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Microbiology Spectrum Jun 2024The Atacama Desert is the oldest and driest desert on Earth, encompassing great temperature variations, high ultraviolet radiation, drought, and high salinity, making it...
The Atacama Desert is the oldest and driest desert on Earth, encompassing great temperature variations, high ultraviolet radiation, drought, and high salinity, making it ideal for studying the limits of life and resistance strategies. It is also known for harboring a great biodiversity of adapted life forms. While desertification is increasing as a result of climate change and human activities, it is necessary to optimize soil and water usage, where stress-resistant crops are possible solutions. As many studies have revealed the great impact of the rhizobiome on plant growth efficiency and resistance to abiotic stress, we set up to explore the rhizospheric soils of and desert plants. By culturing these soils and using 16S rRNA amplicon sequencing, we address community taxonomy composition dynamics, stability through time, and the ability to promote lettuce plant growth. The rhizospheric soil communities were dominated by the families Pseudomonadaceae, Bacillaceae, and Planococcaceae for and Porphyromonadaceae and Haloferacaceae for . Nonetheless, the cultures were completely dominated by the Enterobacteriaceae family (up to 98%). Effectively, lettuce plants supplemented with the cultures showed greater size and biomass accumulation. We identified 12 candidates that could be responsible for these outcomes, of which 5 ( and ) were part of the built co-occurrence network. We aim to contribute to the efforts to characterize the microbial communities as key for the plant's survival in extreme environments and as a possible source of consortia with plant growth promotion traits aimed at agricultural applications.IMPORTANCEThe current scenario of climate change and desertification represents a series of incoming challenges for all living organisms. As the human population grows rapidly, so does the rising demand for food and natural resources; thus, it is necessary to make agriculture more efficient by optimizing soil and water usage, thus ensuring future food supplies. Particularly, the Atacama Desert (northern Chile) is considered the most arid place on Earth as a consequence of geological and climatic characteristics, such as the naturally low precipitation patterns and high temperatures, which makes it an ideal place to carry out research that seeks to aid agriculture in future conditions that are predicted to resemble these scenarios. Our main interest lies in utilizing microorganism consortia from plants thriving under extreme conditions, aiming to promote plant growth, improve crops, and render "unsuitable" soils farmable.
Topics: Desert Climate; Soil Microbiology; Rhizosphere; Bacteria; RNA, Ribosomal, 16S; Plant Development; Lactuca; Microbiota; Soil; Biodiversity; Chenopodiaceae
PubMed: 38687070
DOI: 10.1128/spectrum.00056-24 -
Nucleic Acids Research Apr 2021Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some...
Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. KmAgo binds 16-20 nt long 5'-phosphorylated guide molecules with no strict specificity for their sequence and is active in a wide range of temperatures. In bacterial cells, KmAgo is loaded with small DNAs with no obvious sequence preferences suggesting that it can uniformly target genomic sequences. Mismatches between the guide and target sequences greatly affect the efficiency and precision of target cleavage, depending on the mismatch position and the nature of the reacting nucleic acids. Target RNA cleavage by KmAgo depends on the formation of secondary structure indicating that KmAgo can be used for structural probing of RNA. These properties of KmAgo open the way for its use for highly specific nucleic acid detection and cleavage.
Topics: Argonaute Proteins; Bacterial Proteins; DNA, Bacterial; Planococcaceae; Protein Binding; RNA, Bacterial; Substrate Specificity
PubMed: 33744962
DOI: 10.1093/nar/gkab182 -
The ISME Journal Jan 2021Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease...
Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
Topics: Actinobacteria; Bacillus; Bacteria; Firmicutes; Incidence; Solanum lycopersicum; Planococcaceae; Plant Diseases; Ralstonia solanacearum; Rhizosphere; Soil Microbiology
PubMed: 33028974
DOI: 10.1038/s41396-020-00785-x -
Scientific Reports May 2018Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR...
Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34-59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2'-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.
Topics: Amino Acid Sequence; Crystallography, X-Ray; Dihydrodipicolinate Reductase; Kinetics; Models, Molecular; NADP; Planococcaceae; Protein Conformation; Sequence Homology; Substrate Specificity
PubMed: 29786696
DOI: 10.1038/s41598-018-26291-x -
Journal of Applied Microbiology Aug 2011To gain an understanding of the environmental factors that affect the growth of the bacterium Sporosarcina pasteurii, the metabolism of the bacterium and the calcium...
AIMS
To gain an understanding of the environmental factors that affect the growth of the bacterium Sporosarcina pasteurii, the metabolism of the bacterium and the calcium carbonate precipitation induced by this bacterium to optimally implement the biological treatment process, microbial induced calcium carbonate precipitation (MICP), in situ.
METHODS AND RESULTS
Soil column and batch tests were used to assess the effect of likely subsurface environmental factors on the MICP treatment process. Microbial growth and mineral precipitation were evaluated in freshwater and seawater. Environmental conditions that may influence the ureolytic activity of the bacteria, such as ammonium concentration and oxygen availability, as well as the ureolytic activities of viable and lysed cells were assessed. Treatment formulation and injection rate, as well as soil particle characteristics are other factors that were evaluated for impact on uniform induction of cementation within the soils.
CONCLUSIONS
The results of the study presented herein indicate that the biological treatment process is equally robust over a wide range of soil types, concentrations of ammonium chloride and salinities ranging from distilled water to full seawater; on the time scale of an hour, it is not diminished by the absence of oxygen or lysis of cells containing the urease enzyme.
SIGNIFICANCE AND IMPACT OF STUDY
This study advances the biological treatment process MICP towards field implementation by addressing key environmental hurdles faced with during the upscaling process.
Topics: Calcium Carbonate; Chemical Precipitation; Culture Media; Fresh Water; Seawater; Soil; Soil Microbiology; Sporosarcina; Urea; Urease
PubMed: 21624021
DOI: 10.1111/j.1365-2672.2011.05065.x -
Zoological Studies 2021Bacteria are known to have explicit roles within the microbiomes of host tissues, therefore examining these communities may prove useful in assessing host health and...
Bacteria are known to have explicit roles within the microbiomes of host tissues, therefore examining these communities may prove useful in assessing host health and responses to environmental change. The present study contributes to the emerging, yet understudied, field of microbiome research in elasmobranchs. We provide a screening of the culturable bacteria communities found on multiple tissue sites on the body surface of blacktip (), bull (), and tiger () sharks near Miami, Florida. Tissue sites include mouth, gills, skin, and any visible wounds. The study adds to our understanding of the diversity of bacteria present on sharks in comparison to their natural environment. We also compare bacterial groups found within wounds in shark skin to healthy tissue sites on the same individual. Results indicate that wounds on an individual may allow for opportunistic bacteria to invade or overgrow where they would not normally be found, which may have potential health consequences for sharks that become wounded due to fishing practices. Identified bacteria belonged to the , , and phyla, known to be prominent bacterial groups associated with marine organisms. Results indicate shark species-specific differences in bacterial communities, including the presence of bacteria belonging to exclusively on the skin of tiger sharks. To our knowledge, this is the first report of this family in any elasmobranch. While most tissue sites displayed commensal bacteria identified in similar studies, known pathogens belonging to and were identified in the wounds of blacktip and bull sharks. Some bacteria may be normal residents, but the loss of protective dermal denticles due to a wound may allow colonization by pathogens. Continued research is needed to explore microbial communities associated with sharks and their influence on host health.
PubMed: 35774257
DOI: 10.6620/ZS.2021.60-69 -
Scientific Reports Oct 2019We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO) can be tailored by modulating the precipitation kinetics...
We demonstrate for the first time that the morphology and nanomechanical properties of calcium carbonate (CaCO) can be tailored by modulating the precipitation kinetics of ureolytic microorganisms through genetic engineering. Many engineering applications employ microorganisms to produce CaCO. However, control over bacterial calcite morphology and material properties has not been demonstrated. We hypothesized that microorganisms genetically engineered for low urease activity would achieve larger calcite crystals with higher moduli. We compared precipitation kinetics, morphology, and nanomechanical properties for biogenic CaCO produced by two Escherichia coli (E. coli) strains that were engineered to display either high or low urease activity and the native producer Sporosarcina pasteurii. While all three microorganisms produced calcite, lower urease activity was associated with both slower initial calcium depletion rate and increased average calcite crystal size. Both calcite crystal size and nanoindentation moduli were also significantly higher for the low-urease activity E. coli compared with the high-urease activity E. coli. The relative resistance to inelastic deformation, measured via the ratio of nanoindentation hardness to modulus, was similar across microorganisms. These findings may enable design of novel advanced engineering materials where modulus is tailored to the application while resistance to irreversible deformation is not compromised.
Topics: Calcium Carbonate; Chemical Precipitation; Crystallization; Escherichia coli; Kinetics; Metabolic Engineering; Microscopy, Electron, Scanning; Organisms, Genetically Modified; Sporosarcina; Urease; X-Ray Diffraction
PubMed: 31604977
DOI: 10.1038/s41598-019-51133-9 -
Brazilian Journal of Microbiology :... Jul 2009Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus...
Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary trees. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus) of Bacillaceae, so some Bacillus species in Group 9: B. salarius, B. qingdaonensis and B. thermcloacae might not belong to Bacillus. Four Bacillus species, B. schlegelii, B. tusciae, B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups.
PubMed: 24031394
DOI: 10.1590/S1517-838220090003000013 -
Molecules (Basel, Switzerland) Oct 2018Phenolic inhibitors generated during alkaline pretreatment of lignocellulosic biomasses significantly hinder bacterial growth and subsequent biofuel and biochemical...
Phenolic inhibitors generated during alkaline pretreatment of lignocellulosic biomasses significantly hinder bacterial growth and subsequent biofuel and biochemical production. Water rinsing is an efficient method for removing these compounds. Nevertheless, this method often generates a great amount of wastewater, and leads to the loss of solid fiber particles and fermentable sugars. LAM0618, a recently identified microorganism, was herein shown to be able to efficiently transform phenolic compounds (syringaldehyde, hydroxybenzaldehyde, and vanillin) into less toxic acids. Taking advantage of these properties, a biodetoxification method was established by inoculating LAM0618 into the NH₃/H₂O₂-pretreated unwashed corn stover to degrade phenolic inhibitors and weak acids generated during the pretreatment. Subsequently, 33.47 and 17.91 g/L lactic acid was produced by LA204 at 50 °C through simultaneous saccharification and fermentation (SSF) from 8% (/) of NH₃/H₂O₂-pretreated corn stover with or without LAM0618-biodetoxification, indicating biodetoxification significantly increased lactic acid titer and yield. Importantly, using 15% (/) of the NH₃/H₂O₂-pretreated LAM0618-biodetoxified corn stover as a substrate through fed-batch simultaneous saccharification and fermentation, high titer and high yield of lactic acid (84.49 g/L and 0.56 g/g corn stover, respectively, with a productivity of 0.88 g/L/h) were produced by LA204. Therefore, this study reported the first study on biodetoxification of alkaline-pretreated lignocellulosic material, and this biodetoxification method could replace water rinsing for removal of phenolic inhibitors and applied in biofuel and biochemical production using the alkaline-pretreated lignocellulosic bioresources.
Topics: Batch Cell Culture Techniques; Benzaldehydes; Biodegradation, Environmental; Biomass; Bioreactors; Fermentation; Lactic Acid; Lignin; Planococcaceae; Zea mays
PubMed: 30322101
DOI: 10.3390/molecules23102626 -
Applied and Environmental Microbiology May 2012The connection between farm-generated animal waste and the dissemination of antibiotic resistance in soil microbial communities, via mobile genetic elements, remains...
The connection between farm-generated animal waste and the dissemination of antibiotic resistance in soil microbial communities, via mobile genetic elements, remains obscure. In this study, electromagnetic induction (EMI) surveying of a broiler chicken farm assisted soil sampling from a chicken-waste-impacted site and a marginally affected site. Consistent with the EMI survey, a disparity existed between the two sites with regard to soil pH, tetracycline resistance (Tc(r)) levels among culturable soil bacteria, and the incidence and prevalence of several tet and erm genes in the soils. No significant difference was observed in these aspects between the marginally affected site and several sites in a relatively pristine regional forest. When the farm was in operation, tet(L), tet(M), tet(O), erm(A), erm(B), and erm(C) genes were detected in the waste-affected soil. Two years after all waste was removed from the farm, tet(L), tet(M), tet(O), and erm(C) genes were still detected. The abundances of tet(L), tet(O), and erm(B) were measured using quantitative PCR, and the copy numbers of each were normalized to eubacterial 16S rRNA gene copy numbers. tet(L) was the most prevalent gene, whereas tet(O) was the most persistent, although all declined over the 2-year period. A mobilizable plasmid carrying tet(L) was identified in seven of 14 Tc(r) soil isolates. The plasmid's hosts were identified as species of Bhargavaea, Sporosarcina, and Bacillus. The plasmid's mobilization (mob) gene was quantified to estimate its prevalence in the soil, and the ratio of tet(L) to mob was shown to have changed from 34:1 to 1:1 over the 2-year sampling period.
Topics: Animals; Bacillales; Bacterial Proteins; Chickens; DNA, Bacterial; Feces; Molecular Sequence Data; Plasmids; Polymerase Chain Reaction; Sequence Analysis, DNA; Soil Microbiology; Sporosarcina; Tetracycline Resistance
PubMed: 22389375
DOI: 10.1128/AEM.07763-11