in all ponds. Zebrafish embryos reared with pond water had high mortality and diverse malformations. Among the ponds analyzed, Araçagi showed the highest lethality (an average of 62.9 ± 0.8%), followed by Boqueirão (lethality average of 62.5 ± 0.8%). Here, we demonstrate that water from ponds undergoing extremely drought conditions have an abundance of potentially harmful cyanobacteria and their toxins. Our findings are consistent with a scenario in which polluted drinking water poses a great risk to human health.

Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.

Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.