Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis

Albuquerque, Luciana; Johnson, Megan; Schümann, Peter; Rainey, Fred A.; Costa, Milton S. da

doi:10.1016/j.syapm.2014.03.001

Cited by 46 publications

(35 citation statements)

References 22 publications

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“…1B), suggesting that Family I (order Subsection III) may be an important dietary resource for R. auricularia . Many of the Cyanobacteria bacteria found in the snail gut, including Leptolyngbya , Nostoc , and Pleurocapsa , Microcoleus , Gemmobacter , Exiguobacterium , and Rubrobacter , are of environmental origin, such as fresh water and soil (Hagemann et al, 2015; Lv et al, 2017; Strahsburger et al, 2018; Albuquerque et al, 2014). …”

Section: Discussionmentioning

confidence: 99%

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

Chen

Chang

et al. 2018

PeerJ

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Due to its wide distribution across the world, the snail Radix auricularia plays a central role in the transferal of energy and biomass by consuming plant biomass in freshwater systems. The gut microbiota are involved in the nutrition, digestion, immunity, and development of snails, particularly for cellulolytic bacteria, which greatly contribute to the digestion of plant fiber. For the first time, this study characterized the gut bacterial communities of R. auricularia, as well as predicted functions, using the Illumina Miseq platform to sequence 16S rRNA amplicons. Both juvenile snails (JS) and adult snails (AS) were sampled. The obtained 251,072 sequences were rarefied to 214,584 sequences and clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria (JS: 36.0%, AS: 31.6%) and Cyanobacteria (JS: 16.3%, AS: 19.5%), followed by Chloroflexi (JS: 9.7%, AS: 13.1%), Firmicutes (JS: 14.4%, AS: 6.7%), Actinobacteria (JS: 8.2%, AS: 12.6%), and Tenericutes (JS: 7.3%, AS: 6.2%). The phylum Cyanobacteria may have originated from the plant diet instead of the gut microbiome. A total of 52 bacterial families and 55 genera were found with >1% abundance in at least one sample. A large number of species could not be successfully identified, which could indicate the detection of novel ribotypes or result from insufficient availability of snail microbiome data. The core microbiome consisted of 469 OTUs, representing 88.4% of all sequences. Furthermore, the predicted function of bacterial community of R. auricularia performed by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States suggests that functions related to metabolism and environmental information processing were enriched. The abundance of carbohydrate suggests a strong capability of the gut microbiome to digest lignin. Our results indicate an abundance of bacteria in both JS and AS, and thus the bacteria in R. auricularia gut form a promising source for novel enzymes, such as cellulolytic enzymes, that may be useful for biofuel production. Furthermore, searching for xenobiotic biodegradation bacteria may be a further important application of these snails.

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Section: Discussionmentioning

confidence: 99%

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

Chen

Chang

et al. 2018

PeerJ

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“…This might be because of their distinctly different physiology; members of the genus Streptomyces (and some Mycobacterium spp. also) exhibit mycelial growth, whereas the deep-branching Actinobacteria (Rubrobacter and Conexibacter) have rod-or coccoid-shaped cells (Monciardini et al, 2003;Albuquerque et al, 2014). The latter forms of cell morphology enable deep-branching Actinobacteria to cope with desiccation, whereas the vegetative hyphae of mycelial prokaryotes are injured rapidly by desiccation (Williams et al, 1972).…”

Section: Discussionmentioning

confidence: 99%

Extreme effects of drought on composition of the soil bacterial community and decomposition of plant tissue

Tóth

Táncsics

Kriszt

et al. 2017

European J Soil Science

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Summary The decomposition of soil organic matter, as an essential part of nutrient cycling, has a crucial role in maintaining soil fertility and the regulation of climate. This function of the soil is likely to be affected by extreme weather events that are expected to be more frequent and severe in the future. We conducted an experiment from March 2014 to March 2015 to test the effects of extreme drought on composition of the bacterial community and decomposition of plant tissue with soil microclimate variables such as soil temperature and moisture. Precipitation was excluded for a 5‐month period by transparent roofs. To follow organic matter decomposition, we used the tea bag method. Soil samples were taken to determine the effects of extreme drought on the bacterial community 6 months after the dry period (mid‐term). Drought plots were drier (P < 0.001) and warmer (P < 0.001) than control plots as a consequence of the extreme drought treatment. The permanova test showed that the dry period altered soil bacterial communities accordingly (Fpermanova = 10.36, P = 0.002). However, there was no significant difference between the control and drought‐treated plots 6 months after the dry period in terms of bacterial alpha diversity. Furthermore, rates of organic matter decomposition in the control plots were significantly larger by an average of 93.7% than in the drought plots. The results also indicated that soil temperature and moisture had significant effects on decomposition. Overall, the findings demonstrate clearly the response of soil bacteria and soil function to experimental drought. The strong effect of changes in precipitation and increasing temperature on mass loss suggests that extreme weather events, such as extreme droughts, can markedly change the composition of soil bacterial communities and processes of decomposition. This effect is expected to be more pronounced during dry periods of increasing severity and frequency. Highlights We studied the effects of extreme drought on plant tissue decay and soil bacterial diversity. Microbial degradation of organic matter was followed by the novel tea bag method. Changes in soil microclimate altered bacterial community structure and decomposition. Microbiota and soil function were markedly affected by extreme weather events like droughts.

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“…Due to the unique presence of these three proteins in the chlorophototrophs, BLAST searches with their sequences provide important diagnostic tools to determine the presence of photosynthesis (or its remnants) in other bacterial lineages. The BLASTp searches with the sequences of these proteins reported in the present work have revealed that homologs showing high degree of sequence and structural similarity to the BchB and BchN proteins are present in members of the genus Rubrobacter, which is a part of the phylum Actinobacteria (Yarza et al 2008;Gao and Gupta 2012;Egas et al 2014;Albuquerque et al 2014). The branching pattern in phylogenetic trees and the sequence characteristics of the Rubrobacter BchB/BchN homologs indicate that the genes for these proteins are not derived by lateral gene transfers from other phyla of photosynthetic bacteria and that they likely represent ancestral forms of the BchB/ BchN proteins.…”

Section: Introductionmentioning

confidence: 68%

“…Results presented here show that homologs showing high degree of sequence similarity to the BchB and BchN proteins are present in two sequenced Rubrobacter species (R. xylanophilus and R. radiotolerans), belonging to the phylum Actinobacteria (family Rubrobaceteraceae, order Rubrobacterales) (Yarza et al 2008;Gao and Gupta 2012;Egas et al 2014;Albuquerque et al 2014). The phylum Actinobacteria is composed of high G?C Grampositive bacteria (Goodfellow et al 2011;Gao and Gupta 2012), and there is no prior indication of the presence of photosynthesis, or any evidence pertaining to it, in the members of this phylum.…”

Section: Discussionmentioning

confidence: 92%

“…In addition to R. radiotolerans and R. xylanophilus, four additional species are currently part of this genus (viz. R. taiwanensis, R. calidifulminis, R. naiadicus, and R. bracarensis) (Carreto et al 1996;Chen et al 2004;Albuquerque et al 2014;Kampfer et al 2014). The cells from most species of this genus show light-to bright-pink coloration.…”

Section: Discussionmentioning

confidence: 99%

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Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

Gupta

Khadka

2015

Photosynth Res

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Homologs showing high degree of sequence similarity to the three subunits of the protochlorophyllide oxidoreductase enzyme complex (viz. BchL, BchN, and BchB), which carries out a central role in chlorophyll-bacteriochlorophyll (Bchl) biosynthesis, are uniquely found in photosynthetic organisms. The results of BLAST searches and homology modeling presented here show that proteins exhibiting a high degree of sequence and structural similarity to the BchB and BchN proteins are also present in organisms from the high G+C Gram-positive phylum of Actinobacteria, specifically in members of the genus Rubrobacter (R. x ylanophilus and R. r adiotolerans). The results presented exclude the possibility that the observed BLAST hits are for subunits of the nitrogenase complex or the chlorin reductase complex. The branching in phylogenetic trees and the sequence characteristics of the Rubrobacter BchB/BchN homologs indicate that these homologs are distinct from those found in other photosynthetic bacteria and that they may represent ancestral forms of the BchB/BchN proteins. Although a homolog showing high degree of sequence similarity to the BchL protein was not detected in Rubrobacter, another protein, belonging to the ParA/Soj/MinD family, present in these bacteria, exhibits high degree of structural similarity to the BchL. In addition to the BchB/BchN homologs, Rubrobacter species also contain homologs showing high degree of sequence similarity to different subunits of magnesium chelatase (BchD, BchH, and BchI) as well as proteins showing significant similarity to the BchP and BchG proteins. Interestingly, no homologs corresponding to the BchX, BchY, and BchZ proteins were detected in the Rubrobacter species. These results provide the first suggestive evidence that some form of photosynthesis either exists or was anciently present within the phylum Actinobacteria (high G+C Gram-positive) in members of the genus Rubrobacter. The significance of these results concerning the origin of the Bchl-based photosynthesis is also discussed.

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Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis

Cited by 46 publications

References 22 publications

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

Extreme effects of drought on composition of the soil bacterial community and decomposition of plant tissue

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis

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