scholarly journals The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

2016 ◽  
Vol 82 (12) ◽  
pp. 3572-3581 ◽  
Author(s):  
Kevin C. Lee ◽  
Matthew B. Stott ◽  
Peter F. Dunfield ◽  
Curtis Huttenhower ◽  
Ian R. McDonald ◽  
...  
Keyword(s):  
Microbial Community ◽  
Genomic Sequence ◽  
Geographic Distance ◽  
Taupo Volcanic Zone ◽  
Rrna Gene ◽  
Volcanic Zone ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Local Selection ◽  
Stochastic Dispersal

ABSTRACTChthonomonas calidiroseaT49Tis a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that theC. calidiroseagenome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of fourC. calidiroseaisolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation inC. calidirosearelative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of theC. calidiroseaisolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms ofC. calidiroseadistribution. This dispersal and extinction mechanism is likely not limited toC. calidiroseabut may shape the populations and genomes of many other low-abundance free-living taxa.IMPORTANCEThis study compares the genomic sequence variations and metabolisms of four strains ofChthonomonas calidirosea, a rare thermophilic bacterium from the phylumArmatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the fourC. calidiroseastrains were isolated.C. calidiroseawas previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, theC. calidiroseagenome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting thatC. calidiroseagenotypes are not primarily determined by adaptive evolution. Instead, the presence ofC. calidiroseamay be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

scholarly journals Burkholderia insulsa sp. nov., a facultatively chemolithotrophic bacterium isolated from an arsenic-rich shallow marine hydrothermal system

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 189-194 ◽  
Author(s):  
Antje Rusch ◽  
Shaer Islam ◽  
Pratixa Savalia ◽  
Jan P. Amend
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shallow Marine Hydrothermal System ◽  
Type Strains

Enrichment cultures inoculated with hydrothermally influenced nearshore sediment from Papua New Guinea led to the isolation of an arsenic-tolerant, acidophilic, facultatively aerobic bacterial strain designated PNG-AprilT. Cells of this strain were Gram-stain-negative, rod-shaped, motile and did not form spores. Strain PNG-AprilT grew at temperatures between 4 °C and 40 °C (optimum 30–37 °C), at pH 3.5 to 8.3 (optimum pH 5–6) and in the presence of up to 2.7 % NaCl (optimum 0–1.0 %). Both arsenate and arsenite were tolerated up to concentrations of at least 0.5 mM. Metabolism in strain PNG-AprilT was strictly respiratory. Heterotrophic growth occurred with O2 or nitrate as electron acceptors, and aerobic lithoautotrophic growth was observed with thiosulfate or nitrite as electron donors. The novel isolate was capable of N2-fixation. The respiratory quinones were Q-8 and Q-7. Phylogenetically, strain PNG-AprilT belongs to the genus Burkholderia and shares the highest 16S rRNA gene sequence similarity with the type strains of Burkholderia fungorum (99.8 %), Burkholderia phytofirmans (98.8 %), Burkholderia caledonica (98.4 %) and Burkholderia sediminicola (98.4 %). Differences from these related species in several physiological characteristics (lipid composition, carbohydrate utilization, enzyme profiles) and DNA–DNA hybridization suggested the isolate represents a novel species of the genus Burkholderia , for which we propose the name Burkholderia insulsa sp. nov. The type strain is PNG-AprilT ( = DSM 28142T = LMG 28183T).

Tree ferns and tea trees in biogeochemical exploration for epithermal Au and Ag in New Zealand

2019 ◽  
Vol 20 (3) ◽  
pp. 299-314
Author(s):  
C. E. Dunn ◽  
A. B. Christie
Keyword(s):  
Common Species ◽  
Taupo Volcanic Zone ◽  
Geothermal Area ◽  
Volcanic Zone ◽  
Tree Fern ◽  
Content Type ◽  
Tea Tree ◽  
Tree Ferns ◽  
Supplementary Material ◽  
Epithermal Au

Biogeochemical orientation surveys were undertaken at low sulphidation epithermal Au–Ag occurrences in the Hauraki Goldfield–Coromandel Volcanic Zone and the Taupo Volcanic Zone, and at the Waiotapu active geothermal area in the Taupo Volcanic Zone. Several plant species were sampled, including the foliage of tree ferns and tea trees. The ferns – silver fern (ponga), rough tree fern (wheki) and black tree fern (mamaku) – were ubiquitous and were the easiest species to sample, although tea tree was the dominant genus at Waiotapu. At the Waiotapu geothermal area, significantly higher concentrations of Ag, Au, Sb, As, Cs and Rb were present in samples close to Champagne Pool than elsewhere, confirming its location as the main outflow source of Au, Ag and their pathfinder elements. The fern survey areas at Luck at Last mine, Pine Sinter and Ohui in the Coromandel Volcanic Zone each exhibited biogeochemical anomalies, which successfully highlighted most of the known quartz veins and provided additional anomalies for further investigation. Rough tree fern was the most common species at Goldmine Hill, Puhipuhi (Taupo Volcanic Zone). Although this species absorbs lower concentrations of many elements than the silver fern, the spatial distribution of elements is of greater significance than their absolute concentrations. The highest Au, Ag, As and Al concentrations occurred in samples from a ridge extending WNW from Goldmine Hill. Sb and Bi were at anomalous levels in an area peripheral to the precious metal anomalies, indicating the potential zonation of elements distal from the Au and Ag deposits.Supplementary material: The full datasets on the fern and tea tree chemistry, including quality assurance/quality control and multi-element plots, are available free of charge through the GNS Science website (search for Dunn) at http://shop.gns.cri.nz/publications/science-reports/.

scholarly journals Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

2013 ◽  
Vol 80 (2) ◽  
pp. 757-765 ◽  
Author(s):  
Amber M. Koskey ◽  
Jenny C. Fisher ◽  
Mary F. Traudt ◽  
Ryan J. Newton ◽  
Sandra L. McLellan
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Fecal Indicator ◽  
Fecal Samples ◽  
Content Type

ABSTRACTGulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such asEscherichia coliand enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.EnterococcaceaeandEnterobacteriaceaewere the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealedCatellicoccus marimammaliumas the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcusindoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified asEnterococcusspp., 1.2% were identified asStreptococcusspp., and none were identified asC. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions ofC. marimammalium16S rRNA gene sequences (>50-fold) relative to typical mEI culturableEnterococcusspp.C. marimammaliumtherefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.

scholarly journals Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

2013 ◽  
Vol 79 (12) ◽  
pp. 3601-3609 ◽  
Author(s):  
Henglin Cui ◽  
Kun Yang ◽  
Eulyn Pagaling ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Temporal Variation ◽  
Beach Sand ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Fecal Indicator ◽  
Bacterial Populations ◽  
Mass Unit ◽  
Content Type ◽  
Beach Water

ABSTRACTRecent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with totalVibrioin all beach zones but less significantly with total bacterial density andEscherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.

Rhabdothermincola sediminis gen. nov., sp. nov., a new actinobacterium isolated from hot spring sediment, and emended description of the family Iamiaceae

2019 ◽  
Vol 71 (3) ◽  
Author(s):  
Ze-Tao Liu ◽  
Jian-Yu Jiao ◽  
Lan Liu ◽  
Meng-Meng Li ◽  
Yu-Zhen Ming ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Hot Spring ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

One thermophilic bacterium, designated strain SYSU G02662T, was isolated from hot spring sediment sampled in Tibet, PR China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G02662T showed the highest sequence similarity to Actinomarinicola tropica SCSIO 58843T (95.1 %). The strain could be differentiated from other species of the family Iamiaceae by its distinct phenotypic and genotypic characteristics. Cells of strain SYSU G02662T were aerobic, Gram-staining-positive and short rodshaped. Growth occurred optimally at 45 °C and pH 7.0. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The respiratory quinone was MK-9 (H8), while the major fatty acids (>10 %) were C16 : 0, C17 : 0, C18 : 0 and iso-C16 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The G+C content of the genomic DNA was 70.5 % based on the draft genomic sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G02662T represents a novel species of a novel genus in the family Iamiaceae , for which the name Rhabdothermincola sediminis gen. nov., sp. nov. is proposed. The type strain of the proposed novel species is SYSU G02662T (=CGMCC 4.7688T=KCTC 49500T).

Transcrustal Magmatic Systems: Evidence from Andesites of the Southern Taupo Volcanic Zone

2021 ◽  
pp. jgs2020-204
Author(s):  
Christopher Svoboda ◽  
Tyrone O. Rooney ◽  
Guillaume Girard ◽  
Chad Deering
Keyword(s):  
Field Work ◽  
Scoria Cone ◽  
Taupo Volcanic Zone ◽  
Volcanic Zone ◽  
Content Type ◽  
Supplementary Material ◽  
Temperature And Pressure ◽  
Compositional Diversity ◽  
Lower Crustal ◽  
Hot Zone

Studies synthesizing field work, numerical simulations, petrology, geochemistry, and geophysical observations indicate that the compositional diversity of arc lavas results from evolution of mantle-derived magmas by mixing, assimilation, and fractional crystallization. This evolution occurs within complexes called transcrustal magmatic systems. The mafic lower parts of such zones, called hot zones, are difficult to probe. However, a satellite vent near the stratovolcano Ruapehu in the southern Taupo Volcanic Zone (New Zealand) comprises materials that may originate from a hot zone. Magnesian andesites (Mg#64-69) from the Ohakune scoria cone contain primitive olivine (Fo85-91), high Mg# clinopyroxene (Mg#81-88), and orthopyroxene (Mg#76-83), but lack plagioclase. Disequilibrium of Ohakune crystals and groundmass suggests that the crystal cargo of Ohakune andesites was scavenged from deeper and more primitive levels of the magmatic system. Mineral constraints on temperature and pressure indicate that the hot zone initially formed at mid- to lower-crustal pressures (3.5-7.0±2.8 kbar). We interpret the mafic mineralogy and presence of disequilibrium features as evidence that these andesites and their crystal cargo are products of a hot zone in the middle to lower crust. Products of the hot zone may appear before products of the systems that form the bases of mature stratovolcanoes such as Ruapehu.Supplementary material:https://doi.org/10.6084/m9.figshare.c.5494984

Xanthobacter oligotrophicus sp.nov., isolated from paper mill sewage

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ekaterina N. Tikhonova ◽  
Denis S. Grouzdev ◽  
Irina K. Kravchenko
Keyword(s):  
Type Species ◽  
Paper Mill ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Carbohydrate Utilization ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Bacterium Strain

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29kT, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5–0.7×1.7–3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-β-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C18:1 ω7, C19:0 cyclo and C16:0. The genomic DNA G+C content was 67.95 mol%. Strain 29kT was able to grow at 4–37 °C (optimum, 30 °C), at pH 6.0–8.5 (optimum, pH 6.5–7.0) and at salinities of 0–0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29kT could grow chemolithoautotrophically in mineral media under an atmosphere of H2, O2 and CO2 as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Xanthobacter with Xanthobacter autotrophicus 7cT (99.9% similarity) and Xanthobacter viscosus 7dT (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA–DNA hybridization values of 92.7 and 44.9%, respectively, of the 29kT to the genome of the most closely related species, X. autotrophicus 7cT, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Xanthobacter oligotrophicus sp. nov. The type strain is 29kT (=KCTC 72777T=VKM B-3453T).

Luteolibacter ambystomatis sp. nov., isolated from the skin of an Anderson’s salamander (Ambystoma andersoni)

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Hans-Jürgen Busse ◽  
Peter Kämpfer ◽  
Michael Peter Szostak ◽  
Joachim Spergser
Keyword(s):  
Type Species ◽  
Genomic Sequence ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
Genomic Sequence Analysis ◽  
Hydroxylated Fatty Acids

A bacterial strain designated 32AT was isolated from the skin of an Anderson’s salamander (Ambystoma andersoni) and subjected to a comprehensive taxonomic study. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase- and urease-negative, and catalase-positive. 16S rRNA gene sequence comparisons placed the strain in the genus Luteolibacter with highest sequence similarities to Luteolibacter pohnpeiensis A4T-83T (95.2%), Luteolibacter gellanilyticus CB-286403T (95.1%) and Luteolibacter cuticulihirudinis E100T (94.9%). Genomic sequence analysis revealed a size of 5.3 Mbp, a G+C-content of 62.2 mol% and highest ANI values with Luteolibacter luteus (71.2%), Luteolibacter yonseiensis (71.4%) and L. pohnpeiensis (69.5%). In the polyamine pattern, 1,3-diaminopropane and spermidine were predominant. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system was composed of the major menaquinones MK-9 and MK-10. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, the unidentified aminolipid AL2, the unidentified phospholipid PL2 and the unidentified aminophospholipid APL1. The fatty acid profile contained major amounts of iso-C14:0, iso-C16:0, C16 : 0 and C16 : 1 ω9c. In addition, C14 : 0, C15:0, anteiso-C15 : 0, summed feature 2 (C14 : 0 3OH and/or iso-C16 : 0 I), and the hydroxylated fatty acids iso-C14 : 0 3OH, iso-C16 : 0 3OH and C16 : 0 3-OH were detected. Physiologically, strain 32AT is distinguishable from its next relatives. Based on phylogenetic, genomic, physiological and chemotaxonomic data, strain 32AT represents a novel species of the genus Luteolibacter for which we propose the name Luteolibacter ambystomatis sp. nov. The type strain is 32AT (=CCM 9141T=LMG 32214T).

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