scholarly journals Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Izabela Mujakić ◽  
Adrian-Ştefan Andrei ◽  
Tanja Shabarova ◽  
Lívia Kolesár Fecskeová ◽  
Michaela M. Salcher ◽  
...  
Keyword(s):  
Close Association ◽  
Gene Clusters ◽  
Gobi Desert ◽  
Rrna Gene ◽  
Natural Environments ◽  
Freshwater Species ◽  
Freshwater Lakes ◽  
Unique Type ◽  
Content Type ◽  
Bacterial Phyla

ABSTRACT Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota. They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes’ epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments. IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria. We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.

Acuticoccus mangrovi sp. nov., with an antibacterial property, isolated from mangrove sediment

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Zhe Li ◽  
Wenjin Hu ◽  
Shushi Huang ◽  
Yuanlin Huang ◽  
Fei Li ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Amino Acid Identity ◽  
Mangrove Sediment ◽  
Species Discrimination ◽  
Rrna Gene ◽  
Beibu Gulf ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Sequence Relatedness

A Gram-stain-negative, aerobic, milky white bacterium, designated B2012T, was isolated from mangrove sediment collected at Beibu Gulf, South China Sea. Antimicrobial activity assay revealed that the isolate possesses the capability of producing antibacterial compounds. Strain B2012T shared the highest 16S rRNA gene sequence relatedness (96.9–95.5 %) with members of the genus Acuticoccus . The isolate and all known Acuticoccus species contain Q-10 as the main respiratory quinone and have the same polar lipid components (phosphatidylcholine, unidentified glycolipid, unidentified lipid, unidentified amino lipid and phosphatidylglycerol). However, genomic relatedness referred by values of average nucleotide identity, digital DNA–DNA hybridization, average amino acid identity and the percentage of conserved proteins between strain B2012T and other type strains of the genus Acuticoccus were below the proposed thresholds for species discrimination. The genome of strain B2012T was assembled into 65 scaffolds with an N50 size of 244239 bp, resulting in a 5.5 Mb genome size. Eight secondary metabolite biosynthetic gene clusters were detected in this genome, including three non-ribosomal peptide biosynthetic loci encoding yet unknown natural products. Strain B2012T displayed moderately halophilic and alkaliphilic properties, growing optimally at 2–3 % (w/v) NaCl concentration and at pH 8–9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, C16 : 0 dimethyl aldehyde (DMA) and C16 : 0. Combined data from phenotypic, genotypic and chemotaxonomic analyses suggested that strain B2012T represents a novel species of the genus Acuticoccus , for which the name Acuticoccus mangrovi sp. nov. is proposed. The type strain of the type species is B2012T (=MCCC 1K04418T=KCTC 72962T).

scholarly journals A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment

2018 ◽  
Vol 84 (22) ◽  
Author(s):  
Jonah E. Einson ◽  
Asha Rani ◽  
Xiaomeng You ◽  
Allison A. Rodriguez ◽  
Clifton L. Randell ◽  
...  
Keyword(s):  
Cultural History ◽  
Bacterial Communities ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Production Facility ◽  
Production Environment ◽  
Content Type ◽  
Bacterial Phyla ◽  
Fermented Vegetables

ABSTRACTFermented vegetables are highly popular internationally in part due to their enhanced nutritional properties, cultural history, and desirable sensorial properties. In some instances, fermented foods provide a rich source of the beneficial microbial communities that could promote gastrointestinal health. The indigenous microbiota that colonize fermentation facilities may impact food quality, food safety, and spoilage risks and maintain the nutritive value of the product. Here, microbiomes within sauerkraut production facilities were profiled to characterize variance across surfaces and to determine the sources of these bacteria. Accordingly, we used high-throughput sequencing of the 16S rRNA gene in combination with whole-genome shotgun analyses to explore biogeographical patterns of microbial diversity and assembly within the production facility. Our results indicate that raw cabbage and vegetable handling surfaces exhibit more similar microbiomes relative to the fermentation room, processing area, and dry storage surfaces. We identified biomarker bacterial phyla and families that are likely to originate from the raw cabbage and vegetable handling surfaces. Raw cabbage was identified as the main source of bacteria to seed the facility, with human handling contributing a minor source of inoculation.LeuconostocandLactobacillaceaedominated all surfaces where spontaneous fermentation occurs, as these taxa are associated with the process. Wall, floor, ceiling, and barrel surfaces host unique microbial signatures. This study demonstrates that diverse bacterial communities are widely distributed within the production facility and that these communities assemble nonrandomly, depending on the surface type.IMPORTANCEFermented vegetables play a major role in global food systems and are widely consumed by various global cultures. In this study, we investigated an industrial facility that produces spontaneous fermented sauerkraut without the aid of starter cultures. This provides a unique system to explore and track the origins of an “in-house” microbiome in an industrial environment. Raw vegetables and the surfaces on which they are handled were identified as the likely source of bacterial communities rather than human contamination. As fermented vegetables increase in popularity on a global scale, understanding their production environment may help maintain quality and safety goals.

scholarly journals Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

2012 ◽  
Vol 78 (10) ◽  
pp. 3744-3752 ◽  
Author(s):  
Boojala Vijay B. Reddy ◽  
Dimitris Kallifidas ◽  
Jeffrey H. Kim ◽  
Zachary Charlop-Powers ◽  
Zhiyang Feng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Natural Product ◽  
Gene Sequence ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Type I ◽  
Adenylation Domain ◽  
Biosynthetic Gene ◽  
Bacterial Phyla

ABSTRACTThe number of bacterial species estimated to exist on Earth has increased dramatically in recent years. This newly recognized species diversity has raised the possibility that bacterial natural product biosynthetic diversity has also been significantly underestimated by previous culture-based studies. Here, we compare 454-pyrosequenced nonribosomal peptide adenylation domain, type I polyketide ketosynthase domain, and type II polyketide ketosynthase alpha gene fragments amplified from cosmid libraries constructed using DNA isolated from three different arid soils. While 16S rRNA gene sequence analysis indicates these cloned metagenomes contain DNA from similar distributions of major bacterial phyla, we found that they contain almost completely distinct collections of secondary metabolite biosynthetic gene sequences. When grouped at 85% identity, only 1.5% of the adenylation domain, 1.2% of the ketosynthase, and 9.3% of the ketosynthase alpha sequence clusters contained sequences from all three metagenomes. Although there is unlikely to be a simple correlation between biosynthetic gene sequence diversity and the diversity of metabolites encoded by the gene clusters in which these genes reside, our analysis further suggests that sequences in one soil metagenome are so distantly related to sequences in another metagenome that they are, in many cases, likely to arise from functionally distinct gene clusters. The marked differences observed among collections of biosynthetic genes found in even ecologically similar environments suggest that prokaryotic natural product biosynthesis diversity is, like bacterial species diversity, potentially much larger than appreciated from culture-based studies.

scholarly journals Genome-based analyses reveal the presence of 12 heterotypic synonyms in the genus Streptomyces and emended descriptions of Streptomyces bottropensis, Streptomyces celluloflavus, Streptomyces fulvissimus, Streptomyces glaucescens, Streptomyces murinus, and Streptomyces variegatus

2020 ◽  
Vol 70 (6) ◽  
pp. 3924-3929 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Venkatakrishnan Sivaraj Saravanan ◽  
Wah-Seng See-Too
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Genus Streptomyces ◽  
Content Type ◽  
Link Type ◽  
Streptomyces Glaucescens

Phylogenetic analysis based on 16S rRNA gene sequences of the genus Streptomyces showed the presence of six distinguishable clusters, with 100 % sequence similarity values among strains in each cluster; thus they shared almost the same evolutionary distance. This result corroborated well with the outcome of core gene (orthologous gene clusters) based genome phylogeny analysis of 190 genomes including the Streptomyces species in those six clusters. These preeminent results led to an investigation of genome-based indices such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI) and average amino acid identity (AAI) for the strains in those six clusters. Certain strains recorded genomic indices well above the threshold values (70 %, 95–96 % and >95 % for dDDH, ANI and AAI, respectively) determined for species affiliation, suggesting only one type strain belongs to described species and the other(s) may need to be reduced in taxa to a later heterotypic synonym. To conclude, the results of comprehensive analyses based on phylogenetic and genomic indices suggest that the following six reclassifications are proposed: Streptomyces flavovariabilis as a later heterotypic synonym of Streptomyces variegatus ; Streptomyces griseofuscus as a later heterotypic synonym of Streptomyces murinus ; Streptomyces kasugaensis as a later heterotypic synonym of Streptomyces celluloflavus ; Streptomyces luridiscabiei as a later heterotypic synonym of Streptomyces fulvissimus ; Streptomyces pharetrae as a later heterotypic synonym of Streptomyces glaucescens ; and Streptomyces stelliscabiei as a later heterotypic synonym of Streptomyces bottropensis .

Micromonospora humida sp. nov., exhibiting antimicrobial potential, isolated from riverside soil

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Jun Sik Ra ◽  
Min Ji Kim ◽  
Dong Hyeon Lee ◽  
Ji Won Jeong ◽  
Seung Bum Kim
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Clusters ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
The 16S Rrna Gene

An actinobacterial strain designated MMS20-R1-14T was isolated from a riverside soil sample. Colonies on agar plates were orange to strong orange brown in colour, which later became black. The cells grew at 10–40 °C (optimum, 37 °C), pH 5.0–11.0 (pH 8.0) and in the presence of 0–4 % NaCl (1 %). The 16S rRNA gene sequence of strain MMS20-R1-14T showed highest similarities to Micromonospora wenchangensis CCTCC AA 2012002T (99.51 %) and Micromonospora rifamycinica AM105T (99.37 %). The orthoANI values between strain MMS20-R1-14T and the two type strains were 95.72 and 90.99 %, and the digital DNA–DNA hybridization values were 63.6 and 40.8 %, respectively, thus confirming the distinction of strain MMS20-R1-14T from its mostly related species. The DNA G+C content of strain MMS20-R1-14T was 72.9 mol%. The strain contained meso-diaminopimelic acid as the major cell-wall amino acid, and the characteristic whole-cell sugars were arabinose, xylose, glucose, ribose and rhamnose. The main cellular fatty acids were C18 : 1  ω9c, iso-C15 : 0 and iso-C16 : 0, the diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the predominant menaquinones were MK-10(H4) and MK-10(H6), all of which were consistent with those of Micromonospora . Strain MMS20-R1-14T showed antimicrobial activity against a range of bacterial and yeast species. The genome of the strain was found to contain 33 potential biosynthetic gene clusters for secondary metabolites, thus showing a high potential as a producer of bioactive compounds. On the basis of these phenotypic, genotypic and chemotaxonomic data, strain MMS20-R1-14T merits recognition as representing a novel species of the genus Micromonospora , for which the name Micromonospora humida sp. nov. (type strain=MMS20 R1-14T=KCTC 49541T=JCM 34494T) is proposed.

scholarly journals Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1882-1889 ◽  
Author(s):  
Henk C. den Bakker ◽  
Steven Warchocki ◽  
Emily M. Wright ◽  
Adam F. Allred ◽  
Christina Ahlstrom ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Amino Acid Sequences ◽  
Rrna Gene ◽  
Natural Environments ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
A Genome

Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average blast nucleotide identity (ANIb) of less than 85 % to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria ; (i) a clade representing Listeria monocytogenes , L. marthii , L. innocua , L. welshimeri , L. seeligeri and L. ivanovii , which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188T = DSM 26686T = LMG 28120T = BEI NR-42633T) and Listeria floridensis sp. nov. (type strain FSL S10-1187T = DSM 26687T = LMG 28121T = BEI NR-42632T), (iii) a clade consisting of Listeria rocourtiae , L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210T = FSL F6-0969T = DSM 26689T = LMG 28123T = BEI NR-42630T), Listeria grandensis sp. nov. (type strain TTU A1-0212T = FSL F6-0971T = DSM 26688T = LMG 28122T = BEI NR-42631T) and Listeria riparia sp. nov. (type strain FSL S10-1204T = DSM 26685T = LMG 28119T = BEI NR- 42634T) and (iv) a clade containing Listeria grayi . Genomic and phenotypic data suggest that the novel species are non-pathogenic.

scholarly journals Quantification of Endospore-Forming Firmicutes by Quantitative PCR with the Functional Genespo0A

2013 ◽  
Vol 79 (17) ◽  
pp. 5302-5312 ◽  
Author(s):  
Matthieu Bueche ◽  
Tina Wunderlin ◽  
Ludovic Roussel-Delif ◽  
Thomas Junier ◽  
Loic Sauvain ◽  
...  
Keyword(s):  
Quantitative Pcr ◽  
High Sensitivity ◽  
Primer Design ◽  
Rrna Gene ◽  
Natural Environments ◽  
Natural Habitats ◽  
Content Type ◽  
Wide Range ◽  
Primer Sets ◽  
Reliable Quantification

ABSTRACTBacterial endospores are highly specialized cellular forms that allow endospore-formingFirmicutes(EFF) to tolerate harsh environmental conditions. EFF are considered ubiquitous in natural environments, in particular, those subjected to stress conditions. In addition to natural habitats, EFF are often the cause of contamination problems in anthropogenic environments, such as industrial production plants or hospitals. It is therefore desirable to assess their prevalence in environmental and industrial fields. To this end, a high-sensitivity detection method is still needed. The aim of this study was to develop and evaluate an approach based on quantitative PCR (qPCR). For this, the suitability of functional genes specific for and common to all EFF were evaluated. Seven genes were considered, but onlyspo0Awas retained to identify conserved regions for qPCR primer design. An approach based on multivariate analysis was developed for primer design. Two primer sets were obtained and evaluated with 16 pure cultures, including representatives of the generaBacillus,Paenibacillus,Brevibacillus,Geobacillus,Alicyclobacillus,Sulfobacillus,Clostridium, andDesulfotomaculum, as well as with environmental samples. The primer sets developed gave a reliable quantification when tested on laboratory strains, with the exception ofSulfobacillusandDesulfotomaculum. A test using sediment samples with a diverse EFF community also gave a reliable quantification compared to 16S rRNA gene pyrosequencing. A detection limit of about 104cells (or spores) per gram of initial material was calculated, indicating this method has a promising potential for the detection of EFF over a wide range of applications.

scholarly journals Genome Sequence of the Unusual Purple Photosynthetic Bacterium Phaeovibrio sulfidiphilus, Only Distantly Related to Rhodospirillaceae, Reveals Unique Genes for Respiratory Nitrate Reduction and Glycerol Metabolism

2020 ◽  
Vol 9 (49) ◽  
Author(s):  
S. Dubey ◽  
T. E. Meyer ◽  
J. A. Kyndt
Keyword(s):  
Nitrate Reduction ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Bacterium ◽  
Gene Clusters ◽  
Glycerol Metabolism ◽  
Freshwater Species ◽  
Content Type ◽  
Purple Photosynthetic Bacteria ◽  
Purple Photosynthetic Bacterium ◽  
Unique Genes

ABSTRACT Phaeovibrio sulfidiphilus was reported to be a divergent member of the purple photosynthetic bacteria with limited ability to metabolize organic compounds. Whole-genome-based analysis shows that it is indeed only distantly related to freshwater species of Rhodospirillaceae. Unexpectedly, the genome contains unique gene clusters for potential respiratory nitrate reduction and anaerobic glycerol metabolism.

scholarly journals Causal Relationship between Microbial Ecology Dynamics and Proteolysis during Manufacture and Ripening of Protected Designation of Origin (PDO) Cheese Canestrato Pugliese

2014 ◽  
Vol 80 (14) ◽  
pp. 4085-4094 ◽  
Author(s):  
Ilaria De Pasquale ◽  
Maria Calasso ◽  
Leonardo Mancini ◽  
Danilo Ercolini ◽  
Antonietta La Storia ◽  
...  
Keyword(s):  
Causal Relationship ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Content Type ◽  
Bacterial Phyla ◽  
Biolog Ecoplates ◽  
Protected Designation Of Origin ◽  
Physiological Profiles ◽  
Microbial Groups

ABSTRACTPyrosequencing of the 16S rRNA gene, community-level physiological profiles determined by the use of Biolog EcoPlates, and proteolysis analyses were used to characterize Canestrato Pugliese Protected Designation of Origin (PDO) cheese. The number of presumptive mesophilic lactococci in raw ewes' milk was higher than that of presumptive mesophilic lactobacilli. The numbers of these microbial groups increased during ripening, showing temporal and numerical differences. Urea-PAGE showed limited primary proteolysis, whereas the analysis of the pH 4.6-soluble fraction of the cheese revealed that secondary proteolysis increased mainly from 45 to 75 days of ripening. This agreed with the concentration of free amino acids. Raw ewes' milk was contaminated by several bacterial phyla:Proteobacteria(68%; mainlyPseudomonas),Firmicutes(30%; mainlyCarnobacteriumandLactococcus),Bacteroidetes(0.05%), andActinobacteria(0.02%). Almost the same microbial composition persisted in the curd after molding. From day 1 of ripening onwards, the phylumFirmicutesdominated.Lactococcusdominated throughout ripening, and most of theLactobacillusspecies appeared only at 7 or 15 days. At 90 days,Lactococcus(87.2%),Lactobacillus(4.8%; mainlyLactobacillus plantarumandLactobacillus sakei), andLeuconostoc(3.9%) dominated. The relative utilization of carbon sources by the bacterial community reflected the succession. This study identified strategic phases that characterized the manufacture and ripening of Canestrato Pugliese cheese and established a causal relationship between mesophilic lactobacilli and proteolysis.

Promicromonospora thailandica sp. nov., isolated from marine sediment

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2140-2144 ◽  
Author(s):  
Chitti Thawai ◽  
Takuji Kudo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Sequence Similarity ◽  
Close Association ◽  
Biochemical Properties ◽  
Andaman Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain S7F-02T, which produced primary branched hyphae and fragmented into V- and Y-shaped bacillary cells, was isolated from marine sediment collected in the Andaman Sea, Trang Province, Thailand. Lysine was found to be the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars of strain S7F-02T were ribose, arabinose and glucose. The characteristic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H4). The predominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain S7F-02T was 70.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S7F-02T should be classified in the genus Promicromonospora . This strain formed a close association with Promicromonospora citrea DSM 43110T, with which it shared 99.2 % 16S rRNA gene sequence similarity. DNA–DNA hybridization data together with physiological and biochemical properties showed that strain S7F-02T could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain S7F-02T is considered to represent a novel species of the genus Promicromonospora , for which the name Promicromonospora thailandica sp. nov. is proposed. The type strain is S7F-02T ( = BCC 41922T = JCM 17130T).

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