A New Zealand species of the trans-Tasman centipede order Craterostigmomorpha (Arthropoda : Chilopoda) corroborated by molecular evidence

2008 ◽  
Vol 22 (1) ◽  
pp. 1 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Gonzalo Giribet
Keyword(s):  
New Zealand ◽  
Species Diversity ◽  
16S Rrna ◽  
Malpighian Tubules ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
28S Rrna ◽  
Long Distance ◽  
Geographic Structure ◽  
Coi Sequences

Craterostigmus tasmanianus Pocock, 1902, is the sole species in the centipede order Craterostigmomorpha and the focus of much phylogenetic research in Chilopoda. Originally named from Tasmania, Craterostigmus from New Zealand was first considered conspecific with Tasmanian samples based on external morphology, though recent anatomical studies have argued for a deep divergence between New Zealand and Tasmanian Craterostigmus, and a high-ranking taxonomic separation has been advocated. Unambiguous diagnostic nucleotide characters in nuclear ribosomal 18S and 28S rRNA genes as well as in the mitochondrial 16S rRNA, together with the significantly smaller size of New Zealand individuals, the arrangement of supernumerary Malpighian tubules, and patterns in leg spinosity, permit distinction of a New Zealand species, Craterostigmus crabilli, sp. nov. In addition, phylogenetic analysis of four markers (the aforementioned markers plus cytochrome c oxidase subunit I) suggests differentiation of C. tasmanianus from the New Zealand specimens. Combination of the nuclear ribosomal genes and mitochondrial 16S rRNA and COI sequences retrieves a geographic pattern within C. crabilli, sp. nov. in which geographic proximity is decoupled from closest affinities, although the 16S rRNA dataset alone shows more geographic structure. The genetic pattern observed, where among species diversity (for both mitochondrial markers) is equivalent to, or greater than, the within species diversity, is not consistent with a recent long-distance dispersal event, and a relictual Gondwanan distribution is the most plausible alternative.

scholarly journals Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

2013 ◽  
Vol 80 (5) ◽  
pp. 1684-1691 ◽  
Author(s):  
Baozhan Wang ◽  
Yan Zheng ◽  
Rong Huang ◽  
Xue Zhou ◽  
Dongmei Wang ◽  
...  
Keyword(s):  
16S Rrna ◽  
Buoyant Density ◽  
Stable Isotope Probing ◽  
Acidic Soil ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTAll cultivated ammonia-oxidizing archaea (AOA) within theNitrososphaeracluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence ofNitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth ofNitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis ofamoAgenes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that13CO2assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both13C-labeledamoAand 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strainsNitrososphaera viennensisEN76 and JG1 within theNitrososphaeracluster. Our results provide strong evidence for the adaptive growth ofNitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.

A distinct phoronid larva: morphological and molecular evidence

2013 ◽  
Vol 27 (6) ◽  
pp. 622 ◽  
Author(s):  
Elena N. Temereva ◽  
Tatiana V. Neretina
Keyword(s):  
Rrna Genes ◽  
Molecular Characteristics ◽  
Molecular Evidence ◽  
28S Rrna ◽  
Vostok Bay ◽  
Distinctive Features ◽  
Marine Communities ◽  
Close Relationship ◽  
Phoronopsis Harmeri ◽  
World Fauna

Phoronids can be a major component of benthic and planktonic marine communities. Currently, the phoronid world fauna includes ten recognised species, known from adults; however, at least 32 larval forms have been described or documented. This study examined the morphology and 18S rRNA and 28S rRNA genes of two phoronid larvae abundant in Vostok Bay, Sea of Japan. One type was identified as the larval stage of Phoronopsis harmeri, although some distinctive features of this larva differ from the typical description. The morphological and molecular characteristics of the other larva did not match those of described species. According to our morphological results, this second actinotroch larva belongs to the genus Phoronis, but differs morphologically and molecularly from all the known species in the genus, all of which are represented in GenBank for the markers employed here. Taken together, our data suggest that the second actinotroch larva belongs to an undescribed phoronid species. The adult form of this actinotroch has never been identified, but our data suggest a close relationship with Phoronis pallida. The existence of a putative new phoronid species is also confirmed by presence of competent phoronid larvae, which are found in different aquatic areas, have a unique set of morphological features, and whose belonging is still not established.

scholarly journals Molecular Evidence for an Active Microbial Methane Cycle in Subsurface Serpentinite-Hosted Groundwaters in the Samail Ophiolite, Oman

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Emily A. Kraus ◽  
Daniel Nothaft ◽  
Blake W. Stamps ◽  
Kaitlin R. Rempfert ◽  
Eric T. Ellison ◽  
...  
Keyword(s):  
Low Temperature ◽  
16S Rrna ◽  
Microbial Activity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Evidence ◽  
Metagenomic Sequencing ◽  
Production Of Hydrogen ◽  
Genes Encoding ◽  
Subsurface Waters

ABSTRACT Serpentinization can generate highly reduced fluids replete with hydrogen (H2) and methane (CH4), potent reductants capable of driving microbial methanogenesis and methanotrophy, respectively. However, CH4 in serpentinized waters is thought to be primarily abiogenic, raising key questions about the relative importance of methanogens and methanotrophs in the production and consumption of CH4 in these systems. Herein, we apply molecular approaches to examine the functional capability and activity of microbial CH4 cycling in serpentinization-impacted subsurface waters intersecting multiple rock and water types within the Samail Ophiolite of Oman. Abundant 16S rRNA genes and transcripts affiliated with the methanogenic genus Methanobacterium were recovered from the most alkaline (pH, >10), H2- and CH4-rich subsurface waters. Additionally, 16S rRNA genes and transcripts associated with the aerobic methanotrophic genus Methylococcus were detected in wells that spanned varied fluid geochemistry. Metagenomic sequencing yielded genes encoding homologs of proteins involved in the hydrogenotrophic pathway of microbial CH4 production and in microbial CH4 oxidation. Transcripts of several key genes encoding methanogenesis/methanotrophy enzymes were identified, predominantly in communities from the most hyperalkaline waters. These results indicate active methanogenic and methanotrophic populations in waters with hyperalkaline pH in the Samail Ophiolite, thereby supporting a role for biological CH4 cycling in aquifers that undergo low-temperature serpentinization. IMPORTANCE Serpentinization of ultramafic rock can generate conditions favorable for microbial methane (CH4) cycling, including the abiotic production of hydrogen (H2) and possibly CH4. Systems of low-temperature serpentinization are geobiological targets due to their potential to harbor microbial life and ubiquity throughout Earth’s history. Biomass in fracture waters collected from the Samail Ophiolite of Oman, a system undergoing modern serpentinization, yielded DNA and RNA signatures indicative of active microbial methanogenesis and methanotrophy. Intriguingly, transcripts for proteins involved in methanogenesis were most abundant in the most highly reacted waters that have hyperalkaline pH and elevated concentrations of H2 and CH4. These findings suggest active biological methane cycling in serpentinite-hosted aquifers, even under extreme conditions of high pH and carbon limitation. These observations underscore the potential for microbial activity to influence the isotopic composition of CH4 in these systems, which is information that could help in identifying biosignatures of microbial activity on other planets.

Phylogeny of bethylid wasps (Hymenoptera: Bethylidae) inferred from 28S and 16S rRNA genes

2010 ◽  
Vol 41 (1) ◽  
pp. 55-73 ◽  
Author(s):  
Martin Carr ◽  
Peter Mayhew ◽  
J. Peter Young
Keyword(s):  
16S Rrna ◽  
Strong Support ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Monophyletic Clade ◽  
Outgroup Species ◽  
Molecular Studies ◽  
Mitochondrial 16S Rrna Gene

AbstractWe conduct the first molecular studies of the higher level phylogeny of bethylid wasps (Hymenoptera: Bethylidae). Sequences of the 500-bp D2/D3 expansion regions of the nuclear 28S rRNA gene are obtained for 33 bethylid species in 18 genera covering all four commonly recognized subfamilies, and an additional 13 outgroup species. A 450-bp sequence of the mitochondrial 16S rRNA gene is obtained for a smaller subset of those species. Strong support is found for the monophyly of Bethylidae, and for Bethylinae as the sister to the other bethylid subfamilies. Pristocerinae are supported as monophyletic. A species of Mesitiinae clusters with the Sclerodermini (sensu lato), these two strongly supported as a monophyletic clade. The Epyrini are supported as monophyletic, but our data do not demonstrate whether Pristocerinae or the Mesitiinae+Sclerodermini clade are their closest relatives. Kishino–Hasegawa tests reject the monophyly of the Epyrinae. Our results are consistent with Kieffer's original five major subtaxa of Bethylidae.

scholarly journals A troglobitic species of the centipede Cryptops (Chilopoda, Scolopendromorpha) from northwestern Botswana

ZooKeys ◽  
2020 ◽  
Vol 977 ◽  
pp. 25-40 ◽  
Author(s):  
Gregory D. Edgecombe ◽  
Nesrine Akkari ◽  
Edward C. Netherlands ◽  
Gerhard Du Preez
Keyword(s):  
South Africa ◽  
New Species ◽  
New Zealand ◽  
16S Rrna ◽  
Molecular Phylogenetics ◽  
18S Rrna ◽  
Temperate Species ◽  
28S Rrna ◽  
Oxidase Subunit ◽  
A New Species

A new species of Cryptops, C. (Cryptops) legagussp. nov., occurs in caves in the Koanaka and Gcwihaba Hills in northwestern Botswana. Bayesian molecular phylogenetics using 18S rRNA, 28S rRNA, 16S rRNA and cytochrome c oxidase subunit I corroborates a morphological assignment to the subgenus Cryptops and closest affinities to southern temperate species in South Africa, Australia and New Zealand. The new species is not conspicuously modified as a troglomorph.

scholarly journals Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11364
Author(s):  
Bruno R. Sampieri ◽  
Pedro E. Vieira ◽  
Marcos A. L. Teixeira ◽  
Victor C. Seixas ◽  
Paulo R. Pagliosa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Diversity ◽  
Sequence Data ◽  
Atlantic Coast ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
28S Rrna ◽  
Morphological Examination ◽  
Separate Species ◽  
The Way

The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported.

scholarly journals Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats

2016 ◽  
Vol 83 (2) ◽  
Author(s):  
K. Hokynar ◽  
E. J. Vesterinen ◽  
T. M. Lilley ◽  
A. T. Pulliainen ◽  
S. J. Korhonen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
23S Rrna ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Pcr Targeting

ABSTRACT Chlamydia-like organisms (CLOs) are recently identified members of the Chlamydiales order. CLOs share intracellular lifestyles and biphasic developmental cycles, and they have been detected in environmental samples as well as in various hosts such as amoebae and arthropods. In this study, we screened bat feces for the presence of CLOs by molecular analysis. Using pan-Chlamydiales PCR targeting the 16S rRNA gene, Chlamydiales DNA was detected in 54% of the specimens. PCR amplification, sequencing, and phylogenetic analysis of the 16S rRNA and 23S rRNA genes were used to classify positive specimens and infer their phylogenetic relationships. Most sequences matched best with Rhabdochlamydia species or uncultured Chlamydia sequences identified in ticks. Another set of sequences matched best with sequences of the Chlamydia genus or uncultured Chlamydiales from snakes. To gain evidence of whether CLOs in bat feces are merely diet borne, we analyzed insects trapped from the same location where the bats foraged. Interestingly, the CLO sequences resembling Rhabdochlamydia spp. were detected in insect material as well, but the other set of CLO sequences was not, suggesting that this set might not originate from prey. Thus, bats represent another potential host for Chlamydiales and could harbor novel, previously unidentified members of this order. IMPORTANCE Several pathogenic viruses are known to colonize bats, and recent analyses indicate that bats are also reservoir hosts for bacterial genera. Chlamydia-like organisms (CLOs) have been detected in several animal species. CLOs have high 16S rRNA sequence similarity to Chlamydiaceae and exhibit similar intracellular lifestyles and biphasic developmental cycles. Our study describes the frequent occurrence of CLO DNA in bat feces, suggesting an expanding host species spectrum for the Chlamydiales. As bats can acquire various infectious agents through their diet, prey insects were also studied. We identified CLO sequences in bats that matched best with sequences in prey insects but also CLO sequences not detected in prey insects. This suggests that a portion of CLO DNA present in bat feces is not prey borne. Furthermore, some sequences from bat droppings not originating from their diet might well represent novel, previously unidentified members of the Chlamydiales order.

Molecular phylogeny of sea-skaters (Halobates Eschscholtz, 1822), relationship between Halobatini and Metrocorini, and a catalogue of the subfamily Halobatinae (Hemiptera: Heteroptera: Gerridae)

2020 ◽  
Vol 51 (2) ◽  
pp. 139-240 ◽  
Author(s):  
Cristian Román-Palacios ◽  
Jakob Damgaard ◽  
Lanna Cheng ◽  
Felipe Ferraz Figueiredo Moreira ◽  
Terumi Ikawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Common Ancestor ◽  
Open Ocean ◽  
Rrna Genes ◽  
28S Rrna ◽  
The Common ◽  
Geographic Distributions

We investigated the phylogenetic relationships among seven of the ten Halobatinae genera (Heteroptera: Gerridae) based on COI+II, 16S rRNA, and 28S rRNA genes. Our analyses recovered monophyly of Halobatinae, and suggested paraphyly of Metrocorini caused by the position of Ventidius and Esakia. Since our phylogenies did not infer monophyly of the subgenus Halobates (s.str.) within Halobatini, we synonymized Austrobates and Halobates (Hilliella) with Halobates. We confirmed that (1) the limnic lifestyle of Metrocorini was ancestral in Halobatinae, (2) the marine lifestyle evolved only once in the common ancestor of Asclepios + Halobates, (3) the limnic lifestyle of some members of Halobates was independently derived from marine ancestors, and that (4) the open ocean was colonized at least three times in Halobates. A catalogue of Halobatinae organized according to an updated classification is presented, including all known geographic distributions, bibliographical references, and additional notes to all species of the subfamily.

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