Enhanced copper-resistance gene repertoire in Alteromonas macleodii strains isolated from copper-treated marine coatings

Copper is prevalent in coastal ecosystems due to its use as an algaecide and as an anti-fouling agent on ship hulls. Alteromonas spp. have previously been shown to be some of the early colonizers of copper-based anti-fouling paint but little is known about the mechanisms they use to overcome this initial copper challenge. The main models of copper resistance include the Escherichia coli chromosome-based Cue and Cus systems; the plasmid-based E. coli Pco system; and the plasmid-based Pseudomonas syringae Cop system. These were all elucidated from strains isolated from copper-rich environments of agricultural and/or enteric origin. In this work, copper resistance assays demonstrated the ability of Alteromonas macleodii strains CUKW and KCC02 to grow at levels lethal to other marine bacterial species. A custom database of Hidden Markov Models was designed based on proteins from the Cue, Cus, and Cop/Pco systems and used to identify potential copper resistance genes in CUKW and KCC02. Comparative genomic analyses with marine bacterial species and bacterial species isolated from copper-rich environments demonstrated that CUKW and KCC02 possess genetic elements of all systems, oftentimes with multiple copies, distributed throughout the chromosome and mega-plasmids. In particular, two copies of copA (the key player in cytoplasmic detoxification), each with its own apparent MerR-like transcriptional regulator, occur on a mega-plasmid, along with multiple copies of Pco homologs. Genes from both systems were induced upon exposure to elevated copper levels (100 μM– 3 mM). Genomic analysis identified one of the merR-copA clusters occurs on a genomic island (GI) within the plasmid, and comparative genomic analysis found that either of the merR-copA clusters, which also includes genes coding for a cupredoxin domain-containing protein and an isoprenylcysteine methyltransferase, occurs on a GI across diverse bacterial species. These genomic findings combined with the ability of CUKW and KCC02 to grow in copper-challenged conditions are couched within the context of the genome flexibility of the Alteromonas genus.

RNA-seq Insights Into the Impact of Alteromonas macleodii on Isochrysis galbana

Phycospheric bacteria may be the key biological factors affecting the growth of algae. However, the studies about interaction between Isochrysis galbana and its phycospheric bacteria are limited. Here, we show that a marine heterotrophic bacterium, Alteromonas macleodii, enhanced the growth of I. galbana, and inhibited non-photochemical quenching (NPQ) and superoxide dismutase (SOD) activities of this microalgae. Further, we explored this phenomenon via examining how the entire transcriptomes of I. galbana changed when it was co-cultured with A. macleodii. Notable increase was observed in transcripts related to photosynthesis, carbon fixation, oxidative phosphorylation, ribosomal proteins, biosynthetic enzymes, and transport processes of I. galbana in the presence of A. macleodii, suggesting the introduction of the bacterium might have introduced increased production and transport of carbon compounds and other types of biomolecules. Besides, the transcriptome changed largely corresponded to reduced stress conditions for I. galbana, as inferred from the depletion of transcripts encoding DNA repair enzymes, superoxide dismutase (SOD) and other stress-response proteins. Taken together, the presence of A. macleodii mainly enhanced photosynthesis and biosynthesis of I. galbana and protected it from stress, especially oxidative stress. Transfer of fixed organic carbon, but perhaps other types of biomolecules, between the autotroph and the heterotroph might happen in I. galbana-A. macleodii co-culture. The present work provides novel insights into the transcriptional consequences of I. galbana of mutualism with its heterotrophic bacterial partner, and mutually beneficial associations existing in I. galbana-A. macleodii might be explored to improve productivity and sustainability of aquaculture algal rearing systems.

Prochlorococcus exudate stimulates heterotrophic bacterial competition with rival phytoplankton for available nitrogen

The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients, and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and co-culture when nutrients were replete. However, in nitrogen-limited medium Prochlorococcus outgrew Synechococcus, but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen, but only if stimulated by exudate released by Prochlorococcus, or if a proxy organic carbon source was provided. Analysis of a nitrate reductase mutant Alteromonas suggested that Alteromonas outcompetes Synechococcus for nitrate, during which co-cultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in the nutrient-limited regions of the ocean.

Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean

It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::kmr, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.

Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter , Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains

Species of the Alteromonas and Marinobacter genera are heterotrophic Gammaproteobacteria that are part of the marine microbial ecosystem. In this study, four strains were isolated from two nonaxenic Synechococcus cultures and were sequenced. Few studies of these two genera have been reported. Therefore, genomic data of Alteromonadaceae are valuable for the study of heterotroph-phototroph dynamics in marine bacterial communities.

Transcriptomic Study of Substrate-Specific Transport Mechanisms for Iron and Carbon in the Marine Copiotroph Alteromonas macleodii

ABSTRACT Iron is an essential micronutrient for all microbial growth in the marine environment, and in heterotrophic bacteria, iron is tightly linked to carbon metabolism due to its central role as a cofactor in enzymes of the respiratory chain. Here, we present the iron- and carbon-regulated transcriptomes of a representative marine copiotroph, Alteromonas macleodii ATCC 27126, and characterize its cellular transport mechanisms. ATCC 27126 has distinct metabolic responses to iron and carbon limitation and, accordingly, uses distinct sets of TonB-dependent transporters for the acquisition of iron and carbon. These distinct sets of TonB-dependent transporters were of a similar number, indicating that the diversity of carbon and iron substrates available to ATCC 27126 is of a similar scale. For the first time in a marine bacterium, we have also identified six characteristic inner membrane permeases for the transport of siderophores via an ATPase-independent mechanism. An examination of the distribution of specific TonB-dependent transporters in 31 genomes across the genus Alteromonas points to niche specialization in transport capacity, particularly for iron. We conclude that the substrate-specific bioavailability of both iron and carbon in the marine environment will likely be a key control on the processing of organic matter through the microbial loop. IMPORTANCE As the major facilitators of the turnover of organic matter in the marine environment, the ability of heterotrophic bacteria to acquire specific compounds within the diverse range of dissolved organic matter will affect the regeneration of essential nutrients such as iron and carbon. TonB-dependent transporters are a prevalent cellular tool in Gram-negative bacteria that allow a relatively high-molecular-weight fraction of organic matter to be directly accessed. However, these transporters are not well characterized in marine bacteria, limiting our understanding of the flow of specific substrates through the marine microbial loop. Here, we characterize the TonB-dependent transporters responsible for iron and carbon acquisition in a representative marine copiotroph and examine their distribution across the genus Alteromonas. We provide evidence that substrate-specific bioavailability is niche specific, particularly for iron complexes, indicating that transport capacity may serve as a significant control on microbial community dynamics and the resultant cycling of organic matter.

Alteromonas portus sp. nov., an alginate lyase-excreting marine bacterium

An alginate lyase-excreting bacterium, designated strain HB161718T, was isolated from coastal sand collected from Tanmen Port in Hainan, PR China. Cells were Gram-stain-negative rods and motile with a single polar flagellum. Its major isoprenoid quinone was ubiquinone 8 (Q-8), and its cellular fatty acid profile mainly consisted of C16 : 1 ω7c and/or C16 : 1 ω6c, C18 : 1 ω6c and/or C18 : 1 ω7c, C16 : 0, C17 : 0 10-methyl and C16 : 0 N alcohol. The G+C content of the genomic DNA was 44.1 mol%. 16S rRNA gene sequence analysis suggested that strain HB161718T belonged to the genus Alteromonas , sharing 99.5, 99.4, 99.2, 98.9 and 98.5 % sequence similarities to its closest relatives, Alteromonas macleodii JCM 20772T, Alteromonas gracilis 9a2T, Alteromonas australica H17T, Alteromonas marina SW-47T and Alteromonas mediterranea DET, respectively. The low values of DNA–DNA hybridization and average nucleotide identity showed that it formed a distinct genomic species. The combined phenotypic and molecular features supported the conclusion that strain HB161718T represents a novel species of the genus Alteromonas , for which the name Alteromonas portus sp. nov. is proposed. The type strain is HB161718T (=CGMCC 1.13585T=JCM 32687T).

Isolation and Identification of Symbiont Microorganisms from Bioluminescent Marine Life

Bioluminescence means the ability of animals or plants to naturally produce light. The three known ways by which bioluminescence is produced are through specific cells called photocytes, bioluminescent glands in tissues and symbiotic bioluminescent microorganisms. Bioluminescence in Loligo duvaucelii is known to be caused by the presence of symbiotic microorganisms in bioluminescent sacs. There is a need to compile more information on bioluminescent symbiotic microorganisms on marine life in Indonesia and their potential. This study aims to determine the species of bioluminescent microorganisms on squid and fish, namely Loligo sp. and Loligo edulis from the waters of Jepara and the Bombay duck (Harpadon nehereus) from the Strait of Malacca, Indonesia and their potential. The samples were collected by isolating the microorganisms from the luminescent organs, after which the bioluminescent microorganisms were used in the research. This research consisted of antimicrobial tests against pathogenic microorganisms which were conducted qualitatively. The bioluminescent microorganisms were identified using biochemical assay and molecular assay (16S rRNA PCR). Tests results from Loligo sp. symbiotic microorganisms found two isolates which showed antimicrobial activities against pathogenic Multi Drug Resistant (MDR) microorganisms, namely uncultured bacterium clone 1P-1-G05 against Escherichia coli with 32.59 mm of inhibitory zone and Uncultured bacterium clone 3g10a against Enterobacter sp. with 28.44 mm of inhibitory zone. The bioluminescent symbiont microorganisms in Loligo edulis, which was identified to be Photobacterium phosphoreum, showed antimicrobial activities against Vibrio harveyi, E. coli, Staphylococcus aureus, and Bacillus sp. Bioluminescent symbiotic microorganisms on H. nehereus identified Alteromonas macleodii, which showed gamma hemolysis on the blood agar test.