The relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated.
A novel bacterium, strain MUSC 273(T), was isolated from mangrove sediments of the Tanjung Lumpur river in the state of Pahang in peninsular Malaysia. The bacterium was yellow-pigmented, Gram-negative, rod-shaped and non-spore-forming. The taxonomy of strain MUSC 273(T) was studied by a polyphasic approach and the organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence of strain MUSC 273(T) showed the highest sequence similarity to those of Novosphingobium indicum H25(T) (96.8 %), N. naphthalenivorans TUT562(T) (96.4 %) and N. soli CC-TPE-1(T) (95.9 %) and lower sequence similarity to members of all other species of the genus Novosphingobium. Furthermore, in phylogenetic analyses based on the 16S rRNA gene sequence, strain MUSC 273(T) formed a distinct cluster with members of the genus Novosphingobium. DNA-DNA relatedness of strain MUSC 273(T) to the type strains of the most closely related species, N. indicum MCCC 1A01080(T) and N. naphthalenivorans DSM 18518(T), was 29.2 % (reciprocal 31.0 %) and 17 % (reciprocal 18 %), respectively. The major respiratory quinone was ubiquinone Q-10, the major polyamine was spermidine and the DNA G+C content was 63.3±0.1 mol%. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine and sphingoglycolipid. The major fatty acids were C18 : 1ω7c, C17 : 1ω6c, C16 : 0, C15 : 0 2-OH and C16 : 1ω7c. Comparison of BOX-PCR fingerprints indicated that strain MUSC 273(T) represented a unique DNA profile. The combined genotypic and phenotypic data showed that strain MUSC 273(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium malaysiense sp. nov. is proposed. The type strain is MUSC 273(T) ( = DSM 27798(T) = MCCC 1A00645(T) = NBRC 109947(T)).
The Caligidae is a family of parasitic copepods containing over 30 recognised genera. They are commercially important parasites as they cause disease in numerous finfish aquaculture facilities globally. Morphological features are used to distinguish between the genera and Pseudocaligus has traditionally been differentiated from Caligus solely by the presence of a much reduced form of the fourth thoracic leg. Currently there are numerous DNA sequences available for Caligus spp. but only the type species, Pseudocaligus brevipedis, has molecular data available, so systematic studies using molecular phylogenetic analyses have been limited.
This study aimed to isolate and identify Lactobacillus in the honey stomach of honeybee Apis dorsata. Samples of honeybee were collected from A. dorsata colonies in different bee trees and Lactobacillus bacteria isolated from honey stomachs. Ninety two isolates were Gram-stained and tested for catalase reaction. By using bacterial universal primers, the 16S rDNA gene from DNA of bacterial colonies amplified with polymerase chain reaction (PCR). Forty-nine bacterial 16S rDNA gene were sequenced and entrusted in GenBank. Phylogenetic analysis showed they were different phylotypes of Lactobacillus. Two of them were most closely relevant to the previously described species Lactobacillus plantarum. Other two phylotypes were identified to be closely related to Lactobacillus pentosus. However, only one phylotype was found to be distantly linked to the Lactobacillus fermentum. The outcomes of the present study indicated that L. plantarum, L. pentosus, and L. fermentum were the dominant lactobacilli in the honey stomach of honeybee A. dorsata collected during the dry season from Malaysia forest area - specifically "Melaleuca in Terengganu".
A novel actinobacterial strain, designated MUSC 201T, was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201T represented a novel lineage within the class Actinobacteria. Strain MUSC 201T formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1%), Aeromicrobium (92.7-94.6%), Marmoricola (92.5-93.1%) and Kribbella (91.5-92.4%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3γ. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5:0.9:1.0:1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18:1ω9c (30.8%), C16:0 (24.1%), and 10-methyl C18:0 (13.9%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201T (=DSM 27763T=MCCC 1A00646T=NBRC 109973T).
Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202(T) and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter. Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838(T) (97.9-98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963(T) and Acinetobacter bouvetii 4B02(T) (85.4-87.6 and 78.1-82.7 %, respectively). Strain 11-0202(T) displayed low DNA-DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter. The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter: summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3-27.2 %), C18 : 1ω9c (19.9-22.1 %), C16 : 0 (15.2-22.0 %) and C12 : 0 (9.2-14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202(T) ( = KCTC 32033(T) = JCM 18512(T)).
The diversity of specific bacteria taxa, such as the actinomycetes, has not been reported from the Antarctic island of Barrientos. The diversity of actinomycetes was estimated with two different strategies that use PCR-denaturing gradient gel electrophoresis. First, a PCR was applied, using a group-specific primer that allows selective amplification of actinomycete sequences. Second, a nested-PCR approach was used that allows the estimation of the relative abundance of actinomycetes within the bacterial community. Molecular identification, which was based on 16S rDNA sequence analysis, revealed eight genera of actinomycetes, Actinobacterium, Actinomyces, an uncultured Actinomycete, Streptomyces, Leifsonia, Frankineae, Rhodococcus, and Mycobacterium. The uncultured Actinomyces sp and Rhodococcus sp appear to be the prominent genera of actinomycetes in Barrientos Island soil. PCR-denaturing gradient gel electrophoresis patterns were used to look for correlations between actinomycete abundance and environmental characteristics, such as type of rookery and vegetation. There was a significant positive correlation between type of rookery and abundance of actinomycetes; soil samples collected from active chinstrap penguin rookeries had the highest actinomycete abundance. Vegetation type, such as moss, which could provide a microhabitat for bacteria, did not correlate significantly with actinomycete abundance.
Microbial diversity within formation water and oil from two compartments in Bokor oil reservoir from a Malaysian petroleum oil field was examined. A total of 1,056 16S rRNA gene clones were screened from each location by amplified ribosomal DNA restriction analysis. All samples were dominated by clones affiliated with Marinobacter, some novel Deferribacteraceae genera and various clones allied to the Methanococci. In addition, either Marinobacterium- or Pseudomonas-like operational taxonomic units were detected from either compartment. A systematic comparison with the existing pertinent studies was undertaken by analysing the microbial amplicons detected and the PCR primers used. The analyses demonstrated that bacterial communities were site specific, while Archaea co-occurred more frequently. Amplicons related to Marinobacter, Marinobacterium and Pseudomonas were detected in a number of the studies examined, suggesting they may be ubiquitous members in oil reservoirs. Further analysis of primers used in those studies suggested that most primer pairs had fairly broad but low matches across the bacterial and archaeal domains, while a minority had selective matches to certain taxa or low matches to all the microbial taxa tested. Thus, it indicated that primers may play an important role in determining which taxa would be detected.
A diesel-degrading bacterium has been isolated from a diesel-polluted site. The isolate was tentatively identified as Staphylococcus aureus strain DRY11 based on partial 16S rDNA molecular phylogeny and Biolog GP microplate panels and Microlog database. Isolate 11 showed an almost linear increase in cellular growth with respect to diesel concentrations with optimum growth occurring at 4% (v/v) diesel concentration. Optimization studies using different nitrogen sources showed that the best nitrogen source was potassium nitrite. Sodium nitrite was optimum at 1.2 g l(-1) and higher concentrations were strongly inhibitory to cellular growth. The optimal pH that supported growth of the bacterium was between 7.5 to 8.0 and the isolate exhibited optimal broad temperature supporting growth on diesel from 27 to 37 degrees C. An almost complete removal of diesel components was seen from the reduction in hydrocarbon peaks observed using Solid Phase Microextraction Gas Chromatography analysis after 5 days of incubation. The characteristics of this bacterium suggest that it is suitable for bioremediation of diesel spills and pollutions in the tropics.
A single Leptospira strain (designated Bejo-Iso9(T)) was isolated from a soil sample taken in Johor, Malaysia. The isolate showed motility and morphology typical of the genus Leptospira under dark-field microscopy. Cells were found to be 10-13 microm in length and 0.2 microm in diameter, with a wavelength of 0.5 microm and an amplitude of approximately 0.2 microm. Phenotypically, strain Bejo-Iso9(T) grew in Ellinghausen-McCullough-Johnson-Harris medium at 13, 30 and 37 degrees C, and also in the presence of 8-azaguanine. Serologically, strain Bejo-Iso9(T) produced titres towards several members of the Tarassovi serogroup, but was found to be serologically unique by cross-agglutinin absorption test and thus represented a novel serovar. The proposed name for this serovar is Malaysia. Phylogenetic analysis of 16S rRNA gene sequences placed this novel strain within the radiation of the genus Leptospira, with sequence similarities within the range 90.4-99.5% with respect to recognized Leptospira species. DNA-DNA hybridization against the three most closely related Leptospira species was used to confirm the results of the 16S rRNA gene sequence analysis. The G+C content of the genome of strain Bejo-Iso9(T) was 36.2 mol%. On the basis of phenotypic, serological and phylogenetic data, strain Bejo-Iso9(T) represents a novel species of the genus Leptospira, for which the name Leptospira kmetyi sp. nov. is proposed. The type strain is Bejo-Iso9(T) (=WHO LT1101(T)=KIT Bejo-Iso9(T)).
This study for the first time provides insight into the bacterial community in the benthic region of the Off-Terengganu Coastline, which is considered to be anthropogenically polluted due to heavy fishing vessel commotion. Subsurface bacteria were randomly collected from two locations at different depths and were examined using the 16S rDNA V3-V4 marker gene on the Illumina™ Miseq platform. In addition, the physiochemical parameters of the sediment were also measured. Surprisingly, the results show a high diversity of sulfur-oxidizing bacteria in the surveyed area, where Sulfurovum sp. was identified to predominate the overall bacterial community. The physiochemical parameters reveal insufficient evidence of hydrothermal vents in the surveyed area. However, there are traces of hydrocarbon pollutants such as gasoline, diesel, and mineral oil in this area. It is assumed that sediment accumulation in the lee of breakwater plays an important role in trapping the runoff from the nearby harbor, which includes oil spills. Based on the common knowledge, Sulvurofum sp. is a native bacterium that exists in deep hydrothermal vents and volcanic territories. Although the reason for the abundance of Sulfurovum sp. in the surveyed area is still unclear, there is a possibility that metabolic adaptation plays an important role in regulating hydrocarbon pollutants for survival. The work presented in this paper therefore has profound implications for future studies on Sulfurovum sp. versatility. However, future research is needed to strengthen the findings of this study and to provide a better evidence regarding the metabolic response of this bacterium toward hydrocarbon pollutants.
The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).
The morphotaxonomy of Rhipicephalus microplus complex has been challenged in the last few years and prompted many biologists to adopt a DNA-based method for distinguishing the members of this group. In the present study, we used a mitochondrial DNA analysis to characterise the genetic assemblages, population structure and dispersal pattern of R. microplus from Southeast Asia, the region where the species originated.
Lactic acid bacteria (LAB) are the predominant micro-organisms in tempoyak, a Malaysian acid-fermented condiment. In a study on the diversity of LAB in this product, three isolates could not be identified using SDS-PAGE of whole-cell proteins or API 50 CH. The taxonomic position of the three isolates was clarified in the present study. 16S rDNA sequencing classified a representative strain in the genus Lactobacillus, clearly separated from all known species, and most closely related to the Lactobacillus reuteri phylogenetic group. DNA-DNA hybridization experiments and an extensive phenotypic description confirm that the strains represent a single and separate novel species among the obligately heterofermentative lactobacilli. The three isolates are distinguished at the intra-species level by plasmid profiling, pulsed-field gel electrophoresis of macro-restriction fragments and biochemical features. The name Lactobacillus durianis sp. nov. is proposed for the novel taxon and the type strain is LMG 19193T (= CCUG 45405T).
Five strains of phytase-producing, gram-negative, non-spore-forming, non-motile, small, stout, rod-shaped, strictly anaerobic, fermentative bacteria were isolated from the rumens of cattle in Malaysia. All five strains had morphological, physiological and biochemical features in common. Although these strains had many physiological and biochemical characteristics that were identical to those of the Mitsuokella multacida type strain (ATCC 27723T), they could be distinguished from this species by means of the following characteristics: a smaller cell size (1.2-2.4 microm long and 0.6-0.8 microm wide); a lower final pH value (3.8-4.0) in peptone/yeast extract/glucose broth; inhibition by 0.001% brilliant green; insensitivity to kanamycin (100 microg ml(-1)) and penicillin (10 microg ml(-1)); a higher optimum growth temperature (approx. 42 degrees C); the ability to grow at 45 and 47 degrees C; the ability to ferment glycerol, sorbitol and amidon; and the inability to ferment mannitol, rhamnose, D-tagatose and melezitose. The G+C content of the type strain (M 9T) of these five strains was 56.9 mol%. Analysis of the 16S rRNA gene sequence of type strain M 9T indicated that the strain falls within the genus Mitsuokella. The sequence similarity between type strain M 9T and Mitsuokella multacida was 98.7%. The DNA-DNA relatedness between type strain M 9T and Mitsuokella multacida type strain DSM 20544T (= ATCC 27723T) was 63.8%, indicating that, in spite of a high level of similarity for the 16S rRNA gene sequence, type strain M 9T is independent of Mitsuokella multacida at the species level. On the basis of these results, a new species, Mitsuokella jalaludinii sp. nov., is proposed for these strains. The type strain is M 9T (= DSM 13811T = ATCC BAA-307T).
Paralactobacillus selangorensis gen. nov., sp. nov. is described. This organism, isolated from a Malaysian food ingredient called chili bo, is an obligatory homofermentative, rod-shaped lactic acid bacterium. The G+C content is 46.1-46.2+/-0.3 mol%. Earlier 16S rRNA studies showed that this organism constitutes a new taxon distantly related to the Lactobacillus casei-Pediococcus group. A phenotypic description that distinguishes Paralactobacillus selangorensis from other genera of lactic acid bacteria is presented. The type strain of Paralactobacillus selangorensis is LMG 17710T.
Pulsed field gel electrophoresis analysis of genomic DNA was used to investigate genetic diversity among Dichelobacter nodosus from footrot in sheep in Malaysia. Twelve Dichelobacter nodosus strains isolated from lesion materials from infected sheep were confirmed as Dichelobacter nodosus by polymerase chain reaction technique using the species-specific Dichelobacter nodosus 16S RNA sequence Ac and C as primers. Pulsed field gel electrophoresis banding profiles using restriction enzymes ApaI (5'GGGCCC3'), SfiI (5'GGCCNNNNNGGCC3') and SmaI ('5CCCGGG3') enabled the 12 Dichelobacter nodosus strains to be differentiated into eight different PFGE patterns and thus genome-types, with F (coefficient of similarity) values ranging from 0.17 to 1.0 (ApaI), 0.14 to 1.0 (SfiI) and 0.22 to 1.0 (SmaI). Strains with origin in different farms were shown to have different PFGE patterns (two strains, M7 and M8 were the only exception). On the basis of their PFGE, all field strains used in the study differed from the reference strains. Our data revealed that there are several clonal types of Dichelobacter nodosus isolates and indicated that there is probably more than one source of this pathogen on the farms studied. The study showed that strains of D. nodosus exhibited considerable genetic diversity using this method and that genomic analysis by pulsed field gel electrophoresis was useful in discriminating the D. nodosus strains.
This study determined the effect of light intensity and photoperiod on the dry cell weight and total amount of carotenoids in four isolates of purple non-sulfur bacteria obtained from shaded and exposed microhabitats of a mangrove ecosystem in Kota Kinabalu, Sabah, Malaysia. The initial isolation of the bacteria was carried out using synthetic 112 medium under anaerobic conditions (2.5 klx) at 30 ± 2°C. On the basis of colony appearance, cell morphology, gram staining, motility test, and 16S rRNA gene sequencing analyses, all four bacteria were identified as Afifella marina. One of the bacterial isolates, designated as Af. marina strain ME, which was extracted from an exposed mud habitat within the mangrove ecosystem, showed the highest yield in dry cell weight (4.32± 0.03 g/l) as well as total carotenoids (0.783 ± 0.002 mg/g dry cell weight). These values were significantly higher than those for dry cell weight (3.77 ± 0.02g/l ) and total carotenoid content (0.706 ± 0.008 mg/g) produced by the isolates from shaded habitats. Further analysis of the effect of 10 levels of light intensity on the growth characteristics of Af. marina strain ME showed that the optimum production of dry cell weight and total carotenoids was achieved at different light intensities and incubation periods. The bacterium produced the highest dry cell weight of 4.98 g/l at 3 klx in 72 h incubation, but the carotenoid production of 0.783 mg/g was achieved at 2.5 klx in 48 h incubation. Subsequent analysis of the effect of photoperiod on the production of dry cell weight and total carotenoids at optimum light intensities (3 and 2.5 klx, respectively) revealed that 18 and 24 h were the optimum photoperiods for the production of dry cell weight and total carotenoids, respectively. The unique growth characteristics of the Af. marina strain ME can be exploited for biotechnology applications.
The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An α-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86-92% similar to known sequences.