-
Frontiers in Microbiology 2022Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of...
Malic acid is a component of the rhizosphere exudate and is vital for crop growth. However, little information is available about the effects of external applications of malic acid on the nutrient absorption and quality of grape fruit, and few studies have been performed on the relationship between the changes in the rhizosphere microbial community and nutrient absorption and fruit quality of grapes after adding malic acid. Here, the LM (low concentration of malic acid) and HM (high concentration of malic acid) treatments comprised 5% and 10% malic acid (the ratio of acid to the total weight of the fertilizer) combined with NPK fertilizer, respectively. Applying malic acid changed the grape rhizosphere microbial community structure and community-level physiological profile (CLPP) significantly, and HM had a positive effect on the utilization of substrates. The microbial community structure in the rhizosphere of the grapes with added malic acid was closely related to the CLPP. The N and P content in the leaves and fruits increased after applying malic acid compared to the control, while K content in the fruits increased significantly. In addition, malic acid significantly reduced the weight per fruit, significantly increased soluble sugar content (SSC) and vitamin C content of the fruit, and significantly improved the fruit sugar-acid ratio and grape tasting score. Moreover, the principal component analysis and grape nutrient and fruit quality scores showed that grape nutrients and fruit quality were significantly affected by malic acid and ranked as 5% malic acid > 10% malic acid > control. Pearson's correlation heatmap of microbial composition, nutrient absorption and fruit quality of the grapes showed that the grape microbial community was closely related to grape nutrients and fruit quality. Adding malic acid was positively correlated to , , and . Furthermore, , , and were closely related to grape nutrient absorption and fruit quality. and were positively correlated with total soluble sugar, while and were positively correlated with titratable acid. Hence, and were the key bacteria that played a major role in grape fruit quality and nutrient absorption after applying malic acid water-soluble fertilizer.
PubMed: 35663858
DOI: 10.3389/fmicb.2022.850807 -
PloS One 2021Microbial-induced calcium carbonate precipitation (MICP) is a biological process inducing biomineralization of CaCO3. This can be used to form a solid, concrete-like...
Microbial-induced calcium carbonate precipitation (MICP) is a biological process inducing biomineralization of CaCO3. This can be used to form a solid, concrete-like material. To be able to use MICP successfully to produce solid materials, it is important to understand the formation process of the material in detail. It is well known that crystallization surfaces can influence the precipitation process. Therefore, we present in this contribution a systematic study investigating the influence of calcite seeds on the MICP process. We focus on the changes in the pH and changes of the optical density (OD) signal measured with absorption spectroscopy to analyze the precipitation process. Furthermore, optical microscopy was used to visualize the precipitation processes in the sample and connect them to changes in the pH and OD. We show, that there is a significant difference in the pH evolution between samples with and without calcite seeds present and that the shape of the pH evolution and the changes in OD can give detailed information about the mineral precipitation and transformations. In the presented experiments we show, that amorphous calcium carbonate (ACC) can also precipitate in the presence of initial calcite seeds and this can have implications for consolidated MICP materials.
Topics: Biomineralization; Calcium Carbonate; Carbonates; Chemical Precipitation; Construction Materials; Microscopy; Minerals; Soil; Sporosarcina
PubMed: 33561160
DOI: 10.1371/journal.pone.0240763 -
PloS One 2022Auxospore production is a sexual reproductive strategy by diatoms to re-attain normal size after the size-reducing effect of clonal reproduction. Aside from the minimum...
Auxospore production is a sexual reproductive strategy by diatoms to re-attain normal size after the size-reducing effect of clonal reproduction. Aside from the minimum size threshold used as a sex clock by diatoms, the environmental or chemical triggers that can induce sex in diatoms are still not well understood. Here we investigated the influence of six marine bacteria from five families on the production of sexual cells and auxospores of the ubiquitous marine polar centric diatom, Odontella sp. Microbiome association and co-occurrence with the diatom in culture and in nature were investigated using 16S rRNA amplicon sequencing. Indole acetic acid (IAA) secretion, a phytohormone that regulates plants' growth and sexual development, was explored as a potential inducer of sexual reproduction in Odontella and compared between bacterial associates. We found that Odontella co-cultured with Flavobacteriaceae (Polaribacter and Cellulophaga) have significantly more sexual cells and auxospores than bacteria-free Odontella and Odontella co-cultured with other bacteria from Vibrionaceae (Vibrio), Pseudoalteromonadaceae (Pseudoalteromonas), Rhodobacteraceae (Sulfitobacter), or Planococcaceae (Planococcus) family. Differences in IAA secretion were observed between bacterial isolates, but this did not correspond consistently with the diatom's clonal growth or production of sexual cells and auxospores. Microbiome composition survey of Odontella cultures showed that the diatom harbors homologous sequences of the four bacterial isolates at varying proportions, with Sulfitobacter and Polaribacter at high abundances. Microbiome surveys at Santa Cruz Wharf, Monterey Bay, from 2014-2015 showed that Odontella abundance is positively correlated with Flavobacteriaceae and Rhodobacteraceae abundances. Our study demonstrates that specific members of the diatom microbiome can enhance the host's sexual reproduction, with the interkingdom interaction driven by partner compatibility and long-term association. Sex-enhancing bacteria may even be needed by the diatom host to carry out the optimal inducement of sex under normal conditions, allowing for size restitution and maintaining genetic diversity in culture and in nature.
Topics: Humans; Animals; Diatoms; RNA, Ribosomal, 16S; Plant Growth Regulators; Microbiota; Arthropods; Reproduction; Rhodobacteraceae
PubMed: 36260629
DOI: 10.1371/journal.pone.0276305 -
Microbial Cell Factories Oct 2021Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to...
BACKGROUND
Members of the genus Planococcus have been revealed to utilize and degrade solvents such as aromatic hydrocarbons and alkanes, and likely to acquire tolerance to solvents. A yellow marine bacterium Planococcus maritimus strain iso-3 was isolated from an intertidal sediment that looked industrially polluted, from the Clyde estuary in the UK. This bacterium was found to produce a yellow acyclic carotenoid with a basic carbon 30 (C) structure, which was determined to be methyl 5-glucosyl-5,6-dihydro-4,4'-diapolycopenoate. In the present study, we tried to isolate and identify genes involved in carotenoid biosynthesis from this marine bacterium, and to produce novel or rare C-carotenoids with anti-oxidative activity in Escherichia coli by combinations of the isolated genes.
RESULTS
A carotenoid biosynthesis gene cluster was found out through sequence analysis of the P. maritimus genomic DNA. This cluster consisted of seven carotenoid biosynthesis candidate genes (orf1-7). Then, we isolated the individual genes and analyzed the functions of these genes by expressing them in E. coli. The results indicated that orf2 and orf1 encoded 4,4'-diapophytoene synthase (CrtM) and 4,4'-diapophytoene desaturase (CrtNa), respectively. Furthermore, orf4 and orf5 were revealed to code for hydroxydiaponeurosporene desaturase (CrtNb) and glucosyltransferase (GT), respectively. By utilizing these carotenoid biosynthesis genes, we produced five intermediate C-carotenoids. Their structural determination showed that two of them were novel compounds, 5-hydroxy-5,6-dihydro-4,4'-diaponeurosporene and 5-glucosyl-5,6-dihydro-4,4'-diapolycopene, and that one rare carotenoid 5-hydroxy-5,6-dihydro-4,4'-diapolycopene is included there. Moderate singlet oxygen-quenching activities were observed in the five C-carotenoids including the two novel and one rare compounds.
CONCLUSIONS
The carotenoid biosynthesis genes from P. maritimus strain iso-3, were isolated and functionally identified. Furthermore, we were able to produce two novel and one rare C-carotenoids in E. coli, followed by positive evaluations of their singlet oxygen-quenching activities.
Topics: Antioxidants; Carotenoids; Escherichia coli; Genes, Bacterial; Planococcaceae
PubMed: 34627253
DOI: 10.1186/s12934-021-01683-3 -
Nucleic Acids Research Feb 2021Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA...
Argonaute (Ago) proteins are conserved nucleic acid-guided proteins present in all domains of life. Eukaryotic Argonaute proteins (eAgos) are key players in RNA interference pathways and function as RNA-guided RNA endonucleases at physiological temperatures. Although eAgos are considered to evolve from prokaryotic Argonaute proteins (pAgos), previously studied pAgos were unable to catalyze RNA-guided RNA cleavage at physiological temperatures. Here, we describe a distinctive pAgo from mesophilic bacteria Kurthia massiliensis (KmAgo). KmAgo utilizes DNA guides to cleave single-stranded DNA (ssDNA) and RNA targets with high activity. KmAgo also utilizes RNA guides to cleave ssDNA and RNA targets at moderate temperatures. We show that KmAgo can use 5' phosphorylated DNA guides as small as 9-mers to cut ssDNA and RNA, like Clostridium butyricum Ago. Small DNA binding confers remarkable thermostability on KmAgo, and we can suppress the guide-independent plasmid processing activity of empty KmAgo by elevating the DNA guide loaded temperature. Moreover, KmAgo performs programmable cleavage of double-stranded DNA and highly structured RNA at 37°C. Therefore, KmAgo can be regarded as a DNA-guided programmable omnipotent nuclease for cleaving most types of nucleic acids efficiently. This study broadens our understanding of Ago proteins and could expand the pAgo-based DNA and RNA manipulation toolbox.
Topics: Argonaute Proteins; Bacterial Proteins; Cations, Divalent; DNA Breaks, Double-Stranded; DNA, Single-Stranded; Planococcaceae; RNA; Temperature
PubMed: 33444443
DOI: 10.1093/nar/gkaa1278 -
Biomolecules Feb 2022Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo...
Prokaryotic Argonautes (pAgos) from mesophilic bacteria are attracting increasing attention for their genome editing potential. So far, it has been reported that KmAgo from can utilize DNA and RNA guide of any sequence to effectively cleave DNA and RNA targets. Here we find that three active pAgos, which have about 50% sequence identity with KmAgo, possess typical DNA-guided DNA target cleavage ability. Among them, RsuAgo from is mainly explored for which can cleave both DNA and RNA targets. Interestingly, RsuAgo-mediated RNA target cleavage occurs only with short guide DNAs in a narrow length range (16-20 nt), and mismatches between the guide and target sequence greatly affect the efficiency of RNA target cleavage. RsuAgo-mediated target cleavage shows a preference for a guide strand with a 5'-terminal A residue. Furthermore, we have found that RsuAgo can cleave double-stranded DNA in a low-salt buffer at 37 °C. These properties of RsuAgo provide a new tool for DNA and RNA manipulation at moderate temperatures.
Topics: Argonaute Proteins; Bacteria; Bacterial Proteins; DNA; Endonucleases; Planococcaceae; RNA
PubMed: 35327547
DOI: 10.3390/biom12030355 -
Animals : An Open Access Journal From... Mar 2021Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at...
Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae () and Ruminococcaceae () were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.
PubMed: 33803934
DOI: 10.3390/ani11030819 -
Biology Oct 2023The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied...
The Barents Sea is one of the most rapidly changing Arctic regions, with an unprecedented sea ice decline and increase in water temperature and salinity. We have studied the diversity of prokaryotic communities using 16S metabarcoding in the western and northeastern parts of the Barents Sea along the Kola Section and the section from Novaya Zemlya to Franz Joseph Land. The hypothesis-independent clustering method revealed the existence of two distinct types of communities. The most common prokaryotic taxa were shared between two types of communities, but their relative abundance was different. It was found that the geographic location of the sampling sites explained more than 30% of the difference between communities, while no statistically significant correlation between environmental parameters and community composition was found. The representatives of the , and genera were dominant in samples from both types of communities. The first type of community was also dominated by members of , , and an unclassified representative of the family. The second type of community also had a significant proportion of , SAR92, SAR11 Clade I, NS9, and SUP05 representatives. The origin of these communities can be explained by the influence of environmental factors or by the different origins of water masses. This research highlights the importance of studying biogeographic patterns in the Barents Sea in comparison with those in the North Atlantic and Arctic Ocean prokaryote communities.
PubMed: 37887020
DOI: 10.3390/biology12101310 -
Scientific Reports Dec 2023This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing...
This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing 3N-BBM medium was inoculated with Microglena sp., Tetradesmus obliquus, and Desmodesmus subspicatus mixture with a density of 1.0 × 10 cells/mL and the consortium was cultivated for 30 days. Then, the bioreactor was semi-continuously fed with liquid digestate with hydraulic retention time (HRT) of 30 days, and the treatment process was continued for the next 15 weeks. The change in the microalgal and cyanobacterial species domination was measured in regular intervals using cell counting with droplet method on a microscope slide. At the end of the experiment, Desmonostoc sp. cyanobacteria (identified with 16S ribosomal RNA genetical analysis) as well as Tetradesmus obliquus green algae along with Rhodanobacteraceae and Planococcaceae bacteria (determined with V3-V4 16sRNA metagenomic studies) dominated the microbial community in the photobioreactor. The experiment demonstrated high treatment efficiency, since nitrogen and soluble COD were removed by 89.3 ± 0.5% and 91.2 ± 1.6%, respectively, whereas for phosphates, 72.8 ± 2.1% removal rate was achieved.
Topics: Photobioreactors; Waste Disposal, Fluid; Microalgae; Vegetables; Anaerobiosis; Cyanobacteria; Nitrogen; Chlorophyceae; Biomass
PubMed: 38114556
DOI: 10.1038/s41598-023-50173-6 -
Nature Communications Apr 2021Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild...
Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.
Topics: Animals; Buffaloes; Communicable Diseases; DNA, Bacterial; Feces; Feeding Behavior; Firmicutes; Gastrointestinal Microbiome; Incidence; Metagenomics; Phylogeny; Planococcaceae; Prevalence; RNA, Ribosomal, 16S; South Africa; Symbiosis
PubMed: 33859184
DOI: 10.1038/s41467-021-22510-8