Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment

Comparative proteomics of biofilm development in Pseudoalteromonas tunicata discovers a distinct family of Ca2+-dependent adhesins

The marine bacterium, Pseudoalteromonas tunicata, is a useful model for studying biofilm development due to its ability to colonize and form biofilms on a variety of marine and eukaryotic host-associated surfaces. However, the pathways responsible for P. tunicata biofilm formation are not fully understood, in part due to a lack of functional information for a large proportion of its proteome. We used comparative shotgun proteomics to explore P. tunicata biofilm development from the planktonic phase throughout early, middle, and late biofilm stages. A total of 248 biofilm-associated proteins were identified, including many hypothetical proteins, as well as previously known P. tunicata biofilm-related proteins, such as the autocidal enzyme AlpP, violacein proteins, S-layer protein SLR4, and various pili proteins. We further investigated the top identified biofilm-associated protein, a previously uncharacterized 1,600-amino acid protein (EAR30327), which we designate as "BapP." Based on AlphaFold modeling and genomic context analysis, we predicted BapP as a distinct Ca2+-dependent biofilm adhesin. Consistent with this prediction, a ΔbapP knockout mutant was defective in forming both pellicle- and surface-associated biofilms and rescued by re-insertion of bapP into the genome. Similar to the mechanisms of RTX Bap-like adhesins, BapP-mediated biofilm formation was influenced by Ca2+ levels, and BapP is potentially exported by a Type 1 secretion system. Ultimately, our work not only provides a useful proteomic data set for studying biofilm development in an ecologically relevant organism but also adds to our knowledge of bacterial adhesin diversity, emphasizing Bap-like proteins as widespread determinants of biofilm formation in bacteria.

IMPORTANCE

Understanding how bacteria form biofilms is essential because biofilms play a crucial role in bacterial survival and interaction with their environments. The marine bacterium Pseudoalteromonas tunicata is a valuable model for studying biofilm formation, as it colonizes diverse marine surfaces and host organisms. By identifying proteins involved in biofilm development, our study sheds light on the specific proteins that help P. tunicata transition from a free-swimming state to a stable biofilm. This work highlights the role of a large, calcium-dependent protein, BapP, which we found to be essential for biofilm stability and structure. This protein and hundreds of others identified provide new insights into bacterial adhesion mechanisms, expanding our understanding of biofilm formation in marine environments and potentially informing broader studies on biofilm-related processes in other bacteria.

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.

New investigation of encoding secondary metabolites gene by genome mining of a marine bacterium, Pseudoalteromonas viridis BBR56

Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425-CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA-DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.

The impact of interspecific competition on the genomic evolution of Phaeobacter inhibens and Pseudoalteromonas tunicata during biofilm growth

Interspecific interactions in biofilms have been shown to cause the emergence of community-level properties. To understand the impact of interspecific competition on evolution, we deep-sequenced the dispersal population of mono- and co-culture biofilms of two antagonistic marine bacteria (Phaeobacter inhibens 2.10 and Pseudoalteromononas tunicata D2). Enhanced phenotypic and genomic diversification was observed in the P. tunicata D2 populations under both mono- and co-culture biofilms in comparison to P. inhibens 2.10. The genetic variation was exclusively due to single nucleotide variants and small deletions, and showed high variability between replicates, indicating their random emergence. Interspecific competition exerted an apparent strong positive selection on a subset of P. inhibens 2.10 genes (e.g., luxR, cobC, argH, and sinR) that could facilitate competition, while the P. tunicata D2 population was genetically constrained under competition conditions. In the absence of interspecific competition, the P. tunicata D2 replicate populations displayed high levels of mutations affecting the same genes involved in cell motility and biofilm formation. Our results show that interspecific biofilm competition has a complex impact on genomic diversification, which likely depends on the nature of the competing strains and their ability to generate genetic variants due to their genomic constraints.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.

Genomic Analysis of Two Cold-Active Pseudoalteromonas Phages Isolated from the Continental Shelf in the Arctic Ocean

Cold-active bacteriophages are bacterial viruses that infect and replicate at low temperatures (≤4 °C). Understanding remains limited of how cold-active phage-host systems sustain high viral abundance despite the persistently low temperatures in pelagic sediments in polar seas. In this study, two Pseudoalteromonas phages, ACA1 and ACA2, were isolated from sediment core samples of the continental shelf in the western Arctic Ocean. These phages exhibited successful propagation at a low temperature of 1 °C and displayed typical myovirus morphology with isometric icosahedral heads and contractile tails. The complete genome sequences of phages ACA1 and ACA2 were 36,825 bp and 36,826 bp in size, respectively, sharing almost the same gene content. These are temperate phages encoding lysogeny-related proteins such as anti-repressor, immunity repressor and integrase. The absence of cross-infection between the host strains, which were genomically distinct Pseudoalteromonas species, can likely be attributed to heavy divergence in the anti-receptor apparently mediated by an associated diversity-generating retroelement. HHpred searching identified genes for all of the structural components of a P2-like phage (family Peduoviridae), although the whole of the Peduoviridae family appeared to be divided between two anciently diverged tail modules. In contrast, Blast matching and whole genome tree analysis are dominated by a nonstructural gene module sharing high similarity with Pseudoalteromonas phage C5a (founder of genus Catalunyavirus). This study expands the knowledge of diversity of P2-like phages known to inhabit Peudoalteromonas and demonstrates their presence in the Arctic niche.

Isolation and genome sequencing of a novel lytic Pseudoalteromonas phage SL20

Phage SL20, a novel lytic Pseudoalteromonas phage, was isolated from the coastal waters of the Yellow Sea, China. The microbiological characterization demonstrated that phage SL20 was relatively stable from 35 to 55 °C and the optimal pH was approximately 6.0. A latent period of approximately 24 min was indicated by a one-step growth curve. The burst size was approximately 12 ± 3 PFU/cell. The genome had a length of 120,295 bp with a G + C content of 35.84%, and predicted 95 ORFs. The phylogenetic tree based on DNA helicase showed that Pseudoalteromonas phage SL20 was related to the Pseudoalteromonas phage H101 and was a member of the family Shandongvirus. The isolation and genomic analysis of SL20 has improved our understanding of host-phage interactions and the ecology of the marine bacteria Pseudoalteromonas.

Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick

Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.

Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups

Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of 13C and 15N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in 13C and 15N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.

Molecular Relationships in Biofilm Formation and the Biosynthesis of Exoproducts in Pseudoalteromonas spp

Most members of the Pseudoalteromonas genus have been isolated from living surfaces as members of epiphytic and epizooic microbiomes on marine macroorganisms. Commonly Pseudoalteromonas isolates are reported as a source of bioactive exoproducts, i.e., secondary metabolites, such as exopolymeric substances and extracellular enzymes. The experimental conditions for the production of these agents are commonly associated with sessile metabolic states such as biofilms or liquid cultures in the stationary growth phase. Despite this, the molecular mechanisms that connect biofilm formation and the biosynthesis of exoproducts in Pseudoalteromonas isolates have rarely been mentioned in the literature. This review compiles empirical evidence about exoproduct biosynthesis conditions and molecular mechanisms that regulate sessile metabolic states in Pseudoalteromonas species, to provide a comprehensive perspective on the regulatory convergences that generate the recurrent coexistence of both phenomena in this bacterial genus. This synthesis aims to provide perspectives on the extent of this phenomenon for the optimization of bioprospection studies and biotechnology processes based on these bacteria.

Metaproteomics reveals unique metabolic niches of dominant bacterial groups in response to rapid regime shifts during a mixed dinoflagellate bloom

The dynamics of bacterial composition and metabolic activity during a distinct phytoplankton bloom have been reported. However, there is limited information on the bacterial community response to drastic environmental changes caused by species succession during a mixed-species bloom. This study investigated active bacterial groups and metabolic activity during a mixed bloom formed by dinoflagellates Prorocentrum obtusidens and Karenia mikimotoi using a metaproteomic approach. Bacterial community structure and dominant bacterial groups varied rapidly with the bloom regime shifts caused by species succession. Pseudoalteromonas and Vibrio dominated the bacterial community in the P. obtusidens-dominated regime, while Alteromonas, Cytophaga-Flavobacteria-Bacteroides (CFB) group, and marine Roseobacter clade (MRC) were the major contributors in other regimes, with the most abundant taxa being Alteromonas in the K. mikimotoi-dominated regime and the CFB group in the dissipation regime. Specific metabolic niches and unique substrate specificity of different bacterial groups enabled them to dominate and thrive in different bloom regimes. High metabolic plasticity in signal response, substrate utilization, motility, and adhesion are essential for bacteria to respond to drastic bloom regime shift, and the predominance of specific bacteria under unique bloom regimes may be the result of long-term coevolution between bacteria and bloom-forming phytoplankton species.

New Report: Genome Mining Untaps the Antibiotics Biosynthetic Gene Cluster of Pseudoalteromonas xiamenensis STKMTI.2 from a Mangrove Soil Sediment

The marine bacterium Pseudoalteromonas xiamenensis STKMTI.2 was isolated from a mangrove soil sediment on Setokok Island, Batam, Indonesia. The genome of this bacterium consisted of 4,563,326 bp (GC content: 43.2%) with 1 chromosome, 2 circular plasmids, 2 linear plasmids, 4,824 protein-coding sequences, 25 rRNAs, 104 tRNAs, 4 ncRNAs, and 1 clustered, regularly interspaced, short palindromic repeated (CRISPR). This strain possessed cluster genes which are responsible for the production of brominated marine pyrroles/phenols (bmp), namely, bmp8 and bmp9. Other gene clusters responsible for the synthesis of secondary metabolites were identified using antiSMASH and BAGEL4, which yielded five results, namely, non-ribosomal peptides, polyketide-like butyrolactone, Lant class I, and RiPP-like, detected in chromosome 1, while prodigiosin was detected in the unnamed plasmid 5. This suggests that these whole genome data will be of remarkable importance for the improved understanding of the biosynthesis of industrially important bioactive and antibacterial compounds produced by P. xiamenensis STKMTI.2.

Draft Genome Sequencing of Pseudoalteromonas tetraodonis Strain kknpp56, a Potent Biofilm-Forming Bacterium Isolated from Early-Stage Marine Biofilm

Pseudoalteromonas tetraodonis strain kknpp56 is an exopolysaccharide (EPS)-producing marine bacterium that forms potent biofilm. To determine the biosynthesis pathways involved in the EPS production of this bacterium, whole-genome sequencing was performed. The complete genome comes from one chromosome containing 3.72 Mbp of DNA with a G+C content of 41%.

The Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid

Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this study extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.

Assessment of the environmental compatibility and antifouling performance of an innovative biocidal and foul-release multifunctional marine coating

The control of marine biofouling has raised serious environmental concerns, thus the continuous release of toxic and persistent biocidal agents applied as anti-biofouling coatings have triggered the search for non-toxic strategies. However, most of them still lack rigorous evaluation of their ecotoxicity and antifouling effects under real scenarios and their correlation with simulated assays. In this work, the biocide releasing risk and ecotoxicity of a biocidal and foul-release polydimethylsiloxane (PDMS)-based marine coating containing grafted Econea biocide (<0.6 wt.%) were evaluated under simulated real mechanical wear conditions at a pilot-scale system, and under extreme wear scenarios (washability settings). The coating system demonstrated low environmental impact against the model Vibrio fischeri bacterium and marine algae, associated with the effective biocide grafting in the coating matrix and subsequent biocide release minimization. This multifunctional coating system also showed auspicious antifouling (AF) effects, with an AF performance index significantly higher (API > 89) than a single foul-release system (AF < 40) after two and half years at a real immersion scenario in the Portuguese shore of the Atlantic Ocean. These field results corroborated the antibiofilm performance evaluated with Pseudoalteromonas tunicata at simulated dynamic marine conditions after seven-week assays. This eco-friendly multifunctional strategy, validated by both simulated testing conditions and real field tests, is believed to be a powerful tool for the development of AF technologies and a potential contribution to the quest for new environmentally friendly antifouling solutions.

Two Distinct Bacterial Biofilm Components Trigger Metamorphosis in the Colonial Hydrozoan Hydractinia echinata

In marine environments, the bacterially induced metamorphosis of larvae is a widespread cross-kingdom communication phenomenon that is critical for the persistence of many marine invertebrates. However, the majority of inducing bacterial signals and underlying cellular mechanisms remain enigmatic. The marine hydroid Hydractinia echinata is a well-known model system for investigating bacterially stimulated larval metamorphosis, as larvae transform into the colonial adult stage within 24 h of signal detection. Although H. echinata has served as a cell biological model system for decades, the identity and influence of bacterial signals on the morphogenic transition remained largely unexplored. Using a bioassay-guided analysis, we first determined that specific bacterial (lyso)phospholipids, naturally present in bacterial membranes and vesicles, elicit metamorphosis in Hydractinia larvae in a dose-response manner. Lysophospholipids, as single compounds or in combination (50 μM), induced metamorphosis in up to 50% of all larvae within 48 h. Using fluorescence-labeled bacterial phospholipids, we demonstrated that phospholipids are incorporated into the larval membranes, where interactions with internal signaling cascades are proposed to occur. Second, we identified two structurally distinct exopolysaccharides of bacterial biofilms, the new Rha-Man polysaccharide from Pseudoalteromonas sp. strain P1-9 and curdlan from Alcaligenes faecalis, to induce metamorphosis in up to 75% of tested larvae. We also found that combinations of (lyso)phospholipids and curdlan induced transformation within 24 h, thereby exceeding the morphogenic activity observed for single compounds and bacterial biofilms. Our results demonstrate that two structurally distinct, bacterium-derived metabolites converge to induce high transformation rates of Hydractinia larvae and thus may help ensure optimal habitat selection. IMPORTANCE Bacterial biofilms profoundly influence the recruitment and settlement of marine invertebrates, critical steps for diverse marine processes such as the formation of coral reefs, the maintenance of marine fisheries, and the fouling of submerged surfaces. However, the complex composition of biofilms often makes the characterization of individual signals and regulatory mechanisms challenging. Developing tractable model systems to characterize these coevolved interactions is the key to understanding fundamental processes in evolutionary biology. Here, we characterized two types of bacterial signaling molecules, phospholipids and polysaccharides, that induce the morphogenic transition. We then analyzed their abundance and combinatorial activity. This study highlights the general importance of multiple bacterial signal converging activity in development-related cross-kingdom signaling and poses the question of whether complex lipids and polysaccharides are general metamorphic cues for cnidarian larvae.

Population structure, activity potential and ecotype partitioning of Pseudoalteromonas along the vertical water column of the New Britain Trench

Microbial degradation of organic matter along the vertical profile of the water column is a major process driving the carbon cycle in the ocean. Pseudoalteromonas has been identified as a dominant genus in pelagic marine environments worldwide, playing important roles in the remineralization of organic carbon. However, the current understanding of Pseudoalteromonas was mainly based on shallow water populations or cultivated species. This study analyzed for the first time the structure, activity potential and ecotypes differentiation of Pseudoalteromonas in the water column of the New Britain Trench (NBT) down to 6000 m. Analysis on diversities of the 16S rRNA gene and their transcripts showed that Pseudoalteromonas was greatly enriched in deep-sea waters and showed high activity potentials. The deep-sea Pseudoalteromonas were significantly different from their shallow-water counterparts, suggesting an obvious ecotype division along with the vertical profile. Phylogenetic analysis on the 16S rRNA gene and hsp60 gene of 219 Pseudoalteromonas strains isolated from different depths further showed that the vertical ecotype division could even occur at the strain level, which might be a result of long-term adaptation to environmental conditions at different depths. The discovered depth-specific strains provide valuable models for further studies on adaptation, evolution and functions of the deep-sea Pseudoalteromonas.

Evolutionary Trajectory of the Replication Mode of Bacterial Replicons

Chromosome replication is an essential process for cell division. The mode of chromosome replication has important impacts on the structure of the chromosome and replication speed.

As typical bacterial replicons, circular chromosomes replicate bidirectionally and circular plasmids replicate either bidirectionally or unidirectionally. Whereas the finding of chromids (plasmid-derived chromosomes) in multiple bacterial lineages provides circumstantial evidence that chromosomes likely evolved from plasmids, all experimentally assayed chromids were shown to use bidirectional replication. Here, we employed a model system, the marine bacterial genus Pseudoalteromonas, members of which consistently carry a chromosome and a chromid. We provide experimental and bioinformatic evidence that while chromids in a few strains replicate bidirectionally, most replicate unidirectionally. This is the first experimental demonstration of the unidirectional replication mode in bacterial chromids. Phylogenomic and comparative genomic analyses showed that the bidirectional replication evolved only once from a unidirectional ancestor and that this transition was associated with insertions of exogenous DNA and relocation of the replication terminus region (ter2) from near the origin site (ori2) to a position roughly opposite it. This process enables a plasmid-derived chromosome to increase its size and expand the bacterium’s metabolic versatility while keeping its replication synchronized with that of the main chromosome. A major implication of our study is that the uni- and bidirectionally replicating chromids may represent two stages on the evolutionary trajectory from unidirectionally replicating plasmids to bidirectionally replicating chromosomes in bacteria. Further bioinformatic analyses predicted unidirectionally replicating chromids in several unrelated bacterial phyla, suggesting that evolution from unidirectionally to bidirectionally replicating replicons occurred multiple times in bacteria.

Developing New Marine Antifouling Surfaces: Learning from Single-Strain Laboratory Tests

The development of antifouling (AF) technology for marine environments is an area of intense research given the severe economic and ecological effects of marine biofouling. Preliminary data from in vitro assays is frequently used to screen the performance of AF coatings. It is intuitive that microbial composition plays a major role in surface colonization. The rationale behind this study is to investigate whether using a mixed population for the in vitro tests yields substantially different results than using single strains during initial screening. A polymeric coating was tested against single- and dual-species cultures of two common microfouler organisms for 49 days. A bacterium (Pseudoaltermonas tunicata) and a cyanobacterium (Cyanobium sp. LEGE 10375) were used in this study. Linear regression analysis revealed that Cyanobium sp. biofilms were significantly associated with a higher number of cells, wet weight, thickness, and biovolume compared to dual-species biofilms. P. tunicata alone had a biofilm growth kinetics similar to dual-species biofilms, although the P. tunicata–Cyanobium sp. mixture developed less dense and thinner biofilms compared to both single-species biofilms. Cyanobium sp. LEGE 10375 biofilms provided the worst-case scenario, i.e., the conditions that caused higher biofilm amounts on the surface material under test. Therefore, it is likely that assessing the AF performance of new coatings using the most stringent conditions may yield more robust results than using a mixed population, as competition between microfouler organisms may reduce the biofilm formation capacity of the consortium.

Delivering Beneficial Microorganisms for Corals: Rotifers as Carriers of Probiotic Bacteria

The use of Beneficial Microorganisms for Corals (BMCs) to increase the resistance of corals to environmental stress has proven to be effective in laboratory trials. Because direct inoculation of BMCs in larger tanks or in the field can be challenging, a delivery mechanism is needed for efficient transmission of the BMC consortium. Packaged delivery mechanisms have been successfully used to transmit probiotics to other organisms, including humans, lobsters, and fish. Here, we tested a method for utilizing rotifers of the species Brachionus plicatilis for delivery of BMCs to corals of the species Pocillopora damicornis. Epifluorescence microscopy combined with a live/dead cell staining assay was used to evaluate the viability of the BMCs and monitor their in vivo uptake by the rotifers. The rotifers efficiently ingested BMCs, which accumulated in the digestive system and on the body surface after 10 min of interaction. Scanning electron microscopy confirmed the adherence of BMCs to the rotifer surfaces. BMC-enriched rotifers were actively ingested by P. damicornis corals, indicating that this is a promising technique for administering coral probiotics in situ. Studies to track the delivery of probiotics through carriers such as B. plicatilis, and the provision or establishment of beneficial traits in corals are the next proof-of-concept research priorities.

Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions

Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.

Combating Parasitic Nematode Infections, Newly Discovered Antinematode Compounds from Marine Epiphytic Bacteria

Parasitic nematode infections cause debilitating diseases and impede economic productivity. Antinematode chemotherapies are fundamental to modern medicine and are also important for industries including agriculture, aquaculture and animal health. However, the lack of suitable treatments for some diseases and the rise of nematode resistance to many available therapies necessitates the discovery and development of new drugs. Here, marine epiphytic bacteria represent a promising repository of newly discovered antinematode compounds. Epiphytic bacteria are ubiquitous on marine surfaces where they are under constant pressure of grazing by bacterivorous predators (e.g., protozoans and nematodes). Studies have shown that these bacteria have developed defense strategies to prevent grazers by producing toxic bioactive compounds. Although several active metabolites against nematodes have been identified from marine bacteria, drug discovery from marine microorganisms remains underexplored. In this review, we aim to provide further insight into the need and potential for marine epiphytic bacteria to become a new source of antinematode drugs. We discuss current and emerging strategies, including culture-independent high throughput screening and the utilization of Caenorhabditis elegans as a model target organism, which will be required to advance antinematode drug discovery and development from marine microbial sources.

Prokaryotic Diversity and Distribution Along Physical and Nutrient Gradients in the Tunisian Coastal Waters (South Mediterranean Sea)

Prokaryotes play an important role in biogeochemical cycling in marine ecosystems, but little is known about their diversity and composition, and how they may contribute to the ecological functioning of coastal areas in the South Mediterranean Sea. This study investigated bacterial and archaeal community diversity in seawater samples along the Tunisian coast subject to important physicochemical disturbances. The 16S amplicon sequencing survey revealed higher prokaryotic diversity in the northern Tunisian bays than in southeastern waters (Gulf of Gabès). The major taxonomic groups identified in all samples were Alphaproteobacteria (40.9%), Gammaproteobacteria (18.7%), Marine Group II Euryarchaeota (11.3%), and Cyanobacteria (10.9%). Among them, the relative abundance of Alteromonadales, Prochlorococcus, and some clades of Pelagibacterales (SAR11) significantly differed between the northern and the southern bays, whereas no difference was observed across coastal waters in the archaeal Candidatus Poseidoniales (MGII), Synechococcus, and Pelagibacteraceae (SAR11 clade Ia), for which no relationship was observed with the environmental variables. Both Pseudoalteromonas and Alteromonas levels increased with the increasing salinity, density and nutrients (NH₄ ⁺ and/or PO₄ ^3-) gradients detected toward the southern waters, while the SAR11 clades Ib and IV and Prochlorococcus, decreased in the shallow, salty and nutrient-rich coastal waters of the Gulf of Gabès. Rhodobacteraceae was positively correlated with Synechococcus and chlorophyll levels, suggesting a relationship with phytoplankton biomass. The present study provides the first insights into planktonic prokaryotic community composition in the South Mediterranean Sea through the analysis of Tunisian seawaters, which may support further investigations on the role of bacterioplankton in the biogeochemistry of these ecosystems.

Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component

S‐layers are paracrystalline proteinaceous lattices that surround prokaryotic cells, forming a critical interface between the cells and their extracellular environment. Here, we report the discovery of a novel S‐layer protein present in the Gram‐negative marine organism, Pseudoalteromonas tunicata D2. An uncharacterized protein (EAR28894) was identified as the most abundant protein in planktonic cultures and biofilms. Bioinformatic methods predicted a beta‐helical structure for EAR28894 similar to the Caulobacter S‐layer protein, RsaA, despite sharing less than 20% sequence identity. Transmission electron microscopy revealed that purified EAR28894 protein assembled into paracrystalline sheets with a unique square lattice symmetry and a unit cell spacing of ~9.1 nm. An S‐layer was found surrounding the outer membrane in wild‐type cells and completely removed from cells in an EAR28894 deletion mutant. S‐layer material also appeared to be “shed” from wild‐type cells and was highly abundant in the extracellular matrix where it is associated with outer membrane vesicles and other matrix components. EAR28894 and its homologs form a new family of S‐layer proteins that are widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio, and found exclusively in marine metagenomes. We propose the name Slr4 for this novel protein family.

Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery

Secondary metabolites can be viewed as a chemical language, facilitating communication between microorganisms. From an ecological point of view, this metabolite exchange is in constant flux due to evolutionary and environmental pressures. From a biomedical perspective, the chemistry is unsurpassed for its antibiotic properties. Genome sequencing of microorganisms has revealed a large reservoir of Biosynthetic Gene Clusters (BGCs); however, linking these to the secondary metabolites they encode is currently a major bottleneck to chemical discovery. This linking of genes to metabolites with experimental validation will aid the elicitation of silent or cryptic (not expressed under normal laboratory conditions) BGCs. As a result, this will accelerate chemical dereplication, our understanding of gene transcription and provide a comprehensive resource for synthetic biology. This will ultimately provide an improved understanding of both the biosynthetic and chemical space. In recent years, integrating these complex metabolomic and genomic data sets has been achieved using a spectrum of manual and automated approaches. In this review, we cover examples of these approaches, while addressing current challenges and future directions in linking these data sets.

Phage-specific metabolic reprogramming of virocells

Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.

Diversity and Distribution of Bacteria Producing Known Secondary Metabolites

There is an increasing interest in the utilisation of marine bioactive compounds as novel biopharmaceuticals and agrichemicals; however, little is known about the environmental distribution for many of these molecules. Here, we aimed to elucidate the environmental distribution and to detect the biosynthetic gene clusters in environmental samples of four bioactive compounds, namely violacein, tropodithietic acid (TDA), tambjamine and the antibacterial protein AlpP. Our database analyses revealed high bacterial diversity for AlpP and violacein producers, while TDA-producing bacteria were mostly associated with marine surfaces and all belonged to the roseobacter group. In contrast, the tambjamine cluster was only found in the genomes of two Pseudoalteromonas species and in one terrestrial species belonging to the Cupriavidus genus. Using a PCR-based screen of different marine samples, we detected TDA and violacein genes associated with the microbiome of Ulva and Protohyale niger and tambjamine genes associated with Nodilittorina unifasciata; however, alpP was not detected. These results highlight the variable distribution of the genes encoding these four bioactive compounds, including their detection from the surface of multiple marine eukaryotic hosts. Determining the natural distribution of these gene clusters will help to understand the ecological importance of these metabolites and the bacteria that produce them.

Prokaryotic niche partitioning between suspended and sinking marine particles

Suspended particles are major organic carbon substrates for heterotrophic microorganisms in the mesopelagic ocean (100-1000 m). Nonetheless, communities associated with these particles have been overlooked compared with sinking particles, the latter generally considered as main carbon transporters to the deep ocean. This study is the first to differentiate prokaryotic communities associated with suspended and sinking particles, collected with a marine snow catcher at four environmentally distinct stations in the Scotia Sea. Amplicon sequencing of 16S rRNA gene revealed distinct prokaryotic communities associated with the two particle-types in the mixed-layer (0-100 m) and upper-mesopelagic zone (mean dissimilarity 42.5% ± 15.2%). Although common remineralising taxa were present within both particle-types, gammaproteobacterial Pseudomonadales and Vibrionales, and alphaproteobacterial Rhodobacterales were found enriched in sinking particles up to 32-fold, while Flavobacteriales (Bacteroidetes) favoured suspended particles. We propose that this niche-partitioning may be driven by organic matter properties found within both particle-types: K-strategists, specialised in the degradation of complex organic compounds, thrived on semi-labile suspended particles, while generalists r-strategists were adapted to the transient labile organic contents of sinking particles. Differences between the two particle-associated communities were more pronounced in the mesopelagic than in the surface ocean, likely resulting from exchanges between particle-pools enabled by the stronger turbulence.

A First Study of the Virulence Potential of a Bacillus subtilis Isolate From Deep-Sea Hydrothermal Vent

Bacillus subtilis is the best studied Gram-positive bacterium, primarily as a model of cell differentiation and industrial exploitation. To date, little is known about the virulence of B. subtilis. In this study, we examined the virulence potential of a B. subtilis strain (G7) isolated from the Iheya North hydrothermal field of Okinawa Trough. G7 is aerobic, motile, endospore-forming, and requires NaCl for growth. The genome of G7 is composed of one circular chromosome of 4,216,133 base pairs with an average GC content of 43.72%. G7 contains 4,416 coding genes, 27.5% of which could not be annotated, and the remaining 72.5% were annotated with known or predicted functions in 25 different COG categories. Ten sets of 23S, 5S, and 16S ribosomal RNA operons, 86 tRNA and 14 sRNA genes, 50 tandem repeats, 41 mini-satellites, one microsatellite, and 42 transposons were identified in G7. Comparing to the genome of the B. subtilis wild type strain NCIB 3610^T, G7 genome contains many genomic translocations, inversions, and insertions, and twice the amount of genomic Islands (GIs), with 42.5% of GI genes encoding hypothetical proteins. G7 possesses abundant putative virulence genes associated with adhesion, invasion, dissemination, anti-phagocytosis, and intracellular survival. Experimental studies showed that G7 was able to cause mortality in fish and mice following intramuscular/intraperitoneal injection, resist the killing effect of serum complement, and replicate in mouse macrophages and fish peripheral blood leukocytes. Taken together, our study indicates that G7 is a B. subtilis isolate with unique genetic features and can be lethal to vertebrate animals once being introduced into the animals by artificial means. These results provide the first insight into the potential harmfulness of deep-sea B. subtilis.

Complete genome sequences of pooled genomic DNA from 10 marine bacteria using PacBio long-read sequencing

BACKGROUND

High-quality, completed genomes are important to understand the functions of marine bacteria. PacBio sequencing technology provides a powerful way to obtain high-quality completed genomes. However individual library production is currently still costly, limiting the utility of the PacBio system for high-throughput genomics. Here we investigate how to generate high-quality genomes from pooled marine bacterial genomes.

RESULTS

Pooled genomic DNA from 10 marine bacteria were subjected to a single library production and sequenced with eight SMRT cells on the PacBio RS II sequencing platform. In total, 7.35 Gbp of long-read data was generated, which is equivalent to an approximate 168× average coverage for the input genomes. Genome assembly showed that eight genomes with average nucleotide identities (ANI) lower than 91.4% can be assembled with high-quality and completion using standard assembly algorithms (e.g. HGAP or Canu). A reference-based reads phasing step was developed and incorporated to assemble the complete genomes of the remaining two marine bacteria that had an ANI > 97% and whose initial assemblies were highly fragmented.

CONCLUSIONS

Ten complete high-quality genomes of marine bacteria were generated. The findings and developments made here, including the reference-based read phasing approach for the assembly of highly similar genomes, can be used in the future to design strategies to sequence pooled genomes using long-read sequencing.

Microbial Population Changes in Decaying Ascophyllum nodosum Result in Macroalgal-Polysaccharide-Degrading Bacteria with Potential Applicability in Enzyme-Assisted Extraction Technologies

Seaweeds are of significant interest in the food, pharmaceutical, and agricultural industries as they contain several commercially relevant bioactive compounds. Current extraction methods for macroalgal-derived metabolites are, however, problematic due to the complexity of the algal cell wall which hinders extraction efficiencies. The use of advanced extraction methods, such as enzyme-assisted extraction (EAE), which involve the application of commercial algal cell wall degrading enzymes to hydrolyze the cell wall carbohydrate network, are becoming more popular. Ascophyllum nodosum samples were collected from the Irish coast and incubated in artificial seawater for six weeks at three different temperatures (18 °C, 25 °C, and 30 °C) to induce decay. Microbial communities associated with the intact and decaying macroalga were examined using Illumina sequencing and culture-dependent approaches, including the novel ichip device. The bacterial populations associated with the seaweed were observed to change markedly upon decay. Over 800 bacterial isolates cultured from the macroalga were screened for the production of algal cell wall polysaccharidases and a range of species which displayed multiple hydrolytic enzyme activities were identified. Extracts from these enzyme-active bacterial isolates were then used in EAE of phenolics from Fucus vesiculosus and were shown to be more efficient than commercial enzyme preparations in their extraction efficiencies.

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9^T (ATCC 43555^T), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.

Dissemination of Genetic Acquisition/Loss Provides a Variety of Quorum Sensing Regulatory Properties in Pseudoalteromonas

A bstract: Quorum sensing (QS) enables single-celled bacteria to communicate with chemical signals in order to synchronize group-level bacterial behavior. Pseudoalteromonas are marine bacteria found in versatile environments, of which QS regulation for their habitat adaptation is extremely fragmentary. To distinguish genes required for QS regulation in Pseudoalteromonas, comparative genomics was deployed to define the pan-genomics for twelve isolates and previously-sequenced genomes, of which acyl-homoserine lactone (AHL)-based QS traits were characterized. Additionally, transposon mutagenesis was used to identify the essential QS regulatory genes in the selected Pseudoalteromonas isolate. A remarkable feature showed that AHL-based colorization intensity of biosensors induced by Pseudoalteromonas most likely correlates with QS regulators genetic heterogeneity within the genus. This is supported by the relative expression levels of two of the main QS regulatory genes (luxO and rpoN) analyzed in representative Pseudoalteromonas isolates. Notably, comprehensive QS regulatory schema and the working model proposed in Pseudoalteromonas seem to phylogenetically include the network architectures derived from Escherichia coli, Pseudomonas, and Vibrio. Several associated genes were mapped by transposon mutagenesis. Among them, a right origin-binding protein-encoding gene (robp) was functionally identified as a positive QS regulatory gene. This gene lies on a genomic instable region and exists in the aforementioned bioinformatically recruited QS regulatory schema. The obtained data emphasize that the distinctly- and hierarchically-organized mechanisms probably target QS association in Pseudoalteromonas dynamic genomes, thus leading to bacterial ability to accommodate their adaption fitness and survival advantages.

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

Acidification increases abundances of Vibrionales and Planctomycetia associated to a seaweed-grazer system: potential consequences for disease and prey digestion efficiency

Ocean acidification significantly affects marine organisms in several ways, with complex interactions. Seaweeds might benefit from rising CO₂ through increased photosynthesis and carbon acquisition, with subsequent higher growth rates. However, changes in seaweed chemistry due to increased CO₂ may change the nutritional quality of tissue for grazers. In addition, organisms live in close association with a diverse microbiota, which can also be influenced by environmental changes, with feedback effects. As gut microbiomes are often linked to diet, changes in seaweed characteristics and associated microbiome can affect the gut microbiome of the grazer, with possible fitness consequences. In this study, we experimentally investigated the effects of acidification on the microbiome of the invasive brown seaweed Sargassum muticum and a native isopod consumer Synisoma nadejda. Both were exposed to ambient CO₂ conditions (380 ppm, pH 8.16) and an acidification treatment (1,000 ppm, pH 7.86) for three weeks. Microbiome diversity and composition were determined using high-throughput sequencing of the variable regions V5-7 of 16S rRNA. We anticipated that as a result of acidification, the seaweed-associated bacterial community would change, leading to further changes in the gut microbiome of grazers. However, no significant effects of elevated CO₂ on the overall bacterial community structure and composition were revealed in the seaweed. In contrast, significant changes were observed in the bacterial community of the grazer gut. Although the bacterial community of S. muticum as whole did not change, Oceanospirillales and Vibrionales (mainly Pseudoalteromonas) significantly increased their abundance in acidified conditions. The former, which uses organic matter compounds as its main source, may have opportunistically taken advantage of the possible increase of the C/N ratio in the seaweed under acidified conditions. Pseudoalteromonas, commonly associated to diseased seaweeds, suggesting that acidification may facilitate opportunistic/pathogenic bacteria. In the gut of S. nadejda, the bacterial genus Planctomycetia increased abundance under elevated CO₂. This shift might be associated to changes in food (S. muticum) quality under acidification. Planctomycetia are slow-acting decomposers of algal polymers that could be providing the isopod with an elevated algal digestion and availability of inorganic compounds to compensate the shifted C/N ratio under acidification in their food.

In conclusion, our results indicate that even after only three weeks of acidified conditions, bacterial communities associated to ungrazed seaweed and to an isopod grazer show specific, differential shifts in associated bacterial community. These have potential consequences for seaweed health (as shown in corals) and isopod food digestion. The observed changes in the gut microbiome of the grazer seem to reflect changes in the seaweed chemistry rather than its microbial composition.

Seafood spoilage microbiota and associated volatile organic compounds at different storage temperatures and packaging conditions

Seafood comprising of both vertebrate and invertebrate aquatic organisms are nutritious, rich in omega-3 fatty acids, essential vitamins, proteins, minerals and form part of healthy diet. However, despite the health and nutritional benefits, seafood is highly perishable. Spoilage of seafood could be as a result of microbial activity, autolysis or chemical oxidation. Microbial activity constitutes more spoilage than others. Spoilage bacteria are commonly Gram negative and produce off odours and flavours in seafood as a result of their metabolic activities. Storage temperature, handling and packaging conditions affect microbial growth and thus the shelf-life of seafood. Due to the complexity of the microbial communities in seafood, culture dependent methods of detection may not be useful, hence the need for culture independent methods are necessary to understand the diversity of microbiota and spoilage process. Similarly, the volatile organic compounds released by spoilage bacteria are not fully understood in some seafood. This review therefore highlights current knowledge and understanding of seafood spoilage microbiota, volatile organic compounds, effects of storage temperature and packaging conditions on quality of seafood.

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept

Viruses influence the ecology and evolutionary trajectory of microbial communities. Yet our understanding of their roles in ecosystems is limited by the paucity of model systems available for hypothesis generation and testing. Further, virology is limited by the lack of a broadly accepted conceptual framework to classify viral diversity into evolutionary and ecologically cohesive units. Here, we introduce genomes, structural proteomes, and quantitative host range data for eight Pseudoalteromonas phages isolated from Helgoland (North Sea, Germany) and use these data to advance a genome-based viral operational taxonomic unit (OTU) definition. These viruses represent five new genera and inform 498 unaffiliated or unannotated protein clusters (PCs) from global virus metagenomes. In a comparison of previously sequenced Pseudoalteromonas phage isolates (n = 7) and predicted prophages (n = 31), the eight phages are unique. They share a genus with only one other isolate, Pseudoalteromonas podophage RIO-1 (East Sea, South Korea) and two Pseudoalteromonas prophages. Mass-spectrometry of purified viral particles identified 12–20 structural proteins per phage. When combined with 3-D structural predictions, these data led to the functional characterization of five previously unidentified major capsid proteins. Protein functional predictions revealed mechanisms for hijacking host metabolism and resources. Further, they uncovered a hybrid sipho-myovirus that encodes genes for Mu-like infection rarely described in ocean systems. Finally, we used these data to evaluate a recently introduced definition for virus populations that requires members of the same population to have >95% average nucleotide identity across at least 80% of their genes. Using physiological traits and genomics, we proposed a conceptual model for a viral OTU definition that captures evolutionarily cohesive and ecologically distinct units. In this trait-based framework, sensitive hosts are considered viral niches, while host ranges and infection efficiencies are tracked as viral traits. Quantitative host range assays revealed conserved traits within virus OTUs that break down between OTUs, suggesting the defined units capture niche and fitness differentiation. Together these analyses provide a foundation for model system-based hypothesis testing that will improve our understanding of marine copiotrophs, as well as phage–host interactions on the ocean particles and aggregates where Pseudoalteromonas thrive.

Mechanisms for Pseudoalteromonas piscicida-Induced Killing of Vibrios and Other Bacterial Pathogens

Pseudoalteromonas piscicida is a Gram-negative gammaproteobacterium found in the marine environment. Three strains of pigmented P. piscicida were isolated from seawater and partially characterized by inhibition studies, electron microscopy, and analysis for proteolytic enzymes. Growth inhibition and death occurred around colonies of P. piscicida on lawns of the naturally occurring marine pathogens Vibrio vulnificus, Vibrio parahaemolyticus, Vibrio cholerae, Photobacterium damselae, and Shewanella algae Inhibition also occurred on lawns of Staphylococcus aureus but not on Escherichia coli O157:H7 or Salmonella enterica serovar Typhimurium. Inhibition was not pH associated, but it may have been related to the secretion of a cysteine protease with strong activity, as detected with a synthetic fluorogenic substrate. This diffusible enzyme was secreted from all three P. piscicida strains. Direct overlay of the Pseudoalteromonas colonies with synthetic fluorogenic substrates demonstrated the activity of two aminopeptidase Bs, a trypsin-like serine protease, and enzymes reactive against substrates for cathepsin G-like and caspase 1-like proteases. In seawater cultures, scanning electron microscopy revealed numerous vesicles tethered to the outer surface of P. piscicida and a novel mechanism of direct transfer of these vesicles to V. parahaemolyticus Vesicles digested holes in V. parahaemolyticus cells, while the P. piscicida congregated around the vibrios in a predatory fashion. This transfer of vesicles and vesicle-associated digestion of holes were not observed in other bacteria, suggesting that vesicle binding may be mediated by host-specific receptors. In conclusion, we show two mechanisms by which P. piscicida inhibits and/or kills competing bacteria, involving the secretion of antimicrobial substances and the direct transfer of digestive vesicles to competing bacteria.IMPORTANCEPseudoalteromonas species are widespread in nature and reduce competing microflora by the production of antimicrobial compounds. We isolated three strains of P. piscicida and characterized secreted and cell-associated proteolytic enzymes, which may have antimicrobial properties. We identified a second method by which P. piscicida kills V. parahaemolyticus It involves the direct transfer of apparently lytic vesicles from the surface of the Pseudoalteromonas strains to the surface of Vibrio cells, with subsequent digestion of holes in the Vibrio cell walls. Enzymes associated with these vesicles are likely responsible for the digestion of holes in the cell walls. Pseudoalteromonas piscicida has potential applications in aquaculture and food safety, in control of the formation of biofilms in the environment, and in food processing. These findings may facilitate the probiotic use of P. piscicida to inactivate pathogens and may lead to the isolation of enzymes and other antimicrobial compounds of pharmacological value.

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

BACKGROUND

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.

RESULTS

Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.

CONCLUSIONS

This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.

Microbiome analysis shows enrichment for specific bacteria in separate anatomical regions of the deep-sea carnivorous sponge Chondrocladia grandis

The Cladorhizidae is a unique family of carnivorous marine sponges characterised by either the absence or reduction of the aquiferous system and by the presence of specialised structures to trap and digest mesoplanktonic prey. Previous studies have postulated a key role of host-associated bacteria in enabling carnivory in this family of sponges. In this study, we employed high-throughput Illumina-based sequencing to identify the bacterial community associated with four individuals of the deep-sea sponge Chondrocladia grandis sampled in the Gulf of Maine. By characterising the V6 through V8 region of the 16S rRNA gene, we compared the bacterial community composition and diversity in three distinct anatomical regions with predicted involvement in prey capture (sphere), support (axis) and benthic substrate attachment (root). A high abundance of Tenacibaculum, a known siderophore producing bacterial genus, was present in all anatomical regions and specimens. The abundance of Colwellia and Roseobacter was greater in sphere and axis samples, and bacteria from the hydrocarbon-degrading Robiginitomaculum genus were most abundant in the root. This first description of the bacterial community associated with C. grandis provides novel insights into the contribution of bacteria to the carnivorous lifestyle while laying foundations for future cladorhizid symbiosis studies.

Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems

With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.

Advances in Chromobacterium violaceum and properties of violacein-Its main secondary metabolite: A review

Chromobacterium violaceum is important in the production of violacein, like other bacteria, such as Alteromonas, Janthinobacterium, Pseudoalteromonas, Duganella, Collimonas and Escherichia. Violacein is a versatile pigment, where it exhibits several biological activities, and every year, it shows increasing commercially interesting uses, especially for industrial applications in cosmetics, medicines and fabrics. This review on violacein focuses mainly on the last five years of research regarding this target compound and describes production and importance of quorum sensing in C. violaceum, mechanistic aspects of its biosynthesis, monitoring processes, genetic perspectives, pathogenic effects, antiparasitic and antimicrobial activities, immunomodulatory potential and uses, antitumor potential and industrial applications.

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria

Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.

Six Pseudoalteromonas Strains Isolated from Surface Waters of Kabeltonne, Offshore Helgoland, North Sea

Draft genomes are presented for 6 Pseudoalteromonas sp. strains isolated from surface waters at Kabeltonne, Helgoland, a long-term ecological research station in the North Sea. These strains contribute knowledge of the genomic underpinnings of a developing model system to study phage-host dynamics of a particle-associated ocean copiotroph.

Plankton networks driving carbon export in the oligotrophic ocean

The biological carbon pump is the process by which CO₂ is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterised. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria, alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of just a few bacterial and viral genes can predict most of the variability in carbon export in these regions.

Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms

Biofilms are integral to many marine processes but their formation and function may be affected by anthropogenic inputs that alter environmental conditions, including fertilisers that increase nutrients. Density composition and connectivity of biofilms developed in situ (under ambient and elevated nutrients) were compared using 454-pyrosequencing of the 16S gene. Elevated nutrients shifted community composition from bacteria involved in higher processes (eg Pseudoalteromonas spp. invertebrate recruitment) towards more nutrient-tolerant bacterial species (eg Terendinibacter sp.). This may enable the persistence of biofilm communities by increasing resistance to nutrient inputs. A core biofilm microbiome was identified (predominantly Alteromonadales and Oceanospirillales) and revealed shifts in abundances of core microbes that could indicate enrichment by fertilisers. Fertiliser decreased density and connectivity within biofilms indicating that associations were disrupted perhaps via changes to energetic allocations within the core microbiome. Density composition and connectivity changes suggest nutrients can affect the stability and function of these important marine communities.