Mammoth mangrove bacterium has complex cell.

"Eye-opening" discovery challenges evolutionary thinking on microbes.

Leucothrix sargassi sp. nov., isolated from a marine alga [Sargassum natans (L.) Gaillon].

A novel bacterial strain, C3212T, was isolated from a marine alga collected from the sea shore of Yantai, China. The strain was Gram-stain-negative, rod-shaped, aerobic, non-motile, and oxidase- and catalase-positive. Growth was observed at 8-37 °C (optimum, 28 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 1.0-7.0 % (w/v) NaCl (optimum, 4.0 %). The major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids of strain C3212T consisted of diphosphatidylglycerol (cardiolipin), phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified polar lipid. The major fatty acids were C16 : 1ω6c and/or C16 : 1ω7c, and C18 : 1ω6c and/or C18 : 1ω7c. The DNA G+C content of strain C3212T was 44.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Leucothrix pacifica XH122T, Leucothrix arctica IMCC 9719T and Leucothrix mucor DSM 2157T with similarities of 98.0, 97.5 and 94.3 %, respectively. Estimated DNA-DNA hybridization values were 14.2, 20.7 and 13.9 % between strain C3212T and L. pacifica XH122T, L. arctica IMCC 9719T and L. mucor DSM 2157T, respectively. Phenotypic, phylogenetic and genomic analyses revealed that strain C3212T represents a novel species of the genus Leucothrix, for which the name Leucothrix sargassi sp. nov. is proposed. The type strain is C3212T (=MCCC 1K03600T=KCTC 72121T).

Thioflexithrix psekupsensis gen. nov., sp. nov., a filamentous gliding sulfur bacterium from the family Beggiatoaceae.

A sulfur-oxidizing, filamentous, gliding micro-organism, strain D3T, was isolated from a sulfidic spring in Goryachy Klyuch, Krasnodar, Russia. The cell walls were Gram-negative. The new isolate was a microaerophilic facultative anaerobe and an obligate chemolithoautotroph. The pH range for growth was pH 6.8-7.6, with an optimum at pH 7.2. The temperature range for growth was 10-46 °C, with an optimum at 32 °C. The G+C content of DNA was 42.1 mol%. Phylogenetic analysis of the 16S rRNA gene showed that strain D3T belongs to the family Beggiatoaceae, order Thiotrichales and was distantly related to the genera of the family Beggiatoaceae(86-88 % sequence similarity). The major respiratory quinone was ubiquinone-6. Major fatty acids were C18:1 ω7 (37.6 %), C16 : 0 (34.7 %) and C16: 1 ω7 (27.7 %). On the basis of its physiological properties and the results of phylogenetic analysis, strain D3T is considered to represent a novel species of a new genus, for which the name Thioflexithrix psekupsensis gen. nov., sp. nov. is proposed. The type strain is D3T (=KCTC 62399=UNIQEM U981).

Description of a phototrophic bacterium, Thiorhodococcus alkaliphilus sp. nov.

Strain JA878T was purified from a photoheterotrophic enrichment obtained from a sediment sample of a brown pond near Nari Salt Pan, Bhavnagar, Gujarat, India. Cells of the isolate were coccoid, motile by means of single polar flagellum and Gram-stain-negative. The internal photosynthetic membrane architecture was vesicular. Strain JA878T contained bacteriochlorophyll a and spirilloxanthin series of carotenoids with rhodopin (>85 %) as the major component. Strain JA878T grew optimally at pH 10-11, and had no requirement for NaCl (tolerated up to 6 %, w/v) or vitamins for growth. C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c/C18 : 1ω6c and C16 : 0 were identified as the major fatty acids (>10 %). Phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and an unknown polar lipid were identified. Q8 was the predominant quinone system in strain JA878T. The DNA G+C content was 62.4 mol%. Highest 16S rRNA gene sequence similarity through EzTaxon-based blast analysis of strain JA878T was found with the type strains of Thiorhodococcus fuscus (99 %), Thiorhodococcus kakinadensis (98.6 %), Thiohalobacter thiocyanaticus (98.4 %), Thiophaeococcus fuscus (97.3 %) and other members of the class Gammaproteobacteria (<97.3 %), revealing a close affiliation to the genera Thiorhodococcus, Thiohalobacter and Thiophaeococcus. However, the phylogenetic treeing firmly placed the strain in the genus Thiorhodococcus. Phenotypic and chemotaxonomic evidence supported the affiliation of strain JA878T to the genus Thiorhodococcus and not to Thiohalobacter, Thiophaeococcus or other known genera of Chromatiaceae. Distinct physiological, genotypic and chemotaxonomic differences indicate that strain JA878T represents a novel species of the genus Thiorhodococcus, for which the name Thiorhodococcus alkaliphilus sp. nov. is proposed. The type strain is JA878T (=KCTC 15531T=JCM 31245T).

Microbial Community Associated with Thioploca sp. Sheaths in the Area of the Posolski Bank Methane Seep, Southern Baikal.

Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolski Bank cold methane seep (southern Baikal) were -studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica.- Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as in- side and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells-without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic; of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were idenified in the sheath community: Bacteroidetes, Nitro- spira, Chloroflexi, Planctomycetes, Verrucomicrobia,'y-, and 6-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.

Leucothrix pacifica sp. nov., isolated from seawater, and emended description of the genus Leucothrix.

A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, white-pigmented and rod-shaped bacterium, designated strain XH122T, was isolated from a surface seawater sample collected from the South Pacific Gyre (45° 58' E 163° 11' S) during Integrated Ocean Drilling Program Expedition 329.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XH122T belonged to the genus Leucothrix and showed highest 16S rRNA gene sequence similarity to Leucothrix mucor DSM 2157T (94.3%). It showed lower sequence similarities ( < 90.7%) with all other representatives of the class Gammaproteobacteria. Optimal growth occurred in the presence of 2% (w/v) NaCl, at pH 8.0 and at 28 °C. The DNA G+C content of strain XH122T was 46.2 mol%. The major fatty acids were C16 : 0, C16 : 1ω9c and C18 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of data from this polyphasic study, strain XH122T is considered to represent a novel species of the genus Leucothrix, for which the name Leucothrix pacifica sp. nov. is proposed. The type strain is XH122T ( = DSM 25984T = JCM 18388T).

Metatranscriptomic analysis of diminutive Thiomargarita-like bacteria ("Candidatus Thiopilula" spp.) from abyssal cold seeps of the Barbados Accretionary Prism.

Large sulfur-oxidizing bacteria in the family Beggiatoaceae are important players in the global sulfur cycle. This group contains members of the well-known genera Beggiatoa, Thioploca, and Thiomargarita but also recently identified and relatively unknown candidate taxa, including "Candidatus Thiopilula" spp. and "Ca. Thiophysa" spp. We discovered a population of "Ca. Thiopilula" spp. colonizing cold seeps near Barbados at a ∼4.7-km water depth. The Barbados population consists of spherical cells that are morphologically similar to Thiomargarita spp., with elemental sulfur inclusions and a central vacuole, but have much smaller cell diameters (5 to 40 µm). Metatranscriptomic analysis revealed that when exposed to anoxic sulfidic conditions, Barbados "Ca. Thiopilula" organisms expressed genes for the oxidation of elemental sulfur and the reduction of nitrogenous compounds, consistent with their vacuolated morphology and intracellular sulfur storage capability. Metatranscriptomic analysis further revealed that anaerobic methane-oxidizing and sulfate-reducing organisms were active in the sediment, which likely provided reduced sulfur substrates for "Ca. Thiopilula" and other sulfur-oxidizing microorganisms in the community. The novel observations of "Ca. Thiopilula" and associated organisms reported here expand our knowledge of the globally distributed and ecologically successful Beggiatoaceae group and thus offer insight into the composition and ecology of deep cold seep microbial communities.

Macplocimine A, a new 18-membered macrolide isolated from the filamentous sulfur bacteria Thioploca sp.

Macplocimine A (1), a rare naturally occurring 18-membered macrolide, was isolated from the marine-derived filamentous sulfur bacteria Thioploca sp. The structure was determined by a combination of spectroscopic techniques, including HRESIMS, 1D and 2D NMR analyses. 1 features a thymine group, which is attached to an aromatic fused 18-membered macrolide ring structure derived from a polyketide synthase biosynthetic pathway.

Dimorphism in methane seep-dwelling ecotypes of the largest known bacteria.

We present evidence for a dimorphic life cycle in the vacuolate sulfide-oxidizing bacteria that appears to involve the attachment of a spherical Thiomargarita-like cell to the exteriors of invertebrate integuments and other benthic substrates at methane seeps. The attached cell elongates to produce a stalk-like form before budding off spherical daughter cells resembling free-living Thiomargarita that are abundant in surrounding sulfidic seep sediments. The relationship between the attached parent cell and free-living daughter cell is reminiscent of the dimorphic life modes of the prosthecate Alphaproteobacteria, but on a grand scale, with individual elongate cells reaching nearly a millimeter in length. Abundant growth of attached Thiomargarita-like bacteria on the integuments of gastropods and other seep fauna provides not only a novel ecological niche for these giant bacteria, but also for animals that may benefit from epibiont colonization.

A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano.

A mat-forming population of the giant sulfur bacterium Thiomargarita was discovered at the flank of the mud volcano Amon on the Nile Deep Sea Fan in the Eastern Mediterranean Sea. All cells were of a spherical and vacuolated phenotype and internally stored globules of elemental sulfur. With a diameter of 24-65 µm, Thiomargarita cells from the Eastern Mediterranean were substantially smaller than cells of previously described populations. A 16S rRNA gene fragment was amplified and could be assigned to the Thiomargarita-resembling cells by fluorescence in situ hybridization. This sequence is monophyletic with published Thiomargarita sequences but sequence similarities are only about 94%, indicating a distinct diversification. In the investigated habitat, highly dynamic conditions favour Thiomargarita species over other sulfur-oxidizing bacteria. In contrast to Thiomargarita namibiensis populations, which rely on periodic resuspension from sulfidic sediment into the oxygenated water column, Thiomargarita cells at the Amon mud volcano seem to remain stationary at the sediment surface while environmental conditions change around them due to periodic brine flow.

Cocleimonas flava gen. nov., sp. nov., a gammaproteobacterium isolated from sand snail (Umbonium costatum).

A Gram-stain-negative, aerobic, yellow-pigmented, heterotrophic, sulfur-oxidizing, non-motile, rod-shaped bacterium, designated KMM 3898(T), was isolated from an internal tissue of the sand snail Umbonium costatum, collected from the shallow sediments of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KMM 3898(T) formed a distinct phylogenetic lineage within the class Gammaproteobacteria and was most closely related to Leucothrix mucor DSM 2157(T) (89.2 % 16S rRNA gene sequence similarity) and members of the genus Thiothrix (86.7-88.5 %). Chemotaxonomically, strain KMM 3898(T) contained the isoprenoid quinone Q-8, the polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid and the fatty acids C(18 : 1)ω7c, C(16 : 1)ω7c and C(16 : 0) as predominant components (>10 %). The DNA G+C content of strain KMM 3898(T) was 43.4 mol%. On the basis of phenotypic features and phylogenetic analysis, strain KMM 3898(T) represents a novel genus and species, for which the name Cocleimonas flava gen. nov., sp. nov. is proposed. The type strain is KMM 3898(T) (=NRIC 0757(T) =JCM 16494(T)).

Distribution, ecology and molecular identification of Thioploca from Danish brackish water sediments.

The distribution of Thioploca populations was investigated in Danish fjords, brackish lakes and coastal waters. Thioploca was found in three geographically distinct populations, where biomasses reached 33.8+/-14.3 g wet weight m(-2) (mean+/-SD). Mats or lawns were not formed at the sediment surfaces and Thioploca biomasses peaked 4-7 cm into the sediment and extended down to 18 cm depth. Morphology and 16S rRNA gene sequences classified all populations as Thioploca ingrica. A sequence divergence of 1.7-2.2% indicated that T. ingrica comprise at least two genotypes. Physiological analysis showed that T. ingrica accumulate nitrate in concentrations of approximately 3 mM and that bicarbonate and acetate are used as a carbon source. The presence of oxygen promoted carbon incorporation, but T. ingrica could survive up to 3 months without an external supply of nitrate or oxygen. Thioploca ingrica populations were exclusively found close to river outlets in a bioturbated sediment with separate sulphidic spots and worm burrow walls containing nitrate and oxygen. It is hypothesized that the subsurface T. ingrica have a special advantage in this heterogeneous environment using their sheath surrounding the bacterial trichomes when navigating between electron donor and acceptor.

Novel observations of Thiobacterium, a sulfur-storing Gammaproteobacterium producing gelatinous mats.

The genus Thiobacterium includes uncultivated rod-shaped microbes containing several spherical grains of elemental sulfur and forming conspicuous gelatinous mats. Owing to the fragility of mats and cells, their 16S ribosomal RNA genes have not been phylogenetically classified. This study examined the occurrence of Thiobacterium mats in three different sulfidic marine habitats: a submerged whale bone, deep-water seafloor and a submarine cave. All three mats contained massive amounts of Thiobacterium cells and were highly enriched in sulfur. Microsensor measurements and other biogeochemistry data suggest chemoautotrophic growth of Thiobacterium. Sulfide and oxygen microprofiles confirmed the dependence of Thiobacterium on hydrogen sulfide as energy source. Fluorescence in situ hybridization indicated that Thiobacterium spp. belong to the Gammaproteobacteria, a class that harbors many mat-forming sulfide-oxidizing bacteria. Further phylogenetic characterization of the mats led to the discovery of an unexpected microbial diversity associated with Thiobacterium.

[Colorless sulfur bacteria Thioploca from different sites in Lake Baikal].

The colorless sulfur bacteria Thioploca spp. found in Lake Baikal are probably a marker for the influx of subterranean mineralized fluids. Bacteria act as a biological filter; by consuming sulfide in their metabolism, they detoxicate it and maintain the purity of Lake Baikal's water. The bacteria were investigated by various techniques. According to analysis of the 16S rRNA gene fragment, Thioploca sp. from Frolikha Bay, Baikal belongs to the clade of freshwater species found in Lake Biwa and Lake Constance; it is most closely related to Thioploca ingrica.

Physiology and behaviour of marine Thioploca.

Among prokaryotes, the large vacuolated marine sulphur bacteria are unique in their ability to store, transport and metabolize significant quantities of sulphur, nitrogen, phosphorus and carbon compounds. In this study, unresolved questions of metabolism, storage management and behaviour were addressed in laboratory experiments with Thioploca species collected on the continental shelf off Chile. The Thioploca cells had an aerobic metabolism with a potential oxygen uptake rate of 1760 micromol O2 per dm(3) biovolume per h, equivalent to 4.4 nmol O2 per min per mg protein. When high ambient sulphide concentrations (approximately 200 microM) were present, a sulphide uptake of 6220+/-2230 micromol H2S per dm(3) per h, (mean+/-s.e.m., n=4) was measured. This sulphide uptake rate was six times higher than the oxidation rate of elemental sulphur by oxygen or nitrate, thus indicating a rapid sulphur accumulation by Thioploca. Thioploca reduce nitrate to ammonium and we found that dinitrogen was not produced, neither through denitrification nor through anammox activity. Unexpectedly, polyphosphate storage was not detectable by microautoradiography in physiological assays or by staining and microscopy. Carbon dioxide fixation increased when nitrate and nitrite were externally available and when organic carbon was added to incubations. Sulphide addition did not increase carbon dioxide fixation, indicating that Thioploca use excess of sulphide to rapidly accumulate sulphur rather than to accelerate growth. This is interpreted as an adaptation to infrequent high sulphate reduction rates in the seabed. The physiology and behaviour of Thioploca are summarized and the adaptations to an environment, dominated by infrequent oxygen availability and periods of high sulphide abundance, are discussed.

New communities of large filamentous sulfur bacteria in the eastern South Pacific.

New complex communities of morphologically diverse and sometimes abundant large, multicellular, filamentous bacteria were discovered in the oxygen-deficient, organically laden, shelf sediments under the oxygen minimum zone off the coast of the eastern Pacific, i.e., off the coasts of central and northern Chile; central and northern Perú; Roca Redonda, Galápagos Archipielago, Ecuador; and off the Pacific coasts of Panamá and Costa Rica. Similar microbial communities were also observed in the reduced layer of a muddy-sand beach adjacent to a mangrove swamp on Coiba Island, Pacific Panamá, and in the organically laden bottom underneath a salmon culture pen in southern Chile (region X). Of varying morphology, the diameters of the bacteria range from 1 to 10 mum, and their lengths from around 10 mum to usually several hundreds but at times several thousands of micrometers. The new filamentous bacterial component is at least one order of magnitude smaller than the also multicellular "megabacteria" Thioploca spp. and Beggiatoa spp., and is collectively referred to as "macrobacteria". A recent review only mentioned a few of these free-living filamentous bacteria, remarking on their scarcity despite the obvious advantages of a large size. This prokaryote size-window has been rarely investigated optically by researchers; thus, assemblages that appear to have had world-wide distribution probably since pre-Cambrian times have been overlooked.

A cold-loving crenarchaeon is a substantial part of a novel microbial community in cold sulphidic marsh water.

In this paper, we report the identification and first characterization of a novel, cold-loving, prokaryotic community thriving among white-greenish 'streamers' in the cold (c. 10 degrees C) sulphurous water of the marsh Sippenauer Moor near Regensburg, Bavaria, Germany. It consists of the bacterial genus Thiothrix, the bacterium 'Sip100' and one archaeal representative, forming together a unique association structure with a distinct life cycle. Fluorescence in situ hybridization studies have revealed that the archaeal member can be affiliated to the crenarchaeal kingdom ('Cre1'). This crenarchaeon was always observed attached to the bacterial community member 'Sip100'. Extended fluorescence in situ hybridization studies showed that this crenarchaeon was not detected in a free-living form, raising the idea of a probable host-dependent relationship. In line with our fluorescence in situ hybridization studies, novel crenarchaeal 16S rRNA gene sequences were identified in these samples. The design and application of a new in situ cultivation method in the sulphurous water of the marsh allowed first insights into the cohesion mechanisms, lifestyle and chronology of the microbes involved in this prokaryotic community in nature. Our results suggest that hitherto unknown Crenarchaeota thrive in cold sulphidic water and are a substantial part of a synchronized microbial community.

Molecular characterization of microbial communities in Canadian pulp and paper activated sludge and quantification of a novel Thiothrix eikelboomii-like bulking filament.

We examined the microbial community structure and quantified the levels of the filamentous bulking organism Thiothrix eikelboomii in samples of activated sludge mixed liquor suspended solids (MLSS) from Canadian pulp and paper mills. Libraries of chaperonin 60 (cpn60) gene sequences were prepared from MLSS total microbial community DNA and each was compared with cpnDB, a reference database of cpn60 sequences (http://cpndb.cbr.nrc.ca) for assignment of taxonomic identities. Sequences similar to but distinct from the type strain of T. eikelboomii AP3 (ATCC 49788T) (approximately 89% identity over 555 bp) were recovered at high frequency from a mill sample that was experiencing bulking problems at the time of sample collection, which corresponded to microscopic observations using fluorescent in situ hybridization with commercially available 16S rDNA-based probes. We enumerated this strain in five mill-derived MLSS samples using real-time quantitative PCR (qPCR) and found that two samples had high levels of the bulking strain (>1012 genomes/g MLSS) and two contained lower but detectable levels of this organism. None of the mill samples contained cpn60 sequences that were identical to the type strain of T. eikelboomii. This technique shows promise for monitoring pulp and paper mill wastewater treatment systems by detecting and enumerating this strain of T. eikelboomii, which may be specific to pulp and paper mill wastewater treatment systems.

Large sulfur bacteria and the formation of phosphorite.

Phosphorite deposits in marine sediments are a long-term sink for an essential nutrient, phosphorus. Here we show that apatite abundance in sediments on the Namibian shelf correlates with the abundance and activity of the giant sulfur bacterium Thiomargarita namibiensis, which suggests that sulfur bacteria drive phosphogenesis. Sediments populated by Thiomargarita showed sharp peaks of pore water phosphate (/=50 grams of phosphorus per kilogram). Laboratory experiments revealed that under anoxic conditions, Thiomargarita released enough phosphate to account for the precipitation of hydroxyapatite observed in the environment.

Bacterial community associated with black band disease in corals.

Black band disease (BBD) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. While it has been well established that the BBD bacterial mat is dominated by a cyanobacterium, the quantitative composition of the BBD bacterial mat community has not described previously. Terminal-restriction fragment length polymorphism (T-RFLP) analysis was used to characterize the infectious bacterial community of the bacterial mat causing BBD. These analyses revealed that the bacterial composition of the BBD mat does not vary between different coral species but does vary when different species of cyanobacteria are dominant within the mat. On the basis of the results of a new method developed to identify organisms detected by T-RFLP analysis, our data show that besides the cyanobacterium, five species of the division Firmicutes, two species of the Cytophaga-Flexibacter-Bacteroides (CFB) group, and one species of delta-proteobacteria are also consistently abundant within the infectious mat. Of these dominant taxa, six were consistently detected in healthy corals. However, four of the six were found in much higher numbers in BBD mats than in healthy corals. One species of the CFB group and one species of Firmicutes were not always associated with the bacterial communities present in healthy corals. Of the eight dominant bacteria identified, two species were previously found in clone libraries obtained from BBD samples; however, these were not previously recognized as important. Furthermore, despite having been described as an important component of the pathogenetic mat, a Beggiatoa species was not detected in any of the samples analyzed. These results will permit the dominant BBD bacteria to be targeted for isolation and culturing experiments aimed at deciphering the disease etiology.