Use of the
            <i>Verrucomicrobia</i>
            -Specific Probe EUB338-III and Fluorescent In Situ Hybridization for Detection of “
            <i>Candidatus</i>
            Xiphinematobacter” Cells in Nematode Hosts

Vandekerckhove, Tom; Coomans, A.; Cornelis, Karen; Baert, Philippe; Gillis, Monique

doi:10.1128/aem.68.6.3121-3125.2002

Cited by 55 publications

(60 citation statements)

References 23 publications

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“…Many of the OTUs that increase significantly over the chronosequence, such as Bradyrhizobium, Chthoniobacteraceae (genus DA101), Mycobacterium, and Rhodoplanes, indicate increased soil organic matter decomposition and nutrient cycling as conditions become more oligotrophic. Interestingly, we also saw an increase in "Candidatus Xiphinematobacter" in our data, suggest-ing an increase in nematode populations (62) and the potential development of higher trophic levels in the soil ecosystem.…”

Section: Discussionsupporting

confidence: 50%

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

Sun

Song

Avera

et al. 2017

Appl Environ Microbiol

213

109

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Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, ␤-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping ␤-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial ␤-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.KEYWORDS bacteria, chronosequence, cooccurrence networks, disturbance, fungi, reclaimed mine soils, soil microbiota E cologists have been studying the succession dynamics of plant communities for more than a century (1, 2), and the patterns of changes in plant community composition are used as indicators for the restoration of ecosystems (3-5). However,

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Section: Discussionsupporting

confidence: 50%

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

Sun

Song

Avera

et al. 2017

Appl Environ Microbiol

213

109

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“…Members of the candidate genus Xiphinematobacter populate the intestinal epithelia of juvenile nematode worms (66), ectosymbiotic verrucomicrobia on the marine ciliate Euplotidium act as defensive cells (47), and novel verrucomicrobia have been isolated from the human intestine (16), the gut of the sea cucumber (54), marine sponges (57), and the digestive tract of a marine clamworm (14). Previously, we reported the isolation of several novel verrucomicrobia from the guts of wood-eating termites, including the strain we further investigate here, TAV2, which is a member of the Opitutaceae (64).…”

mentioning

confidence: 99%

Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

Wertz

Kim

Breznak

et al. 2012

Appl Environ Microbiol

131

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Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb 3 -type terminal oxidaseencoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono-and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Diplosphaera colitermitum gen. nov., sp. nov., is proposed.

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“…In these nematode species, Wolbachia seems to be required for successful molting as well as for reproduction of the nematode. In only three genera of plant-parasitic nematodes (Heterodera, Globodera and Xiphinema), bacteria-like endosymbionts-other than Wolbachia-have been found (Noel and Atibalentja 2006;Vandekerckhove et al 2002). On the other hand, we can not exclude the possibility of an insertion of Wolbachia genes into the genome of R. similis, as recently has been shown that these inserts can be transcriptionally active (Hotopp et al 2007).…”

Section: Discussionmentioning

confidence: 79%

Exploring the transcriptome of the burrowing nematode Radopholus similis

et al. 2008

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Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more eYcient control measures. For the Wrst high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reXects the nematode population biology. Genes with a role in the parasitism process are identiWed, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three diVerent sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the Wrst molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.Keywords Expressed sequence tag analysis · Trans-spliced leader · Parasitism · G + C content · Wolbachia · Endoparasitic migratory nematode

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Use of the Verrucomicrobia -Specific Probe EUB338-III and Fluorescent In Situ Hybridization for Detection of “ Candidatus Xiphinematobacter” Cells in Nematode Hosts

Cited by 55 publications

References 23 publications

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

Exploring the transcriptome of the burrowing nematode Radopholus similis

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