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The origin of microbial mercury methylation has long been a mystery. Here we employed genome-resolved phylogenetic analyses to decipher the evolution of the mercury methylating gene,hgcAB, constrain the ancestral origin of thehgcoperon, and explain the distribution ofhgcin Bacteria and Archaea. We infer the extent to which vertical inheritance and horizontal gene transfer have influenced the evolution of mercury methylators and hypothesize that evolution of this trait bestowed the ability to produce an antimicrobial compound (MeHg+) on a potentially resource-limited early Earth. We speculate that, in response, the evolution of MeHg+-detoxifying alkylmercury lyase (encoded bymerB) reduced a selective advantage for mercury methylators and resulted in widespread loss ofhgcin Bacteria and Archaea.SignificanceNeurotoxic methylmercury (MeHg+(aq)) is synthesized from HgII(aq)in the environment by microorganisms possessing the gene pairhgcAB. Our phylogenetic analyses elucidate the origin and evolution of thehgcoperon, and support a hypothesis that mercury methylation evolved as an antimicrobial production mechanism, possibly from competition for limited resources on the early Earth. We infer from our analyses thathgchas been primarily vertically inherited in Bacteria and Archaea, with extensive parallel loss, and note that few taxa possessinghgcalso possess the gene encoding for MeHg+demethylation,merB. Our findings support the interpretation thatmerBevolved as a defense mechanism against the evolution of microbial HgII(aq)methylation.

15 pages, 4 figures, 3 tables, supporting Information https://doi.org/10.1111/1755-0998.13687.-- Data availability statement: All metagenomes analysed in this study are in the public domain as described in Table 2, Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes, This work was funded by the Severo Ochoa Excellence Programme postdoctoral fellowship awarded in 2021 to Eric Capo (CEX2019-000928-S), the Swedish Research Council Formas (grant 2018-01031), the EMFF-Blue Economy project MER-CLUB (grant 863584). [...]. Benjamin Peterson was funded as a postdoctoral research associate by the National Science Foundation (award 1935173) during the work in this manuscript.[...]. Oak Ridge National Laboratory is managed by UT-Battelle, LLC under contract no. DE-AC05-00OR22725 with the U.S. Department of Energy (DOE)

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin that accumulates in terrestrial and marine food webs, with potential impacts on human health. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet, British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicts that Marinimicrobia HgcAB proteins contain the highly conserved amino acid sites and folding structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognized.

Marine flavobacteria are specialists for polysaccharide degradation. They dominate in habitats enriched with polysaccharides, but are also prevalent in pelagic environments where polysaccharides are less available. These niches are likely occupied by distinct lineages, but evolutionary processes underlying their niche differentiation remain elusive. Here, genomic analyses and physiological assays indicate that the sister flavobacteria lineages Leeuwenhoekiella and Nonlabens likely explore polysaccharide-rich macroalgae and polysaccharide-poor pelagic niches respectively. Phylogenomic analyses inferred that the niche separation likely occurred anciently and coincided with increased sequence evolutionary rate in Nonlabens compared with Leeuwenhoekiella. Further analyses ruled out the known mechanisms likely driving evolutionary rate acceleration, including reduced selection efficiency, decreased generation time and increased mutation rate. In particular, the mutation rates were determined using an unbiased experimental method, which measures the present-day populations and may not reflect ancestral populations. These data collectively lead to a new hypothesis that an ancestral and transient mutation rate increase resulted in evolutionary rate increase in Nonlabens. This hypothesis was supported by inferring that gains and losses of genes involved in SOS response, a mechanism known to drive transiently increased mutation rate, coincided with evolutionary rate acceleration. Our analyses highlight the evolutionary mechanisms underlying niche differentiation of flavobacteria lineages.

Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn − Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO2, in which microorganisms may play important roles, is followed by agglomeration of MnO2 into nodules. Celeribater manganoxidans DY25T, belonging to family Rhodobacteraceae, has ability to catalyze the formation of MnO2 [ 1 ]. The concentration of MnO2 formed by harvested cells reached 7.08 μM after suspended in 10 mM HEPES (pH 7.5). Genomic and physiological characteristics of strain DY25T provided a better understanding of its Mn-oxidizing mechanism. Fifteen genes (including four multicopper oxidases) may be involved in Mn(II)-oxidation, whereas only three of them can promote this process. Sulfur-oxidizing activity was detected, which may be associated with manganese oxidation. Genes involved in import and export of primary elemental ingredients (C, N, P and S) and metallic elements (e.g. Mn) were discovered, demonstrating its potential roles in the biogeochemical cycle.

Background The Mariana Trench is the deepest known site in the Earth’s oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood. Results Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ2H values of n-C16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from − 79 to − 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source. Conclusions These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment. Electronic supplementary material The online version of this article (10.1186/s40168-019-0652-3) contains supplementary material, which is available to authorized users.

A new marine phage-host system was isolated and further purified from the surface water of the Yellow Sea, China, using the agar overlay method. The host bacterium was identified to be a strain of Pseudoalteromonas marina by its 16S rRNA gene sequence. The phage, named Pseudoalteromonas phage PH103, was characterized and identified by morphological examination, host infection properties, stability, host range, full genome sequencing and bioinformatics analysis. The morphology of phage PH103 demonstrated that the phage is a member of the Siphoviridae family. PH103 showed strong tolerance with a wide range of temperatures (0–60 °C) and pH (3−13). The genome sequencing and bioinformatics analysis found the genome to be 43,190 bp long, with an average GC content of 41.17%. Seventy six ORFs were predicted in the genome, with twenty assigned genes included in the function groups of the host interaction, DNA replication/recombination, DNA packaging/head formation, and phage tail/host recognition. 44.74% of the total genome had no homologous sequence matching, which indicates that phage PH103 is newly identified.

Metagenomics and metatranscriptomics are powerful tools to uncover key microbes and processes driving biogeochemical cycling in natural ecosystems. Currently available databases depicting metabolic functions from metagenomic/metatranscriptomic data are not dedicated to biogeochemical cycles. There are no databases encompass genes involved in the cycling of dimethylsulfoniopropionate (DMSP), an abundant organosulfur compound. Additionally, a recognized normalization mode to estimate and compare the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been available. These limitations impact the ability to accurately relate key microbial driven biogeochemical processes to differences in environmental conditions. Thus, an easy to use specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) and a manually created DMSP cycling gene database. Accurate and specific formulas for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemically-relevant pathways in both text and graphical format. We applied DiTing to metagenomes from simulated data, hydrothermal vents and the Tara Ocean project. The DiTing outputs were consistent with genetic feature of genomes used in simulated benchmark data, and also demonstrated that the predicted functional profiles correlated strongly with changes in environmental conditions. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets.

The Earth&rsquo, s oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0&ndash, 10,500 m) in the Mariana Trench, the deepest natural point in the Earth&rsquo, s oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at &ge, 4000 m layers was slightly larger compared to those at 0&ndash, 2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (&gt, 10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea &alpha, lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in &gt, 10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth&rsquo, s deepest seawater.

Summary Corals are colonized by symbiotic microorganisms that profoundly influence the animal’s health. One noted symbiont is a single‐celled alga (in the dinoflagellate family Symbiodiniaceae), which provides the coral with most of its fixed carbon. Thermal stress increases the production of reactive oxygen species (ROS) by Symbiodiniaceae during photosynthesis. ROS can both damage the algal symbiont’s photosynthetic machinery and inhibit its repair, causing a positive feedback loop for the toxic accumulation of ROS. If not scavenged by the antioxidant network, excess ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating in a process known as bleaching. We use Exaiptasia diaphana as a model for corals and constructed a consortium comprised of E. diaphana–associated bacteria capable of neutralizing ROS. We identified six strains with high free radical scavenging (FRS) ability belonging to the families Alteromonadaceae, Rhodobacteraceae, Flavobacteriaceae and Micrococcaceae. In parallel, we established a consortium of low FRS isolates consisting of genetically related strains. Bacterial whole genome sequences were used to identify key pathways that are known to influence ROS.

Corals are colonized by symbiotic microorganisms that exert a profound influence on the animal’s health. One noted symbiont is a single-celled alga (from the familySymbiodiniaceae), which provides the coral with most of its fixed carbon. During thermal stress, hyperactivity of photosynthesis results in a toxic accumulation of reactive oxygen species (ROS). If not scavenged by the antioxidant network, ROS may trigger a signaling cascade ending with the coral host and algal symbiont disassociating; this process is known as bleaching. Our goal was to construct a probiotic comprised of host-associated bacteria able to neutralize free radicals such as ROS. Using the coral model, the anemoneExaiptasia diaphana, and pure bacterial cultures isolated from the model animal, we identified six strains with high free radical scavenging ability belonging to the familiesAlteromonadaceae, Rhodobacteraceae, Flavobacteriaceae, andMicrococcaceae. In parallel, we established a “negative” probiotic consisting of genetically related strains with poor free radical scavenging capacities. From their whole genome sequences, we explored genes of interest that may contribute to their potential beneficial roles, which may help facilitate the therapeutic application of a bacterial probiotic. In particular, the occurrence of key pathways that are known to influence ROS in each of the strains has been inferred from the genomes sequences and are reported here.IMPORTANCECoral bleaching is tightly linked to the production of reactive oxygen species (ROS), which accumulates to a toxic level in algae-harboring host cells leading to coral-algal dissociation. Interventions targeting ROS accumulation, such as the application of exogenous antioxidants, have shown promise for maintaining the coral-algal partnership. With the feasibility of administering antioxidants directly to corals being low, we aim to develop a probiotic to neutralize toxic ROS during a thermal stress event. This probiotic can be tested with corals or a coral model to assess its efficacy in improving coral resistance to environmental stress.

Microbes transform aqueous mercury (Hg) into methylmercury (MeHg), a potent neurotoxin in terrestrial and marine food webs. This process requires the gene pair hgcAB, which encodes for proteins that actuate Hg methylation, and has been well described for anoxic environments. However, recent studies report potential MeHg formation in suboxic seawater, although the microorganisms involved remain poorly understood. In this study, we conducted large-scale multi-omic analyses to search for putative microbial Hg methylators along defined redox gradients in Saanich Inlet (SI), British Columbia, a model natural ecosystem with previously measured Hg and MeHg concentration profiles. Analysis of gene expression profiles along the redoxcline identified several putative Hg methylating microbial groups, including Calditrichaeota, SAR324 and Marinimicrobia, with the last by far the most active based on hgc transcription levels. Marinimicrobia hgc genes were identified from multiple publicly available marine metagenomes, consistent with a potential key role in marine Hg methylation. Computational homology modelling predicted that Marinimicrobia HgcAB proteins contain the highly conserved structures required for functional Hg methylation. Furthermore, a number of terminal oxidases from aerobic respiratory chains were associated with several SI putative novel Hg methylators. Our findings thus reveal potential novel marine Hg-methylating microorganisms with a greater oxygen tolerance and broader habitat range than previously recognised.

BackgroundMarine Group I (MGI)Thaumarchaeota, which play key roles in the global biogeochemical cycling of nitrogen and carbon (ammonia oxidizers), thrive in the aphotic deep sea with massive populations. Recent studies have revealed that MGIThaumarchaeotawere present in the deepest part of oceans—the hadal zone (depth > 6000 m, consisting almost entirely of trenches), with the predominant phylotype being distinct from that in the “shallower” deep sea. However, little is known about the metabolism and distribution of these ammonia oxidizers in the hadal water.ResultsIn this study, metagenomic data were obtained from 0–10,500 m deep seawater samples from the Mariana Trench. The distribution patterns ofThaumarchaeotaderived from metagenomics and 16S rRNA gene sequencing were in line with that reported in previous studies: abundance ofThaumarchaeotapeaked in bathypelagic zone (depth 1000–4000 m) and the predominant clade shifted in the hadal zone. Several metagenome-assembled thaumarchaeotal genomes were recovered, including a near-complete one representing the dominant hadal phylotype of MGI. Using comparative genomics, we predict that unexpected genes involved in bioenergetics, including two distinct ATP synthase genes (predicted to be coupled with H+and Na+respectively), and genes horizontally transferred from other extremophiles, such as those encoding putative di-myo-inositol-phosphate (DIP) synthases, might significantly contribute to the success of this hadal clade under the extreme condition. We also found that hadal MGI have the genetic potential to import a far higher range of organic compounds than their shallower water counterparts. Despite this trait, hadal MDI ammonia oxidation and carbon fixation genes are highly transcribed providing evidence they are likely autotrophic, contributing to the primary production in the aphotic deep sea.ConclusionsOur study reveals potentially novel adaptation mechanisms of deep-sea thaumarchaeotal clades and suggests key functions of deep-seaThaumarchaeotain carbon and nitrogen cycling.

Additional file 1:. Supplementary figures and tables.

The genus Vibrio , belonging to Gammaproteobacteria of the phylum Proteobacteria , is a genetically and ecologically diverse group of heterotrophic bacteria, that are ubiquitous in marine environments, especially in coastal areas. In particular, vibrios dominate, i.e. up to 10% of the readily culturable marine bacteria in these habitats. The distribution of Vibrio spp. is shaped by various environmental parameters, notably temperature, salinity and dissolved organic carbon. Vibrio spp. may utilize a wide range of organic carbon compounds, including chitin (this may be metabolized by most Vibrio spp.), alginic acid and agar. Many Vibrio spp. have very short replication times (as short as ~ 10 min), which could facilitate them developing into high biomass content albeit for relatively short durations. Although Vibrio spp. usually comprise a minor portion (typically ~1% of the total bacterioplankton in coastal waters) of the total microbial population, they have been shown to proliferate explosively in response to various nutrient pulses, e.g., organic nutrients from algae blooms and iron from Saharan dust. Thus, Vibrio spp. may exert large impacts on marine organic carbon cycling especially in marginal seas. Genomics and related areas of investigation will reveal more about the molecular components and mechanisms involved in Vibrio -mediated biotransformation and remineralization processes.

Background Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level. Results Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal gene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the genus. The chitinase A genes were estimated to have evolved along with the genus, and have undergone significant purifying selective force to conserve the ancestral state. Conclusions Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches. Electronic supplementary material The online version of this article (10.1186/s12864-018-4531-2) contains supplementary material, which is available to authorized users.

Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn - Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO

Vibrio species are associated with human health and play important roles in the carbon cycle. The interest in the Vibrio ecology in marine pelagic environments has increased in recent years, and the correlations between the Vibrio community structure and various environmental factors have been demonstrated. However, the identification of planktonic Vibrio species and their relationship with particulate matter are unclear. Here, we elucidated the spatiotemporal dynamics of Vibrio diversity and in relation to environmental factors in the northern Chinese marginal seas, which feature complex and ever-changing environmental conditions. Vibrio abundance derived from quantitative PCR analysis was higher in summer (∼1.4 × 106 copies liter−1) than in winter (∼1.9 × 105 copies liter−1). Interestingly, the average amount of free-living (on a 0.22-μm-pore-size filter membrane) Vibrio was higher (∼3.89 times) than that of particle-associated Vibrio (on a 3-μm-pore-size filter membrane), making it likely that the preferential lifestyle of the planktonic Vibrio community was free living. Shifts in Vibrio community composition identified by high-throughput amplicon sequencing of the Vibrio-specific 16S rRNA gene were observed at both spatial and temporal scales, which were mainly driven by temperature, dissolved oxygen, ammonium, salinity, nitrite, and phosphate. The most prominent operational taxonomic units in summer were closely related to Vibrio campbellii and Vibrio caribbeanicus and shifted to those affiliated with Vibrio atlanticus in winter. Our study demonstrated abundant and diverse Vibrio populations in the northern Chinese marginal seas, contributing to a better understanding of their potential ecological roles in these ecosystems. IMPORTANCE The dynamics of Vibrio communities have been shown in many marine habitats that are close to land, including estuary or harbor areas. Here, we investigated the spatiotemporal dynamics of Vibrio populations in the northern Chinese marginal seas, spanning a wide spatial scale. We showed that the abundances of the Vibrio population in the present study were higher than those in most previously studied areas and that Vibrio species are more likely to adopt a free-living lifestyle. Moreover, our results expanded upon previous results by showing a clear shift in the dominant Vibrio species from summer to winter, which was mainly attributable to the reduction in the abundance of dominant species in summer. Overall, this work contributes to the understanding of the ecology of the Vibrio communities in the marginal seas.

Labrenzia aggregata LZB033 (Rhodobacteraceae), which produces dimethylsulfoniopropionate (DMSP) and reduces nitrate to nitrogen, was isolated from seawater of the East China Sea. Its genome encodes a large number of transcriptional regulators which may be important for its adaptation to diverse marine environments. The alternative σ(54) factor (RpoN) is a central regulator of many bacteria, regulating the transcription of multiple genes and controlling important cellular functions. However, the exact role of RpoN in Labrenzia spp. is unknown. In this study, an in-frame rpoN deletion mutant was constructed in LZB033, and the function of RpoN was determined. To systematically identify RpoN-controlled genes, we performed a detailed analysis of gene expression differences between the wild-type strain and the ΔrpoN mutant using RNA sequencing. The expression of 175 genes was shown to be controlled by RpoN. Subsequent phenotypic assays showed that the ΔrpoN mutant was attenuated in flagellar biosynthesis and swimming motility, utilized up to 13 carbon substrates differently, lacked the ability to assimilate malic acid, and displayed markedly decreased biofilm formation. In addition, stress response assays showed that the ΔrpoN mutant was impaired in the ability to survive under different challenge conditions, including osmotic stress, oxidative stress, temperature changes, and acid stress. Moreover, both the DMSP synthesis and catabolism rates of LZB033 decreased after rpoN was knocked out. Our work provides essential insight into the regulatory function of RpoN, revealing that RpoN is a key determinant for LZB033 flagellar formation, motility, biofilm formation, and environmental fitness, as well as DMSP production and degradation. IMPORTANCE This study established an in-frame gene deletion method in the alphaproteobacterium Labrenzia aggregata LZB033 and generated an rpoN gene mutant. A comparison of the transcriptomes and phenotypic characteristics between the mutant and wild-type strains confirmed the role of RpoN in L. aggregata LZB033 flagellar formation, motility, biofilm formation, and carbon usage. Most importantly, RpoN is a key factor for survival under different environmental challenge conditions. Furthermore, the ability to synthesize and metabolize dimethylsulfoniopropionate (DMSP) was related to RpoN. These features revealed RpoN to be an important regulator of stress resistance and survival for L. aggregata LZB033 in marine environments.

Supplementary figures and tables (DOCX 3821 kb)

Supplementary methods (DOCX 33 kb)

Figure S2. COGs classification of the specific genomes of V. rotiferianus B64D1 and V. mediterranei QT6D1. Designations of functional categories: [A] RNA processing and modification, [B] chromatin structure and dynamics, [C] energy production and conversion, [D] cell cycle control and mitosis, [E] amino acid metabolism and transport, [F] nucleotide metabolism and transport, [G] carbohydrate metabolism and transport, [H] coenzyme metabolism, [I] lipid metabolism, [J] translation, [K] transcription, [L] replication and repair, [M] cell wall/membrane/envelope biogenesis, [N] Cell motility, [O] post-translational modification, protein turnover, chaperone functions, [P] Inorganic ion transport and metabolism, [Q] secondary metabolites biosynthesis, transport and catabolism, [R] general functional prediction only, [S] function unknown, [T] signal transduction, [U] intracellular trafficking and secretion, [V] Defense mechanisms, [W] Extracellular structures, [Y] nuclear structure, [Z] cytoskeleton. (PDF 822Â kb)

Figure S3. Pan genome tree. The tree was created based on the presence or absence of gene clusters in the 20 complete Vibrio genomes. The number at each node denotes the bootstrap value based on 1000 replicates. The color red and yellow are corresponding to the core genome tree, suggesting the discrepancy between core and pan genome trees. (PDF 194Â kb)

Figure S6. Genes related to the chitin-degrading process in 20 vibrios with complete genomes. Each column indicates a chitin metabolism-related gene family, with the family name indicating the predicted function. The number in the box indicates the copy number of that gene family in the corresponding genome. (PDF 282Â kb)

Figure S1. Pan and core plot of the 20 Vibrio species with complete genomes. Accumulation curves for (A) the number of genes in common or (B) total number of genes are plotted. The grey dots represent 10 different random input sequences of genomes, and the extrapolated limiting value for core genes is shown as a dashed line. Equations which can be used to fit the curves are shown above the plot respectively. (PDF 1023Â kb)

Figure S4. Neighbor-joining phylogenetic tree of the 20 vibrios genomes based on 16S rRNA gene. The number at each node denotes the bootstrap value based on 1000 replicates. S. denitrificans OS217 was used as the outgroup. Bar, 0.01 substitutions per site. (PDF 186Â kb)

Figure S5. Heatmap presentation of pairwise average nucleotide identity of the 19 Vibrio species with complete genomes. The genomes are hierarchical clustered according to the values of rows. The clusters present in blue and orange are corresponding to the core genome tree. (PDF 212Â kb)

Table S1. General features of the 20 complete genomes of Vibrio species analyzed. (DOCX 48Â kb)

Table S2. General features of the 13 marine bacteria complete genomes used to compare with Vibrio. (DOCX 34Â kb)

Background South Pacific Gyre (SPG) is the largest and clearest gyre in the world, where the concentration of surface chlorophyll a and primary production are extremely low. Aquimarina longa SW024T was isolated from surface water of the SPG center. To understand how this bacterium could survive in this ultra-oligotrophic oceanic environment and its function in biogeochemical cycle, we sequenced the genome of A. longa SW024T and performed extensive genomic analyses. Methods Genomic DNA was extracted and sequenced using Illumina Hiseq 2000 and Miseq platform. Genome annotation, genomic comparison and phylogenetic analyses were performed with the use of multiple bioinformatics tools like: BLAST+ 2.2.24, Glimmer3.0, RAST server, Geneious 4.8.5, ClustalW2 and MEGA5. Physiological and morphological features were tested by bacterial culture, electron microscopy, fluorescence microscopy and exopolysaccharides extraction. Results Analysis of seven Aquimarina genomes and 30 other genomes of Flavobacteriaceae isolated from seawater showed that most of the strains had low DNA G + C contents, and Aquimarina had larger genomes than other strains. Genome comparison showed varying genomic properties among seven Aquimarina genomes, including genome sizes and gene contents, which may warrant their specific adaptive strategies. Genome of A. longa SW024T was further compared with the genomes of two other Aquimarina species which were also isolated from the SPG and A. longa SW024T appeared to have much more genes related to replication, recombination and repair. As a copiotroph, A. longa SW024T is long in length, and possesses large genome size and diverse transporters. However, it has also evolved many properties to survive in the oligotrophic marine environment. This bacterium grew better on solid medium than in liquid medium, suggesting it may be liable to attach to particle surfaces in order to survive in the nutrient-limiting environment. Gliding motility and the capacity to degrade various polymers possibly allow the bacterium to grow on detritus particles and use polymeric substances as carbon and energy sources. Moreover, genes related to carbon, nitrogen, and sulfur metabolisms were identified, which showed that A. longa SW024T might be involved in various elemental cycles. Conclusions Genomic comparison of Aquimarina genus exhibits comprehensive capabilities of the strains to adapt to diverse marine environments. The genomic characteristics of A. longa SW024T reveal that it evolves various strategies to cope with both copiotrophic and ultra-oligotrophic marine environment, which provides a better understanding of the survival abilities of bacteria in prevalent and even extreme oceanic environments. Furthermore, carbon, nitrogen and sulfur utilization of A. longa SW024T may represent its potential functions in the global biogeochemical cycle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2005-3) contains supplementary material, which is available to authorized users.

Summary of genomic information of 30 Flavobacteriaceae genomes. (DOCX 21 kb)