RESUMEN
Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.
Asunto(s)
Carbono , Genoma Bacteriano , Carbono/metabolismo , Filogenia , Genómica/métodos , Planctomycetales/genética , Planctomycetales/clasificación , Planctomycetales/metabolismo , Bacterias/genética , Bacterias/clasificación , Bacterias/metabolismo , Metabolismo EnergéticoRESUMEN
One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.
Asunto(s)
Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano , Ácidos Grasos , Lagos , Filogenia , Planctomycetales , ARN Ribosómico 16S , Análisis de Secuencia de ADN , Lagos/microbiología , ARN Ribosómico 16S/genética , Ácidos Grasos/análisis , Ácidos Grasos/química , ADN Bacteriano/genética , Planctomycetales/genética , Planctomycetales/clasificación , Planctomycetales/aislamiento & purificación , Federación de Rusia , Genoma Bacteriano/genética , Sedimentos Geológicos/microbiología , AnaerobiosisRESUMEN
Climate change is altering the frequency and severity of drought events. Recent evidence indicates that drought may produce legacy effects on soil microbial communities. However, it is unclear whether precedent drought events lead to ecological memory formation, i.e., the capacity of past events to influence current ecosystem response trajectories. Here, we utilize a long-term field experiment in a mountain grassland in central Austria with an experimental layout comparing 10 years of recurrent drought events to a single drought event and ambient conditions. We show that recurrent droughts increase the dissimilarity of microbial communities compared to control and single drought events, and enhance soil multifunctionality during drought (calculated via measurements of potential enzymatic activities, soil nutrients, microbial biomass stoichiometry and belowground net primary productivity). Our results indicate that soil microbial community composition changes in concert with its functioning, with consequences for soil processes. The formation of ecological memory in soil under recurrent drought may enhance the resilience of ecosystem functioning against future drought events.
Asunto(s)
Sequías/estadística & datos numéricos , Microbiota/fisiología , Microbiología del Suelo , Suelo/química , Agua/análisis , Acidobacteria/clasificación , Acidobacteria/genética , Acidobacteria/aislamiento & purificación , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Altitud , Austria , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Biomasa , Carbono/análisis , Chloroflexi/clasificación , Chloroflexi/genética , Chloroflexi/aislamiento & purificación , Pradera , Humanos , Nitrógeno/análisis , Fósforo/análisis , Planctomycetales/clasificación , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , Azufre/análisis , Verrucomicrobia/clasificación , Verrucomicrobia/genética , Verrucomicrobia/aislamiento & purificaciónRESUMEN
Four strains of Planctomycetes, (JC636, JC649, JC650T, JC657T) which are all salt and alkali tolerant, pink coloured, with spherical to oval shaped, Gram-stain-negative, non-motile cells were isolated from different regions of Chilika lagoon, India. All strains have obligate requirement for N-acetylglucosamine (NAG) and share highest 16S rRNA gene sequence identity with members of the genus Tautonia (<95%) of the family Isosphaeraceae. The 16S rRNA gene sequence identity between strains was >99.5%. Respiratory quinone for all the strains was MK6. Major fatty acids of all the strains were C18:1ω9c, C16:0 and C18:0. Major polar lipid of the strain JC650T was phosphatidylethanolamine, while, phosphatidylcholine and phosphatidylglycerol for strain JC657T. Spermidine was the only common polyamine for all the four strains. Strains JC657T, JC636 and JC649 shared highest phenotypic similarity along with 100% 16S rRNA gene sequence identity. Strains JC657T, JC636 and JC649 differed from strain JC650T phenotypically, chemotaxonomically and genotypically, thus belong to a different species. The genomic size of strain JC650T and JC657T are 7.06â¯Mb and 6.96â¯Mb with DNA Gâ¯+â¯C content of 63.9 and 62.7â¯mol%, respectively. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strains JC650T and JC657T (together with strains JC636, JC649) belong to the genus Tautonia and constitute two novel species for which we propose the names Tautonia marina sp. nov., and Tautonia rosea sp. nov., respectively. These two novel species are represented by the type strains JC650T (=KCTC 72177Tâ¯=â¯NBRC 113885T) and JC657T (=KCTC 72597Tâ¯=â¯NBRC 113883T) respectively.
Asunto(s)
Filogenia , Planctomycetales/clasificación , Microbiología del Agua , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , India , Hibridación de Ácido Nucleico , Fosfolípidos/química , Pigmentación , Planctomycetales/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMEN
Two axenic cultures of Planctomycetes were isolated from distinct geographical regions of the east coast of India. The two closely related strains (JC640 and CH01) showed <93.3% 16S rRNA gene sequence identity with members of the genus Roseimaritima followed by Rhodopirellula (<91%). Both strains displayed non-canonical cell morphology of Planctomycetes, such as rod shaped cells with division by lateral budding. Both strains showed crateriform structures on their surfaces and cells lack fimbriae. The genomes have a size of about 5.76 Mb and DNA G+C content of 63.6mol%. Phylogenetic analysis based on 16S rRNA gene sequence and 92 core genes based RAxML phylogenetic tree place both the strains in the family Pirellulaceae and indicated Roseimaritima sediminicola as their closest relative. The AAI and POCP values differentiate both strains from rest of the members of the family Pirellulaceae. The axenic cultures of both strains were able to grow up to 8-10 passages and subsequently the cells became non-viable with pleomorphic shapes. Supported by genomic, phylogenetic and morphological differences, we conclude that both strains belong to a novel genus. However, since the new isolates lost their viability on passaging, we propose the novel genus as "Candidatus Laterigemmans" gen. nov. and the novel species as "Candidatus Laterigemmans baculatus" sp. nov.
Asunto(s)
Filogenia , Planctomycetales/clasificación , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , India , Planctomycetales/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
Asunto(s)
Bacteroidetes/clasificación , Cianobacterias/clasificación , Microbiota/genética , Planctomycetales/clasificación , Poríferos/microbiología , Proteobacteria/clasificación , Animales , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Biodiversidad , Clima , Cambio Climático , Cianobacterias/genética , Cianobacterias/aislamiento & purificación , Calor , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Termotolerancia/genéticaRESUMEN
Two pink-coloured, oxidase-catalase-positive, salt and alkali-tolerant planctomycetal strains (JC635T and JC645T) with pear to spherical-shaped, Gram-stain-negative, motile cells were isolated from Chilika lagoon, India. Both strains share highest 16S rRNA gene sequence identity with members of the genus Rhodopirellula (< 94%) and Roseimaritima (< 94%) of the family Pirellulaceae. The 16S rRNA sequence identity between the strains JC635T and JC645T is 96.1%. Respiratory quinone for both strains is MK6. Major fatty acids are C18:1ω9c and C16:0. Major polar lipids are phosphatidylethanolamine, phosphatidylcholine, unidentified amino lipids and an unidentified lipid. The genomic size of strain JC635T and JC645T are 7.95 Mb and 8.2 Mb with DNA G + C content of 55.1âand 60.0 mol%, respectively. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that both strains belong to a novel genus Roseiconus gen. nov. and constitute two novel species for which we propose the names Roseiconus nitratireducens sp. nov. and Roseiconus lacunae sp. nov. The two novel species are represented by the type strains JC645T (= KCTC 72174T = NBRC 113879T) and JC635T (= KCTC 72164T = NBRC 113875T), respectively.
Asunto(s)
Filogenia , Planctomycetales/clasificación , Agua de Mar/microbiología , Composición de Base , Ácidos Grasos/análisis , India , Planctomycetales/genética , ARN Ribosómico 16S/genética , Especificidad de la Especie , Microbiología del AguaRESUMEN
Thirteen novel planctomycetal strains were isolated from five different aquatic sampling locations. These comprise the hydrothermal vent system close to Panarea Island (Italy), a biofilm on the surface of kelp at Monterey Bay (CA, USA), sediment and algae on Mallorca Island (Spain) and Helgoland Island (Germany), as well as a seawater aquarium in Braunschweig, Germany. All strains were shown to belong to the genus Gimesia. Their genomes cover a size range from 7.22 to 8.29 Mb and have a G+C content between 45.1 and 53.7%. All strains are mesophilic (Topt 26-33 °C) with generation times between 12 and 32 h. Analysis of fatty acids yielded palmitic acid (16:0) and a fatty acid with the equivalent chain length of 15.817 as major compounds. While five of the novel strains belong to the already described species Gimesia maris and Gimesia chilikensis, the other strains belong to novel species, for which we propose the names Gimesia alba (type strain Pan241wT = DSM 100744T = LMG 31345T = CECT 9841T = VKM B-3430T), Gimesia algae (type strain Pan161T = CECT 30192T = STH00943T = LMG 29130T), Gimesia aquarii (type strain V144T = DSM 101710T = VKM B-3433T), Gimesia fumaroli (type strain Enr17T = DSM 100710T = VKM B-3429T) and Gimesia panareensis (type strain Enr10T = DSM 100416T = LMG 29082T). STH numbers refer to the Jena Microbial Resource Collection (JMRC).
Asunto(s)
Organismos Acuáticos/aislamiento & purificación , Ecosistema , Planctomycetales/clasificación , Planctomycetales/aislamiento & purificación , Organismos Acuáticos/citología , Organismos Acuáticos/genética , Organismos Acuáticos/fisiología , California , ADN Bacteriano , Ácidos Grasos/análisis , Alemania , Italia , Filogenia , Planctomycetales/citología , Planctomycetales/fisiología , ARN Ribosómico 16S , Análisis de Secuencia de ADN , EspañaRESUMEN
A novel strain of Planctomycetes, designated JC670T, was isolated from a high altitude (~ 2900 m above sea level) soil sample collected from Garhwal region in the Western Himalaya. Colonies of this strain were observed to be light pink coloured with spherical to oval shaped cells having crateriform structures distributed all over the cell surface. The cells divide by budding. Strain JC670T was found to grow well at pH 7.0 and pH 8.0 and to tolerate up to 2% NaCl (w/v). MK6 was the only respiratory quinone identified. The major fatty acids of strain JC670T were identified as C18:1ω9c, C18:0 and C16:0, and phosphatidylcholine, two unidentified phospholipids and six unidentified lipids are present as the polar lipids. The polyamines putrescine and sym-homospermidine were detected. Strain JC670T shows high 16S rRNA gene sequence identity (95.4%) with Paludisphaera borealis PX4T. The draft genome size of strain JC670T is 7.97 Mb, with G + C content of 70.4 mol%. Based on phylogenetic analyses with the sequences of ninety-two core genes, low dDDH value (20.6%), low gANI (76.8%) and low AAI (69.1%) results, differential chemotaxonomic and physiological properties, strain JC670T (= KCTC 72850T = NBRC 114339T) is recognised as the type strain of a new species of the genus Paludisphaera, for which we propose the name Paludisphaera soli sp. nov.
Asunto(s)
Altitud , Planctomycetales/clasificación , Planctomycetales/aislamiento & purificación , Microbiología del Suelo , Técnicas de Tipificación Bacteriana , ADN Bacteriano/genética , Ácidos Grasos/análisis , Fosfolípidos/análisis , Filogenia , Planctomycetales/genética , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADNRESUMEN
Planctomycetes of the family Gemmataceae are characterized by large genome sizes and cosmopolitan distribution in freshwater and terrestrial environments but their ecological functions remain poorly understood. In this study, we characterized a novel representative of this family, strain PL17T, which was isolated from a littoral tundra wetland and was capable of growth on xylan and cellulose. Cells of this isolate were represented by pink-pigmented spheres that multiplied by budding and occurred singly or in short chains and aggregates. Strain PL17T was obligately aerobic, mildly acidophilic chemoorganotrophic bacterium, which displayed good tolerance of low temperatures. The major fatty acids were C18:0, C16:1ω5, and ßOH-C16:1; the major polar lipid was trimethylornithine. The genome of strain PL17T consisted of a 9.83 Mb chromosome and a 24.69kb plasmid. The G+C contents of the chromosomal and plasmid DNA were 67.4 and 62.3mol%, respectively. Over 8900 potential protein-coding genes were identified in the genome including a putative cellulase that contains a domain from the GH5 family of glycoside hydrolases. The genome of strain PL17T contained one linked and one unlinked rRNA operons with 16S rRNA gene sequences displaying 94.5% similarity to that in Gemmata obscuriglobus UQM2246T. Based on the results of comparative phenotypic, chemotaxonomic and phylogenomic analyses, we propose to classify strain PL17T (= CECT 9407T=VKM B-3467T) as representing a novel genus and species of the family Gemmataceae, Frigoriglobus tundricola gen. nov., sp. nov.
Asunto(s)
Bacterias Aerobias Gramnegativas/clasificación , Bacterias Aerobias Gramnegativas/aislamiento & purificación , Tundra , Humedales , Bacterias , Técnicas de Tipificación Bacteriana , Composición de Base , Celulosa/metabolismo , Frío , ADN Bacteriano/química , ADN Bacteriano/genética , Ácidos Grasos/análisis , Genes Bacterianos , Genes de ARNr , Genoma Bacteriano , Bacterias Aerobias Gramnegativas/genética , Bacterias Aerobias Gramnegativas/fisiología , Lípidos/análisis , Redes y Vías Metabólicas/genética , Filogenia , Planctomycetales/clasificación , Planctomycetales/genética , ARN Ribosómico 16S/genética , Xilanos/metabolismoRESUMEN
The fjords of west Spitsbergen Svalbard, Arctic Norway, are undergoing a transformation as the impact of nutrient rich warmer Atlantic water is significantly altering the primary production and subsequently the carbon pool. Members of the phylum Planctomycetes are ubiquitous in marine systems and are important in the mineralization of organic matter. Hence, the phylogenetic diversity and distribution pattern of Planctomycetes in the surface sediments of a high Arctic fjord, the Kongsfjorden were studied. Further, considering the release of ammonium as a part of mineralization, the diversity of bacterial community involved in anaerobic ammonium oxidation (anammox) was also evaluated. The highly diverse Planctomycetes community, which consisted mainly of uncultivated and uncharacterized Planctomycetes, was observed in the study area with a total of 162 OTUs. The major genera observed were Blastopirellula (13.3%), Gimesia (13%), Rhodopirellula (10%), Planctomicrobium (2%) and Thermogutta (1.6%). Functional prediction revealed the dominance of carbohydrate metabolism genes and the presence of gene clusters for production of secondary metabolites and xenobiotic degradation. Anammox bacterial sequences were detected from all the samples with a total of 52 OTUs. Most of the OTUs belonged to the genus Candidatus Scalindua and three distinct clusters were observed in the phylogenetic tree, (a) Ca. Scalindua brodae (49%), (b) Ca. Scalindua wagneri (31%) and (c) Ca. Scalindua marina (12%) based on their phylogenic distance. Our findings suggest the existence of highly diverse Planctomycetes and anammox bacterial community with regional variants in the sediments of Kongsfjorden.
Asunto(s)
Bacterias/clasificación , Crecimiento Quimioautotrófico/fisiología , Estuarios , Sedimentos Geológicos/microbiología , Filogenia , Planctomycetales/clasificación , Agua de Mar/microbiología , Compuestos de Amonio , Anaerobiosis , Regiones Árticas , Océano Atlántico , Bacterias/genética , ADN Bacteriano , Microbiota , Planctomycetales/genética , ARN Ribosómico 16S/genéticaRESUMEN
Bacterial strains of the phylum Planctomycetes occur ubiquitously, but are often found on surfaces of aquatic phototrophs, e.g. alga. Despite slower growth, planctomycetes are not outcompeted by faster-growing bacteria in biofilms on such surfaces; however, strategies allowing them to compensate for slower growth have not yet been investigated. Here, we identified stieleriacines, a class of N-acylated tyrosines produced by the novel planctomycete Stieleria maiorica Mal15T, and analysed their effects on growth of the producing strain and bacterial species likely co-occurring with strain Mal15T. Stieleriacines reduced the lag phase of Mal15T and either stimulated or inhibited biofilm formation of two bacterial competitors, indicating that Mal15T employs stieleriacines to specifically alter microbial biofilm composition. The genetic organisation of the putative stieleriacine biosynthetic cluster in strain Mal15T points towards a functional link of stieleriacine biosynthesis to exopolysaccharide-associated protein sorting and biofilm formation.
Asunto(s)
Antibacterianos/farmacología , Biopelículas/crecimiento & desarrollo , Bacterias Grampositivas/crecimiento & desarrollo , Planctomycetales/clasificación , Agua de Mar/microbiología , Tirosina/farmacología , Acilación , Antibacterianos/química , Biopelículas/efectos de los fármacos , Bacterias Grampositivas/efectos de los fármacos , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Planctomycetales/metabolismo , Tirosina/químicaRESUMEN
A Gram-stain-negative, stalked, oval-shaped and budding bacterial strain, designated E7T, was isolated from a deep-sea water sample collected from the Northwest Indian Ocean. The novel strain was strictly aerobic, and catalase- and oxidase-positive. It grew at 6-40 °C (optimum 30 °C) and pH 5.5-8.0 (optimum pH 7.0-7.5). The strain required 0.5-9.0â% (w/v) NaCl (optimum 3.0-5.0â%) for growth. Aesculin, starch, pectin and Tween 20 were hydrolysed. Based on 16S rRNA gene sequence analysis, strain E7T showed the highest similarity with Gimesia maris DSM 8797T (97.5â%). The average nucleotide identity and in silico DNA-DNA hybridization values between strain E7T and G. maris DSM 8797T were 78.0 and 19.3â%, respectively. The predominant cellular fatty acids of strain E7T were C16â:â0 and summed feature 3 (comprising C16â:â1ω7c and/or C16â:â1ω6c). The major respiratory quinone was menaquinone-6 (MK-6) and the major polar lipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), phosphatidyldimethylethanolamine (PDME), phosphatidylcholine (PC) and diphosphatidylglycerol (DPG). The genomic DNA G+C content of strain E7T was 52.8 mol%. On the basis of phylogenetic inference and phenotypic characteristics, it is proposed that strain E7T represents a novel species of the genus Gimesia, for which the name Gimesia benthica sp. nov. is proposed. The type strain is E7T (=CGMCC 1.16119T=KCTC 72737T).
Asunto(s)
Filogenia , Planctomycetales/clasificación , Agua de Mar/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Océano Índico , Hibridación de Ácido Nucleico , Fosfolípidos/química , Planctomycetales/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMEN
A Gram-stain-negative, aerobic, non-motile, salt- and alkali-tolerant, pear to oval shaped, rosette-forming, white coloured, bacterium, designated as strain JC646T, was isolated from a sediment sample collected from Chilika lagoon, India. Strain JC646T reproduced through budding, grew well at up to pH 9.0 and tolerated up to 7â% NaCl. Strain JC 646T utilized α-d-glucose, fumarate, lactose, sucrose, fructose, d-galactose, mannose, maltose and d-xylose as carbon sources. Peptone, l-isoleucine, l-serine, l-lysine, l-glutamic acid, l-aspartic acid, dl-threonine and l-glycine were used by the strain as nitrogen sources for growth. The respiratory quinone was MK6. Major fatty acids were C16â:â1 ω7c/C16â:â1 ω6c and C16â:â0. The polar lipids of strain JC646T comprised phosphatidyl-dimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified amino lipid and two unidentified lipids. Strain JC646T had highest (97.3â%) 16S rRNA gene sequence identity to the only species of the genus Gimesia, Gimesia maris DSM 8797T. The genome of strain JC646T was 7.64 Mbp with a DNA G+C content of 53.2 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 housekeeping genes. Based on phylogenetic analyses, digital DNA-DNA hybridization (19.0â%), genome average nucleotide identity (74.5â%) and average amino acid identity/percentageof conserved proteins (77â%) results, chemotaxonomic characteristics, and differential physiological properties, strain JC646T is recognized as representing a new species of the genus Gimesia, for which we propose the name Gimesia chilikensis sp. nov. The type strain is JC646T (=KCTC 72175T=NBRC 113881T).
Asunto(s)
Sedimentos Geológicos/microbiología , Filogenia , Planctomycetales/clasificación , Aguas Salinas , Microbiología del Agua , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , India , Hibridación de Ácido Nucleico , Fosfolípidos/química , Planctomycetales/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMEN
The phylum Planctomycetes comprises bacteria with peculiar and very unique characteristics among prokaryotes. In marine environments, macroalgae biofilms are well known for harboring planctomycetal diversity. Here, we describe a novel isolate obtained from the biofilm of the red alga Chondrus crispus collected at a rocky beach in Porto, Portugal. The novel strain LzC2T is motile, rosette-forming with spherical- to ovoid-shaped cells. LzC2T forms magenta- to pinkish-colored colonies in M13 and M14 media. Transmission and scanning electron microscopy observations showed a division by polar and lateral budding. Mother cells are connected to the daughter cells by a tubular neck-like structure. The strain requires salt for growth. Vitamins are not required for growth. Optimal growth occurs from 15 to 30°C and within a pH range from 5.5 to 10.0. Major fatty acids are anteiso-C15:0 (54.2%) and iso-C15:0 (19.5%). Phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid represent the main lipids and menaquinone 6 (MK-6) is the only quinone present. 16S rRNA gene-based phylogenetic analysis supports the affiliation to the phylum Planctomycetes and family Planctomycetaceae, with Alienimonas as the closest relative. Strain LzC2T shares 97% 16S rRNA gene sequence similarity with Alienimonas californiensis. LzC2T has a genome size of 5.3 Mb and a G+C content of 68.3%. Genotypic and phenotypic comparison with the closest relatives strongly suggest that LzC2T (=CECT 30038T=LMG XXXT) is a new species of the genus Alienimonas, for which we propose the name Alienimonas chondri sp. nov., represented by LzC2T as type strain. 16S rRNA gene accession number: GenBank=MN757873.1. Genome accession number: GenBank=WTPX00000000.
Asunto(s)
Biopelículas , Planctomycetales/clasificación , Planctomycetales/genética , Rhodophyta , Algas Marinas/clasificación , Algas Marinas/genética , Biopelículas/crecimiento & desarrollo , Ácidos Grasos/análisis , Ácidos Grasos/química , Genoma Bacteriano , Genómica/métodos , Filogenia , Planctomycetales/aislamiento & purificación , Planctomycetales/ultraestructura , ARN Ribosómico 16S/genética , Rhodophyta/crecimiento & desarrollo , Algas Marinas/aislamiento & purificación , Algas Marinas/ultraestructuraRESUMEN
The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.
Asunto(s)
Bacterias , Plancton , Poliaminas/metabolismo , Agua de Mar/microbiología , Actinobacteria/clasificación , Actinobacteria/genética , Actinobacteria/aislamiento & purificación , Bacterias/clasificación , Bacterias/genética , Bacterias/aislamiento & purificación , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Cianobacterias/clasificación , Cianobacterias/genética , Cianobacterias/aislamiento & purificación , Golfo de México , Metagenómica , Microbiota , Nitrógeno/metabolismo , Filogenia , Planctomycetales/clasificación , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Plancton/metabolismo , Plancton/microbiología , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Agua de Mar/química , TranscriptomaRESUMEN
Strain JC651T was isolated from a sediment sample collected from Chilika lagoon, which is one of the world's most important brackish water lakes with estuarine characteristics. Colonies of this strain are light pink and cells are Gram-stain negative, spherical to pear shaped and form rosettes. Strain JC651T grows well up to pH 9.0 and tolerates up to 5â% NaCl (w/v). The respiratory quinone is MK6. The detected major fatty acids are C18â:â1 ω9c and C16â:â0. Its polar lipids are diphosphatidylglycerol, an unidentified phospholipid, phosphatidylglycerol and phosphatidylcholine. Strain JC651T shows highest 16S rRNA gene sequence similarity (97.8%) to the type species of the genus Roseimaritima, Roseimaritima ulvae UC8T. The genome size of strain JC651T is 6.2 Mb with a G+C content of 62.4 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 core genes. Based on the phylogenetic analyses, low digital DNA-DNA hybridization values (19.5%), low (74.9%) genome average nucleotide identity results, chemotaxonomic characteristics and differential physiological properties, strain JC651T is recognized as a new species of the genus Roseimaritima for which we propose the name Roseimaritima sediminicola sp. nov. The type strain is JC651T (=KCTC 72178T=NBRC 113926T).
Asunto(s)
Lagos/microbiología , Filogenia , Planctomycetales/clasificación , Aguas Salinas , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , India , Hibridación de Ácido Nucleico , Fosfolípidos/química , Pigmentación , Planctomycetales/aislamiento & purificación , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMEN
The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the ß-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.
Asunto(s)
Amoníaco/metabolismo , Acuicultura/métodos , Chromatiaceae/metabolismo , Genes Bacterianos , Nitratos/metabolismo , Penaeidae/fisiología , Contaminantes Químicos del Agua/metabolismo , Alphaproteobacteria/clasificación , Alphaproteobacteria/genética , Alphaproteobacteria/aislamiento & purificación , Animales , Bacteroidetes/clasificación , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Biodegradación Ambiental , Chromatiaceae/genética , Deltaproteobacteria/clasificación , Deltaproteobacteria/genética , Deltaproteobacteria/aislamiento & purificación , Ecosistema , Gammaproteobacteria/clasificación , Gammaproteobacteria/genética , Gammaproteobacteria/aislamiento & purificación , Humanos , Consorcios Microbianos/genética , Planctomycetales/clasificación , Planctomycetales/genética , Planctomycetales/aislamiento & purificación , Proteobacteria/clasificación , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética , Contaminación del Agua/prevención & control , Calidad del AguaRESUMEN
The family Gemmataceae accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52T, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52T was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were C18â:â1É·7c, C18â:â0 and ßOH-C16:0; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52T was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52T displayed only 86.0-89.8â% 16S rRNA gene sequence similarity to taxonomically described Gemmataceae planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, Limnoglobus roseus gen. nov., sp. nov. The type strain is strain PX52T (=KCTC 72397T=VKM B-3275T).