Microbiome analyses of 12 psyllid species of the family Psyllidae identified various bacteria including Fukatsuia and Serratia symbiotica, known as secondary symbionts of aphids

Abstract Background Psyllids (Hemiptera: Psylloidea) comprise a group of plant sap-sucking insects that includes important agricultural pests. They have close associations not only with plant pathogens, but also with various microbes, including obligate mutualists and facultative symbionts. Recent studies are revealing that interactions among such bacterial populations are important for psyllid biology and host plant pathology. In the present study, to obtain further insight into the ecological and evolutionary behaviors of bacteria in Psylloidea, we analyzed the microbiomes of 12 psyllid species belonging to the family Psyllidae (11 from Psyllinae and one from Macrocorsinae), using high-throughput amplicon sequencing of the 16S rRNA gene. Results The analysis showed that all 12 psyllids have the primary symbiont, Candidatus Carsonella ruddii (Gammaproteobacteria: Oceanospirillales), and at least one secondary symbiont. The majority of the secondary symbionts were gammaproteobacteria, especially those of the family Enterobacteriaceae (order: Enterobacteriales). Among them, symbionts belonging to “endosymbionts3”, which is a genus-level monophyletic group assigned by the SILVA rRNA database, were the most prevalent and were found in 9 of 11 Psyllinae species. Ca. Fukatsuia symbiotica and Serratia symbiotica, which were recognized only as secondary symbionts of aphids, were also identified. In addition to other Enterobacteriaceae bacteria, including Arsenophonus, Sodalis, and “endosymbionts2”, which is another genus-level clade, Pseudomonas (Pseudomonadales: Pseudomonadaceae) and Diplorickettsia (Diplorickettsiales: Diplorickettsiaceae) were identified. Regarding Alphaproteobacteria, the potential plant pathogen Ca. Liberibacter europaeus (Rhizobiales: Rhizobiaceae) was detected for the first time in Anomoneura mori (Psyllinae), a mulberry pest. Wolbachia (Rickettsiales: Anaplasmataceae) and Rickettsia (Rickettsiales: Rickettsiaceae), plausible host reproduction manipulators that are potential tools to control pest insects, were also detected. Conclusions The present study identified various bacterial symbionts including previously unexpected lineages in psyllids, suggesting considerable interspecific transfer of arthropod symbionts. The findings provide deeper insights into the evolution of interactions among insects, bacteria, and plants, which may be exploited to facilitate the control of pest psyllids in the future.

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Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽

10.3390/metabo11080482 ◽

2021 ◽

Vol 11 (8) ◽

pp. 482

Author(s):

Jae-Kwon Jo ◽

Seung-Ho Seo ◽

Seong-Eun Park ◽

Hyun-Woo Kim ◽

Eun-Ju Kim ◽

...

Keyword(s):

Gut Microbiota ◽

Relative Abundance ◽

High Fat Diet ◽

Amplicon Sequencing ◽

Gas Chromatography Mass Spectrometry ◽

Control Group ◽

Rrna Gene ◽

High Fat ◽

Underlying Mechanisms ◽

Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

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Microbiota Analysis of an Environmental Slurry and Its Potential Role as a Reservoir of Bovine Digital Dermatitis Pathogens

Applied and Environmental Microbiology ◽

10.1128/aem.00244-17 ◽

2017 ◽

Vol 83 (11) ◽

Cited By ~ 3

Author(s):

Kirstine Klitgaard ◽

Mikael L. Strube ◽

Anastasia Isbrand ◽

Tim K. Jensen ◽

Martin W. Nielsen

Keyword(s):

Dairy Herd ◽

Amplicon Sequencing ◽

Dairy Herds ◽

Rrna Gene ◽

Digital Dermatitis ◽

Bacterial Populations ◽

Associated Bacteria ◽

Content Type ◽

Next Generation Sequencing Technology ◽

Route Of Transmission

ABSTRACT At present, very little information exists regarding what role the environmental slurry may play as an infection reservoir and/or route of transmission for bovine digital dermatitis (DD), a disease which is a global problem in dairy herds. To investigate whether DD-related bacteria belong to the indigenous microbiota of the dairy herd environment, we used deep amplicon sequencing of the 16S rRNA gene in 135 slurry samples collected from different sites in 22 dairy farms, with and without DD-infected cows. Both the general bacterial populations and digital dermatitis-associated Treponema were targeted in this study. The results revealed significant differences in the bacterial communities between the herds, with only 12 bacterial taxa shared across at least 80% of all the individual samples. These differences in the herd microbiota appeared to reflect mainly between-herd variation. Not surprisingly, the slurry was dominated by ubiquitous gastrointestinal bacteria, such as Ruminococcaceae and Lachnospiraceae. Despite the low relative abundance of spirochetes, which ranged from 0 to 0.6%, we were able to detect small amounts of bacterial DNA from DD-associated treponemes in the slurry. However, the DD-associated Treponema spp. were detected only in samples from herds with reported DD problems. These data indicate that treponemes involved in the pathogenesis of DD are not part of the normal environmental microflora in dairy herds without clinical DD and, consequently, that slurry is not a primary reservoir of infection. IMPORTANCE Bovine digital dermatitis (DD), a dermal disease which causes lameness in dairy cattle, is a serious problem worldwide. To control this disease, the infection reservoirs and transmission routes of DD pathogens need to be clarified. The dairy herd slurry may be a pathogen reservoir of DD-associated bacteria. The rationale for the present study was, therefore, to examine whether DD-associated bacteria are always present in slurry or if they are found only in DD-afflicted herds. The results strongly indicated that DD Treponema spp. are not part of the indigenous slurry and, therefore, do not comprise an infection reservoir in healthy herds. This study applied next-generation sequencing technology to decipher the microbial compositions of environmental slurry of dairy herds with and without digital dermatitis.

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Anaerobic microbial LCFA degradation in bioreactors

Water Science & Technology ◽

10.2166/wst.2008.090 ◽

2008 ◽

Vol 57 (3) ◽

pp. 439-444 ◽

Cited By ~ 18

Author(s):

D. Z. Sousa ◽

M. A. Pereira ◽

J. I. Alves ◽

H. Smidt ◽

A. J. M Stams ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Rrna Gene ◽

Cloning And Sequencing ◽

16S Rrna Gene Analysis ◽

Sulfate Reducing ◽

Bacterial Consortia ◽

Enrichment Cultures ◽

The Family ◽

Insight Into

This paper reviews recent results obtained on long-chain fatty acids (LCFA) anaerobic degradation. Two LCFA were used as model substrates: oleate, a mono-unsaturated LCFA, and palmitate, a saturated LCFA, both abundant in LCFA-rich wastewaters. 16S rRNA gene analysis of sludge samples submitted to continuous oleate- and palmitate-feeding followed by batch degradation of the accumulated LCFA demonstrated that bacterial communities were dominated by members of the Clostridiaceae and Syntrophomonadaceae families. Archaeal populations were mainly comprised of hydrogen-consuming microorganisms belonging to the genus Methanobacterium, and acetate-utilizers from the genera Methanosaeta and Methanosarcina. Enrichment cultures growing on oleate and palmitate, in the absence or presence of sulfate, gave more insight into the major players involved in the degradation of unsaturated and saturated LCFA. Syntrophomonas-related species were identified as predominant microorganisms in all the enrichment cultures. Microorganisms clustering within the family Syntrophobacteraceae were identified in the methanogenic and sulfate-reducing enrichments growing on palmitate. Distinct bacterial consortia were developed in oleate and palmitate enrichments, and observed differences might be related to the different degrees of saturation of these two LCFA. A new obligately syntrophic bacterium, Syntrophomonas zehnderi, was isolated from an oleate-degrading culture and its presence in oleate-degrading sludges detected by 16S rRNA gene cloning and sequencing.

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Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0249 ◽

2020 ◽

Author(s):

Yingwu Shi ◽

Hongmei Yang ◽

Min Chu ◽

Xinxiang Niu ◽

Xiangdong Huo ◽

...

Keyword(s):

Community Structure ◽

Endophytic Bacteria ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Populations ◽

Operational Taxonomic Units ◽

Cotton Sample ◽

Endophytic Bacterial Community ◽

V3 Region ◽

Illumina Amplicon Sequencing

Endophytic bacteria may be important for plant health and other ecologically relevant functions of cotton. However, the endophytic bacterial community structure and diversity in cotton is still poorly characterized. We investigated the community structure of endophytic bacteria in cotton roots growing in Xinjiang, China, using the Illumina amplicon sequencing. A total of 60.84 M effective sequences of 16S rRNA gene V3 region were obtained from cotton samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in cotton, that is, 81-338 OTUs in a cotton sample, at 3% cutoff level and sequencing depth of 50000 sequences. We identified 23 classes from the resulting 2,723,384 sequences. Gammaproteobacteria were the dominant class in all cottons, followed by Alphaproteobacteria, Actinobacteria and Bacilli. A marked difference in the diversity of endophytic bacteria in cotton for different growth periods was evident. The greatest number of OTUs was detected during seedling (654 OTUs) and budding (381 OTUs). Endophytic bacteria diversity was reduced during flowering (350 OTUs) and boll-opening (351 OTUs). 217 OTUs were common to all four periods. There were more tags of Pantoea in Shihezi than other locations. While there were more tags of Erwinia in Hami than other locations. The dynamics of endophytic bacteria communities were influenced by plant growth stage. These results show the complexity of the bacterial populations present in inner tissues of cotton.

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Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa043 ◽

2020 ◽

Vol 96 (4) ◽

Cited By ~ 2

Author(s):

César Ruiz ◽

Marcela Villegas-Plazas ◽

Olivier P Thomas ◽

Howard Junca ◽

Thierry Pérez

Keyword(s):

Extreme Environments ◽

Amplicon Sequencing ◽

Sponge Species ◽

Rrna Gene ◽

Microbiome Composition ◽

16S Amplicon Sequencing ◽

Ecological Success ◽

Specific Community ◽

First Time ◽

The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

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Identification and Cultivation of Anaerobic, Syntrophic Long-Chain Fatty Acid-Degrading Microbes from Mesophilic and Thermophilic Methanogenic Sludges

Applied and Environmental Microbiology ◽

10.1128/aem.02053-06 ◽

2006 ◽

Vol 73 (4) ◽

pp. 1332-1340 ◽

Cited By ~ 71

Author(s):

Masashi Hatamoto ◽

Hiroyuki Imachi ◽

Akiyoshi Ohashi ◽

Hideki Harada

Keyword(s):

Fatty Acid ◽

Enrichment Culture ◽

Stable Isotope Probing ◽

Chain Fatty Acid ◽

Rrna Gene ◽

Long Chain Fatty Acid ◽

Bacterial Populations ◽

Enrichment Cultures ◽

The Family ◽

Long Chain

ABSTRACT We investigated long-chain fatty acid (LCFA)-degrading anaerobic microbes by enrichment, isolation, and RNA-based stable isotope probing (SIP). Primary enrichment cultures were made with each of four LCFA substrates (palmitate, stearate, oleate, or linoleate, as the sole energy source) at 55ï¿½C or 37ï¿½C with two sources of anaerobic granular sludge as the inoculum. After several transfers, we obtained seven stable enrichment cultures in which LCFAs were converted to methane. The bacterial populations in these cultures were then subjected to 16S rRNA gene-based cloning, in situ hybridization, and RNA-SIP. In five of seven enrichment cultures, the predominant bacteria were affiliated with the family Syntrophomonadaceae. The other two enrichment cultures contained different bacterial populations in which the majority of members belonged to the phylum Firmicutes and the class Deltaproteobacteria. After several attempts to isolate these dominant bacteria, strain MPA, belonging to the family Syntrophomonadaceae, and strain TOL, affiliated with the phylum Firmicutes, were successfully isolated. Strain MPA converts palmitate to acetate and methane in syntrophic association with Methanospirillum hungatei. Even though strain TOL assimilated [13C]palmitate in the original enrichment culture, strain TOL has not shown the ability to degrade LCFAs after isolation. These results suggest that microbes involved in the degradation of LCFAs under methanogenic conditions might not belong only to the family Syntrophomonadaceae, as most anaerobic LCFA-degrading microbes do, but may also be found in phylogenetically diverse bacterial groups.

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Phylogenetic position of Coronastrum ellipsoideum and description of Parachlorella hussii sp. nov.

Biologia ◽

10.2478/s11756-011-0056-8 ◽

2011 ◽

Vol 66 (4) ◽

Cited By ~ 14

Author(s):

Christina Bock ◽

Marie Pažoutová ◽

Lothar Krienitz

Keyword(s):

Molecular Data ◽

Phylogenetic Position ◽

Rrna Gene ◽

Combined Approach ◽

Molecular Analyses ◽

Phylogenetic Studies ◽

The Family ◽

Its Rrna Gene ◽

Molecular Phylogenetic ◽

First Time

AbstractFollowing traditional morphological concepts, the genus Coronastrum is considered to be a rare member of the Scenedesmaceae (Chorophyceae). This classification may be called into question when molecular data are taken into account as well. Recent molecular phylogenetic studies revealed the polyphyletic origin of the family Scenedesmaceae within the Chlorophyceae and Trebouxiophyceae. In a combined approach of morphological analyses, SSU/ITS rRNA gene phylogeny and comparison of the ITS secondary structure, we analysed the systematics of Coronastrum strains available in public strain collections. Our molecular analyses revealed a new subclade within the Chlorella clade of the Chlorellaceae consisting of Coronastrum ellipsoideum, two strains with Dictyosphaerium-like morphology and one strain which fits the description of the genus Parachlorella. Four additional strains formed together a new lineage within the genus Parachlorella in the Parachlorella clade of the Chlorellaceae. These strains differ from the already known Parachlorella species in complementary base changes within the ITS2 and are here described for the first time as Parachlorella hussii sp. nov.

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A STUDY OF THE SYSTEMATICS OF THE WATER MITE FAMILY PIONIDAE (PROSTIGMATA: PARASITENGONA)

Memoirs of the Entomological Society of Canada ◽

10.4039/entm10898fv ◽

1976 ◽

Vol 108 (S98) ◽

pp. 1-249 ◽

Cited By ~ 14

Author(s):

Ian M. Smith

Keyword(s):

Morphological Data ◽

Water Mite ◽

Male Adult ◽

The Family ◽

Species Groups ◽

Three New Species ◽

First Time ◽

Insight Into ◽

Mite Family

AbstractA phylogeny is proposed for the 30 species groups in the 13 genera here included in the family Pionidae. The phylogeny is based upon a detailed analysis of available morphological data for larval and adult stages according to the methodology advocated by Hennig. This methodology is outlined and discussed. The proposed phylogeny provides the basis for a revised classification of the pionids and permits new insight into certain biological manifestations of phylogeny, namely habitat diversification, life history modification, and geographic distribution, in the group.Original descriptions are provided for the larvae of 41 pionid species (20 for the first time) representing 24 species groups in eight genera. Three new species, Wettina ontario n. sp., Forelia pinguipalpis n. sp., and Tiphys cooki n. sp., are described along with the previously undescribed male adult of Pseudofeltria multipora Cook and female adults of Forelia cayuga Habeeb and Forelia onondaga Habeeb. Keys and new diagnoses are presented for pionid genera and species groups. Keys to the larvae and adults, and new distributional data, are included for the pionid species known to occur in Ontario.

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The evolution of realized niches within freshwater Synechococcus

10.1101/678375 ◽

2019 ◽

Author(s):

Nicolas Tromas ◽

Zofia E. Taranu ◽

Mathieu Castelli ◽

Juliana S. M. Pimentel ◽

Daniel A. Pereira ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Environmental Parameters ◽

Amplicon Sequencing ◽

Fundamental Question ◽

Rrna Gene ◽

Biological Interactions ◽

Sequencing Data ◽

Evolutionary Time ◽

Genus Level

SummaryUnderstanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely-related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely-related taxa share more similar niches, and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely-related Synechococcus (in the continuous range of 93-100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.Originality-Significance StatementWe address a fundamental question in ecology and evolution: how do niche preferences change over evolutionary time? Using time-series analysis of 16S rRNA gene amplicon sequencing data, we develop an approach to highlight the importance of biotic factors in defining realized niches, and show how niche preferences change proportionally with the 16S gene molecular clock within the genus Synechococcus. Ours is also one of few studies on the ecology of freshwater Synechococcus, adding significantly to our knowledge about this abundant and widespread lineage of Cyanobacteria.

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Similarity of salivary microbiome in parents and adult children

10.7287/peerj.preprints.27565 ◽

2019 ◽

Author(s):

Kati Sundström ◽

Pashupati P Mishra ◽

Mikko J Pyysalo ◽

Terho Lehtimäki ◽

Pekka J Karhunen ◽

...

Keyword(s):

Adult Children ◽

Bacterial Communities ◽

Bacterial Species ◽

Amplicon Sequencing ◽

Human Saliva ◽

Oral Microbiome ◽

Rrna Gene ◽

Genus Level ◽

Abundant Genus ◽

Dna Profiles

Background: Human saliva contains approximately 700 bacterial species but the relatedness of salivary bacteria from parents to adult children is not investigated in humans. The objectives were to investigate the entirety of salivary bacterial DNA profiles and whether and how families share these profiles and also compare these communities between adult parent-off-spring pairs using 16S rRNA gene amplicon sequencing. Results: The most abundant phyla in two separate families were Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria. Family ties explained 13 % of the variance between individuals’ bacterial communities (R2=0.13; P=0.001). Mothers shared more OTUs with their adult children compared to fathers, but this linkage seemed to be weaker in the family with older adult children. We identified 29 differentially abundant genus level OTUs (FDR < 0.05) between the families, which accounted for 31 % of the total identified genus level OTUs Conclusions: Our results indicate that adult family members share bacterial communities and adult children were more similar to mothers than fathers. Our results suggest implicitly that a similarity in oral microbiome between parent-child pairs is present, but may change over time.

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