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Journal of Environmental Management Jul 2024Chromium contamination from abandoned industrial sites and inadequately managed waste disposal areas poses substantial environmental threat. Microbially induced...
Chromium contamination from abandoned industrial sites and inadequately managed waste disposal areas poses substantial environmental threat. Microbially induced carbonate precipitation (MICP) has shown promising, eco-friendly solution to remediate Cr(VI) and divalent heavy metals. In this study, MICP was carried out for chromium immobilization by an ureolytic bacterium Arthrobacter creatinolyticus which is capable of reducing Cr(VI) to less toxic Cr(III) via extracellular polymeric substances (EPS) production. The efficacy of EPS driven reduction was confirmed by cellular fraction analysis. MICP carried out in aqueous solution with 100 ppm of Cr(VI) co-precipitated 82.21% of chromium with CaCO and the co-precipitation is positively correlated with reduction of Cr(VI). The organism was utilized to remediate chromium spiked sand and found that MICP treatment decreased the exchangeable fraction of chromium to 0.54 ± 0.11% and increased the carbonate bound fraction to 26.1 ± 1.15% compared to control. XRD and SEM analysis revealed that Cr(III) produced during reduction, influenced the polymorph selection of vaterite during precipitation. Evaluation of MICP to remediate Cr polluted soil sample collected from Ranipet, Tamil Nadu also showed effective immobilization of chromium. Thus, A. creatinolyticus proves to be viable option for encapsulating chromium contaminated soil via MICP process, and effectively mitigating the infiltration of Cr(VI) into groundwater and adjacent water bodies.
PubMed: 38955041
DOI: 10.1016/j.jenvman.2024.121300 -
Vavilovskii Zhurnal Genetiki I Selektsii Jun 2024We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average...
Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.).
We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.
PubMed: 38952705
DOI: 10.18699/vjgb-24-35 -
International Journal of Biological... Jun 2024p-Hydroxybenzoate hydroxylase (PHBH) catalyzes the ortho-hydroxylation of 4-hydroxybenzoate (4-HB) to protocatechuate (PCA). PHBHs are commonly known as homodimers, and...
p-Hydroxybenzoate hydroxylase (PHBH) catalyzes the ortho-hydroxylation of 4-hydroxybenzoate (4-HB) to protocatechuate (PCA). PHBHs are commonly known as homodimers, and the prediction of pyridine nucleotide binding and specificity remains an ongoing focus in this field. Therefore, our study aimed to determine the dimerization interface in AspPHBH from Arthrobacter sp. PAMC25564 and identify the canonical pyridine nucleotide-binding residues, along with coenzyme specificity, through site-directed mutagenesis. The results confirm a functional dimeric assembly from a tetramer that appeared in the crystallographic asymmetric unit identical to that established in previous studies. Furthermore, AspPHBH exhibits coenzyme versatility, utilizing both NADH and NADPH, with a preference for NADH. Rational engineering experiments demonstrated that targeted mutations in coenzyme surrounding residues profoundly impact NADPH binding, leading to nearly abrogated enzymatic activity compared to that of NADH. R50, R273, and S166 emerged as significant residues for NAD(P)H binding, having a near-fatal impact on NADPH binding compared to NADH. Likewise, the E44 residue plays a critical role in determining coenzyme specificity. Overall, our findings contribute to the fundamental understanding of the determinants of PHBH's active dimeric conformation, coenzyme binding and specificity holding promise for biotechnological advancements.
PubMed: 38944083
DOI: 10.1016/j.ijbiomac.2024.133268 -
ACS Applied Materials & Interfaces Jun 2024The catalytic efficiency of enzymes can be harnessed as an environmentally friendly solution for decontaminating various xenobiotics and toxins. However, for some...
The catalytic efficiency of enzymes can be harnessed as an environmentally friendly solution for decontaminating various xenobiotics and toxins. However, for some xenobiotics, several enzymatic steps are needed to obtain nontoxic products. Another challenge is the low durability and stability of many native enzymes in their purified form. Herein, we coupled peptide-based encapsulation of bacterial phosphotriesterase with soil-originated bacteria, sp. 4Hβ as an efficient system capable of biodegradation of paraoxon, a neurotoxin pesticide. Specifically, recombinantly expressed and purified methyl parathion hydrolase (MPH), with high hydrolytic activity toward paraoxon, was encapsulated within peptide nanofibrils, resulting in increased shelf life and retaining ∼50% activity after 132 days since purification. Next, the addition of sp. 4Hβ, capable of degrading para-nitrophenol (PNP), the hydrolysis product of paraoxon, which is still toxic, resulted in nondetectable levels of PNP. These results present an efficient one-pot system that can be further developed as an environmentally friendly solution, coupling purified enzymes and native bacteria, for pesticide bioremediation. We further suggest that this system can be tailored for different xenobiotics by encapsulating the rate-limiting key enzymes followed by their combination with environmental bacteria that can use the enzymatic step products for full degradation without the need to engineer synthetic bacteria.
PubMed: 38920304
DOI: 10.1021/acsami.4c06501 -
Water Science and Technology : a... Jun 2024This paper centers on the preparation and characterization of both a clay support and a faujasite zeolite membrane. Additionally, the study explores the development of...
This paper centers on the preparation and characterization of both a clay support and a faujasite zeolite membrane. Additionally, the study explores the development of bacterial media to assess the performance of these prepared membranes. The faujasite zeolite membrane was created using the hydrothermal method, involving the deposition of a faujasite layer to fine-tune the pore sizes of the clay support. The clay supports were crafted from clay which was sieved to particle size Φ ≤ 63 μm, and compacted with 3.0 wt.% activated carbon, then sintered at 1,000 °C. Distilled water fluxes revealed a decrease from 1,500 L m h to a minimum of 412 L m h after 180 min of filtration. Both membranes were characterized by XRF, XRD, FTIR, adsorption-desorption of nitrogen (N), and SEM-EDS. PCR technique was used for the identification of the isolated sp., and the retention of the bacteria on the clay support and the faujasite zeolite membrane were found to be 96 and 99%, respectively. The results showed that the faujasite zeolite membrane passed the clay support due to a narrow pore size of the faujasite zeolite membrane of 2.28 nm compared to 3.55 nm for the clay supports.
Topics: Zeolites; Arthrobacter; Wastewater; Membranes, Artificial; Filtration; Water Purification
PubMed: 38877622
DOI: 10.2166/wst.2024.175 -
Microbiology Resource Announcements Jun 2024Janeemi is a bacteriophage that infects B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted...
Janeemi is a bacteriophage that infects B-2880, which was isolated from soil collected in New York City. The genome has a length of 43,877 bp and contains 69 predicted genes. Based on gene content similarity to phages in the actinobacteriophage database, Janeemi is assigned to phage cluster AZ1.
PubMed: 38860811
DOI: 10.1128/mra.00177-24 -
FEMS Microbiology Ecology Jun 2024Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown...
Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We demonstrated that plant growth characteristics were strongly related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce IAA and siderophores) exhibited greater relative abundance in high- and medium performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, Azohydromonas. Conversely, the network within low performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.
PubMed: 38839598
DOI: 10.1093/femsec/fiae088 -
Cellular and Molecular Biology... Jun 2024Piceatannol, resveratrol's derivative, and a valuable polyphenol has managed to become one of the most remarkable candidate molecules for drug development research, with...
Piceatannol, resveratrol's derivative, and a valuable polyphenol has managed to become one of the most remarkable candidate molecules for drug development research, with its high bioactive properties and higher stability. On the other hand, the very low amount of piceatannol in plants which are its natural source increases the cost and limits the commercialization possibilities of the product. To overcome this bottleneck, a limited number of studies have recently shown that it is possible to produce piceatannol from the resveratrol precursor much cheaper by regioselective hydroxylation catalyzed by bacteria isolated from the soil, and the search for new bacteria of similar nature in new ecosystems has gained popularity. The aim of our study, which was prepared within this framework, is the bacterial isolate with regioselective hydroxylation potential obtained as a result of selective isolation steps; determination of resveratrol hydroxylation potentials and piceatannol product yields, investigation of possibilities to increase piceatannol yield with optimization trials and identification of isolates with the highest yield. For this purpose, 200 bacterial isolates capable of resveratrol hydroxylation were obtained from soil samples taken from Erzurum (Turkey) and its surroundings by using selective media. In the continuation of the study; resveratrol hydroxylation trials were carried out with these isolates and 55 active isolates capable of producing piceatannol by regioselective hydroxylation were selected. Then, yield improvement studies of active isolates were carried out by using different carbon sources and optimizing the culture conditions. As a result, a culture collection was created by identifying the 6 most active bacterial isolates with commercialization potential using conventional and molecular methods. These are 4 Gram-positive (Rhodococcus sp., Rhodococcus erythropolis, Paeniglutamicibacter sp., Arthrobacter sp.) and 2 Gram-negative (Shinella sp., Ensifer adhaerens) bacterial isolates. As a result of the optimization studies, three of these isolates used phenol as a biocatalyst, while the other three increased the production yield of piceatannol by using 4-hydroxyphenylacetic acid.
Topics: Stilbenes; Soil Microbiology; Bacteria; Resveratrol; Turkey; Hydroxylation
PubMed: 38836684
DOI: 10.14715/cmb/2024.70.6.5 -
Journal of Environmental Management Jun 2024To investigate the impact and mechanism of Cd-tolerant bacteria in soil on promoting Cd accumulation in Ageratum conyzoides L., we verified the impact of inoculating two...
To investigate the impact and mechanism of Cd-tolerant bacteria in soil on promoting Cd accumulation in Ageratum conyzoides L., we verified the impact of inoculating two strains, B-1 (Burkholderia contaminans HA09) and B-7 (Arthrobacter humicola), on Cd accumulation in A. conyzoides through a pot experiment. Additionally, we investigated the dissolution of CdCO and nutrient elements, as well as the release of indoleacetic acid (IAA) by the two strains. The results showed that both strains can significantly improve the dissolution of CdCO. Strains B-1 and B-7 had obvious effect of dissolving phosphorus, which was 5.63 and 2.76 times higher than that of the control group, respectively. Strain B-7 had significant effect of dissolution potassium, which was 1.79 times higher than that of the control group. Strains B-1 and B-7 had significant nitrogen fixation effect, which was 29.53 and 44.39 times higher than that of the control group, respectively. In addition, inoculating with strain B-1 and B-7 significantly increased the Cd extraction efficiency of A. conyzoides (by 114% and 45% respectively) through enhancing Cd accumulation and the biomass of A. conyzoides. Furthermore, the inoculation of strain B-1 and B-7 led to a significant increase in the activities of CAT and SOD, as well as the content of chlorophyll a and total chlorophyll in the leaves of A. conyzoides. To sum up, strain B-1 and B-7 can promote the phytoremediation efficiency of A. conyzoides on Cd by promoting the biomass and Cd accumulation of A. conyzoides.
Topics: Cadmium; Biodegradation, Environmental; Arthrobacter; Soil Pollutants; Ageratum; Burkholderia; Indoleacetic Acids
PubMed: 38833921
DOI: 10.1016/j.jenvman.2024.121250 -
Microbiological Research Aug 2024This study aims to investigate the effect of isolated drought-tolerant rhizobacteria, spanning various groups, such as nitrogen-fixing bacteria (NFB), phosphate...
This study aims to investigate the effect of isolated drought-tolerant rhizobacteria, spanning various groups, such as nitrogen-fixing bacteria (NFB), phosphate solubilizing bacteria (PSB), and other plant growth promoting rhizobacteria (PGPR), on the growth of wheat (Triticum durum) plants, focusing on various morphological and physiological responses under moderate drought and low-P availability. Among 343 rhizobacterial morphotypes, 16 exhibited tolerance to NaCl and PEG-6000. These included 8 PSB, 4 NFB, and 4 osmotolerant-PGPR groups, distributed across 14 different genera. Biochemical characterization showcased diverse PGP capabilities, particularly in P solubilization. The dynamic responses of drought-tolerant PSB to salt and PEG-6000-induced drought stress involved variations in organic acid (OA) secretion, with specific acids, including palmitic, lactic, and stearic, playing crucial roles in enhancing available P fractions. Inoculation with rhizobacteria significantly increased both shoot (SDW) and root (RDW) dry weights of wheat plants, as well as rhizosphere available P. PSB (Arthrobacter oryzae) emerged as the most effective strain, plausibly due to its positive impact on root morphological traits (length, surface, and volume). Other isolates, PSB (Priestia flexa), PSB (Bacillus haynesii), and particularly PGPR (Arthrobacter pascens) significantly increased shoot P content (up to 68.91 %), with a 2-fold increase in chlorophyll content. The correlation analysis highlighted positive associations between SDW, shoot P content, chlorophyll content index (CCI), and leaf area. Additionally, a negative correlation emerged between microbial biomass P and root morphophysiological parameters. This pattern could be explained by reduced competition between plants and rhizobacteria for accessible P, as indicated by low microbial biomass P and strong plant growth. Our investigation reveals the potential of drought-tolerant rhizobacteria in enhancing wheat resilience to moderate drought and low-P conditions. This is demonstrated through exceptional performance in influencing root architecture, P utilization efficiency, and overall plant physiological parameters. Beyond these outcomes, the innovative isolation procedure employed, targeting rhizobacteria from diverse groups, opens new avenues for targeted isolation techniques. This unique approach contributes to the novelty of our study, offering promising prospects for targeted bioinoculants in mitigating the challenges of drought and P deficiency in wheat cultivation.
Topics: Triticum; Droughts; Soil Microbiology; Rhizosphere; Plant Roots; Phosphates; Bacteria; Phosphorus; Stress, Physiological
PubMed: 38824819
DOI: 10.1016/j.micres.2024.127795