scholarly journals Genetic Diversity and Horizontal Transfer of Genes Involved in Oxidation of Reduced Phosphorus Compounds by Alcaligenes faecalis WM2072

2005 ◽  
Vol 71 (1) ◽  
pp. 290-296 ◽  
Author(s):  
Marlena M. Wilson ◽  
William W. Metcalf
Keyword(s):  
Pseudomonas Stutzeri ◽  
Alcaligenes Faecalis ◽  
Phosphorus Compounds ◽  
Rrna Gene ◽  
Sequencing Data ◽  
16S Rrna Gene Analysis ◽  
Evolutionary Selection ◽  
Selection For ◽  
Phosphite Dehydrogenase

ABSTRACT Enrichment was performed to isolate organisms that could utilize reduced phosphorus compounds as their sole phosphorus sources. One isolate that grew well with either hypophosphite or phosphite was identified by 16S rRNA gene analysis as a strain of Alcaligenes faecalis. The genes required for oxidation of hypophosphite and phosphite by this organism were identified by using transposon mutagenesis and include homologs of the ptxD and htxA genes of Pseudomonas stutzeri WM88, which encode an NAD-dependent phosphite dehydrogenase (PtxD) and 2-oxoglutarate-dependent hypophosphite dioxygenase (HtxA). This organism also has the htxB, htxC, and htxD genes that comprise an ABC-type transporter, presumably for hypophosphite and phosphite transport. The role of these genes in reduced phosphorus metabolism was confirmed by analyzing the growth of mutants in which these genes were deleted. Sequencing data showed that htxA, htxB, htxC, and htxD are virtually identical to their homologs in P. stutzeri at the DNA level, indicating that horizontal gene transfer occurred. However, A. faecalis ptxD is very different from its P. stutzeri homolog and represents a new ptxD lineage. Therefore, this gene has ancient evolutionary roots in bacteria. These data suggest that there is strong evolutionary selection for the ability of microorganisms to oxidize hypophosphite and phosphite.

scholarly journals Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

2020 ◽  
Vol 30 (1) ◽  
Author(s):  
Rashid Pervez ◽  
Showkat Ahmad Lone ◽  
Sasmita Pattnaik
Keyword(s):  
Insect Pests ◽  
Entomopathogenic Nematode ◽  
Alcaligenes Faecalis ◽  
Symbiotic Bacteria ◽  
Rrna Gene ◽  
Main Body ◽  
Associated Bacteria ◽  
Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

scholarly journals PSXIII-29 Farm of origin has a major influence on the colonic microbiome but alterations due to selection for feed efficiency are also evident

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 475-475
Author(s):  
Stafford Vigors ◽  
Torres Sweeney
Keyword(s):  
Feed Efficiency ◽  
Hypervariable Region ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Nutrient Digestibility ◽  
Major Influence ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Selection For

Abstract While the intestinal microbiota is functionally important in nutrient digestibility and animal performance, the role of the microbiome in influencing feed efficiency is not well characterised. The objective of this experiment was to determine the relative influence of feed efficiency and farm of origin on the pig colonic microbiome. Animals were sourced from two geographically distinct locations in Ireland (farm A + B) and evaluated to identify pigs divergent in feed efficiency. The 8 most efficient (LRFI) & 8 least efficient (HRFI) pigs from farm A and 12 LRFI & 12 HRFI pigs from farm B were slaughtered. Colonic digesta was collected for sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed on the Illumina MiSeq. Alpha diversity differed between the farms in this study with pigs from farm A having greater diversity based on Shannon and InvSimpson measures compared to pigs from farm B (P < 0.05). In agreement with this observation, pigs grouped by farm of origin rather than RFI in the beta diversity analysis. However, despite variation between farms, interesting taxonomic differences were identified between RFI groups. Within the phylum Bacteroidetes, the LRFI pigs had increased abundance of two families BS11 (P < 0.05) and a tendency towards increased Bacteroidaceae (P < 0.10) relative to the HRFI group. At genus level, the LRFI pigs had a tendency towards increased Bacteroides and CF231 (P < 0.10). In conclusion, while farm of origin has a substantial influence on microbial diversity in the pig colon, a microbial signature indicative of feed efficiency status was evident.

Greenhouse gas emissions from a Mediterranean floodplain forest: the role of tree emissions under a changing flooding regime.

2020 ◽  
Author(s):  
Sílvia Poblador ◽  
Elisabet Martínez-Sancho ◽  
Mateu Menéndez-Serra ◽  
Emilio O. Casamayor ◽  
Marc Estiarte ◽  
...  
Keyword(s):  
Greenhouse Gas ◽  
Ghg Emissions ◽  
Floodplain Forest ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Riparian Trees ◽  
Riparian Tree ◽  
Moisture Conditions ◽  
Aerobic Soil

<p>The increase of greenhouse gas (GHG) emissions into the atmosphere is promoting and accelerating climate warming. Among GHG sources, soils are an important natural source of GHG to the atmosphere through aerobic soil respiration that release carbon dioxide (CO<sub>2</sub>). However, in riparian areas, soils can also release relevant amounts of methane (CH<sub>4</sub>) and nitrous oxide (N<sub>2</sub>O) through anaerobic processes promoted by high groundwater levels or flooded conditions. Recent studies have highlighted the role of trees in CH<sub>4</sub> emissions, but little is still known about the origin of these emissions, the processes involved, and their contribution to the global carbon and nitrogen cycles. To shed light on this issue, we measured GHG emissions (i.e. CO<sub>2</sub>, CH<sub>4</sub>, and N<sub>2</sub>O) from the stems of two riparian tree species (Fraxinus agustifolia and Quercus robur) located along a gradient of soil moisture conditions (i.e. from wet to completely flooded soils) in a Mediterranean floodplain forest. Moreover, we also analyzed the isotopic carbon signature of the GHG emitted and the microbial communities inhabiting within tree stems by 16S rRNA gene analysis. Our results showed that CH<sub>4</sub> emitted by riparian tree stems was 100-fold higher at the flooded than at wet soil locations, while CO<sub>2</sub> and N<sub>2</sub>O emissions did not vary across moisture conditions. When considering together emissions form soil surface and tree stems under flooded conditions, riparian trees contributed up to 20%, 40% and 60% of the total CH<sub>4</sub>, CO<sub>2</sub>, and N<sub>2</sub>O emissions, respectively. Keeling plots suggested that CO<sub>2</sub> emitted through tree stems was produced within the soil compartment and thus transported to the atmosphere through the tree stems, whereas CH<sub>4</sub> emissions may have a different origin. However, methanogens were almost absent on the wood microbiome. The substantially higher presence of methanotrophs on the wood than on the soil compartment suggested that, despite CH<sub>4</sub> emitted by stems could come from soil microbial activity, the microbial consumption of that CH<sub>4</sub> within the tree stem could have changed its isotopic signature. Overall, our findings suggest that the riparian trees growing in this Mediterranean floodplain forest may mainly act as passive transporters of GHG produced in soils instead of being active GHG producers.</p>

scholarly journals Presence of Two Different Active nirS Nitrite Reductase Genes in a Denitrifying Thauera sp. from a High-Nitrate-Removal-Rate Reactor

2005 ◽  
Vol 71 (9) ◽  
pp. 5642-5645 ◽  
Author(s):  
Claudia Etchebehere ◽  
James Tiedje
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Nitrite Reductase ◽  
Removal Rate ◽  
Nitrate Removal ◽  
Pseudomonas Stutzeri ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences

ABSTRACT The nirS nitrite reductase genes were studied in two strains (strains 27 and 28) isolated from two denitrifying reactors and characterized as Thauera according to their 16S rRNA gene sequences. Strain 28 contains a single nirS sequence, which is related to the nirS of Thauera mechernichensis, and strain 27 contains two nirS sequences; one is similar to the nirS sequence from Thauera mechernichensis (gene 2), but the second one (gene 8) is from a separate clade with nirS from Pseudomonas stutzeri, Azoarcus species, Alcaligenes faecalis, and other Thauera species. Both genes were expressed, but gene 8 was constitutively expressed while gene 2 was positively regulated by nitrate.

scholarly journals Dominant egg surface bacteria of Holotrichia oblita (Coleoptera: Scarabaeidae) inhibit the multiplication of Bacillus thuringiensis and Beauveria bassiana

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kui Wang ◽  
Qi Liu ◽  
Chunqin Liu ◽  
Lili Geng ◽  
Guirong Wang ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Bacterial Community ◽  
Beauveria Bassiana ◽  
Composition Analysis ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
16S Rrna Gene Analysis ◽  
Initial Development ◽  
Adaptation Ability

AbstractHolotrichia oblita (Coleoptera: Scarabaeidae) and some other scarab beetles are the main soil-dwelling pests in China. Bacillus thuringiensis (Bt) and Beauveria bassiana (Bb) are entomopathogens that have been used as biocontrol agents of various pests. However, scarab larvae especially H. oblita exhibited strong adaptability to these pathogens. Compared to other scarabs, H. oblita could form a specific soil egg case (SEC) structure surrounding its eggs, and young larvae complete the initial development process inside this structure. In this study, we investigated the role of SEC structure and microorganisms from SEC and egg surface in pathogen adaptability. 16S rRNA gene analysis revealed low bacterial richness and high community unevenness in egg surface, with Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria dominating. In terms of OTUs composition analysis, the data show that the egg surface contains a large number of unique bacteria, indicating that the egg bacterial community may be derived from maternal transmission. Furthermore, we found that all culturable bacteria isolated from egg surface possessed antimicrobial activity against both Bt and Bb. The Pseudomonas bacteria with a significantly higher abundance in egg surface showed strong Bt- and Bb antagonistic ability. In conclusion, this study demonstrated a unique and antimicrobial bacterial community of H. oblita egg surface, which may contribute to its adaptability. Furthermore, the specific SEC structure surrounding the H. oblita eggs will provide a stable microenvironment for the eggs and egg surface bacteria, which probably provides more advantages for H. oblita adaptation ability.

scholarly journals Identification and characterization of potential compost degrading bacteria from agro-waste

2021 ◽  
Vol 17 (1) ◽  
pp. 26-32
Author(s):  
Saldatul As Wani Mohd Khalif ◽  
Nurul Zahidah Nordin ◽  
Nadiawati Alias
Keyword(s):  
Skim Milk ◽  
Pseudomonas Stutzeri ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Agricultural Industry ◽  
Degrading Bacteria ◽  
Industrial Waste Management ◽  
Global Economic Growth

Agricultural industry plays a significant role in the global economic growth. It is estimated more than 15% of total waste in Asia are contributed by agro waste. Bacteria is known as one of the useful organisms actively found to surround the waste industry. They are considered as chemical decomposers and act as driving agent of composting that changes the chemistry of organic waste to simple compounds. Thus, this study was conducted to isolate and identify potential compostdegrading bacteria from agriculture waste at several sampling areas in Besut district, Terengganu, Malaysia. A total of 49 bacteria strains were isolated using Tryptic Soya Agar (TSA) from seven groups of raw agro wastes (paddy husk, paddy straw, paddy soil, rock melon waste, rock melon soil, corn waste, and corn soil). Primary screening for potential enzyme production was carried out using selective media containing different substrates (sucrose, xylan, starch, skim milk, and pectin). Only 13 bacterial strains were found positive for protease, nine bacteria strains positive for xylanase, and three bacteria strains were found positive for amylase. Identification of bacteria strains were performed using phenotypic, biochemical tests, and genotypic approaches by 16S rRNA gene sequence. Based on NCBI BLAST analysis, we have identified several bacteria strains: Bacillus cereus (strain B), Alcaligenes faecalis (strain C), Micrococcus sp. (strain D), Pseudomonas stutzeri (strain E), Enterobacter cloacae (strain G), and Serratia marcescens (strain J). Strain F and strain H were identified under distinct family of Enterobacteriaceae, while strain I was identified from Pseudomonadeles order which might represent a new type of proteobacteria strain. These potential waste degrading bacteria could be further analyzed and studies for their true potential in many areas including agriculture and industrial waste management as an approach to reduce waste accumulation in eco-friendly way.

scholarly journals Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

scholarly journals Microbiome of Odontogenic Abscesses

2021 ◽  
Vol 9 (6) ◽  
pp. 1307
Author(s):  
Sebastian Böttger ◽  
Silke Zechel-Gran ◽  
Daniel Schmermund ◽  
Philipp Streckbein ◽  
Jan-Falco Wilbrand ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Minor Role ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
16S Rrna Gene Analysis ◽  
Odontogenic Infections ◽  
Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

scholarly journals Sarocladium and Lecanicillium Associated with Maize Seeds and Their Potential to Form Selected Secondary Metabolites

Biomolecules ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 98
Author(s):  
Lidia Błaszczyk ◽  
Agnieszka Waśkiewicz ◽  
Karolina Gromadzka ◽  
Katarzyna Mikołajczak ◽  
Jerzy Chełkowski
Keyword(s):  
Large Subunit ◽  
Solid Substrate ◽  
Rrna Gene ◽  
Decenoic Acid ◽  
Bioactive Substances ◽  
Lecanicillium Lecanii ◽  
Maize Seeds ◽  
Internally Transcribed Spacer ◽  
First Time

The occurrence and diversity of Lecanicillium and Sarocladium in maize seeds and their role in this cereal are poorly understood. Therefore, the present study aimed to investigate Sarocladium and Lecanicillium communities found in endosphere of maize seeds collected from fields in Poland and their potential to form selected bioactive substances. The sequencing of the internally transcribed spacer regions 1 (ITS 1) and 2 (ITS2) and the large-subunit (LSU, 28S) of the rRNA gene cluster resulted in the identification of 17 Sarocladium zeae strains, three Sarocladium strictum and five Lecanicillium lecanii isolates. The assay on solid substrate showed that S. zeae and S. strictum can synthesize bassianolide, vertilecanin A, vertilecanin A methyl ester, 2-decenedioic acid and 10-hydroxy-8-decenoic acid. This is also the first study revealing the ability of these two species to produce beauvericin and enniatin B1, respectively. Moreover, for the first time in the present investigation, pyrrocidine A and/or B have been annotated as metabolites of S. strictum and L. lecanii. The production of toxic, insecticidal and antibacterial compounds in cultures of S. strictum, S. zeae and L. lecanii suggests the requirement to revise the approach to study the biological role of fungi inhabiting maize seeds.

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