Effects of ammonium and nitrite on growth and competitive fitness of cultivated methanotrophic bacteria.

The effects of nitrite and ammonium on cultivated methanotrophic bacteria were investigated. Methylomicrobium album ATCC 33003 outcompeted Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels, whereas cultures with high ammonium levels allowed Methylocystis sp. to compete more easily. M. album pure cultures and cocultures consumed nitrite and produced nitrous oxide, suggesting a connection between denitrification and nitrite tolerance.

Molecular ecological analysis of planktonic bacterial communities in constructed wetlands invaded by Culex (Diptera: Culicidae) mosquitoes.

The succession of the planktonic bacterial community during the colonization by Culex (Diptera: Culicidae) mosquitoes of 0.1-ha treatment wetlands was studied using denaturing gradient gel electrophoresis (DGGE) methodology. Relationships between apparent bacterial diversity and ecological factors (water quality, total bacterial counts, and immature mosquito abundance) were determined during a 1-mo flooding period. Analysis of DGGE banding patterns indicated that days postflooding and temporal changes in water quality were the primary and secondary determinants, respectively, of diversity in bacterial communities. Lower levels of diversity were associated with later postflood stages and increases in ammoniacal nitrogen concentration and total bacterial counts. Diversity was therefore most similar for bacteria present on the same sampling date at wetland locations with similar flooding regimes and water quality, suggesting that wastewater input was the driving force shaping bacterial communities. Comparatively small changes in bacterial diversity were connected to natural processes as water flowed through the wetlands. Greater immature mosquito abundance coincided with less diverse communities composed of greater total numbers of bacteria. Five individual DGGE bands were directly associated with fluctuations in mosquito production, and an additional 16 bands were associated with hydrological aspects of the environment during the rise and fall of mosquito populations. A marked decline in mosquito numbers 21 d after inundation may have masked associations of bacterial communities and mosquito recruitment into the sparsely vegetated wetlands. DGGE was an effective tool for the characterization of bacteria in mosquito habitat in our study, and its potential application in mosquito ecology is discussed.

Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae.

Three novel heterotrophic, Gram-negative, yellow-pigmented, aerobic, gliding, oxidase- and catalase-positive bacteria were isolated from algae collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied represented members of the family Flavobacteriaceae and showed 93.5-93.8 % similarity with their closest relative, Psychroserpens burtonensis. The DNA G+C content of the strains was 34-37 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C(15 : 0), anteiso-C(15 : 0), iso-C(15 : 1), iso-C(16 : 0)-3OH and iso-C(17 : 0)-3OH. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the newly described bacteria have been assigned to the new genus Winogradskyella gen. nov., as Winogradskyella thalassocola sp. nov. (type strain, KMM 3907T=KCTC 12221T=LMG 22492T=DSM 15363T), Winogradskyella epiphytica sp. nov. (type strain, KMM 3906T=KCTC 12220T=LMG 22491T=CCUG 47091T) and Winogradskyella eximia sp. nov. (type strain, KMM 3944T (=KCTC 12219T=LMG 22474T).

Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment.

An actinobacterial strain was isolated from marine sediment taken from the Troitsa Bay of the Gulf of Peter the Great, East Siberian Sea, and subjected to a taxonomic investigation. The isolate, designated KMM 3905T, was Gram-positive, aerobic, non-motile and coccoid. The strain tolerated up to 15 % NaCl in growth media, although its presence was not essential for growth. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification in the genus Kocuria. The strain formed an independent phylogenetic line in the 16S rRNA gene tree encompassed by members of Kocuria. Comparison of phenotypic characteristics also supported its assignment to a novel species within Kocuria. The name Kocuria marina sp. nov. (type strain KMM 3905T = KCTC 9943T) is proposed for this halotolerant actinobacterium from the marine environment.

A viable microbial community in a subglacial volcanic crater lake, Iceland.

We describe a viable microbial community in a subglacial lake within the Grímsvötn volcanic caldera, Iceland. We used a hot water drill to penetrate the 300-m ice shelf and retrieved lake water and volcanic tephra sediments. We also acquired samples of borehole water before and after penetration to the lake, overlying glacial ice and snow, and water from a nearby subaerial geothermal lake for comparative analyses. Lake water is at the freezing point and fresh (total dissolved solids = 260 mg L(-1)). Detectable numbers of cells were found in samples of the lake water column and tephra sediments: 2 x 10(4) ml(-1) and 4 x 10(7) g(-1), respectively. Plate counts document abundant cold-adapted cultivable organisms in the lake water, but not in the borehole (before penetration) or glacial ice. Denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments amplified from genomic DNA extracted from Grímsvötn samples indicates that the lake community is distinct from the assemblages of organisms in borehole water (before penetration) and the overlying ice and snow. Sequencing of selected DGGE bands revealed that many sequences are highly similar to known psychrophilic organisms or cloned DNA from other cold environments. Significant uptake of 14C-labeled bicarbonate occurred in dark, low-temperature incubations of lake water samples, indicating the presence of autotrophs. Acetylene reduction assays under similar incubation conditions showed no significant nitrogen fixation potential by lake water samples. This may be a consequence of the inhibition of diazotrophy by nitrogen in the lake.

Maribacter gen. nov., a new member of the family Flavobacteriaceae, isolated from marine habitats, containing the species Maribacter sedimenticola sp. nov., Maribacter aquivivus sp. nov., Maribacter orientalis sp. nov. and Maribacter ulvicola sp. nov.

Six novel gliding, heterotrophic, Gram-negative, yellow-pigmented, aerobic, oxidase- and catalase-positive bacteria were isolated from the green alga Ulva fenestrata, sea water and a bottom sediment sample collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied were members of the family Flavobacteriaceae. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacteria have been assigned to the new genus Maribacter gen. nov., as Maribacter sedimenticola sp. nov., Maribacter orientalis sp. nov., Maribacter aquivivus sp. nov. and Maribacter ulvicola sp. nov., with the type strains KMM 3903T (=KCTC 12966T=CCUG 47098T), KMM 3947T (=KCTC 12967T=CCUG 48008T), KMM 3949T (=KCTC 12968T=CCUG 48009T) and KMM 3951T (=KCTC 12969T=DSM 15366T), respectively.

Arenibacter certesii sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata.

The taxonomic position of a novel, marine, heterotrophic, aerobic, pigmented, non-motile bacterium that was isolated from a green alga, Ulva fenestrata, inhabiting the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strain, KMM 3941T, is a member of the genus Arenibacter. The results of DNA-DNA hybridization experiments, supported by phenotypic and chemotaxonomic data, showed that the isolate represents a novel species of the genus Arenibacter, for which the name Arenibacter certesii sp. nov. is proposed. The type strain is KMM 3941T (=KCTC 12113T=CCUG 48006T).

Algibacter lectus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from green algae.

Three strains of the marine, gliding, pigmented, facultatively anaerobic, heterotrophic, Gram-negative bacteria were isolated from the green algae Acrosiphonia sonderi (Kütz) Kornm and Ulva fenestrata Ruprecht inhabiting the Sea of Japan. 16S rDNA sequence analysis indicated that the strains were members of the family Flavobacteriaceae, in which they occupied separate lineages. The predominant cellular fatty acids were i15 : 0, a15 : 0, i15 : 1, 15 : 0, 15 : 1omega6c, i15 : 0 3-OH and i17 : 0 3-OH. The DNA base compositions were 31-33 mol% G+C. Based on the phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the novel bacteria should be placed in a novel taxon as Algibacter lectus gen. nov., sp. nov. with type strain KMM 3902G (=KCTC 12103T=DSM 15365T).

Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata.

Two heterotrophic, aerobic, Gram-negative, pigmented and non-motile marine bacteria that were isolated from the green alga Ulva fenestrata were studied by polyphasic taxonomic methods. 16S rDNA sequence analysis indicated that strain KMM 3912T formed a distinct lineage within the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacteria were classified as Ulvibacter litoralis gen. nov., sp. nov. The type strain is KMM 3912T (=KCTC 12104T=CCUG 47093T).

Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm.

The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kütz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).

Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment.

Three bacterial strains were isolated from sea-water samples taken from Amursky Bay of the Gulf of Peter the Great, East Sea. The isolates, designated KMM 3670, KMM 3673(T) and KMM 3928, were Gram-positive, non-motile, aerobic, non-spore-forming, irregular, rod-shaped actinobacteria. They grew well at mesophilic temperatures and neutral pH and tolerated up to 10 % NaCl, although salt was not essential for growth. The three strains shared all morphological properties and most physiological characteristics tested. Based on subsequent chemotaxonomic and phylogenetic analyses, it was evident that the strains represented a distinctive taxon in the family Microbacteriaceae. The strains contained a major amount of menaquinone with 11 isoprene units; lysine and ornithine were the major cell-wall diamino acids. In 16S rDNA analysis, the three strains formed an independent phylogenetic lineage within the tree encompassed by members of the family Microbacteriaceae. It is notable that the tested strains form the first described taxon of Microbacteriaceae that inhabits a marine aquatic environment. The three strains evidently merit recognition as a single species of a novel genus in the family Microbacteriaceae, for which the name Salinibacterium amurskyense gen. nov., sp. nov. (type strain, KMM 3673(T)=KCTC 9931(T)) is proposed.

Rapid screening for freshwater bacterial groups by using reverse line blot hybridization.

The identification of phylogenetic clusters of bacteria that are common in freshwater has provided a basis for probe design to target important freshwater groups. We present a set of 16S ribosomal RNA gene-based oligonucleotide probes specific for 15 of these freshwater clusters. The probes were applied in reverse line blot hybridization, a simple method that enables the rapid screening of PCR products from many samples against an array of probes. The optimized assay was made stringent to discriminate at approximately the single-mismatch level. This made 10 of the probes highly specific, with at least two mismatches to the closest noncluster member in the global database. Screening of PCR products from bacterioplankton of 81 diverse lakes from Belgium, The Netherlands, Denmark, Sweden, and Norway showed that the respective probes were reactive against 5 to 100% of the lake samples. Positive reactivity of six highly specific probes showed that bacteria from actinobacterial clusters ACK-M1 and Sta2-30 and from verrucomicrobial cluster CLO-14 occurred in at least 90% of the investigated lakes. Furthermore, bacteria from alpha-proteobacterial cluster LD12 (closely related to the marine SAR11 cluster), beta-proteobacterial cluster LD28 and cyanobacterial cluster Synechococcus 6b occurred in more than 70% of the lakes. Reverse line blot hybridization is a new tool in microbial ecology that will facilitate research on distribution and habitat specificity of target species at relatively low costs.

Burkholderia sordidicola sp. nov., isolated from the white-rot fungus Phanerochaete sordida.

Two bacterial strains associated with the white-rot fungus Phanerochaete sordida were subjected to taxonomic investigation. The isolates, designated KCTC 12081(T) and KCTC 12082, were Gram-negative, non-motile, non-spore-forming and ovoid to rod-shaped. The strains contained major amounts of hexadecanoic acid, cyclo-heptadecanoic acid and omega-7-cis-octadecenoic acid in their cell envelopes. Strain KCTC 12081(T) contained ubiquinone-8 as the major isoprenoid quinone and the G+C content of its genomic DNA was 61.3 mol%. Morphological and chemotaxonomic properties of the strains were consistent with classification in the genus BURKHOLDERIA: In a comparison of 16S rDNA sequence, KCTC 12081(T) shared 100 % similarity with KCTC 12082 and both strains formed a distinct phylogenetic lineage within the genus BURKHOLDERIA: The two strains were also differentiated from other species of this genus by fatty acid composition and phenotypic properties. DNA-DNA relatedness data further supported the separation of the new isolates from closely related species. It is therefore proposed that strains KCTC 12081(T) (=JCM 11778(T)) and KCTC 12082 be recognized as a novel species, for which the name Burkholderia sordidicola sp. nov. is proposed.