Genus Planctomyces Research Articles

Effects of Diet on the Gut Microbial Communities of Nile Tilapia (Oreochromis niloticus) Across Their Different Life Stages

Nile tilapia (Oreochromis niloticus) is one of the most important commercial freshwater fish in China, and dietary transition occurs in their different life stages. The gut microbiota is important to host health. The relationships among the diet, gut microbiota, and development of tilapia are not well known. In the present study, we attempted to understand how diet is associated with microbiota community dynamics during the development of tilapia. The first experiment was performed under standard laboratory feeding operation to determine the effect of diet transition on intestinal microbiota. In the second experiment, tilapia were fed with Artemia or plant-based dry (PBD) food from the fish started feeding to their late juvenile stage (90 days post-fertilization). The results in the first experiment showed that feeding habit transition in juvenile fish had a low effect on the microbiota of the tilapia intestine. In the second experiment, plant-based food negatively affected the survival rate and intestinal development of tilapia. The phylum Planctomycetes was dominant in juvenile fish fed PBD food. The phylum Fusobacteria was dominant in the juvenile fish fed Artemia. At the genus level, Gemmobacter, Pirellula, and Planctomyces, belonging to the phylum Planctomycetes, were significantly abundant in the guts of fish fed the PBD food diet. Cetobacterium of the phylum Fusobacteria was dominant in juvenile fish fed Artemia. Thus, we can conclude that diet types have a great effect on the microbiota of tilapia intestine in their early life stages. The intestinal microflora of tilapia was established in juvenile tilapia, approximately 2 months after hatching. Our results provide useful information for the experimental design of studies on the microbial community of the tilapia gut. We suggest that modulation of gut microbiota of tilapia could be performed in their early life.

Taxonomic and functional profiling of nitrifying biofilms in freshwater, brackish and marine RAS biofilters

In recirculating aquaculture systems (RAS), the crucial step of eliminating toxic N compounds like ammonia and nitrite is mediated via nitrifying microorganisms and takes place in biofilters. In this study, analyses of microorganisms colonizing biocarriers of nine moving-bed biofilters of three different RAS operated with freshwater, brackish or marine process water uncovered site specific communities. Illumina-based amplicon sequencing of the V4-region of the 16S rRNA gene revealed a high microbial diversity with 1000–2500 species-level operational taxonomic units (OTUs) in all biofilters with the highest diversity in the brackish RAS. Proteobacteria, Bacteriodetes, Plantomycetes, Chloroflexi and Nitrospirae represented the most abundant phyla. 76 out of 674 known genera occurred in all nine biofilters and were defined as core-taxa, including nitrifying bacteria (Nitrosomonas and Nitrospira) as well as members of the (heterotrophic) genera Planctomyces, Blastopirellula, Nannocystis and Lewinella. Nitrifying communities composed of different, closely related and so far uncultured members of Nitrosomonas and Nitrospira were identified, strongly indicating that several potentially novel ammonia and nitrite oxidizing species are present in RAS biofilters. Relatives of known comammox Nitrospira were detected in the brackish biofilters, revealing 94–99 % identity of the 16S rRNA gene sequence to Ns. inopinata. Salinity tolerance tests with biocarriers derived from biofilters of the three distinct RAS showed an unexpected broad physiological flexibility with regard to salinity. Nitrification performance of freshwater nitrifiers was drastically reduced with increasing salinity and nearly completely inhibited at 15 PSU, while the brackish and marine nitrifiers showed a high resistance and maintained nitrification activity in a broad range of salt concentrations. This data can help to improve the nitrification process in RAS with changing salinity of the process water.

The effects of warming and ocean acidification on growth, photosynthesis, and bacterial communities for the marine invasive macroalga Caulerpa taxifolia

AbstractCaulerpa taxifolia is a pantropical green benthic marine macroalga, and one of the best known marine invasive species in temperate coastal habitats. In Australia, this species has been introduced to seven estuaries along New South Wales and one in South Australia. How this alga will perform under future climate change scenarios is however not well defined. This study experimentally assessed the effects of ocean acidification and global warming on the growth, photosynthetic performance and the bacterial community on two populations of C. taxifolia, one native and one invasive. A range of complex significant interactive effects between pH, temperature, and initial plant size on the growth of C. taxifolia were observed, but no effect of population origin and photosystem II (PSII) fluorescence quantum yield parameters were detected. No significant effects of the treatment combinations were observed on bacterial community richness or diversity. Only one bacterial species out of 1087 present on the algae showed significant changes between pH treatments at high temperature (24°C). This bacterium belonged to the genus Planctomyces and its relative abundance was more than 10 times higher in samples with low pH compared to the control. Higher plant growth was observed under all higher pCO2 and lower pH conditions suggesting that C. taxifolia will benefit from climate change, posing a potential higher risk in invaded locations.

Bacterial diversity in the sediment of Crescent Moon Spring, Kumtag Desert, Northwest China

Desert lake, a unique oasis in desert ecosystems, harbours different bacterial communities. Thus, it is considered as a hub of bacterial diversity. In this study, bacterial diversity in the sediment of Crescent Moon Spring, Kumtag Desert, Northwest China was analyzed using high-throughput amplicon pyrosequencing analysis. The sequences of the most abundant OUTs (Operational Taxonomic Units) in the sediment of Crescent Moon Spring were compared with the sequences of those most abundant OUTs of various origins from NCBI GenBank database to detect the origins of bacteria in the sediment of Crescent Moon Spring. Also, bacterial compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems (including desert lakes) worldwide were compared using cluster analysis to determine the possible factors affecting bacterial compositions. In total, 11,855 sequences were obtained and 30 phyla were identified. At the phylum level, the dominant phylum was Proteobacteria with α-Proteobacteria being the first dominant class and the second dominant phylum was Planctomycetes. Our finding that α-Proteobacteria being the first dominant class of Proteobacteria and Planctomycetes being the second dominant phyla are somewhat contradictory with reports from other desert lake sediments. This difference could be resulted from water hydration and conductivity, as well as oligotrophic conditions of Crescent Moon Spring. At the genus level, Rhodobacter, Caldilinea, Planctomyces, and Porphyrobacter were the dominant genera in the sediment of Crescent Moon Spring. Comparisons on sequences of the most abundant OUTs (including OTU3615, OTU6535, and OTU6646) between sediment of Crescent Moon Spring and various origins from NCBI GenBank database indicate that the origins of bacteria in the sediment of Crescent Moon Spring are likely from the underground water. Furthermore, cluster analysis on comparisons of bacteria compositions between sediment of Crescent Moon Spring and other desert and lake ecosystems (including desert lakes) worldwide shows that at regional scales, bacterial compositions may be mainly affected by geographical patterns, precipitation amounts, and pH values. Collectively, our results provide new knowledge on the bacterial diversity in desert lake ecosystems.

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.

Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.

Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands

Three strains of budding, ellipsoid-shaped and rosette-forming bacteria were isolated from acidic Sphagnum-dominated boreal wetlands of northern Russia and were designated strains MPL7T, MOB77 and SB2. The presence of crateriform pits and numerous fibrillar appendages on the cell surface and an unusual spur-like projection on one pole of the cell indicated a planctomycete morphotype. These isolates are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.2 and 7.5 (with an optimum at pH 5.0-6.2) and at temperatures between 4 and 32 degrees C (optimum 15-26 degrees C). The major fatty acids are C16:0 and C16:1omega7c; the major quinone is MK-6. The G+C content of the DNA is 54.4-56.5 mol%. Strains MPL7T, MOB77 and SB2 possess nearly identical 16S rRNA gene sequences and belong to the planctomycete lineage defined by the genus Planctomyces, being most closely related to Planctomyces limnophilus DSM 3776T (86.9-87.1% sequence similarity). However, strain MPL7T showed only 28% DNA-DNA hybridization with P. limnophilus DSM 3776T. Compared with currently described members of the genus Planctomyces, the isolates from northern wetlands do not form long and distinctive stalks, have greater tolerance of acidic conditions and low temperatures, are more sensitive to NaCl, lack pigmentation and degrade a wider range of biopolymers. The data therefore suggest that strains MPL7T, MOB77 and SB2 represent a novel genus and species, for which the name Schlesneria paludicola gen. nov., sp. nov., is proposed. Strain MPL7T (=ATCC BAA-1393T=VKM B-2452T) is the type strain of Schlesneria paludicola.

Microbial diversity in the marine sponge Aplysina cavernicola (formerly Verongia cavernicola) analyzed by fluorescence in situ hybridization (FISH)

We have employed electronmicroscopical methods (SEM, TEM) to document the microbial community associated with the marine sponge Aplysina cavernicola (formerly Verongia cavernicola, class Demospongiae). Five dominant bacterial types were identified, three of which resemble the morphotypes originally described by Vacelet (1975). One bacterial type possesses morphological properties that are characteristic of the genus Planctomyces. In addition, morphologically uniform bacteria which reside inside the nuclei of host cells were observed. Using in situ hybridization with fluorescently labelled rRNA probes directed against known bacterial groups, the phylogenetic affiliation of the mesohyl bacteria was assessed. It could be shown that the vast majority of mesohyl bacteria belongs to the domain Bacteria with a low GC content. Among the Bacteria, the delta-Proteobacteria were most abundant, followed by the gamma-Proteobacteria and representatives of the Bacteroides cluster. Clusters of Gram-positive bacteria with a high GC content were also found consistently in low amounts. No hybridization signal was obtained with probes specific to the domain Archaea, to the alpha- and beta-Proteobacteria and to the Cytophaga/Flavobacterium cluster. This study describes for the first time the application of the “top-to-bottom approach” using 16S rRNA probes and in situ hybridization to assess the microbial diversity in Aplysina sponges.

Assignment of ATCC 27377 to Pirella gen. nov. as Pirella staleyi comb. nov.

The necessity to rename strain ATCC 27377T (T = type strain), Pasteuria ramosa sensu Staley, led Starr and his associates to propose placing this organism in the genus Planctomyces. Morphological and physiological observations, as well as deoxyribonucleic acid base composition and 16S ribosomal ribonucleic acid oligomer analyses, clearly showed that strain ATCC 27377T differs significantly from species belonging to the genus Planctomyces. Therefore, we propose that strain ATCC 27377T be renamed Pirella staleyi and afforded the position of the type strain of the type species of the newly created genus Pirella. The generic and species descriptions are emended. The request of Starr et al. (Int. J. Syst. Bacteriol. 33:666–671, 1983) for the conservation of Pasteuria ramosa is supported.

Planctomyces stranskae (ex Wawrik 1952) sp. nov., nom. rev. and Planctomyces guttaeformis (ex Hortobagyi 1965) sp. nov., nom. rev.

Two related but recognizably different forms belonging to morphotype V of the Blastocaulis-Planctomyces group of budding bacteria were observed during the summer of 1983 in two eutrophic man-made ponds in Tempe, Ariz. Each of these forms can be assigned to previously described species of the genus Planctomyces; because these forms were not included in the 1980 Approved Lists of Bacterial Names (Skerman et al., ed., Int. J. Syst. Bacterid. 30:225–420), they need to be formally revived. One of these forms (morphotype Vb) is assigned to Planctomyces stranskae (ex Wawrik 1952) sp. nov., nom. rev.; the other form (morphotype Va) is assigned to Planctomyces guttaeformis (ex Hortobágyi 1965) sp. nov., nom. rev. Neither species has been cultivated axenically; hence, both are based on type descriptive material.

Two Identical Genera of Budding and Stalked Bacteria: Planctomyces Gimesi 1924 and Blastocaulis Henrici and Johnson 1935

Planctomyces bekefii Gimesi 1924 was originally described as a planktonic, freshwater fungus. Its spherical bodies on thin stalks were interpreted as sporangia. Colonies of this organism were compared to pine needles whose pointed ends were attached to a common base. Blastocaulis spaerica Henrici and Johnson 1935 is a planktonic, freshwater bacterium of a morphology and size identical to that of the former organism; both organisms occur in the same habitat and at the same time. Because of their rather unique morphology, the organisms are easily recognized. Depositions of ferric hydroxide occasionally thicken the stalks of the two forms. Recent observations on living material have confirmed the original descriptions. As a result of a comparison of the characteristics of the organisms, both are here considered to be identical. Although Planctomyces bekefii has been described as a fungus and its description lacks physiological details, priority must be given to this name, of which B. sphaerica must be considered a later subjective synonym. Because these organisms are the type species of their respective genera, the generic names are also regarded as subjective synonyms, and Planctomyces Gimesi 1924 has priority over Blastocaulis Henrici and Johnson 1935. An amended description of Planctomyces is presented. Besides P. bekefii Gimesi 1924, the following species are currently recognized as belonging to Planctomyces and are described herein: P. gracilis Horrotbagyi 1965, P. condensatus Skuja 1964, and P. kljasmensis comb. nov (basionym: Gallionella kljasmensis Razumov 1949). A key to these species is given. The taxonomic placement of other named organisms which either are or have been associated with the genus Planctomyces is discussed.