Axial Differences in Community Structure ofCrenarchaeota and Euryarchaeota in the Highly Compartmentalized Gut of the Soil-Feeding TermiteCubitermes orthognathus

ABSTRACT Methanogenesis represents an important electron sink reaction in the hindgut of soil-feeding termites. This is the first comprehensive analysis of the archaeal community structure within the highly compartmentalized intestinal tract of a humivorous insect, combining clonal analysis and terminal restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the archaeal communities in the different gut compartments of Cubitermes orthognathus. We found that the morphological and physicochemical heterogeneity of the gut is reflected in a large phylogenetic diversity and pronounced axial differences in the composition of the archaeal gut microbiota, notably among those clones or ribotypes that could be assigned to methanogenic taxa. Comparative analysis of the relative frequencies of different archaeal lineages among the small-subunit rRNA gene (SSU rDNA) clones and their corresponding T-RF indicated that the archaeal community in the anterior, extremely alkaline hindgut compartment (P1) consists mainly of members of theMethanosarcinaceae, whereasMethanobacteriaceae andMethanomicrobiales predominate in the subsequent, more posterior compartments (P3/4a and P4b). The relative abundance ofThermoplasmales increased towards the rectum (P5). SSU rDNA sequences representing Crenarchaeota, which have not yet been reported to occur in the intestinal tracts of arthropods, were detected in all gut sections. We discuss how the spatial distribution of methanogenic populations may be linked to axial heterogeneity in the physicochemical gut conditions and to functional adaptations to their respective ecological niches.

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Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

Applied and Environmental Microbiology ◽

10.1128/aem.64.12.5064-5066.1998 ◽

1998 ◽

Vol 64 (12) ◽

pp. 5064-5066 ◽

Cited By ~ 21

Author(s):

Clifford F. Brunk ◽

Nicole Eis

Keyword(s):

Internal Standard ◽

Pcr Amplification ◽

Quantitative Measure ◽

Pcr Primers ◽

Small Subunit ◽

Ssu Rdna ◽

Rdna Sequence ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

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Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.059899-0 ◽

2014 ◽

Vol 64 (Pt_2) ◽

pp. 680-688 ◽

Cited By ~ 6

Author(s):

Xinpeng Fan ◽

Saleh A. Al-Farraj ◽

Feng Gao ◽

Fukang Gu

Keyword(s):

Phylogenetic Analyses ◽

Eastern China ◽

Small Subunit ◽

Ssu Rdna ◽

Contractile Vacuole ◽

Phylogenetic Position ◽

Rrna Gene ◽

Small Subunit Rrna ◽

North West ◽

Rdna Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

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Kinetic Bias in Estimates of Coastal Picoplankton Community Structure Obtained by Measurements of Small-Subunit rRNA Gene PCR Amplicon Length Heterogeneity

Applied and Environmental Microbiology ◽

10.1128/aem.64.11.4522-4529.1998 ◽

1998 ◽

Vol 64 (11) ◽

pp. 4522-4529 ◽

Cited By ~ 267

Author(s):

Marcelino Suzuki ◽

Michael S. Rappé ◽

Stephen J. Giovannoni

Keyword(s):

Clone Library ◽

Fluorescence Emission ◽

Small Subunit ◽

Ssu Rdna ◽

Rrna Genes ◽

Rrna Gene ◽

Length Variation ◽

Small Subunit Rrna ◽

Gene Frequencies ◽

Rdna Sequences

ABSTRACT Marine bacterioplankton diversity was examined by quantifying natural length variation in the 5′ domain of small-subunit (SSU) rRNA genes (rDNA) amplified by PCR from a DNA sample from the Oregon coast. This new technique, length heterogeneity analysis by PCR (LH-PCR), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. Relationships between the sizes of amplicons and gene phylogeny were predicted by an analysis of 366 SSU rDNA sequences from cultivated marine bacteria and from bacterial genes cloned directly from environmental samples. LH-PCR was used to compare the distribution of bacterioplankton SSU rDNAs from a coastal water sample with that of an SSU rDNA clone library prepared from the same sample and also to examine the distribution of genes in the PCR products from which the clone library was prepared. The analysis revealed that the relative frequencies of genes amplified from natural communities are highly reproducible for replicate sets of PCRs but that a bias possibly caused by the reannealing kinetics of product molecules can skew gene frequencies when PCR product concentrations exceed threshold values.

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Intercontinental distribution of a new trypanosome species from Australian endemic Regent Honeyeater (Anthochaera phrygia)

Parasitology ◽

10.1017/s0031182016000329 ◽

2016 ◽

Vol 143 (8) ◽

pp. 1012-1025 ◽

Cited By ~ 8

Author(s):

JAN ŠLAPETA ◽

VICTORIA MORIN-ADELINE ◽

PAUL THOMPSON ◽

DENISE MCDONELL ◽

MICHAEL SHIELS ◽

...

Keyword(s):

Captive Breeding ◽

Small Subunit ◽

Ssu Rdna ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Small Subunit Rrna Gene ◽

Screening Protocol ◽

Parasitological Survey ◽

Manorina Melanocephala ◽

Baseline Health

SUMMARYEstablishing a health screening protocol is fundamental for successful captive breeding and release of wildlife. The aim of this study was to undertake a parasitological survey focusing on the presence of trypanosomes in a cohort of Regent Honeyeaters, Anthochaera phrygia, syn. Xanthomyza phrygia (Aves: Passeriformes) that are part of the breeding and reintroduction programme carried out in Australia. We describe a new blood parasite, Trypanosoma thomasbancrofti sp. n. (Kinetoplastida: Trypanosomatidae) with prevalence of 24·4% (20/81) in a captive population in 2015. The sequence of the small subunit rRNA gene (SSU rDNA) and kinetoplast ultrastructure of T. thomasbancrofti sp. n. are the key differentiating characteristics from other Trypanosoma spp. T. thomasbancrofti sp. n. is distinct from Trypanosoma cf. avium found in sympatric Noisy Miners (Manorina melanocephala). The SSU rDNA comparison suggests an intercontinental distribution of T. thomasbancrofti sp. n. and Culex mosquitoes as a suspected vector. Currently, no information exists on the effect of T. thomasbancrofti sp. n. on its hosts; however, all trypanosome-positive birds remain clinically healthy. This information is useful in establishing baseline health data and screening protocols, particularly prior to release to the wild.

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Spatial-temporal dynamics and influencing factors of archaeal communities in the sediments of Lancang River cascade reservoirs (LRCR), China

PLoS ONE ◽

10.1371/journal.pone.0253233 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253233

Author(s):

Bo Yuan ◽

Wei Wu ◽

Mengjing Guo ◽

Xiaode Zhou ◽

Shuguang Xie

Keyword(s):

Community Structure ◽

16S Rrna ◽

Large Scale ◽

Temporal Dynamics ◽

Archaeal Community ◽

Rrna Gene ◽

Regulated Rivers ◽

Cascade Reservoirs ◽

Lancang River ◽

Archaeal Communities

The spatial and temporal distribution of the archaeal community and its driving factors in the sediments of large-scale regulated rivers, especially in rivers with cascade hydropower development rivers, remain poorly understood. Quantitative PCR (qPCR) and Illumina MiSeq sequencing of the 16S rRNA archaeal gene were used to comprehensively investigate the spatiotemporal diversity and structure of archaeal community in the sediments of the Lancang River cascade reservoirs (LRCR). The archaeal abundance ranged from 5.11×104 to 1.03×106 16S rRNA gene copies per gram dry sediment and presented no temporal variation. The richness, diversity, and community structure of the archaeal community illustrated a drastic spatial change. Thaumarchaeota and Euryyarchaeota were the dominant archaeal phyla in the sediments of the cascade rivers, and Bathyarchaeota was also an advantage in the sediments. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and carbon and nitrogen metabolism in downstream reservoirs, indicating that anthropogenic pollution discharges might act as the dominant selective force to alter the archaeal communities. Nitrate and C/N ratio were found to play important roles in the formation of the archaeal community composition. In addition, the sediment archaeal community structure was also closely related to the age of the cascade reservoir and hydraulic retention time (HRT). This finding indicates that the engineering factors of the reservoir might be the greatest contributor to the archaeal community structure in the LRCR.

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Analysis of primary structure loops from Hairpins 35 and 48 of the Nematoda SSU rRNA gene provides further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida

Zootaxa ◽

10.11646/zootaxa.3208.1.3 ◽

2012 ◽

Vol 3208 (1) ◽

pp. 41 ◽

Cited By ~ 2

Author(s):

ZENGQI ZHAO ◽

DONGMEI LI ◽

THOMAS R. BUCKLEY

Keyword(s):

Primary Structure ◽

Phylogenetic Analyses ◽

Small Subunit ◽

Ssu Rdna ◽

Rrna Gene ◽

Ssu Rrna ◽

Rdna Sequences ◽

Evolutionarily Conserved ◽

De Man ◽

Nucleotide Transition

A comparison of small subunit (SSU) rDNA sequences has revealed that a rare nucleotide transition A→G and a trans-version G→Y occurred simultaneously in the evolutionarily conserved loops of Hairpins 35 and 48 of the SSU rRNA geneof Tripylina Brzeski 1963, Trischistoma Cobb 1913 and Rhabdolaimus de Man 1880. The same pair of substitutions oc-curred in all Enoplida analysed but not in other nematodes. This evidence from the primary structure of Hairpins 35 and48 indicates that Tripylina, Trischistoma and Rhabdolaimus are members of Enoplida, supporting previous phylogenetic analyses.

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Seasonal Dynamics of Bathyarchaeota-Dominated Benthic Archaeal Communities Associated with Seagrass (Zostera japonica) Meadows

Journal of Marine Science and Engineering ◽

10.3390/jmse9111304 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1304

Author(s):

Pengyuan Liu ◽

Haikun Zhang ◽

Zenglei Song ◽

Yanyan Huang ◽

Xiaoke Hu

Keyword(s):

Community Structure ◽

Seasonal Changes ◽

Archaeal Community ◽

Rrna Gene ◽

Zostera Japonica ◽

Total Organic Nitrogen ◽

Seagrass Meadows ◽

Metabolic Functions ◽

Seagrass Ecosystems ◽

Archaeal Communities

Little is known about the seasonal dynamic of archaeal communities and their potential ecological functions in temperate seagrass ecosystems. In this study, seasonal changes in diversity, community structure, and potential metabolic functions of benthic archaea in surface sediments of two seagrass meadows along the northern Bohai Sea in China were investigated using Miseq sequencing of the 16S rRNA gene and Tax4Fun2 functional prediction. Overall, Crenarchaeota (mainly Bathy-15, Bathy-8, and Bathy-6) dominated, followed by Thermoplasmatota, Asgardarchaeota, and Halobacterota, in terms of alpha diversities and relative abundance. Significant seasonal changes in the entire archaeal community structure were observed. The major phyla Methanobacteria, Nitrosopumilales, and genus Methanolobus had higher proportions in spring, while MBG-D and Bathyarchaeota were more abundant in summer and autumn, respectively. Alpha diversities (Shannon and Simpson) were the highest in summer and the lowest in autumn (ANOVA test, p < 0.05). Salinity, total organic carbon, and total organic nitrogen were the most significant factors influencing the entire archaeal community. Higher cellulose and hemicellulose degradation potentials occurred in summer, while methane metabolism potentials were higher in winter. This study indicated that season had strong effects in modulating bsenthic archaeal diversity and functional potentials in the temperate seagrass ecosystems.

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Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

Microorganisms ◽

10.3390/microorganisms9010021 ◽

2020 ◽

Vol 9 (1) ◽

pp. 21

Author(s):

Abdul Ghafar ◽

Anson V. Koehler ◽

Ross S. Hall ◽

Charles G. Gauci ◽

Robin B. Gasser ◽

...

Keyword(s):

Next Generation Sequencing ◽

Water Buffalo ◽

Hypervariable Region ◽

Small Subunit ◽

Rrna Gene ◽

Next Generation ◽

Small Subunit Rrna ◽

Tropical Theileriosis ◽

Ecological Zones ◽

Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

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Differences in Microbial Activity and Microbial Populations of Peat Associated with Suppression of Damping-Off Disease Caused by Pythium sylvaticum

Applied and Environmental Microbiology ◽

10.1128/aem.00313-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6452-6460 ◽

Cited By ~ 43

Author(s):

Paul J. Hunter ◽

Geoff M. Petch ◽

Leo A. Calvo-Bado ◽

Tim R. Pettitt ◽

Nick R. Parsons ◽

...

Keyword(s):

Microbial Activity ◽

Denaturing Gradient Gel Electrophoresis ◽

Small Subunit ◽

Disease Suppression ◽

Rrna Gene ◽

Damping Off ◽

Small Subunit Rrna ◽

Pythium Sylvaticum ◽

Gradient Gel Electrophoresis ◽

Microbial Groups

ABSTRACT The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

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Detection of Kobe-typeBabesia microtiassociated with Japanese human babesiosis in field rodents in central Taiwan and southeastern mainland China

Parasitology ◽

10.1017/s0031182008004356 ◽

2008 ◽

Vol 135 (6) ◽

pp. 691-699 ◽

Cited By ~ 12

Author(s):

A. SAITO-ITO ◽

N. TAKADA ◽

F. ISHIGURO ◽

H. FUJITA ◽

Y. YANO ◽

...

Keyword(s):

Mainland China ◽

Small Subunit ◽

Human Infection ◽

Babesia Microti ◽

Rrna Gene ◽

Microscopical Examination ◽

Small Subunit Rrna ◽

Central Taiwan ◽

Field Rodents ◽

Human Babesiosis

SUMMARYField rodent surveys forBabesiainfection were performed from 2002 to 2005 in the vicinities of human babesiosis occurrences in Taiwan and mainland China.Babesia microtiwas identified by microscopical examination and/or PCR in 1Rattus coxingaand 1Crocidura horsfieldiiin central Taiwan and in 13Niviventer confucianusand 1Apodemus agrariusin Zhejiang and Fujian Provinces of southeastern China. Of 15B. microtisamples detected by PCR, all except 1 were shown to be the Kobe-type, the aetiological small subunit rRNA gene-type of the first Japanese patient; the exception was also a Kobe-related type. The Kobe-type had been found in rodents only in a few places including the human infection occurrence place in Japan. The internal transcribed spacer 1 to 2 sequences of the Taiwanese and Chinese Kobe-types were very similar to each other but considerably different (approx. 94% pairwise identities) from that of the Japanese Kobe-type. A Taiwanese Kobe-type strain was serologically differentiated from the Kobe strain originating from the Japanese first patient. The distribution of the Kobe-type in the vicinities of human babesiosis occurrences in Taiwan and China as well as in Japan is suggestive of involvement of the Kobe-type in Asian human babesiosis.

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