Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

Dietary Clostridium autoethanogenum protein has dose-dependent influence on the gut microbiota, immunity, inflammation and disease resistance of abalone Haliotis discus hannai

Clostridium autoethanogenum protein (CAP) is an eco-friendly protein source and has great application potential in aquafeeds. The present study aimed to investigate the effects of dietary CAP inclusion on the anti-oxidation, immunity, inflammation, disease resistance and gut microbiota of abalone Haliotis discus hannai after a 110-day feeding trial. Three isonitrogenous and isolipidic diets were formulated by adding 0 % (control), 4.10 % (CAP4.10) and 16.25 % (CAP16.25) of CAP, respectively. A total of 540 abalones with an initial mean body weight of 22.05 ± 0.19 g were randomly distributed in three groups with three replicates per group and 60 abalones per replicate. Results showed that the activities of superoxide dismutase and glutathione peroxidase in the cell-free hemolymph (CFH) were significantly decreased and the content of malondialdehyde in CFH was significantly increased in the CAP16.25 group. The diet with 4.1 % of CAP significantly increased the activities of lysozyme and acid phosphatase in CFH. The expressions of pro-inflammatory genes such as tumor necrosis factor-α (tnf-α), nuclear factor-κb (nf-κb) and toll-like receptor 4 (tlr4) in digestive gland were downregulated, and the expressions of anti-inflammatory genes such as β-defensin and mytimacin 6 in digestive gland were upregulated in the CAP4.10 group. Dietary CAP inclusion significantly decreased the cumulative mortality of abalone after the challenge test with Vibrio parahaemolyticus for 7 days. Dietary CAP inclusion changed the composition of gut microbiota of abalone. Besides, the balance of the ecological interaction network of bacterial genera in the intestine of abalone was enhanced by dietary CAP. The association analysis showed that two bacterial genera Ruegeria and Bacteroides were closely correlated with the inflammatory genes. In conclusion, the 4.10 % of dietary CAP enhanced the immunity and disease resistance as well as inhibited the inflammation of abalone. The 16.25 % of dietary CAP decreased the anti-oxidative capacity of abalone. The structure of the gut microbiota of abalone changed with dietary CAP levels.

Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones

Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.

Acute Ammonia Causes Pathogenic Dysbiosis of Shrimp Gut Biofilms

Acute ammonia exposure has detrimental effects on shrimp, but the underlying mechanisms remain to be fully explored. In the present study, we investigated the impact of acute ammonia exposure on the gut microbiota of the white shrimp Litopenaeus vannamei and its association with shrimp mortality. Exposure to a lethal concentration of ammonia for 48 h resulted in increased mortality in L. vannamei, with severe damage to the hepatopancreas. Ammonia exposure led to a significant decrease in gut microbial diversity, along with the loss of beneficial bacterial taxa and the proliferation of pathogenic Vibrio strains. A phenotypic analysis revealed a transition from the dominance of aerobic to facultative anaerobic strains due to ammonia exposure. A functional analysis revealed that ammonia exposure led to an enrichment of genes related to biofilm formation, host colonization, and virulence pathogenicity. A species-level analysis and experiments suggest the key role of a Vibrio harveyi strain in causing shrimp disease and specificity under distinct environments. These findings provide new information on the mechanism of shrimp disease under environmental changes.

A Comparative Study on Effects of Three Butyric Acid-Producing Additives on the Growth Performance, Non-specific Immunity, and Intestinal Microbiota of the Sea Cucumber Apostichopus japonicus

The providers of butyric acid, Clostridium butyricum (CB), sodium butyrate (SB), and tributyrin (TB), have been extensively studied as aquafeed additives in recent years. However, no comparative study has been reported on the probiotic effects of CB, SB, and TB as feed additives on sea cucumber (Apostichopus japonicus). A 63-day feeding trial was performed to assess the effects of dietary live cells of C. butyricum (CB group, the basal diet supplemented with 1% CB), sodium butyrate (SB group, the basal diet supplemented with 1% SB), and tributyrin (TB group, the basal diet supplemented with 1% TB) on the growth, non-specific immunity, and intestinal microbiota of A. japonicus with a basal diet group as the control. Results indicated that all three additives considerably increased A. japonicus growth, with dietary CB having the optimal growth-promoting effect. Of the seven non-specific enzyme parameters measured in coelomocytes of A. japonicus (i.e., the activities of phagocytosis, respiratory burst, superoxide dismutase, alkaline phosphatase, acid phosphatase, catalase, and lysozyme), dietary CB, SB, and TB considerably increased the activities of six, five, and six of them, respectively. The immune genes (Aj-p105, Aj-p50, Aj-rel, and Aj-lys) expression in the mid-intestine tissues of A. japonicus was significantly increased by all three additives. The CB group had the highest expression of all four genes. Additionally, the relative expression of Aj-p105, Aj-p50, and Aj-lys genes was significantly up-regulated in the three additive groups after stimulation with inactivated Vibrio splendidus. Dietary CB enhanced the intestinal microbial diversity and richness in A. japonicus while dietary TB decreased them. Meanwhile, dietary CB, SB, and TB significantly enhanced the abundance of Firmicutes, unclassified_f_Rhodobacteraceae, and Proteobacteria, respectively, while dietary CB and SB reduced the abundance of Vibrio. Dietary CB and SB improved the stability of microbial ecosystem in the intestine of A. japonicus. In contrast, dietary TB appeared to have a negative effect on the stability of intestinal microbial ecosystem. All three additives improved the intestinal microbial functions associated with energy production and immunity regulation pathways, which may contribute directly to growth promotion and non-specific immunity enhancement in A. japonicus. Collectively, in terms of enhancing growth and non-specific immunity, as well as improving intestinal microbiota, dietary live cells of C. butyricum exhibited the most effective effects in A. japonicus.

Homogeneous environmental selection mainly determines the denitrifying bacterial community in intensive aquaculture water

Nitrate reduction by napA (encodes periplasmic nitrate reductase) bacteria and nitrous oxide reduction by nosZ (encodes nitrous oxide reductase) bacteria play important roles in nitrogen cycling and removal in intensive aquaculture systems. This study investigated the diversity, dynamics, drivers, and assembly mechanisms of total bacteria as well as napA and nosZ denitrifiers in intensive shrimp aquaculture ponds over a 100-day period. Alpha diversity of the total bacterial community increased significantly over time. In contrast, the alpha diversity of napA and nosZ bacteria remained relatively stable throughout the aquaculture process. The community structure changed markedly across all groups over the culture period. Total nitrogen, phosphate, total phosphorus, and silicate were identified as significant drivers of the denitrifying bacterial communities. Network analysis revealed complex co-occurrence patterns between total, napA, and nosZ bacteria which fluctuated over time. A null model approach showed that, unlike the total community dominated by stochastic factors, napA and nosZ bacteria were primarily governed by deterministic processes. The level of determinism increased with nutrient loading, suggesting the denitrifying community can be manipulated by bioaugmentation. The dominant genus Ruegeria may be a promising candidate for introducing targeted denitrifiers into aquaculture systems to improve nitrogen removal. Overall, this study provides important ecological insights into aerobic and nitrous oxide-reducing denitrifiers in intensive aquaculture, supporting strategies to optimize microbial community structure and function.

Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing

Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.

Peroxiredoxin-4 supplementation modulates the immune response, shapes the intestinal microbiome, and enhances AHPND resistance in Penaeus vannamei

Peroxiredoxin-4 from Penaeus vannamei (LvPrx4) is considered a damage-associated molecular pattern (DAMP) that can activate the expression of immune-related genes through the Toll pathway. We previously demonstrated that the recombinant LvPrx4 (rLvPrx4) can enhance shrimp resistance against Vibrio parahaemolyticus, causing acute hepatopancreatic necrosis disease (VP_AHPND), which causes great production losses in shrimp farming. Herein, we showed that the rLvPrx4 had a thermal tolerance of around 60 °C and that the ionic strength had no noticeable effect on its activity. We discovered that feeding a diet containing rLvPrx4 to shrimp for three weeks increased the expression of the immune-related genes LvPEN4 and LvVago5. Furthermore, pre-treatment with rLvPrx4 feeding could significantly prolong shrimp survival following the VP_AHPND challenge. The shrimp intestinal microbiome was then characterized using PCR amplification of the 16S rRNA gene and Illumina sequencing. Three weeks of rLvPrx4 supplementation altered the bacterial community structure (beta diversity) and revealed the induction of differentially abundant families, including Cryomorphaceae, Flavobacteriaceae, Pirellulaceae, Rhodobacteraceae, and Verrucomicrobiaceae, in the rLvPrx4 group. Metagenomic predictions indicated that some amino acid metabolism pathways, such as arginine and proline metabolism, and genetic information processing were significantly elevated in the rLvPrx4 group compared to the control group. This study is the first to describe the potential use of rLvPrx4 supplementation to enhance shrimp resistance to VP_AHPND and alter the composition of a beneficial bacterial community in shrimp, making rLvPrx4 a promising feed supplement as an alternative to antibiotics for controlling VP_AHPND infection in shrimp aquaculture.

Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture

Background

Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host's health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management.

Methods

In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage.

Results

We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected in the natural seawater. This highlights the great importance of the microbial composition of the lagoon on the rearing water microbiota. Considering the larval stage and larval survival we highlight that several genera: Nautella, Leisingera, Ruegerira, Alconivorax, Marinobacter and Tenacibaculum, could be beneficial for the larval survival and may, in the rearing water, overcome the r-strategist microorganisms and/or putative pathogens. Members of these genera might also act as probiotics for the larvae. Marivita, Aestuariicocccus, HIMB11 and Nioella, appeared to be unfavorable for the larval survival and could be associated with upcoming and occurring larval mortalities. All these specific biomarkers of healthy or unhealthy larvae, could be used as early routine detection proxies in the natural seawater and then during the first days of larval rearing, and might help to manage the rearing water microbiota and to select beneficial microorganisms for the larvae.

Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation

Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.

Mutation-induced infections of phage-plasmids

Phage-plasmids are extra-chromosomal elements that act both as plasmids and as phages, whose eco-evolutionary dynamics remain poorly constrained. Here, we show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in a population of marine Roseobacter. Recurrent loss-of-function mutations in the phage repressor that controls prophage induction leads to constitutively lytic phage-plasmids that spread rapidly throughout the population. The entire phage-plasmid genome is packaged into virions, which were horizontally transferred by re-infecting lysogenized cells, leading to an increase in phage-plasmid copy number and to heterozygosity in a phage repressor locus in re-infected cells. However, the uneven distribution of phage-plasmids after cell division (i.e., segregational drift) leads to the production of offspring carrying only the constitutively lytic phage-plasmid, thus restarting the lysis-reinfection-segregation life cycle. Mathematical models and experiments show that these dynamics lead to a continuous productive infection of the bacterial population, in which lytic and lysogenic phage-plasmids coexist. Furthermore, analyses of marine bacterial genome sequences indicate that the plasmid backbone here can carry different phages and disseminates trans-continentally. Our study highlights how the interplay between phage infection and plasmid genetics provides a unique eco-evolutionary strategy for phage-plasmids.

Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms

Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, we provide evidence that bacteria within various Roseobacter lineages are important for thiosulfate oxidation in marine biofilms. We isolate and sequence the genomes of 54 biofilm-associated Roseobacter strains, finding conserved sox gene clusters for thiosulfate oxidation and plasmids, pointing to a niche-specific lifestyle. Analysis of global ocean metagenomic data suggests that Roseobacter strains are abundant in biofilms and mats on various substrates, including stones, artificial surfaces, plant roots, and hydrothermal vent chimneys. Metatranscriptomic analysis indicates that the majority of active sox genes in biofilms belong to Roseobacter strains. Furthermore, we show that Roseobacter strains can grow and oxidize thiosulfate to sulfate under both aerobic and anaerobic conditions. Transcriptomic and membrane proteomic analyses of biofilms formed by a representative strain indicate that thiosulfate induces sox gene expression and alterations in cell membrane protein composition, and promotes biofilm formation and anaerobic respiration. We propose that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.

The potential to produce tropodithietic acid by Phaeobacter inhibens affects the assembly of microbial biofilm communities in natural seawater

Microbial secondary metabolites play important roles in biotic interactions in microbial communities and yet, we do not understand how these compounds impact the assembly and development of microbial communities. To address the implications of microbial secondary metabolite production on biotic interactions in the assembly of natural seawater microbiomes, we constructed a model system where the assembly of a natural seawater biofilm community was influenced by the addition of the marine biofilm forming Phaeobacter inhibens that can produce the antibiotic secondary metabolite tropodithietic acid (TDA), or a mutant incapable of TDA production. Because of the broad antibiotic activity of TDA, we hypothesized that the potential of P. inhibens to produce TDA would strongly affect both biofilm and planktonic community assembly patterns. We show that 1.9 % of the microbial composition variance across both environments could be attributed to the presence of WT P. inhibens, and especially genera of the Bacteriodetes were increased by the presence of the TDA producer. Moreover, network analysis with inferred putative microbial interactions revealed that P. inhibens mainly displayed strong positive associations with genera of the Flavobacteriaceae and Alteromonadaceae, and that P. inhibens acts as a keystone OTU in the biofilm exclusively due to its potential to produce TDA. Our results demonstrate the potential impact of microbial secondary metabolites on microbial interactions and assembly dynamics of complex microbial communities.

Storage and Algal Association of Bacteria That Protect Microchloropsis salina from Grazing by Brachionus plicatilis

Loss of algal production from the crashes of algal mass cultivation systems represents a significant barrier to the economic production of microalgal-based biofuels. Current strategies for crash prevention can be too costly to apply broadly as prophylaxis. Bacteria are ubiquitous in microalgal mass production cultures, however few studies investigate their role and possible significance in this particular environment. Previously, we demonstrated the success of selected protective bacterial communities to save Microchloropsis salina cultures from grazing by the rotifer Brachionus plicatilis. In the current study, these protective bacterial communities were further characterized by fractionation into rotifer-associated, algal-associated, and free-floating bacterial fractions. Small subunit ribosomal RNA amplicon sequencing was used to identify the bacterial genera present in each of the fractions. Here, we show that Marinobacter, Ruegeria, and Boseongicola in algae and rotifer fractions from rotifer-infected cultures likely play key roles in protecting algae from rotifers. Several other identified taxa likely play lesser roles in protective capability. The identification of bacterial community members demonstrating protective qualities will allow for the rational design of microbial communities grown in stable co-cultures with algal production strains in mass cultivation systems. Such a system would reduce the frequency of culture crashes and represent an essentially zero-cost form of algal crop protection.

Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae

In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites, which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis, S26ΔtdaB. Molecular networking demonstrated that other chemical sulfur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found several changes in the physiology of the TDA-deficient mutant, ΔtdaB, compared to the wild type. Growth of the two strains was similar; however, ΔtdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in gene expression and protein abundance related to a type IV secretion system, and to a prophage, and a gene transfer agent in ΔtdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate adaptation to novel niches. We speculate that once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, while filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms. This points to a role of TDA in coordinating colonization and adaptation. IMPORTANCE Despite the broad clinical usage of microbial secondary metabolites with antibiotic activity, little is known about their role in natural microbiomes. Here, we studied the effect of production of the antibiotic tropodithietic acid (TDA) on the producing strain, Phaeobacter piscinae S26, a member of the Roseobacter group. We show that TDA affects several phenotypes of the producing strain, including motility, cell morphology, metal metabolism, and three horizontal gene transfer systems: a prophage, a type IV secretion system, and a gene transfer agent. Together, this indicates that TDA participates in coordinating the colonization process of the producer. TDA is thus an example of a multifunctional secondary metabolite that can mediate complex interactions in microbial communities. This work broadens our understanding of the ecological role that secondary metabolites have in microbial community dynamics.

The ability of Phaeobacter inhibens to produce tropodithietic acid influences the community dynamics of a microalgal microbiome

Microbial secondary metabolites facilitate microbial interactions and are crucial for understanding the complexity of microbial community dynamics. The purpose of the present study was to determine how a secondary metabolite producing marine bacteria or its metabolite deficient mutant affected the microbiome of the marine microalgae Tetraselmis suecica during a 70 day long co-evolution experiment. Using 16S rRNA gene amplicon sequencing, we found that neither the tropodithietic acid (TDA)-producing Phaeobacter inhibens wildtype nor the TDA-deficient mutant had major impacts on the community composition. However, a subset of strains, displayed temporally different relative abundance trajectories depending on the presence of P. inhibens. In particular, a Winogradskyella strain displayed temporal higher relative abundance when the TDA-producing wildtype was present. Numbers of the TDA-producing wildtype were reduced significantly more than those of the mutant over time indicating that TDA production was not an advantage. In communities without the P. inhibens wildtype strain, an indigenous population of Phaeobacter increased over time, indicating that indigenous Phaeobacter populations cannot co-exist with the TDA-producing wildtype. Despite that TDA was not detected chemically, we detected transcripts of the tdaC gene indicating that TDA could be produced in the microbial community associated with the algae. Our work highlights the importance of deciphering longitudinal strain dynamics when addressing the ecological effect of secondary metabolites in a relevant natural community.

Enhancement of growth, survival, immunity and disease resistance in Litopenaeus vannamei, by the probiotic, Lactobacillus plantarum Ep-M17

Green ecological prevention and control technology is a hot spot for aquatic disease research in recent years, and lactic acid bacteria is an important type of probiotic widely used in aquaculture. In this study, a strain of Lactobacillus plantarum Ep-M17 was isolated from the intestine of healthy grouper, which showed good antibacterial activity in vitro. To investigate the application prospects of Ep-M17 as a probiotic, we added it to the diet and fed Litopenaeus vannamei, and then detected its influence on the growth performance, survival rate, disease resistance, intestinal tissue structure, gene transcription, and the flora in the gut of shrimp. The results showed that feeding Ep-M17 increased the specific growth rate, reduced the feed conversion rate, improved the survival rate, and achieved a 76.9% relative protection rate after Vibrio parahaemolyticus E1 infection in shrimp. Histological examination displayed that Ep-M17-fed shrimp had a thick intestinal villi layer, which enhanced the protection against pathogen damage. It was also found that Ep-M17 significantly increased the activity levels of immune and digestion-related enzymes SOD, CAT, TRY, AKP, LIP, and AMS in the gut of shrimp, especially after V. parahaemolyticus E1 infection, these enzymes increased significantly higher than that of control. Transcriptome analysis revealed that Ep-M17 activated significantly differential expression of genes in immune, nutritional, metabolic, and Signal Transduction-related pathways in the gut of shrimp. In addition, Ep-M17 enriched the bacterial diversity of the shrimp gut, with a significant increase in many low-abundance bacterial species, a significant decrease in the number of pathogenic bacteria like Vibrio, and a significant increase in the number of beneficial bacteria. The above results evaluated that Ep-M17 as a potential probiotic can promote the growth and improve the disease resistance of shrimp by regulating the nutritional immune response and flora of the intestine.

Role is in the eye of the beholder-the multiple functions of the antibacterial compound tropodithietic acid produced by marine Rhodobacteraceae

Many microbial secondary metabolites have been studied for decades primarily because of their antimicrobial properties. However, several of these metabolites also possess nonantimicrobial functions, both influencing the physiology of the producer and their ecological neighbors. An example of a versatile bacterial secondary metabolite with multiple functions is the tropone derivative tropodithietic acid (TDA). TDA is a broad-spectrum antimicrobial compound produced by several members of the Rhodobacteraceae family, a major marine bacterial lineage, within the genera Phaeobacter, Tritonibacter, and Pseudovibrio. The production of TDA is governed by the mode of growth and influenced by the availability of nutrient sources. The antibacterial effect of TDA is caused by disruption of the proton motive force of target microorganisms and, potentially, by its iron-chelating properties. TDA also acts as a signaling molecule, affecting gene expression in other bacteria, and altering phenotypic traits such as motility, biofilm formation, and antibiotic production in the producer. In microbial communities, TDA-producing bacteria cause a reduction of the relative abundance of closely related species and some fast-growing heterotrophic bacteria. Here, we summarize the current understanding of the chemical ecology of TDA, including the environmental niches of TDA-producing bacteria, and the molecular mechanisms governing the function and regulation of TDA.

Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition

Supplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-021-00124-9.

Beyond the ABCs—Discovery of Three New Plasmid Types in Rhodobacterales (RepQ, RepY, RepW)

Copiotrophic marine bacteria of the Roseobacter group (Rhodobacterales, Alphaproteobacteria) are characterized by a multipartite genome organization. We sequenced the genomes of Sulfitobacter indolifex DSM 14862^T and four related plasmid-rich isolates in order to investigate the composition, distribution, and evolution of their extrachromosomal replicons (ECRs). A combination of long-read PacBio and short-read Illumina sequencing was required to establish complete closed genomes that comprised up to twelve ECRs. The ECRs were differentiated in stably evolving chromids and genuine plasmids. Among the chromids, a diagnostic RepABC-8 replicon was detected in four Sulfitobacter species that likely reflects an evolutionary innovation that originated in their common ancestor. Classification of the ECRs showed that the most abundant plasmid system is RepABC, followed by RepA, DnaA-like, and RepB. However, the strains also contained three novel plasmid types that were designated RepQ, RepY, and RepW. We confirmed the functionality of their replicases, investigated the genetic inventory of the mostly cryptic plasmids, and retraced their evolutionary origin. Remarkably, the RepY plasmid of S. pontiacus DSM 110277 is the first high copy-number plasmid discovered in Rhodobacterales.

Prevalence of genetically similar Flavobacterium columnare phages across aquaculture environments reveals a strong potential for pathogen control

Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage‐based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden in 2017. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 227 bacterial isolates (from 2013 to 2017) demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole‐genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential for use in phage therapy.

Cryptic niche differentiation of novel sediment ecotypes of Rugeria pomeroyi correlates with nitrate respiration

Marine intertidal sediments fluctuate in redox conditions and nutrient availability, and they are also known as an important sink of nitrogen mainly through denitrification, yet how denitrifying bacteria adapt to this dynamic habitat remains largely untapped. Here, we investigated novel intertidal benthic ecotypes of the model pelagic marine bacterium Ruegeria pomeroyi DSS-3 with a population genomic approach. While differing by only 1.3% at the 16S rRNA gene level, members of the intertidal benthic ecotypes are complete denitrifiers whereas the pelagic ecotype representative (DSS-3) is a partial denitrifier lacking a nitrate reductase. The intertidal benthic ecotypes are further differentiated by using non-homologous nitrate reductases and a different set of genes that allow alleviating oxidative stress and acquiring organic substrates. In the presence of nitrate, the two ecotypes showed contrasting growth patterns under initial oxygen concentrations at 1 vol% versus 7 vol% and supplemented with different carbon sources abundant in intertidal sediments. Collectively, this combination of evidence indicates that there are cryptic niches in coastal intertidal sediments that support divergent evolution of denitrifying bacteria. This knowledge will in turn help understand how these benthic environments operate to effectively remove nitrogen.

Specific Detection of Coral-Associated Ruegeria, a Potential Probiotic Bacterium, in Corals and Subtropical Seawater

Coral microbial flora has been attracting attention because of their potential to protect corals from environmental stresses or pathogens. Although coral-associated bacteria are considered to be acquired from seawater, little is known about the relationships between microbial composition in corals and its surrounding seawater. Here, we tested several methods to identify coral-associated bacteria in coral and its surrounding seawater to detect specific types of Ruegeria species, some of which exhibit growth inhibition activities against the coral pathogen Vibrio coralliilyticus. We first isolated coral-associated bacteria from the reef-building coral Galaxea fascicularis collected at Sesoko Island, Okinawa, Japan, via random colony picking, which showed the existence of varieties of bacteria including Ruegeria species. Using newly constructed primers for colony PCR, several Ruegeria species were successfully isolated from G. fascicularis and seawater. We further investigated the seawater microbiome in association with the distance from coral reefs. By seasonal sampling, it was suggested that the seawater microbiome is more affected by seasonality than the distance from coral reefs. These methods and results may contribute to investigating and understanding the relationships between the presence of corals and microbial diversity in seawater, in addition to the efficient isolation of specific bacterial species from coral or its surrounding seawater.

The Roseobacter-Group Bacterium Phaeobacter as a Safe Probiotic Solution for Aquaculture

Phaeobacter inhibens has been assessed as a probiotic bacterium for application in aquaculture. Studies addressing the efficacy and safety indicate that P. inhibens maintains its antagonistic activity against pathogenic vibrios in aquaculture live cultures (live feed and fish egg/larvae) while having no or a positive effect on the host organisms and a minor impact on the host microbiomes. While P. inhibens produces antibacterial and algicidal compounds, no study has so far found a virulent phenotype of P. inhibens cells against higher organisms. Additionally, an in silico search for antibiotic resistance genes using published genomes of representative strains did not raise concerns regarding the risk for antimicrobial resistance. P. inhibens occurs naturally in aquaculture systems, supporting its safe usage in this environment. In conclusion, at the current state of knowledge, P. inhibens is a "safe-to-use" organism.

The Native Microbiome is Crucial for Offspring Generation and Fitness of Aurelia aurita

All multicellular organisms are associated with a diverse and specific community of microorganisms; consequently, the microbiome is of fundamental importance for health and fitness of the multicellular host. However, studies on microbiome contribution to host fitness are in their infancy, in particular, for less well-established hosts such as the moon jellyfish Aurelia aurita. Here, we studied the impact of the native microbiome on the asexual reproduction and on further fitness traits (health, growth, and feeding) of the basal metazoan due to induced changes in its microbiome. We observed significant impact on all fitness traits analyzed, in particular, in the absence of the protective microbial shield and when challenged with marine potentially pathogenic bacterial isolates. Notable is the identified crucial importance of the native microbiome for the generation of offspring, consequently affecting life cycle decisions. Thus, we conclude that the microbiome is essential for the maintenance of a healthy metaorganism.

All multicellular organisms are associated with microbial communities, ultimately forming a metaorganism. Several studies conducted on well-established model organisms point to immunological, metabolic, and behavioral benefits of the associated microbiota for the host. Consequently, a microbiome can influence the physiology of a host; moreover, microbial community shifts can affect host health and fitness. The present study aimed to evaluate the significance and functional role of the native microbiota for life cycle transitions and fitness of the cnidarian moon jellyfish Aurelia aurita. A comprehensive host fitness experiment was conducted studying the polyp life stage and integrating 12 combinations of treatments with microbiota modification (sterile conditions, foreign food bacteria, and potential pathogens). Asexual reproduction, e.g., generation of daughter polyps, and the formation and release of ephyrae were highly affected in the absence of the native microbiota, ultimately resulting in a halt of strobilation and ephyra release. Assessment of further fitness traits showed that health, growth, and feeding rate were decreased in the absence and upon community changes of the native microbiota, e.g., when challenged with selected bacteria. Moreover, changes in microbial community patterns were detected by 16S rRNA amplicon sequencing during the course of the experiment. This demonstrated that six operational taxonomic units (OTUs) significantly correlated and explained up to 97% of fitness data variability, strongly supporting the association of impaired fitness with the absence/presence of specific bacteria. Conclusively, our study provides new insights into the importance and function of the microbiome for asexual reproduction, health, and fitness of the basal metazoan A. aurita.

Individual and combined toxicogenetic effects of microplastics and heavy metals (Cd, Pb, and Zn) perturb gut microbiota homeostasis and gonadal development in marine medaka (Oryzias melastigma)

Currently, microplastics (MPs) attracted increased attention for their ubiquity and toxic properties. In this study, marine medaka was used to explore the individual and combined toxicity of heavy metals (HMs) and MPs on intestinal bacteria and gonadal development. After exposure to environmentally relevant concentrations of MPs and HMs, significant alterations of intestinal microbiota were found. The MPs treatment reduced the diversity and abundance of intestinal microbiota, while the HMs and MPs-HMs treatments increased them, which were confirmed by the abundance changes of Proteobacteria. According to the KEGG analysis, the metabolism and environmental information processing (EIP) pathways in the microbial community were significantly affected. This study showed that the MPs-HMs treatment caused a higher pollution load on the gut of the marine medaka, and triggered more significant changes of specific bacterial species and gut function in the males. However, during the gonadal development, HMs and MPs-HMs treatments resulted in empty follicles (EF) and follicular atresia (FA), and altered the gene expression levels related to hypothalamic-pituitary-gonadal (HPG) axis. In short, this study demonstrated that the reproductive disturbance was mainly due to HMs, but the combination of MPs and HMs did not strengthen the risk to the gonad development of the marine medaka.

Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage

Ecologically relevant genes generally show patchy distributions among related bacterial genomes. This is commonly attributed to lateral gene transfer, whereas the opposite mechanism-gene loss-has rarely been explored. Pseudogenization is a major mechanism underlying gene loss, and pseudogenes are best characterized by comparing closely related genomes because of their short life spans. To explore the role of pseudogenization in microbial ecological diversification, we apply rigorous methods to characterize pseudogenes in the 279 newly sequenced Ruegeria isolates of the globally abundant Roseobacter group collected from two typical coastal habitats in Hong Kong, the coral Platygyra acuta and the macroalga Sargassum hemiphyllum. Pseudogenes contribute to ~16% of the accessory genomes of these strains. Ancestral state reconstruction reveals that many pseudogenization events are correlated with ancestral niche shifts. Specifically, genes related to resource scavenging and energy acquisition were often pseudogenized when roseobacters inhabiting carbon-limited and energy-poor coral skeleton switched to other resource-richer niches. For roseobacters inhabiting the macroalgal niches, genes for nitrogen regulation and carbohydrate utilization were important but became dispensable upon shift to coral skeleton where nitrate is abundant but carbohydrates are less available. Whereas low-energy-demanding secondary transporters are more favorable in coral skeleton, ATP-driven primary transporters are preferentially kept in the energy-replete macroalgal niches. Moreover, a large proportion of these families mediate organismal interactions, suggesting their rapid losses by pseudogenization as a potential response to host and niche shift. These findings illustrate an important role of pseudogenization in shaping genome content and driving ecological diversification of marine roseobacters.

Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites

A drop of seawater contains numerous microspatial niches at the scale relevant to microbial activities. Examples are abiotic niches such as detrital particles that show different sizes and organic contents, and biotic niches resulting from bacteria-phage and bacteria-phytoplankton interactions. A common practice to investigate the impact of microenvironments on bacterial evolution is to separate the microenvironments physically and compare the bacterial inhabitants from each. It remains poorly understood, however, which microenvironment primarily drives bacterioplankton evolution in the pelagic ocean. By applying a dilution cultivation approach to an undisturbed coastal water sample, we isolate a bacterial population affiliated with the globally dominant Roseobacter group. Although varying at just a few thousand nucleotide sites across the whole genomes, members of this clonal population are diverging into two genetically separated subspecies. Genes underlying speciation are not unique to subspecies but instead clustered at the shared regions that represent ~6% of the genomic DNA. They are primarily involved in vitamin synthesis, motility, oxidative defense, carbohydrate, and amino acid utilization, consistent with the known strategies that roseobacters take to interact with phytoplankton and particles. Physiological assays corroborate that one subspecies outcompetes the other in these traits. Our results indicate that the microenvironments in the pelagic ocean represented by phytoplankton and organic particles are likely important niches that drive the cryptic speciation of the Roseobacter population, though microhabitats contributed by other less abundant pelagic hosts cannot be ruled out.

Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses

Heterotrophic bacteria such as those from the Roseobacter group and genus Alteromonas dominate the hadal zones of oceans; however, we know little about the genomic characteristics and potential metabolic adaptations of hadal trench-dwelling bacteria. Here, we report multiple single amplified genomes (SAGs) belonging to Roseobacter and Alteromonas, recovered from the hadal zone of the Mariana Trench. While phylogenetic analyses show that these hadal SAGs cluster with their surface relatives, an analysis of genomic recruitment indicates that they have higher relative abundances in the hadal zone of the Mariana Trench. Comparative genomic analyses between the hadal SAGs and reference genomes of closely related shallow-water relatives indicate that genes involved in the mobilome (prophages and transposons) are overrepresented among the unique genes of the hadal Roseobacter and Alteromonas SAGs; the functional proteins encoded by this category of genes also shows higher amino acid sequence variation than those encoded by other gene sets within the Roseobacter SAGs. We also found that genes involved in cell wall/membrane/envelope biogenesis, transcriptional regulation, and metal transport may be important for the adaptation of hadal Roseobacter and Alteromonas lineages. These results imply that the modification of cell surface-related proteins and transporters is the major direction of genomic evolution in Roseobacter and Alteromonas bacteria adapting to the hadal environment, and that prophages and transposons may be the key factors driving this process.

Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi

The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health, and homeostasis. Cooperative and competitive interactions between bacteria, due to release of, for example, antibacterial substances and quorum sensing (QS)/quorum quenching (QQ) molecules, ultimately affect the establishment and dynamics of the associated microbial community. Aiming to address interspecies competition of cultivable microbes associated with emerging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi), we performed a classical isolation approach. Overall, 84 bacteria were isolated from A. aurita medusae and polyps, 64 bacteria from M. leidyi, and 83 bacteria from ambient seawater, followed by taxonomically classification by 16S rRNA gene analysis. The results show that A. aurita and M. leidyi harbor a cultivable core microbiome consisting of typical marine ubiquitous bacteria also found in the ambient seawater. However, several bacteria were restricted to one host suggesting host‐specific microbial community patterns. Interbacterial interactions were assessed by (a) a growth inhibition assay and (b) QS interference screening assay. Out of 231 isolates, 4 bacterial isolates inhibited growth of 17 isolates on agar plates. Moreover, 121 of the 231 isolates showed QS‐interfering activities. They interfered with the acyl‐homoserine lactone (AHL)‐based communication, of which 21 showed simultaneous interference with autoinducer 2. Overall, this study provides insights into the cultivable part of the microbiota associated with two environmentally important marine non‐model organisms and into interbacterial interactions, which are most likely considerably involved in shaping a healthy and resilient microbiota.

Osmotic stress induces gut microbiota community shift in fish

Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.

Fine-scale succession patterns and assembly mechanisms of bacterial community of Litopenaeus vannamei larvae across the developmental cycle

BACKGROUND

Microbiome assembly in early life may have a long-term impact on host health. Larval nursery is a crucial period that determines the success in culture of Litopenaeus vannamei, the most productive shrimp species in world aquaculture industry. However, the succession patterns and assembly mechanisms of larval shrimp bacterial community still lack characterization at a fine temporal scale. Here, using a high-frequency sampling strategy and 16S rRNA gene amplicon sequencing, we investigated dynamics of larval shrimp bacterial community and its relationship with bacterioplankton in the rearing water across the whole developmental cycle in a realistic aquaculture practice.

RESULTS

Alpha-diversity of larval shrimp bacteria showed a U-shaped pattern across the developmental cycle with the stages zoea and mysis as the valley. Correspondingly, the compositions of dominant bacterial taxa at the stages nauplius and early postlarvae were more complex than other stages. Remarkably, Rhodobacteraceae maintained the overwhelming dominance after the mouth opening of larvae (zoea I~early postlarvae). The taxonomic and phylogenetic compositions of larval bacterial community both showed stage-dependent patterns with higher rate of taxonomic turnover, suggesting that taxonomic turnover was mainly driven by temporal switching among closely related taxa (such as Rhodobacteraceae taxa). The assembly of larval bacteria was overall governed by neutral processes (dispersal among individuals and ecological drift) at all the stages, but bacterioplankton also had certain contribution during three sub-stages of zoea, when larval and water bacterial communities were most associated. Furthermore, the positive host selection for Rhodobacteraceae taxa from the rearing water during the zoea stage and its persistent dominance and large predicted contribution to metabolic potentials of organic matters at post-mouth opening stages suggest a crucial role of this family in larval microbiome and thus a potential source of probiotic candidates for shrimp larval nursery.

CONCLUSIONS

Our results reveal pronounced succession patterns and dynamic assembly processes of larval shrimp bacterial communities during the developmental cycle, highlighting the importance of the mouth opening stage from the perspective of microbial ecology. We also suggest the possibility and potential timing in microbial management of the rearing water for achieving the beneficial larval microbiota in the nursery practice. Video Abstract.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

Effects of Carbon/Nitrogen Ratio on Growth, Intestinal Microbiota and Metabolome of Shrimp (Litopenaeus vannamei)

Increasing the C/N ratio of input feed has been reported as a practical approach for improving water quality and enhancing shrimp growth through changing the bacterial community of rearing water. However, little is known about the effects of different C/N ratios of feed input on the intestinal microbiota and metabolome of shrimp. In the present study, the effects of three different C/N ratio levels (CN6, CN10, and CN15) maintained by adding sucrose on the growth, intestinal microbiota and metabolome of Litopenaeus vannamei, and bioflocs formation were investigated after 17 days of feeding. The results indicated that higher C/N ratio (10 and 15), especially CN15, of feed input significantly enhance the length and weight of shrimp individuals accompanied by a significant accumulation of bioflocs, compared to that of CN6. The increase of C/N ratio input decreased the α-diversity of the intestinal microbiota and changed the microbial community structure through increasing the relative abundance of Actinobacteria, Rhodobacteraceae (mainly consist of Roseobacter and Paracoccus groups), Alteromonadaceae, and inhibiting the growth of Cyanobacteria, certain Rhodobacteraceae, Mycoplasmataceae and Vibrio. The change of microbial community caused by increasing C/N ratio input was closely associated with various bioactive metabolites of flavonoids, benzenoids, prenol lipids, and indole derivatives, which are benefit for shrimp growth either as an antimicrobial agent or as a nutrient component. Overall, this study demonstrated that manipulating high C/N ratio of feed input helps to the growth of shrimp through increasing the relative abundance of potential beneficial bacteria and the accumulation of various bioactive metabolites to suppress the growth of detrimental bacteria.

The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis

In order to supply human demand for food, the aquaculture industry has been growing fast in the last years, being fish usually cultivated in overcrowded conditions. Hence, to prevent the rapidly disease spreading, antibiotics may be applied to both sick and healthy animals. Due to its broad spectrum, oxytetracycline (OTC) is one of the most used antibiotics in food-production. Yet, although useful to prevent infections, antibiotics may reshape aquatic animals' microbiome, disturbing hosts' welfare. However, the impact of this exposure to the organism microbiome and its surrounding environment is poorly understood. Then, the objective of this study was to analyze in detail the long-term effect of OTC in both zebrafish gut and water microbiomes. Zebrafish adults were exposed, via water, for two months to three concentrations of OTC (0, 10 and 10000 μg/L). Total DNA was extracted from gut and water samples and the V3-V4 region of the bacterial 16 S rRNA gene was sequenced using Illumina technology. Results of alpha and beta-diversity analyses revealed that long-term exposure to OTC impacted both zebrafish gut and water microbiomes. In water samples, effects were observed even at the lowest (10 μg/L) OTC concentration tested resulting in an increase in Deltaproteobacteria, namely the Myxococcales and Bdellovibrionales orders. On the other hand, effects on zebrafish gut were only observed at the highest concentration with the selection of Alphaproteobacteria and Actinobacteria classes. Although these classes are common in fish gut, the increase of Actinobacteria may represent a health problem since some genera like Gordonia are linked to some human infection disease. Nevertheless, in both gut and water, it was observed a decrease in Gamaproteobacteria, probably due to OTC mode of action. In silico functional metagenomic analysis revealed that OTC exposure selected general detoxification mechanisms. In addition, the abundance of functional genes involved in Quorum Sensing (QS) increased under OTC exposure suggesting that QS may help bacteria to survive OTC stress. Thus, future studies should consider post-exposure scenarios for a deeper analysis of the water and zebrafish gut resistome, since bacteria may react differently after exposure ceased.

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.

Tropodithietic acid induces oxidative stress response, cell envelope biogenesis and iron uptake in Vibrio vulnificus

The Roseobacter group is a widespread marine bacterial group, of which some species produce the broad-spectrum antibiotic tropodithietic acid (TDA). A mode of action for TDA has previously been proposed in Escherichia coli, but little is known about its effect on non-producing marine bacteria at in situ concentrations. The purpose of this study was to investigate how a sub-lethal level of TDA affects Vibrio vulnificus at different time points (30 and 60 min) using a transcriptomic approach. Exposure to TDA for as little as 30 min resulted in the differential expression of genes associated with cell regeneration, including the up-regulation of those involved in biogenesis of the cell envelope. Defence mechanisms including oxidative stress defence proteins and iron uptake systems were also up-regulated in response to TDA, while motility-related genes were down-regulated. Gene expression data and scanning electron microscopy imaging revealed a switch to a biofilm phenotype in the presence of TDA. Our study shows that a low concentration of this antibiotic triggers a defence response to reactive oxygen species and iron depletion in V. vulnificus, which indicates that the mode of action of TDA is likely more complex in this bacterium than what is known for E. coli.

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments

BACKGROUND

Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS

Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS

Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities

Bacteria-host interactions are universal in nature and have significant effects on host functionality. Bacterial secondary metabolites are believed to play key roles in such interactions as well as in interactions within the host-associated microbial community. Hence, prominent secondary metabolite-producing bacteria may be strong drivers of microbial community composition in natural host-associated microbiomes. This has, however, not been rigorously tested, and the purpose of this study was to investigate how the secondary metabolite producer Phaeobacter inhibens affects the diversity and composition of microbiomes associated with the microalga Emiliania huxleyi and the European flat oyster, Ostrea edulis. Roseobacters were indigenous to both communities exhibiting relative abundances between 2.8% and 7.0%. Addition of P. inhibens caused substantial changes in the overall structure of the low-complexity microbiome of E. huxleyi, but did not shape microbial community structure to the same degree in the more complex oyster microbiomes. Species-specific interactions occurred in both microbiomes and specifically the abundances of other putative secondary metabolite-producers such as vibrios and pseudoalteromonads were reduced. Thus, the impact of a bioactive strain like P. inhibens on host-associated microbiomes depends on the complexity and composition of the existing microbiome.

Polyurethane, epoxy resin and polydimethylsiloxane altered biofilm formation and mussel settlement

In many environments, biofilms are a major mode and an emergent form of microbial life. Biofilms play crucial roles in biogeochemical cycling and invertebrate recruitment in marine environments. However, relatively little is known about how marine biofilms form on different substrata and about how these biofilms impact invertebrate recruitment. Here, we performed a comparative analysis of a 28-day-old biofilm community on non-coated (a control glass) and coated substrata (polyurethane (PU), epoxy resin (EP) and polydimethylsiloxane (PDMS)) and examined the settlement of Mytilus coruscus plantigrades on these biofilms. PU, EP and PDMS deterred the development of marine biofilms by reducing the biofilm biomass including the biofilm dry weight, cell density of the bacteria and diatoms and chlorophyll a concentrations. Further analysis of bacterial community revealed that EP altered the bacterial community composition compared with that on the glass substrata by reducing the relative abundance of Ruegeria (Alphaproteobacteria) and by increasing the relative abundance of Methylotenera (Betaproteobacteria) and Cyanobacteria in the biofilms. However, bacterial communities developed on PU and PDMS, as well as glass and PU, EP and PDMS did not exhibit differences from each other. The M. coruscus settlement rates on biofilms on PU, EP and PDMS were reduced by 20-41% compared with those on the glass after 28 days. Thus, the tested coatings impacted the development of marine biofilms by altering the biofilm biomass and/or the bacterial community composition. The mussel settlements decreased in the biofilms that formed on the coatings compared with those on non-coated glass.

Understanding the roles of surface proteins in regulation of Lactobacillus pentosus HC-2 to immune response and bacterial diversity in midgut of Litopenaeus vannamei

The interactions of microbiota in the intestines play an important role in promoting or maintaining the health of hosts. The present study aim to investigate the effects of the surface proteins of Lactobacillus pentosus HC-2 on the immune response and the bacterial composition of Litopenaeus vannamei, thus, the immune-related genes, surface condition, HC-2 numbers and the bacteria diversity in midgut were explored after shrimp feeding the normal HC-2 and 5 M -  lithium chloride (LiCl) treated HC-2 for four weeks. Obvious improvements in the intestinal surface were observed in R group than the control group and L group. qPCR analysis demonstrated that the selected immune-related genes of lysozyme, proPO, LGBP, PEN-3α, crustin, and lvLec were significantly up-regulated in group R than in group L. Meanwhile, in the challenge test, shrimp in R group received 72% relative percent survival, which was significantly higher than the L group (RPS = 9%). The bacteria composition analysis showed that the abundance of Proteobacteria were significantly higher in group R and L than in group C, and the Bacteroidetes were significantly higher in group C than in group R and L, whereas the numbers of Chloroflexi were significantly higher in group R than in group C and L. The bacterial community difference analysis revealed that the harmful bacteria such as genus of Vibrio, Tenacibaculu and Thalassobius were decreased and the beneficial bacterium as Ruegeria and Lactobacillus were increased in R group, whereas this phenomenon were not found in L group. Taken together, above results indicating that the surface proteins were indispensable for L. pentosus HC-2 adhesion and colonization in shrimp intestines to improve intestine condition, enhance immune response, competitively exclude the pathogens, and promote the beneficial bacteria growth to protect the shrimp from pathogens infection. The findings in this work will help to promote the understanding of the roles of probiotics in shrimp intestines displaying probiotic-function by regulating the intestinal bacteria.

Potential role of host-derived quorum quenching in modulating bacterial colonization in the moon jellyfish Aurelia aurita

Multicellular organisms can be regarded as metaorganisms, comprising of a macroscopic host interacting with associated microorganisms. Within this alliance, the host has to ensure attracting beneficial bacteria and defending against pathogens to establish and maintain a healthy homeostasis. Here, we obtained several lines of evidence arguing that Aurelia aurita uses interference with bacterial quorum sensing (QS) - quorum quenching (QQ) - as one host defense mechanism. Three A. aurita-derived proteins interfering with bacterial QS were identified by functionally screening a metagenomic library constructed from medusa-derived mucus. Native expression patterns of these host open reading frames (ORFs) differed in the diverse life stages (associated with different microbiota) pointing to a specific role in establishing the developmental stage-specific microbiota. Highly increased expression of all QQ-ORFs in germ-free animals further indicates their impact on the microbiota. Moreover, incubation of native animals with pathogenic bacteria induced expression of the identified QQ-ORFs arguing for a host defense strategy against confronting bacteria by interference with bacterial QS. In agreement, immobilized recombinant QQ proteins induced restructuring of polyp-associated microbiota through changing abundance and operational taxonomic unit composition. Thus, we hypothesize that additional to the immune system host-derived QQ-activities potentially control bacterial colonization.

Quorum Sensing System of Ruegeria mobilis Rm01 Controls Lipase and Biofilm Formation

Quorum sensing (QS) promotes in situ extracellular enzyme (EE) activity via the exogenous signal N-acylhomoserine lactone (AHL), which facilitates marine particle degradation, but the species that engage in this regulatory mechanism remain unclear. Here, we obtained AHL-producing and AHL-degrading strains from marine particles. The strain Ruegeria mobilis Rm01 of the Roseobacter group (RBG), which was capable of both AHL producing and degrading, was chosen to represent these strains. We demonstrated that Rm01 possessed a complex QS network comprising AHL-based QS and quorum quenching (QQ) systems and autoinducer-2 (AI-2) perception system. Rm01 was able to respond to multiple exogenous QS signals through the QS network. By applying self-generated AHLs and non-self-generated AHLs and AI-2 QS signal molecules, we modulated biofilm formation and lipase production in Rm01, which reflected the coordination of bacterial metabolism with that of other species via eavesdropping on exogenous QS signals. These results suggest that R. mobilis might be one of the participators that could regulate EE activities by responding to QS signals in marine particles.

Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean

Epibacterium mobile BBCC367 is a marine bacterium that is common in coastal areas. It belongs to the Roseobacter clade, a widespread group in pelagic marine ecosystems. Species of the Roseobacter clade are regularly used as models to understand the evolution and physiological adaptability of generalist bacteria. E. mobile BBCC367 comprises two chromosomes and two plasmids. We used gel-free shotgun proteomics to assess its protein expression under 16 different conditions, including stress factors such as elevated temperature, nutrient limitation, high metal concentration, and UVB exposure. Comparison of the different conditions allowed us not only to retrieve almost 70% of the predicted proteins, but also to define three main protein assemblages: 584 essential core proteins, 2,144 facultative accessory proteins and 355 specific unique proteins. While the core proteome mainly exhibited proteins involved in essential functions to sustain life such as DNA, amino acids, carbohydrates, cofactors, vitamins and lipids metabolisms, the accessory and unique proteomes revealed a more specific adaptation with the expression of stress-related proteins, such as DNA repair proteins (accessory proteome), transcription regulators and a significant predominance of transporters (unique proteome). Our study provides insights into how E. mobile BBCC367 adapts to environmental changes and copes with diverse stresses.

Characterization of a Novel N-Acylhomoserine Lactonase RmmL from Ruegeria mobilis YJ3

Gram-negative bacteria utilize N-acylhomoserine lactones (AHLs) as quorum sensing (QS) signaling molecules for intercellular communication. Cell-to-cell communication depends on cell population density, and AHL-dependent QS is related to the production of multiple genes including virulence factors. Quorum quenching (QQ), signal inactivation by enzymatic degradation, is a potential strategy for attenuating QS regulated bacterial infections. Both Gram-positive and -negative bacteria have QQ enzymes that can degrade AHLs. In our previous study, strain Ruegeria mobilis YJ3, isolated from healthy shrimp, showed strong AHLs degradative activity. In the current study, an AHL lactonase (designated RmmL) was cloned and characterized from Ruegeria mobilis YJ3. Amino acid sequence analysis showed that RmmL has a conserved “HXHXDH” motif and clusters together with lactonase AidC that belongs to the metallo-β-lactamase superfamily. Recombinant RmmL could degrade either short- or long-chain AHLs in vitro. High-performance liquid chromatography analysis indicated that RmmL works as an AHL lactonase catalyzing AHL ring-opening by hydrolyzing lactones. Furthermore, RmmL can reduce the production of pyocyanin by Pseudomonas aeruginosa PAO1, while for the violacein and the extracellular protease activities by Chromobacterium violaceum CV026 and Vibrio anguillarum VIB72, no significant reduction was observed. This study suggests that RmmL might be used as a therapeutic agent in aquaculture.

Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae

The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.

Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model

An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model. The model simulates 2 × 10⁸ cells, which allows random genetic drift to act in a realistic manner. Each cell has a whole genome subject to base-substitution mutation and recombination, which affect the carbon and nitrogen requirements of DNA and protein pools. Nonsynonymous changes can be functionally deleterious. Together, these factors affect the growth and fitness. Simulations show that experimentally determined mutation bias toward GC is not sufficient to build the GC-rich genome of DSS-3. While nitrogen availability has been repeatedly hypothesized to drive the evolution of GC content in marine bacterioplankton, our model instead predicts that DSS-3 and its ancestors have been evolving in environments primarily limited by carbon.

Characterisation of the l-Cystine β-Lyase PatB from Phaeobacter inhibens: An Enzyme Involved in the Biosynthesis of the Marine Antibiotic Tropodithietic Acid

The l-cystine β-lyase from Phaeobacter inhibens is involved in the biosynthesis of the sulfur-containing antibiotic tropodithietic acid. The recombinant enzyme was obtained by heterologous expression in Escherichia coli and biochemically characterised by unambiguous chemical identification of the products formed from the substrate l-cystine, investigation of the substrate spectrum, determination of the enzyme kinetics, sequence alignment with closely related homologues and site-directed mutagenesis to identify a highly conserved lysine residue that is critical for functionality. PatB from P. inhibens is a new member of the small group of characterised l-cystine β-lyases and the first example of an enzyme with such an activity that is required for the biosynthesis of an antibiotic. A comparison of PatB to previously reported enzymes with l-cystine β-lyase activity from bacteria and plants is given.

Phaeobacter piscinae sp. nov., a species of the Roseobacter group and potential aquaculture probiont

Four heterotrophic, antimicrobial, motile, marine bacterial strains, 27-4^T, 8-1, M6-4.2 and S26, were isolated from aquaculture units in Spain, Denmark and Greece. All four strains produced the antibiotic compound tropodithietic acid, which is a key molecule in their antagonism against fish pathogenic bacteria. Cells of the strains were Gram-reaction-negative, rod-shaped and formed star-shaped aggregates in liquid culture and brown-coloured colonies on marine agar. The predominant cellular fatty acids were C18 : 1ω7c, C16 : 0, C11 methyl C18 : 1ω7c and C16 : 0 2-OH, and the polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an aminolipid, a phospholipid and an unidentified lipid. The strains grew optimally at 31-33 °C. Growth was observed at a salt concentration between 0.5 and 5-6 % NaCl with an optimum at 2-3 %. The pH range for growth of the strains was from pH 6 to 8-8.5 with an optimum at pH 7. Based on 16S rRNA gene sequence analysis, the strains are affiliated with the genus Phaeobacter. The genome sequences of the strains have a DNA G+C content of 60.1 % and share an average nucleotide identity (ANI) of more than 95 %. The four strains are distinct from the type strains of the closely related species Phaeobactergallaeciensis and Phaeobacterinhibens based on an ANI of 90.5-91.7 and 89.6-90.4 %, respectively, and an in silico DNA-DNA hybridization relatedness of 43.9-46.9 and 39.8-41.9 %, respectively. On the basis of phylogenetic analyses as well as phenotypic and chemotaxonomic properties, the isolates are considered to represent a novel species, for which the name Phaeobacter piscinae sp. nov. is proposed. The type strain is 27-4^T (=DSM 103509^T=LMG 29708^T).