Taxonomy of Marine Bacteria: the Genus Beneckea

One-hundred-and-forty-five isolates of marine origin were submitted to an extensive physiological, nutritional, and morphological characterization. All strains were gram-negative, facultatively anaerobic, straight or curved rods which were motile by means of flagella. Glucose was fermented with the production of acid but no gas. Sodium but no organic growth factors were required. None of the strains were able to denitrify or fix molecular nitrogen. The results of nutritional and physiological tests were submitted to a numerical analysis. On the basis of phenotypic similarity, nine groups were established. These groups could be distinguished from one another by multiple, unrelated, phenotypic traits. Six groups which had deoxyribonucleic acid (DNA) containing 45 to 48 moles per cent guanine plus cytosine (GC) were assigned to a redefined genus Beneckea. All of the strains in this genus, when grown in liquid medium, had a single, polar flagellum. When grown on a solid medium, many strains had peritrichous flagella. Two groups were similar to previously described species and were designated B. alginolytica and B. natriegens. The remaining four groups were designated B. campbellii, B. neptuna, B. nereida, and B. pelagia. An additional group of phenotypically similar strains having the properties of the genus Beneckea was not included in the numerical analysis. These strains were readily separable from species of this genus and were designated B. parahaemolytica. Of the remaining groups, one was identified as Photobacterium fischeri. The other group (B-2) which had about 41 moles% GC content in its DNA could not be placed into existing genera.     

Flagellation of“Gluconobacter” melanogenus

Summary Electron-micrographs ofGluconobacter melanogenus strain AC 8 (formerlyG. liquefaciens), andG. melanogenus strain U 4, have conclusively confirmed the findings ofShimwell andCarr (1959),Stouthamer (1960), andLeifson (private communication), that these strains are not polarly flagellatedAcetomonas orGluconobacter strains, but peritrichously flagellated acetate-oxidisingAcetobacter ones. When transferred to the latter genus all evidence that these two genera are derived from a “common pool of ancestors”, as claimed byDe Ley (1961), disappears.     

Mesophilic aerobic Gram negative cellulose degrading bacteria from aquatic habitats and soils

New procedures have been developed for the isolation and purification of aerobic and facultatively anaerobic bacteria able to utilize cellulose as sole source of carbon and energy. Wood pulp medium was used for enrichment, and bacterial cellulose, obtained from cultures of Acetobacter aceti subsp. xylinus , was employed as carbon substrate during purification and for the rapid screening of colonies for cellulolytic activity. The methods have revealed several new groups of Gram negative cellulose-degrading bacteria, including organisms that form differentiated colonies superficially similar to myxobacterial sori. The organisms formed several phenetic clusters, three of which contained reference strains of Cellvibrio fulvus, Pseudomonas fluorescens var. cellulosa and Cytophaga hutchinsonii . No cellulose degrading cluster included non-cellulose degrading strains. Most of the cellulose degraders studied were flagellated and, of these, the majority had polar or lophotrichous flagella, although one cluster included peritrichously flagellated organisms. The cellulose degraders in this study included five organisms that grew on nitrate-free medium; these appeared in two different clusters. A few Gram positive isolates appeared to belong to the genera Streptomyces and Thermoactinomyces .     

Microbial degradation of 1,3-dichlorobenzene.

A gram-negative, peritrichously flagellated rod, tentatively identified as an Alcaligenes sp., was isolated from a mixture of soil and water samples by using 1,3-dichlorobenzene as the sole carbon and energy source. During growth on 1,3-dichlorobenzene, almost stoichiometric amounts of chloride were released. Simultaneous adaptation studies, as well as enzyme studies, indicated that 1,3-dichlorobenzene was metabolized via 3,5-dichloro-cis-1,2-dihydroxycyclohexa-3,5-diene to 3,5-dichlorocatechol. Subsequently, the latter product was cleaved, yielding 2,4-dichloromuconate. No initial hydrolytic step yielding 3-chlorophenol was detected in this species.     

Adsorption kinetics of laterally and polarly flagellated Vibrio.

The adsorption of laterally and polarly flagellated bacteria to chitin was measured, and from the data obtained, a modified Langmuir adsorption isotherm was derived. Results indicated that the adsorption of laterally flagellated Vibrio parahaemolyticus follows the Langmuir adsorption isotherm, a type of adsorption referred to as surface saturation kinetics, when conditions are favorable for the production of lateral flagella. When conditions were not favorable for the production of lateral flagella, bacterial adsorption did not follow the Langmuir adsorption isotherm; instead, proportional adsorption kinetics were observed. The adsorption of some polarly flagellated bacteria exhibited surface saturation kinetics. However, the binding index (the product of the number of binding sites and bacterial affinity to the surface) of polarly flagellated bacteria differed significantly from that of laterally flagellated bacteria, suggesting that polarly flagellated bacteria adsorb to chitin by a different mechanism from that used by the laterally flagellated bacteria. From the results of dual-label adsorption competition experiments, in which polarly flagellated V. cholerae competed with increasing concentrations of laterally flagellated V. parahaemolyticus, it was observed that laterally flagellated bacteria inhibited the adsorption of polarly flagellated bacteria. In contrast, polarly flagellated bacteria enhanced the adsorption of V. cholerae. In competition experiments, where V. parahaemolyticus competed against increasing concentrations of other bacteria, polarly flagellated bacteria enhanced V. parahaemolyticus adsorption significantly, whereas laterally flagellated bacteria only slightly enhanced the process. The direct correlation observed between surface saturation kinetics, the production of lateral flagella, and the ability of laterally flagellated bacteria to inhibit the adsorption of polarly flagellated bacteria suggests that lateral flagella represent a component of bacterial structure that is important in the adsorption of laterally flagellated bacteria to surfaces. A model for adsorption events of laterally flagellated bacteria is proposed, based on the evidence presented.     

Microbial degradation of 1,3-dichlorobenzene

A gram-negative, peritrichously flagellated rod, tentatively identified as an Alcaligenes sp., was isolated from a mixture of soil and water samples by using 1,3-dichlorobenzene as the sole carbon and energy source. During growth on 1,3-dichlorobenzene, almost stoichiometric amounts of chloride were released. Simultaneous adaptation studies, as well as enzyme studies, indicated that 1,3-dichlorobenzene was metabolized via 3,5-dichloro-cis-1,2-dihydroxycyclohexa-3,5-diene to 3,5-dichlorocatechol. Subsequently, the latter product was cleaved, yielding 2,4-dichloromuconate. No initial hydrolytic step yielding 3-chlorophenol was detected in this species.     

Deoxyribonucleic Acid Base Composition of Rothia dentocariosa as Determined by Thermal Denaturation

The moles per cent guanine plus cytosine (GC) of 10 filamentous strains of Rothia dentocariosa ranged from 65.4 to 69.7. Major differences were not observed in the base composition of a filamentous form (69.7 moles% GC) and its coccal variant (68.0 moles% GC).     

Numerical taxonomy of heavy metal-tolerant nonhalophilic bacteria isolated from hypersaline environments.

A total of 232 metal-tolerant bacterial strains were isolated from water and sediment samples collected in different hypersaline environments located in Cádiz, Huelva and Morón de la Frontera (Spain). They were isolated on a medium containing mercury, chromium, cadmium, copper or zinc. These halotolerant isolates were analyzed by numerical taxonomy techniques by using the simple matching (SSM) and Jaccard (SJ) coefficients; clustering was achieved using the unweighted pair group method with averages (UPGMA) algorithm. At the 81% and 83% similarity level, different numbers of phenons were obtained for Gram-negative and Gram-positive halotolerant microorganisms. Most of the 48 Gram-negative metal-tolerant strains studied were grouped into nine phenons, representing the genera Pseudoalteromonas, Alteromonas, Xanthomonas, Pseudomonas, Alcaligenes and Enterobacteria. The 72 Gram-positive metal-tolerant strains grouped into eight phenons, with only 15 strains left unassigned. Most of the isolates were assigned to the genus Bacillus (seven phenons), and one phenon comprised microorganisms with phenotypic characteristics similar to those of the genus Celullomonas.     

Regulation of aspartokinase activity in non-fermentative,marine eubacteria

Summary Cell-free extracts of gram-negative, non-fermentative, marine eubacteria were assayed for aspartokinase activity. The organisms tested included polarly flagellated species and groups which had GC contents in their DNAs of 46 to 64 moles % (Alteromonas, Pseudomonas) as well as species which had peritrichous flagellation and moles % GC contents of 53 to 68 (Alcaligenes). The results of these studies suggested that in all the strains tested, aspartokinase activity was catalyzed by a single enzyme. On the basis of the effect ofl-threonine,l-lysine,l-methionine, andl-isoleucine on activity, five different types of aspartokinases (designated I through V) were delineated. In aspartokinase types I through IV,l-threonine andl-lysine inhibited activity by means of a concerted feedback inhibition; in type V, activity was inhibited byl-threonine but unaffected byl-lysine. In types I, III, and IV,l-threonine andl-lysine alone were inhibitory, while in type II these effectors had virtually no effect on activity when tested singly. Three distinct responses were observed in the presence of two other end products of the aspartate pathway,l-methionine andl-isoleucine. In types I and II, these two amino acids usually stimulated activity and overcame the inhibition byl-threonine andl-lysine; in types IV and V,l-methionine andl-isoleucine had no effect; and in type III these amino acids inhibited activity. The results of this study indicate that the aspartokinases of a number of species and groups of marine bacteria have similarities and differences which should be of use in making future taxonomic groupings.     

Hydroxamate-siderophore production and utilization by marine eubacteria

Siderophore (iron-binding chelator) production was examined in 30 strains of open ocean bacteria from the generaVibrio, Alteromonas, Alcaligenes, Pseudomonas, andPhotobacterium. The results showed that hydroxamate-type siderophore production was widely distributed in various marine species, except for isolates ofAlteromonas macleodii andV. nereis. In all cases, the ability to produce siderophores was under the control of iron levels in the medium and satisfied the iron requirements of the siderophore bioassay organism. On the basis of chemical assay and bacterial bioassays, none of the examined isolates produced phenolate-type siderophores. Several isolates produces siderophores that were neither hydroxamatenor phenolate-type siderophores. Some strains such asAlteromonas communis produce siderophores that could be used by many other isolates. In contrast, the siderophore produced byAlcaligenes venustus had little cross-strain utilization. These findings suggest that the ability to produce siderophores may be common to open ocean bacteria.     

Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism

Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.     

Identification of dimethyl disulfide-forming bacteria isolated from activated sludge

Twenty-four strains with high dimethyl disulfide (DMDS)-forming ability were isolated from activated sludge and identified to the genus level. These bacteria were classified into four groups (A, B, C, and D) by the API ZYM System (API System S.A., Montalieu, France). Group A (three strains) was identified as genus Lactobacillus by the API 20B System, by the method of Cowan and Steel, and by production of lactic acid as confirmed by gas-liquid chromatography. Group B (eight strains) was identified as genus Corynebacterium by API 20B and the Cowan and Steel method. Group C (one strain) was suggested to belong to genus Corynebacterium by the API 20B System. Group D (12 strains) was identified as genus Pseudomonas or Alcaligenes by the API 20B System, as genus Alcaligenes by the Cowan and Steel method, and as Achromobacter group Vd by the API 20NE System. However, on the basis of guanine-plus-cytosine contents in DNA and form of flagella, these strains were identified as genus Pseudomonas. Formation of DMDS from DL-methionine and S-methyl-L-cysteine was tested. DMDS-forming bacteria isolated from activated sludge formed DMDS from both precursors. In genus Pseudomonas, P. aeruginosa could not form DMDS from either precursor, but P. acidovorans, P. alcaligenes, P. pseudoalcaligenes, and P. testosteroni formed DMDS. In genus Alcaligenes, A. denitrificans subsp. xylosoxydans, A. denitrificans subsp. denitrificans, A. faecalis, and A. odorans formed DMDS from both precursors. Achromobacter group Vd formed DMDS from S-methyl-L-cysteine, but could not from DL-methionine.     

A Numerical Taxonomic Study of Pseudomonas-like Bacteria Isolated from Fish in Southeastern Queensland and their Association with Spoilage

Pseudomonas -like bacteria isolated from fresh and spoiling fish in southeastern Queensland were subjected to a wide range of physiological and nutritional tests. The results of these tests, together with those of 20 named strains, were analysed numerically, resulting in the formation of 11 groups. Most of the isolates clustered into group 1 and group 2 which also contained the bulk of the strains able to produce spoilage odours when grown in a tryptic digest of fish muscle at 2°C. Almost all of the group 1 organisms produced sulphydryl type odours, had only 50 mol % G + C and were identified as strains of Alteromonas putrefaciens which were deficient in the ability to produce H₂S detectable in Peptone Iron Agar. Certain of the group 2 strains produced fruity and sulphydryl type odours, but these organisms were not distinguishable from other strains in this group not producing odours. Group 2 strains were highly related to Pseudomonas fragi and were intermediate in properties between Ps. fluorescens and Ps. putida. The remaining nine minor groups contained few organisms able to produce spoilage odours.     

Taxonomy of four marine bacterial strains that produce tetrodotoxin

Four strains of tetrodotoxin-producing bacteria isolated from a red alga and from pufferfish were characterized. Two of these strains are members of the genus Listonella MacDonell and Colwell. The phenotypic characteristics, guanine-plus-cytosine contents, and base sequences of the 16S rRNAs of these organisms indicated that they are members of Listonella pelagia (Vibrio pelagius) biovar II. The other two strains are members of the genus Alteromonas Baumann et al. and the genus Shewanella MacDonell and Colwell. These two strains are mutually distinct and distinct from the previously described Alteromonas and Shewanella species and therefore are placed in new species. The names Shewanella alga and Alteromonas tetraodonis are proposed for these organisms; the type strains are strains OK-1 and GFC, respectively.     

A new anaerobic,sporing, acetate-oxidizing,sulfate-reducing bacterium,Desulfotomaculum (emend.) acetoxidans

Archives of Microbiology - A new strictly anaerobic, polarly flagellated, sporing, acetate-oxidizing, sulfate-reducing bacterium was isolated from anaerobic fresh or sea water mud samples. The...     

Methanogenium,a new genus of marine methanogenic bacteria,and characterization ofMethanogenium cariaci sp. nov. andMethanogenium marisnigri sp. nov.

A new genus of marine methanogenic bacteria and two species within this genus are described.Methanogenium is the proposed genus andMethanogenium cariaci the type species. Cells of the type species are Gram-negative, peritrichously flagellated, irregular cocci with a periodic wall surface pattern. Colonies formed by these bacteria are yellow, circular and umbonate with entire edges. The DNA base composition is 52 mol% guanine plus cytosine. Formate or hydrogen and carbon dioxide serve as substrates for growth. Cells ofMethanogenium marisnigri are of similar shape but smaller diameter thanM. cariaci. The colonies ofM. marisnigri are convex, and the DNA base composition is 61 mol % G+C. Formate or hydrogen and carbon dioxide are growth substrates. Sodium chloride is required for growth of both methanogens.Abbreviations SDS sodium dodecylsulfate - PIPES piperazine-N,N-bis (2 ethanesulfonic acid) - HS-CoM coenzyme M, 2-mercaptoethanesulfonic acid     

The acetic acid bacteria, 1941–1961

Summary Leifson's (1954) differentiation of the acetic acid bacteria into (1)Acetobacter—peritrichously flagellated and acetate oxidising, and (2)Acetomonas—polarly flagellated and acetate non-oxidising, has, by various workers, been (a) fully confirmed, (b) doubted, or only partly accepted, and (c) denied altogether. Also the priority ofAcetomonas overGluconobacter has been questioned, as has also facile mutability inAcetobacter. By a critical comparative review of all the publications concerned, and by the experimental examination of the various cultures claimed to contraveneLeifson's correlation, we have attempted to clarify the confusion, and to give a clear picture of the true position, which is really quite simple. The result of so doing has been to vindicateLeifson's findings in every case, to refute criticism of facile mutability inAcetobacter, and to show whyGluconobacter Asai cannot claim priority overAcetomonas Leifson.     

Surface structures, co-aggregation and adherence phenomena of Streptococcus oralis and related species

Seven strains of Streptococcus oralis were found to possess surface structures. Four strains possessed long fimbriae which ranged in length from 266-366 nm, while the remaining three strains possessed shorter peritrichously distributed fibrils which ranged in length from 80-197 nm. The fibrillar strains were morphologically similar to strains of Streptococcus sanguis I and II and Streptococcus mitis. No strain of S. oralis produced tufts of fibrils like certain strains of S. sanguis I. Strains of Streptococcus milleri produced peritrichously distributed fimbriae which were morphologically dissimilar to the fimbriae produced by S. oralis strains. S. oralis strains were moderately to highly hydrophobic, but hydrophobicity could not be related to adhesion parameters or type or length or density of surface structures. Furthermore, there appeared to be no correlation between type of surface structures and adhesion parameters. Two of the three fibrillar strains of S. oralis and the peritrichously fibrillar strains of S. sanguis, together with one strain of S. milleri, were able to co-aggregate with actinomycetes.     

Taxonomy of the marine,luminous bacteria

Summary One hundred and seventy-three strains of marine, luminous bacteria isolated from sea water, surfaces and intestines of fish, as well as from the luminous organs of fish and squid were submitted to an extensive phenotypic characterization. A numerical analysis of the results grouped these strains into four clusters which were formed on the basis of overall phenotypic similarity. One cluster, which was given the designationBeneckea harveyi, consisted of strains which had a moles% GC content in their DNAs of 46.5±1.3 and a single, sheathed, polar flagellum when grown in liquid medium. Most of these strains had unsheathed, peritrichous flagella in addition to the sheathed, polar flagellum when grown on solid medium. The two phenotypically similar clusters which were assigned the species designationsPhotobacterium phosphoreum andP. mandapamensis consisted of strains which had 1–3 unsheathed, polar flagella and moles % GC contents in their DNAs of 41.5±0.7 and 42.9±0.5, respectively. The cluster designatedP. fischeri contained strains having 2–8 sheathed, polar flagella and a moles % GC content of 39.8±1.1. These four species could be further distinguished on the basis of a number of nutritional properties as well as other phenotypic traits. The assignment of the luminous, marine bacteria to four species was supported by differences in the properties of the luminous system as well as differences in the pattern of regulation of spartokinase activity which are discussed. The speciesB. harveyi was found to be phenotypically similar to a number of previously characterized, non-luminous strains ofBeneckea which should probably be assigned to this species.Non-Standard Abbreviations ASW artificial sea water - ATCC American Type Culture Collection - BM basal medium - BMA basal medium agar - GC guanine plus cytosine - LA luminous medium agar - LB luminous medium broth - MA Difco Marine Agar - NCMB National Collection of Marine Bacteria - PHB poly--hydroxybutyrate - S similarity coefficient - YEB yeast extract broth This paper is part of a dissertation submitted by the senior author to the Graduate Division of the University of Hawaii in partial fulfillment of the requirements for the Ph.D. Degree in Microbiology