Summary of Alteromonas macleodii ATCC 27126, version 29.0

Tier 2 Curated Organism Database

Database Authors

¹SRI International, ²University of Haifa, ³Alfred-Wegener-Institut, ⁴University of Natural Resources and Life Sciences (BOKU), ⁵University of North Carolina, ⁶Scripps Institution of Oceanography, ⁷Israel Oceanographic and Limnological Research Institute, ⁸University of Alabama at Birmingham, ⁹The Weizmann Institute of Science, ¹⁰Hebrew University of Jerusalem, ¹¹Tel Aviv University, ¹²Macquarie University

Summary

Alteromonas macleodii is a marine species within the ecologically and physiologically diverse genus of Alteromonas [Wietz22]. Alteromonas are ubiquitous in all oceans, apart from the Arctic/Antarctic, and usually found associated with particles, where they may form a significant part of the microbial community [Roth21]. They are easily isolated and cultured and known to be associated with a variety of phytoplankton, such as Synechococcus, Prochlorococcus and diatoms [Kearney21]. Alteromonas respond rapidly to changes in environmental conditions, such as the addition of dissolved organic matter and some inorganic nutrients (e.g. [McCarren10]), and a single strain has been shown to be capable of metabolizing almost all of the labile pool of marine organic carbon [Pedler14]. Several studies have characterized A. macleodii phylogeny, genomic diversity and evolutionary dynamics, highlighting how genetic traits are exchanged through genomic islands and plasmids [LopezPerez16, LopezPerez17, Gonzaga12]. Some Alteromonas strains may also have biotechnological applications. Therefore, Alteromonas in general, and A. macleodii in particular, are becoming important model organisms in marine microbiology and biological oceanography. A brief overview of the Alteromonas macleodii species, including several outstanding questions, can be found in [Wietz22].

The type strain Alteromonas macleodii ATCC 27126 was isolated from surface seawater near Hawaii [Baumann72]. It is a non-spore forming, Gram-negative bacterium which requires Na⁺ ions for growth. During exponential growth, the cells are motile, straight rods with unsheathed, polar flagella. ATCC 27126 is unable to fix molecular nitrogen (N₂) or grow chemolithotrophically with molecular hydrogen (H₂) as the sole source of energy and carbon dioxide as the sole source of carbon (C). They are able to produce extracellular amylase, gelatinase, and lipase but not chitinase, in agreement with their potential ecological relevance in the degradation of polysaccharides [Koch19]. A distinctive property of all A. macleodii tested is their inability to grow on tricarboxylic acid cycle intermediates such as succinate, fumarate, citrate, α-ketoglutarate, and aconitate [Baumann72].

Understanding how the information encoded in the genomes of diverse Alteromonas strains drives their ecological dynamics, requires high quality metabolic reconstructions. To begin addressing this need, the metabolic reconstruction of the type strain, A. macleodii ATCC 27126, was improved and curated collaboratively as part of a community "curate-a-thon" at the University of Haifa, Israel (February 5-8, 2023). The curation effort focused on characterizing phenotypic traits considered by the participants of the workshop key for understanding the ecological dynamics of Alteromonas: 1) Degradation and utilization of diverse C sources such as polysaccharides and C1 compounds. We also asked whether they have the genomic capacity to perform mixed acid fermentation, since their association with marine particles could include low-oxygen environments; 2) Utilization of organic N sources such as nucleotides and amino acids; 3) Traits potentially involved in microbial interactions, including the production of siderophores, quorum sensing molecules and reactive oxygen species (ROS)-scavenging enzymes. Data sources used in the curation process included multiple publications, growth media composition, and BIOLOG phenotype plates.

Unpublished phenotypic data is available from Daniel Sher (dsher@univ.haifa.ac.il) pending submission to a database with a DOI.

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 27.0 and MetaCyc [Caspi18] version 27.0 on 08-Dec-2022 13:03:06.

Genome

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
chromosome	3,962	3,829	72	61	4,653,851	RefSeq:NC_018632.1

Ortholog data available?	Yes

Database Contents

Genes	3,962
Pathways	280
Enzymatic Reactions	1,502
Transport Reactions	19
Polypeptides	3,829
Protein Complexes	52
Enzymes	907
Transporters	304
Compounds	1,030
Transcription Units	2,659
tRNAs	52
Protein Features	6,181
GO Terms	4

Database Version

29.0

Taxonomic Lineage	cellular organisms Bacteria <bacteria> Pseudomonadota Gammaproteobacteria Alteromonadales Alteromonadaceae Alteromonas/Salinimonas group Alteromonas Alteromonas macleodii Alteromonas macleodii ATCC 27126
Genetic Code Number	11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLE	SAMN02603229
NCBI BioProject	PRJNA224116
NCBI-Taxonomy	529120
Environment	seawater surface
Geographic Location	Pacific Ocean
Annotation Provider	NCBI RefSeq
Annotation Date	2021-12-19
Annotation Pipeline	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version	5.3
Annotation Comment	Best-placed reference protein set; GeneMarkS-2+