scholarly journals Metagenomic screening for lipolytic genes reveals an ecology-clustered distribution pattern

2021 ◽  
Author(s):  
Mingji Lu ◽  
Dominik Schneider ◽  
Rolf Daniel
Keyword(s):  
Markov Models ◽  
Sequence Similarity ◽  
Ecological Factors ◽  
16S Rrna Genes ◽  
Microbial Consortia ◽  
Rrna Genes ◽  
Lipolytic Enzymes ◽  
Two Samples ◽  
Metagenome Sequencing ◽  
Microbial Groups

AbstractLipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique genes encoding lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integral classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.

scholarly journals Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep

2007 ◽  
Vol 57 (6) ◽  
pp. 1243-1249 ◽  
Author(s):  
Ngoc-Phuc Hua ◽  
Atsuko Kanekiyo ◽  
Katsunori Fujikura ◽  
Hisato Yasuda ◽  
Takeshi Naganuma
Keyword(s):  
Deep Sea ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Cold Seep ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
High Sequence Similarity ◽  
Moderately Halophilic ◽  
Type Strains ◽  
Moderately Halophilic Bacteria

Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1 ω7c alcohol and C18 : 1 ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.

scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

scholarly journals Opening a next-generation black box: ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

2021 ◽  
Author(s):  
Martin Hahn ◽  
Andrea Huemer ◽  
Alexandra Pitt ◽  
Matthias Hoetzinger
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxon Richness ◽  
Large Set ◽  
Free Living ◽  
Environmental Distribution ◽  
Living Bacteria

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster evolving protein-encoding marker to reveal ecological patterns hidden within a single OTU defined by >99% 16S rRNA sequence similarity. The studied taxon, subcluster PnecC of the genus Polynucleobacter, represents a ubiquitous group of planktonic freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. Besides the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. A unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca-rich and Ca-poor habitats, which strongly resembled the vicariance of plant species on silicate and limestone soils. The presented new cultivation-independent approach opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

scholarly journals Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2320-2325 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Moderate Amount ◽  
Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

Alkalibacterium gilvum sp. nov., slightly halophilic and alkaliphilic lactic acid bacterium isolated from soft and semi-hard cheeses

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1471-1478 ◽  
Author(s):  
Morio Ishikawa ◽  
Kazuhide Yamasato ◽  
Kayo Kodama ◽  
Hinako Yasuda ◽  
Mioko Matsuyama ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molar Ratio ◽  
Phylogenetic Position ◽  
Growth Responses ◽  
Cultivation Conditions ◽  
Content Type ◽  
Link Type

Nine novel strains of halophilic and alkaliphilic lactic acid bacteria isolated from European soft and semi-hard cheeses by using a saline, alkaline medium (7 % NaCl, pH 9.5) were taxonomically characterized. The isolates were Gram-stain-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from d-glucose with the production of formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from d-glucose. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth ranged between 2.0 % and 5.0 % (w/v), with a growth range of 0–1 % to 15–17.5 %. The optimum pH for growth ranged between 8.5 and 9.5, with a growth range of 7.0–7.5 to 9.5–10.0. Comparative sequence analysis of the 16S rRNA genes revealed that the isolates occupied a phylogenetic position within the genus Alkalibacterium , showing the highest sequence similarity (98.2 %) to Alkalibacterium kapii T22-1-2T. The isolates constituted a single genomic species with DNA–DNA hybridization values of 79–100 % among the isolates and <29 % between the isolates and other members of the genus Alkalibacterium , from which the isolates were different in motility and flagellation, growth responses to NaCl concentrations and pH, and profiles of sugar fermentation. The DNA G+C contents were between 36.0 and 37.6 mol%. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major components of cellular fatty acids were C14 : 0, C16 : 0 and C16 : 1ω9c. Based on the phenotypic characteristics and genetic distinctness, the isolates are classified as a novel species within the genus Alkalibacterium , for which the name Alkalibacterium gilvum sp. nov. is proposed. The type strain is 3AD-1T ( = DSM 25751T = JCM 18271T).

Thalassobacter stenotrophicus Macián et al. 2005 is a later synonym of Jannaschia cystaugens Adachi et al. 2004, with emended description of the genus Thalassobacter

2005 ◽  
Vol 55 (5) ◽  
pp. 1959-1963 ◽  
Author(s):  
M. J. Pujalte ◽  
M. C. Macián ◽  
D. R. Arahal ◽  
E. Garay
Keyword(s):  
16S Rrna ◽  
Genomic Dna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Traits ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Sequence Comparisons ◽  
Emended Description

The type strains of Jannaschia cystaugens (LMG 22015T) and Thalassobacter stenotrophicus (CECT 5294T) were analysed by means of genomic DNA–DNA hybridization, comparison of 16S rRNA gene sequences and phenotypic properties determined under the same methodological conditions. J. cystaugens LMG 22015T showed DNA–DNA relatedness levels of 72 % when hybridized with the genomic DNA of T. stenotrophicus CECT 5294T. Sequence comparisons revealed that the 16S rRNA genes of the two strains had a similarity of 99·8 %. The cellular fatty acid and polar lipid compositions of the two strains and their DNA mol% G+C contents were almost identical. Bacteriochlorophyll a (Bchl a) and polyhydroxybutyrate were produced by both strains under the same culture conditions. Their closest phylogenetic neighbours were Jannaschia helgolandensis and Jannaschia rubra; however, the low sequence similarity values (95·7–95·9 %) and several important differences in phenotypic traits (ionic requirements, Bchl a production and polar lipids) support the distinction between the genera Thalassobacter and Jannaschia. Thus, we propose the unification of J. cystaugens (LMG 22015T) and T. stenotrophicus (CECT 5294T) as Thalassobacter stenotrophicus (type strain, CECT 5294T=DSM 16310T). An emended description of the genus Thalassobacter is also presented.

scholarly journals Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China

2007 ◽  
Vol 57 (7) ◽  
pp. 1402-1407 ◽  
Author(s):  
M. C. Gutiérrez ◽  
A. M. Castillo ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
Inner Mongolia ◽  
Saline Lake ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Family ◽  
Extremely Halophilic Archaeon

Strain SH-6T was isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl2, for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6T is a member of the family Halobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains of Natronolimnobius innermongolicus and Natronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6T contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C20C20 and C20C25 glycerol diethers together with the glycolipid S2-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6T is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halopiger xanaduensis gen. nov., sp. nov. is proposed. The type strain of Halopiger xanaduensis is SH-6T (=CECT 7173T=CGMCC 1.6379T=JCM 14033T).

Evidence for Iron- and Sulfur-Oxidizing Bacteria and Archaea in a Currently Active Lignite Mining Area of Lusatia (Eastern Germany)

2009 ◽  
Vol 71-73 ◽  
pp. 97-100 ◽  
Author(s):  
H.M. Siebert ◽  
Thore Rohwerder ◽  
Wolfgang Sand ◽  
M. Strzodka ◽  
K.P. Stahmann
Keyword(s):  
16S Rrna ◽  
Mining Area ◽  
16S Rrna Genes ◽  
Open Pit ◽  
Rrna Genes ◽  
Published Data ◽  
Lignite Mining ◽  
Two Samples ◽  
Pure Cultures ◽  
Sulfur Oxidizing

The largest lignite mining area in Europe is located 150 km southeast of Berlin. Acidic lakes exist in this area, known to be caused by marcasite oxidation. Thirty-two samples from the open-pit brown coal-mine Jaenschwalde were analyzed for microorganisms. Cell numbers determined after separation from sand particles revealed concentrations of 102 to 107 microorganisms per g sample. In samples exposed to the air within an hour, up to 4x107 cells were counted. Measurement of metabolic activity by microcalorimetry showed for such samples up to 50 µW per g sand, whereas in heap samples (with low moisture) low or even no activity was measurable. DNA extraction was successful for 28 samples. In 26 samples microbial 16S rRNA genes were amplified by PCR. Acidithiobacillus ferrooxidans and At. thiooxidans specific amplificates were detected by nested PCR in 23 and 10 cases, respectively. A specific signal indicating Leptospirillum ferrooxidans was obtained with nine samples. Random samples were sequenced and showed 96 to 99 % identity with published data of all three species. Surprisingly, in four samples archaeal 16S rRNA genes were amplified by PCR. Sequencing of two samples showed 99 % identity with unidentified or uncultured archaea found in NCBI-databases. Molecular biology results for At. ferrooxidans as well as for At. thiooxidans were supported by successful isolations of pure cultures in 23 cases. Cultivation of the archaea failed so far. These data indicate that iron- and sulfur-oxidizing microorganisms occur at these sites in large numbers. If in addition the evidence for archaea can become verified, a screening for hot spots as the sites of their occurrence would become interesting.

scholarly journals Mucilaginibacter koreensis sp. nov., isolated from leaf mould

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2274-2279 ◽  
Author(s):  
Cheol Su Park ◽  
Kyudong Han ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-staining-negative, strictly aerobic, rod-shaped, pale-pink pigmented bacterial strain, designated TF8T, was isolated from leaf mould in Cheonan, Republic of Korea. Its taxonomic position was determined through a polyphasic approach. Optimal growth occurred on R2A agar without NaCl supplementation, at 25–28 °C and at pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TF8T belongs to the genus Mucilaginibacter in the family Sphingobacteriaceae . The sequence similarity between 16S rRNA genes of strain TF8T and the type strains of other species of the genus Mucilaginibacter ranged from 92.1 to 94.7 %. The closest relatives of strain TF8T were Mucilaginibacter lutimaris BR-3T (94.7 %), M. soli R9-65T (94.5 %), M. litoreus BR-18T (94.5 %), M. rigui WPCB133T (94.0 %) and M. daejeonensis Jip 10T (93.8 %). The major isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0 (33.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 24.8 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 13.0 %). The major polar lipids of TF8T were phosphatidylethanolamine and three unidentified aminophospholipids. The G+C content of the genomic DNA was 46.2 mol%. On the basis of the data presented here, strain TF8T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter koreensis sp. nov. is proposed. The type strain is TF8T ( = KACC 17468T = JCM 19323T).

scholarly journals rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira The GenBank accession numbers of the 16S rDNA gene sequences reported in this paper are AY038032–AY038037.

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 481-496 ◽  
Author(s):  
Isabelle Iteman ◽  
Rosmarie Rippka ◽  
Nicole Tandeau de Marsac ◽  
Michael Herdman
Keyword(s):  
16S Rrna ◽  
16S Rdna ◽  
Genomic Sequence ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Heterocystous Cyanobacteria

The taxonomic coherence and phylogenetic relationships of 11 planktonic heterocystous cyanobacterial isolates were examined by investigating two areas of the rRNA operon, the 16S rRNA gene (rrnS) and the internal transcribed spacer (ITS) located between the 16S rRNA and 23S rRNA genes. The rrnS sequences were determined for five strains, including representatives of Anabaena flos-aquae, Aphanizomenon flos-aquae, Nodularia sp. and two alkaliphilic planktonic members of the genera Anabaenopsis and Cyanospira, whose phylogenetic position was previously unknown. Comparison of the data with those previously published for individual groups of planktonic heterocystous cyanobacteria showed that, with the exception of members assigned to the genus Cylindrospermopsis, all the planktonic strains form a distinct subclade within the monophyletic clade of heterocystous cyanobacteria. Within this subclade five different phylogenetic clusters were distinguished. The phylogenetic groupings of Anabaena and Aphanizomenon strains within three of these clusters were not always consistent with their generic or specific assignments based on classical morphological definitions, and the high degree of sequence similarity between strains of Anabaenopsis and Cyanospira suggests that they may be assignable to a single genus. Ribotyping and additional studies performed on PCR amplicons of the 16S rDNA or the ITS for the 11 planktonic heterocystous strains demonstrated that they all contain multiple rrn operons and ITS regions of variable size. Finally, evidence is provided for intra-genomic sequence heterogeneity of the 16S rRNA genes within most of the individual isolates.

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