Bioactivity,Chemical Profiling,and 16S rRNA-Based Phylogeny of <Emphasis Type="BoldItalic">Pseudoalteromonas</Emphasis> Strains Collected on a Global Research Cruise

One hundred one antibacterial Pseudoalteromonas strains that inhibited growth of a Vibrio anguillarum test strain were collected on a global research cruise (Galathea 3), and 51 of the strains repeatedly demonstrated antibacterial activity. Here, we profile secondary metabolites of these strains to determine if particular compounds serve as strain or species markers and to determine if the secondary metabolite profile of one strain represents the bioactivity of the entire species. 16S rRNA gene similarity divided the strains into two primary groups: One group (51 strains) consisted of bacteria which retained antibacterial activity, 48 of which were pigmented, and another group (50 strains) of bacteria which lost antibacterial activity upon sub-culturing, two of which were pigmented. The group that retained antibacterial activity consisted of six clusters in which strains were identified as Pseudoalteromonas luteoviolacea, Pseudoalteromonas aurantia, Pseudoalteromonas phenolica, Pseudoalteromonas ruthenica, Pseudoalteromonas rubra, and Pseudoalteromonas piscicida. HPLC-UV/VIS analyses identified key peaks, such as violacein in P. luteoviolacea. Some compounds, such as a novel bromoalterochromide, were detected in several species. HPLC-UV/VIS detected systematic intra-species differences for some groups, and testing several strains of a species was required to determine these differences. The majority of non-antibacterial, non-pigmented strains were identified as Pseudoalteromonas agarivorans, and HPLC-UV/VIS did not further differentiate this group. Pseudoalteromonas retaining antibacterial were more likely to originate from biotic or abiotic surfaces in contrast to planktonic strains. Hence, the pigmented, antibacterial Pseudoalteromonas have a niche specificity, and sampling from marine biofilm environments is a strategy for isolating novel marine bacteria that produce antibacterial compounds.     

Anoxygenic phototrophic bacteria of the Kislo-Sladkoe stratified lake (White Sea,Kandalaksha Bay)

The community of anoxygenic phototrophic bacteria (APB) in the water column of the Kislo-Sladkoe stratified lake recently isolated from the sea (White Sea, Kandalaksha Bay) was investigated in September 2010. The water of the sulfide-rich zone was greenish-brown due to intense development of green sulfur bacteria (GSB). Nine APB strains were isolated from the water samples: three belonging to GSB, five, to purple sulfur bacteria (PSB), and one, to purple nonsulfur bacteria (PNB). GSB predominated in the phototrophic community of the chemocline. Unexpectedly, two morphologically different green-colored GSB strains were found to be phylogenetically identical and related to the brown-colored Chlorobium phaeovibrioides (99% similarity according to the 16S rRNA gene sequencing). Homology to the closest green-colored species (Chlorobium luteolum) was 98%. Two morphologically and physiologically similar PSB strains (TcrPS10 and AmPS10) had rounded cells containing okenone and gas vesicles. According to the 16S rRNA gene sequencing, these strains were most closely related (99%) to two different Thiocapsa species: Tca. marina (containing okenonee and no gas vesicles) and Tca. rosea (containing spirilloxanthin and gas vesicles). The remaining isolates of purple bacteria were similar to the already described APB species.     

Ecology and taxonomy of chitinoclasticCytophaga and related chitin-degrading bacteria isolated from an estuary

A total of 103 strains of estuarine, Chitinoclastic bacteria isolated from water, and sediment samples collected from the upper Chesapeake Bay, including 17 freshwater and 11 seawater isolates, were subjected to numerical taxonomy analysis. The isolates included 44 yellow-orange pigmented strains classified asCytophaga-like bacteria (CLB) of theCytophagaceae. Salt requirement of the strains ranged from tolerance to 1% NaCl to an absolute requirement for NaCl, with 1% NaCl satisfying this requirement. The largest phenon consisted of facultatively anaerobic, oligo-nitrophilic, and flexirubin pigment-producing freshwater and estuarine isolates, and included reference strains of bothCytophaga johnsonae Stanier andCytophaga aquatilis Strohl and Tait. Other phena, containing a smaller number of strains, comprised marine and estuarine isolates which did not produce flexirubin pigments, and required organic nitrogen for growth and for production of chitinolytic enzymes. Salt-requiring, flexirubin pigment-producing, chitin-degrading strains were, on occasion, isolated from estuarine samples and represented phena found in estuaries. Most of theCytophaga isolates, as well as chitin-degrading species not of the genusCytophaga that were isolated from Chesapeake Bay, clustered in phena representing previously described species of aerobic, zymogenic, chitinoclastic bacteria. When the frequency of occurrence of features related to environmental parameters, viz., pH, salinity, temperature range of growth, and growth on media lacking organic nitrogen, was calculated, ecological groupings of strains in the 2 major phena of CLB could be distinguished among the estuarine, chitin-degrading bacteria.     

Psychrotrophic amylolytic bacteria from deep sea sediment of Prydz Bay, Antarctic: diversity and characterization of amylases

Seventeen psychrotrophic bacteria with cold-adaptive amylolytic, lipolytic or proteolytic activity were isolated from deep sea sediment of Prydz Bay, Antarctic. They were affiliated with γ-Proteobacteria (12 strains) and gram-positive bacteria (5 strains) as determined by 16S rDNA sequencing. The amylase-producing strains belonged to genus Pseudomonas, Rhodococcus, and Nocardiopsis. Two Pseudomonas strains, 7193 and 7197, which showed highest amylolytic activity were chosen for further study. The optimal temperatures for their growth and amylase-producing were between 15 and 20°C. Both of the purified amylases showed highest activity at 40°C and pH 9.0, and retained 50% activity at 5°C. The SDS-PAGE and zymogram activity staining showed that the molecular mass of strain 7193 and 7197 amylases were about 60 and 50 kDa respectively. The Pseudomonas sp. 7193 amylase hydrolyzed soluble starch into glucose, maltose, maltotriose, and maltotetraose, indicating that it had both activities of α-amylase and glucoamylase. The product hydrolyzed by Pseudomonas sp. 7197 amylase was meltotetraose.     

Thiobacillus plumbophilus spec. nov., a novel galena and hydrogen oxidizer

From an uranium mine three strains of rodshaped, mesophilic, chemolithoautotrophic bacteria were isolated. They grow by oxidation of H₂S, galena (PbS) and H₂. Anglesite (PbSO₄) is formed from galena. No ferrous iron is oxidized by the isolates. They grow between pH 4 and 6.5 at temperatures of about 9 to 41°C (optimum around 27°C). The G+C content of the DNA is around 66 mol %. Based on their ability to oxidize sulfur compounds, the new organisms belong to the genus Thiobacillus. No significant homology with Thiobacillus ferrooxidans and Thiobacillus cuprinus was detected by DNA-DNA hybridization. Therefore the new isolates represent a new species within the genus Thiobacillus. Based on the unusual growth on galena, we name the new species Thiobacillus plumbophilus (type strain Gro 7; DSM 6690).     

Description of the novel perchlorate-reducing bacteria Dechlorobacter hydrogenophilus gen. nov., sp. nov. and Propionivibrio militaris, sp. nov.

Novel dissimilatory perchlorate-reducing bacteria (DPRB) were isolated from enrichments conducted under conditions different from those of all previously described DPRB. Strain LT-1^T was enriched using medium buffered at pH 6.6 with 2-(N-morpholino)ethanesulfonic acid (MES) and had only 95% 16S rRNA gene identity with its closest relative, Azonexus caeni. Strain MP^T was enriched in the cathodic chamber of a perchlorate-reducing bioelectrical reactor (BER) and together with an additional strain, CR (99% 16S rRNA gene identity), had 97% 16S rRNA gene identity with Propionivibrio limicola. The use of perchlorate and other electron acceptors distinguished strains MP^T and CR from P. limicola physiologically. Strain LT-1^T had differences in electron donor utilization and optimum growth temperatures from A. caeni. Strains LT-1^T and MP^T are the first DPRB to be described in the Betaproteobacteria outside of the Dechloromonas and Azospira genera. On the basis of phylogenetic and physiological features, strain LT-1^T represents a novel genus in the Rhodocyclaceae; strain MP^T represents a novel species within the genus Propionivibrio. The names Dechlorobacter hydrogenophilus gen. nov., sp. nov and Propionivibrio militaris sp. nov. are proposed.     

Isolation and characterization of new poly(3HB)‐accumulating star‐shaped cell‐aggregates‐forming thermophilic bacteria

Aims: This study aimed at isolating thermophilic bacteria that utilize cheap carbon substrates for the economically feasible production of poly(3‐hydroxybutyrate), poly(3HB), at elevated temperatures. Methods and Results: Thermophilic bacteria were enriched from an aerobic organic waste treatment plant in Germany, and from hot springs in Egypt. Using the viable colony staining method for hydrophobic cellular inclusions with Nile red in mineral salts medium (MSM) containing different carbon sources, six Gram‐negative bacteria were isolated. Under the cultivation conditions used in this study, strains MW9, MW11, MW12, MW13 and MW14 formed stable star‐shaped cell‐aggregates (SSCAs) during growth; only strain MW10 consisted of free‐living rod‐shaped cells. The phylogenetic relationships of the strains as derived from 16S rRNA gene sequence comparisons revealed them as members of the Alphaproteobacteria. The 16S rRNA gene sequences of the isolates were very similar (>99% similarity) and exhibited similarities ranging from 93 to 99% with the most closely related species that were Chelatococcus daeguensis, Chelatococcus sambhunathii , Chelatococcus asaccharovorans, Bosea minatitlanensis, Bosea thiooxidans and Methylobacterium lusitanum. Strains MW9, MW10, MW13 and MW14 grew optimally in MSM with glucose, whereas strains MW11 and MW12 preferred glycerol as sole carbon source for growth and poly(3HB) accumulation. The highest cell density and highest poly(3HB) content attained were 4·8 g l^?l (cell dry weight) and 73% (w/w), respectively. Cells of all strains grew at temperatures between 37 and 55°C with the optimum growth at 50°C. Conclusions: New PHA‐accumulating thermophilic bacterial strains were isolated and characterized to produce poly(3HB) from glucose or glycerol in MSM at 50°C. SSCAs formation was reported during growth. Significance and Impact of the Study: To the best of our knowledge, this is the first report on the formation of SSCAs by PHA‐accumulating bacteria and also by thermophilic bacteria. PHA‐producing thermophiles can significantly reduce the costs of fermentative PHA production.     

Epibiont foraminifera of Sertella frigida (Waters) (Bryozoa, Cheilostomata) from Terranova Bay, Ross Sea, Antarctica

Several arenaceous and calcareous foraminifera epibionts of Sertella frigida (Waters) (Bryozoa, Cheilostomata), collected in Terranova Bay during the 1989–90 Italian Antarctic expedition, were studied. Arenaceous species, such as Psammosphaera fusca Schulze f. adhearescens Rhumbler, Haplophragmoides canariensis d'Orbigny, Portatrochammina antarctica (Parr), and Trochammina arctica Hedley, Hurdle and Burdett, are a conspicuous component of the epifaunal community. The calcareous foraminifers encrusting S. frigida are mostly represented by Cibicides refulgens Montfort and Rosalina globularis d'Orbigny. Foraminifera were found only in the basal part of the bryozoan colonies. The presence of many juveniles provided evidence that foraminifers were reproducing at the time of sampling. Psammosphaera fusca f. adhaerescens was found exclusively inside the zooids of S. frigida. The large number of individuals associated with the bryozoan suggest that P. fusca f. adhaerescens finds optimum conditions (shelter, food, and grains for shell building) for growth inside the zooids of S. frigida. The other species occurred most commonly adhered to the trabeculae or to the zooid orifices of S. frigida. An elevated position offers a better chance to catch food particles from the overlying water column. Foraminifers could benefit also from bryozoan feeding currents. The availability of resuspended organic material could provide a more consistent source of food in a highly seasonal oligotrophic environment. Received: 8 February 1995/Accepted: 30 June 1996     

Inhibition of Rhizoctonia by endospore forming bacteria indigenous to landscape planting beds

Endospore forming bacteria were collected from root samples of 35 genera of bedding plants growing in established commercial landscape beds in Central Florida. One hundred and twenty-nine bacterial strains associated with 14 species were identified using fatty acid analysis (Microbial Identification System, MIDI). All strains were evaluated for in vitro inhibition of damping off disease caused by the fungus Rhizoctonia solani. The strongest inhibition of Rhizoctonia by soluble exudates in cocultivation was observed with strains belonging to six species: B. cereus, B. pumilus, B. thuringiensis, L. sphaericus, B. amyloliquefaciens, and B. subtilis. Most strains that inhibited Rhizoctonia growth in cocultivation also inhibited growth via volatile compounds. All 129 strains were evaluated for ability to protect impatiens plants from subsequent challenge infection by Rhizoctonia solani. Certain strains of endospore forming bacteria also enhanced plant growth. It is apparent from this study that the Bacillus community associated with bedding plants in established planting beds produce soluble antifungal compounds, volatile antifungal compounds, and enhance plant growth. In developing biological control, it may be a more practical approach to promote or enhance a natural, multifaceted community of Bacillus strains within our planting beds.     

Anaerobic,alkaliphilic, saccharolytic bacterium <Emphasis Type="Italic">Alkalibacter saccharofermentans</Emphasis> gen. nov., sp. nov. from a soda lake in the Transbaikal region of Russia

Three strains of new obligately anaerobic alkaliphilic bacteria have been isolated as a saccharolytic component from the cellulolytic community of alkaline Lake Nizhnee Beloe (Transbaikal region, Russia), a lake with low salt concentration. DNA analysis of these strains showed an interspecies level of DNA similarity of 96–100%. Strain Z-79820 was selected for further investigations. Cells were Gram-positive, asporogenous, nonmotile short rods with pointed ends. The strain was a true alkaliphile: growth occurred from pH 7.2 to 10.2 with the optimum at pH 9.0. Strain Z-79820 was halotolerant and could grow in medium with up to 10% (w/v) NaCl, with the optimum between 0 and 4% NaCl. The new isolate obligately depended on Na⁺ ions in the form of carbonates or chlorides. Total Na⁺ content needed for optimal growth was 0.46 M Na⁺, with a wide range from 0.023–0.9 M Na⁺ at which growth also occurred. The isolate was a mesophile and grew at temperatures from 6 to 50°C (slow growth at 6 and 15°C) with an optimum at 35°C. The organotrophic organism fermented ribose, xylose, glucose, mannose, fructose, sucrose, mannitol, and peptone. The products of glucose fermentation were acetate, ethanol, formate, H₂, and CO₂. Yeast extract was required for some anabolic needs. The DNA G+C content of the type strain Z-79820 was 42.1 mol%. The new bacterium fell into the 16S rRNA gene cluster XV of the Gram-positive bacteria with low G+C content, where it formed an individual branch. Based on its growth characteristics and genotype traits, we propose the new genus and species named Alkalibacter saccharofermentans with the type strain Z-79820 (=DSM14828), Uniqem-218 (Institute Microbiology, RAS; ).     

Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus

Four red-pigmented isolates, with optimum growth temperatures of approximately 55–60 °C and an optimum pH for growth between 7.5 and 8.5, were recovered from hot springs in Central France. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. The new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the glycolipid profile and fatty acid composition because these organisms lacked the hydroxy fatty acids and the glycolipid variant GL-1a found in all other isolates of the species of Meiothermus examined. On the basis of the results presented here we propose the name Meiothermus rufus for the new species, which is represented by strains CAL-4^T (=DSM 22234^T=LMG 24878^T) and CAL-12 (=DSM 22235=LMG 24879). We also propose emending the genus Meiothermus to include strains that have only one glycolipid instead of two glycolipid variants.     

Respiration of Orchomene plebs (Hurley, 1965) and Waldeckia obesa (Chevreux, 1905) from Admiralty Bay (South Shetlands Islands,Antarctic)

Metabolism of Orchomene plebs from Admirably Bay is higher than that of Waldeckia obesa, and similar to that of P. plebs from McMurdo Sound. The range of variation in respiration is highest below freezing which means that these are optimum temperatures for the Amphipoda species under study.     

Comparisons between the biology of two co-occurring species of whiting (Sillaginidae) in a large marine embayment

Synopsis We compare the biology of the tropical species Sillago analis and the temperate species Sillago schomburgkii in Shark Bay, a large subtropical marine embayment on the west coast of Australia. This environment constitutes approximately the southernmost and northernmost limits of the distributions of these two species, respectively. The annuli visible in sectioned otoliths of S. analis and S. schomburgkii form annually. Their numbers were thus used to age the individuals of these two species, which are morphologically very similar and live in the same habitats. Although the growth rates of S. analis and S. schomburgkii are very similar until maturity is attained, they subsequently diverge, with S. schomburgkii investing relatively more energy into somatic growth. The maximum total lengths and ages of both the females (320 mm, 6 years) and males (283 mm, 8 years) of S. analis were not as great as those of the females (383 mm, 9 years) and males (302 mm, 9 years) of S. schomburgkii. In Shark Bay, S. schomburgkii spawns earlier and longer than S. analis, i.e. August–December vs. January–March, which would result in the juveniles of these two species recruiting into nursery areas at different times. In addition, S. schomburgkii spawns earlier and for longer in Shark Bay than in temperate marine waters 800 km further south, presumably reflecting the fact that, in that subtropical embayment, water temperatures over which this species typically spawns are attained earlier and last for longer. However, although environmental conditions in Shark Bay and those temperate marine waters differ markedly, the growth of the corresponding sexes of S. schomburgkii in these two water bodies is similar.     

Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov.

Two methanotrophic bacteria with optimum growth temperatures above 40° C were isolated. Thermotolerant strain LK6 was isolated from agricultural soil, and the moderately thermophilic strain OR2 was isolated from the effluent of an underground hot spring. When compared to the described thermophilic methanotrophs Methylococcus capsulatus and Methylococcus thermophilus, these strains are phenotypically similar to Methylococcus thermophilus. However, their 16S rRNA gene sequences are markedly different from the sequence of Methylococcus thermophilus (∼ 8% divergence) and, together with Methylomonas gracilis, they form a distinct, new genus within the γ-subgroup of the Proteobacteria related to extant Type I methanotrophs. Further phenotypic characterisation showed that the isolates possess particulate methane monooxygenase (pMMO) but do not contain soluble methane monooxygenase. The nucleotide sequence of a gene encoding pMMO (pmoA) was determined for both isolates and for Methylomonas gracilis. PmoA sequence comparisons confirmed the monophyletic nature of this newly recognised group of thermophilic methanotrophs and their relationship to previously described Type I methanotrophs. We propose that strains OR2 and LK6, together with the misclassified thermophilic strains Methylomonas gracilis VKM-14L^T and Methylococcus thermophilus IMV-B3122, comprise a new genus of thermophilic methanotrophs, Methylocaldum gen. nov., containing three new species: Methylocaldum szegediense, Methylocaldum tepidum and Methylocaldum gracile. Received: 2 April 1997 / Accepted: 23 July 1997     

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture‐dependent and PCR‐DGGE methods

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture‐dependent method and PCR‐DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty‐five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.     

Physiological and genomic characterization of a new ‘Candidatus Nitrotoga’ isolate

Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus ‘Candidatus Nitrotoga’ may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the ‘Ca. Nitrotoga’ sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although ‘Ca. Nitrotoga’ have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced ‘Ca. Nitrotoga’ strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus ‘Ca. Nitrotoga’.     

Leptospirillum-Like Bacteria and Evaluation of Their Role in Pyrite Oxidation

Two strains of Leptospirillum-like bacteria isolated from dumps of Alaverdi and Akhtala sulfide ore deposits in Armenia were studied. The optimum and maximum temperatures for the growth of both strains were 37 and 40°C, respectively. The pH optimum was 2.0–2.3. Bacterial growth and ferrous iron oxidation were inhibited by yeast extract. The pyrite-leaching activity of the Leptospirillum-like bacteria under mesophilic conditions was close to that of Acidithiobacillus ferrooxidans and exceeded by 2.0–2.7 times the activity of these moderately thermophilic bacteria at 37°C. The leaching of pyrite by Leptospirillum-like bacteria increased in the presence of sulfur-oxidizing bacteria, particularly, in their association with a thermotolerant sulfur-oxidizing bacterium.     

Estimation of growth and exopolysaccharide production by two soil cyanobacteria,Scytonema tolypothrichoides and Tolypothrix bouteillei as determined by cultivation in irradiance and temperature crossed gradients

Two filamentous cyanobacteria of the genera Scytonema and Tolypothrix were reported to be effective for stabilizing soil in arid areas due to the production of significant amounts of extracellular polysaccharides (EPS). These EPS may also have applications in the biotechnology industry. Therefore, two cyanobacterial species, Scytonema tolypothrichoides and Tolypothrix bouteillei were examined using crossed gradients of temperature (8–40°C) and irradiance (3–21 W m^?2) to identify their temperature and irradiance optima for maximum biomass and EPS production. According to their reported temperature requirements, both strains were considered mesophilic. The optimum growth range of temperature in S. tolypothrichoides (27 to 34°C) was higher than T. bouteillei (22–32°C). The optimum irradiance range for growth of S. tolypothrichoides (9–13 W m^?2) was slightly lower than T. bouteillei (7–18 W m^?2). Maximum EPS production by S. tolypothrichoides occurred at similar temperatures (28–34°C) as T. bouteillei (27–34°C), both slightly higher than for maximum growth. The optimum irradiance range for EPS production was comparable to that for growth in S. tolypotrichoides (8–13 W m^?2), and slightly lower in T. bouteillei (7–17 W m^?2). The Redundancy Analysis confirmed that temperature was the most important controlling factor and protocols for field applications or for mass cultivation can now be developed.     

Identification and succession of lactic acid bacteria during fermentation of 'urutan', a Balinese indigenous fermented sausage

'Urutan' is a Balinese traditional fermented sausage, which is made of lean pork and fat mixed with spices, sugar, and salt. The mixture is stuffed into cleaned pig intestine and fermented under uncontrolled condition during sun drying for 5 days. The investigation showed that lactic acid bacteria (LAB) were the dominating bacteria during 'urutan' fermentation. Among the 71 isolates obtained, lactobacilli dominated by 77.5% and the other 22.5% were pediococci. Based on physiological characteristics, the isolates were classified into 13 groups: nine belonged to the lactobacilli and the other four were pediococci. One isolate representing each group was chosen randomly, and then was identified by 16S rDNA sequence comparison. Phylogenetic relationship positioned three groups to Lactobacillus plantarum and four groups were closely related to L. farciminis. Two groups were identified as obligate heterofermentative lactobacilli: one was L. fermentum and the other was distantly related to L. hilgardii. Two groups belonging to the pediococci were strains of Pediococcus acidilactici and the other two were closely related to P. pentosaceus. A dramatic succession occurred during fermentation of 'urutan'. Three species mainly dominated the process wherein the initial growth was started by L. plantarum then followed by the growth of P. acidilactici, and finally, L. farciminis was found to be predominant at the last stage of fermentation.     

Genotypic characterization of Brochothrix spp. isolated from meat,poultry and fish

Aim: To study genotypic diversity of isolates of Brochothrix thermosphacta recovered from meat, poultry and fish. Methods and Results: A total of 27 bacteria isolated from 19 samples of meat, poultry and fish were identified phenotypically and genotypically using PCR amplification of 16S‐23S rDNA intergenic transcribed spacer (ITS‐PCR), repetitive sequence‐based PCR (rep‐PCR) and 16S rDNA sequencing. Using ITS‐PCR, all bacteria showed the same DNA profile as the reference strains of Br. thermosphacta, allowing typing of the isolates at species level. Using 16S rDNA sequencing, all isolates were identified, at genus and species level, as Br. thermosphacta. Identification as Br. campestris was observed with a lower, but very close, level of similarity. Rep‐PCR was more discriminatory than ITS‐PCR and allowed differentiation of four subgroups among the isolates. Conclusion: Minor genotypic differences among Br. thermosphacta strains from meat, poultry and fish were observed. Significance and Impact of the Study: A rudimentary exploration of genotypic differences of Br. thermosphacta from meat, poultry and fish resulted in preliminary confirmation of the suitability of ITS‐PCR for typing Br. thermosphacta and confirmed the value of rep‐PCR fingerprinting to discriminate between Br. thermosphacta strains.