Microorganisms

2026

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21 pages, 2693 KB

Open AccessArticle

Genome Analysis and Characterization of Formosa bonchosmolovskayae sp. nov. Isolated from Brown and Green Algae, and a Proposal to Reclassify Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 as Xanthomarina New Members

by Olga Nedashkovskaya, Evgeniya Bystritskaya, Yulia Savicheva, Yulia Bronnikova, Nadezhda Otstavnykh, Viacheslav Eremeev, Song-Gun Kim, Natalia Zhukova and Marina Isaeva

Microorganisms 2026, 14(2), 328; https://doi.org/10.3390/microorganisms14020328 - 30 Jan 2026

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Abstract

Two marine bacteria, designated strains 4Alg 33^Tand 3Alg 14/1, were isolated from brown (Saccharina japonica) and green (Ulva fenestrata) macroalgae, respectively. These isolates were aerobic Gram-negative rods exhibiting a gliding motility. The 16S rRNA gene phylogenetic analysis [...] Read more.

Two marine bacteria, designated strains 4Alg 33^Tand 3Alg 14/1, were isolated from brown (Saccharina japonica) and green (Ulva fenestrata) macroalgae, respectively. These isolates were aerobic Gram-negative rods exhibiting a gliding motility. The 16S rRNA gene phylogenetic analysis clearly showed their belonging to the genus Formosa, the family Flavobacteriaceae, and the phylum Bacteroidota. The closest relatives of the new strains were Formosa undariae KCTC 32328^T (99.05%), Formosa arctica IMCC 9485^T (99.05%) and Formosa agariphila KMM 3901^T (98.96%). The ANI and dDDH values between the two new strains were 97.9% and 85.3%, respectively. The AAI values between 4Alg 33^T and Formosa type strains ranged from 80.1% (Formosa haliotis MA1^T) to 91.4% (F. undariae KCTC 32328^T). The cellular fatty acid and polar lipid profiles of the new isolates were generally similar to those of the type strains of Formosa species. The genomes of 4Alg 33^T and 3Alg 14/1 are represented by a circular chromosome of 4,157,724 bp and 4,316,096 bp in size with 3536 and 3879 protein-coding genes, respectively. They shared a DNA G+C content of 34.3 mol% and comprised four rrn operons. The pangenome of the genus Formosa belongs to the open type and is characterized by an abundance of CAZymes. The proportion of CAZyme genes in novel genomes was more than 5%, with a prevalence of glycoside hydrolase genes, suggesting great potential for utilizing marine-derived polysaccharides. Based on the results of polyphasic characterization, the two algal isolates represent a distinct species lineage within the genus Formosa, for which we propose the name Formosa bonchosmolovskayae sp. nov. with the type strain 4Alg 33^T (= KMM 3963^T = KCTC 72008^T). In addition, we have proposed to transfer Formosa maritima Cao et al. 2020 and Bizionia arctica Li et al. 2015 to the genus Xanthomarina Vaidya et al. 2015 as Xanthomarina maritima comb. nov. and Xanthomarina arctica comb. nov. based on a combination of the genomic and phenotypic characteristics. Full article

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18 pages, 2528 KB

Open AccessArticle

Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights

by Kerem Özdemir

Microorganisms 2026, 14(2), 306; https://doi.org/10.3390/microorganisms14020306 - 28 Jan 2026

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Abstract

In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective [...] Read more.

In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27–37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations. Full article

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18 pages, 4322 KB

Open AccessArticle

Genomic Insights into Marinovum sedimenti sp. nov., Isolated from Okhotsk Sea Bottom Sediments, Suggest Plasmid-Mediated Strain-Specific Motility

by Lyudmila Romanenko, Viacheslav Eremeev, Evgeniya Bystritskaya, Peter Velansky, Valeriya Kurilenko and Marina Isaeva

Microorganisms 2026, 14(1), 125; https://doi.org/10.3390/microorganisms14010125 - 7 Jan 2026

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Abstract

Two Gram-negative aerobic halophilic bacteria, designated KMM 9989^T and KMM 9879, were isolated from a bottom sediment sample of the Okhotsk Sea, Russia. The novel strains grew in 0.5–4% NaCl, at 5–35 °C and pH 5.5–10.0. Phylogenetic analyses based on 16S rRNA [...] Read more.

Two Gram-negative aerobic halophilic bacteria, designated KMM 9989^T and KMM 9879, were isolated from a bottom sediment sample of the Okhotsk Sea, Russia. The novel strains grew in 0.5–4% NaCl, at 5–35 °C and pH 5.5–10.0. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences placed strains KMM 9989^T and KMM 9879 within the family Roseobacteraceae, where they were clustered with their closest relative Marinovum algicola KCTC 22095^T. The average nucleotide identity (ANI) between strain KMM 9989^T and Marinovum algicola KCTC 22095^T was 81.4%. The level of digital DNA–DNA hybridization (dDDH) between the novel isolates KMM 9989^T and KMM 9879 was 97%, while between strain KMM 9989^T and Marinovum algicola KCTC 22095^T, it was 27%. Strains KMM 9989^T and KMM 9879 contained Q-10 as the predominant ubiquinone and C_18:1ω7c as the major fatty acid. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified aminolipid, two unidentified phospholipids, and three unidentified lipids. The genomic size of strains KMM 9989^T and KMM 9879 was determined to be 4,040,543 bp and 3,969,839 bp with a DNA GC content of 61.3 and 61.4 mol%, respectively. Both strains contained a common plasmid of 238,277 bp and a strain-specific plasmid (188,734 bp for KMM 9989^T and 118,029 bp for KMM 9879). It is suggested that the motility of KMM 9879 may be mediated by the presence of a complete fla2-type operon in the strain-specific chromid. Thus, based on the phylogenetic analyses and distinctive phenotypic characteristics, the novel marine strains KMM 9989^T and KMM 9879 are proposed to be classified as a novel species Marinovum sedimenti sp. nov. with the strain KMM 9989^T (=KCTC 8835^T) as the type strain of the species. Full article

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2025

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17 pages, 8870 KB

Open AccessArticle

Sulfide Production and Microbial Dynamics in the Water Reinjection System from an Offshore Oil-Producing Platform

by Vitória da Silva Pereira Domingues, Maira Paula de Sousa, Vinicius Waldow, Rubens Akamine, Lucy Seldin and Diogo Jurelevicius

Microorganisms 2026, 14(1), 38; https://doi.org/10.3390/microorganisms14010038 - 23 Dec 2025

Cited by 1 | Viewed by 505

Abstract

In addition to seawater in the injection header (IH) to enhance oil recovery, oil companies reuse produced water (PW), a byproduct of oil extraction, and implement produced water reinjection systems (PWRI). Although the microorganisms in IH are controlled by biocides, PW is generally [...] Read more.

In addition to seawater in the injection header (IH) to enhance oil recovery, oil companies reuse produced water (PW), a byproduct of oil extraction, and implement produced water reinjection systems (PWRI). Although the microorganisms in IH are controlled by biocides, PW is generally treated by flotation to remove oil residues before PWRI. However, IH, PW, and PWRI can be sources of sulfate-reducing bacteria (SRB) related to oil reservoir souring. Here, we evaluated hydrogen sulfide (H₂S) production in IH, PW, and PWRI, as well as the microbial dynamics (most probable number–MPN, quantitative PCR, and amplicon sequencing), of a Brazilian oil reservoir. Results revealed that the highest average H₂S concentration occurred in PW samples. However, the dissolved H₂S threshold concentration of 2 mg L⁻¹ was exceeded in 18% of PW and ~16% of PWRI samples, respectively. Although MPN showed no correlation between H₂S and the number of SRB or total anaerobic heterotrophic bacteria (TAHB), qPCR and microbiome data revealed that the SRB Desulfobacterota was the most abundant in PW and PWRI. Overall, flotation was associated with (i) low microbial control in PW; and (ii) the enrichment of SRB (mainly Desulfobacterota), Thermotogota, and Proteobacteria groups in PWRI. Full article

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29 pages, 4047 KB

Open AccessReview

Phenomenal Diversity of the Photosynthetic Apparatus Evolved in Aerobic Anoxygenic Phototrophs

by Vladimir Yurkov and Katia Messner

Microorganisms 2025, 13(11), 2446; https://doi.org/10.3390/microorganisms13112446 - 25 Oct 2025

Cited by 2 | Viewed by 1451

Abstract

Aerobic anoxygenic phototrophs (AAPs) are intrinsically paradoxical; these species use a pathway commonly found in oxygen-deprived environments called anoxygenic photosynthesis, as a supplementary energy source to their obligately aerobic respiration. At the surface, such a combination seems odd, but AAPs thrive in a [...] Read more.

Aerobic anoxygenic phototrophs (AAPs) are intrinsically paradoxical; these species use a pathway commonly found in oxygen-deprived environments called anoxygenic photosynthesis, as a supplementary energy source to their obligately aerobic respiration. At the surface, such a combination seems odd, but AAPs thrive in a plethora of environments and are phylogenetically broad, suggesting that this feature is advantageous and ecologically valuable. The range of habitats and taxonomy have been reviewed, yet the main element which unites the group, their anoxygenic photosynthesis, which is diverse in its components, has not received the deserved attention. The intricate light-capturing photosynthetic complex forms the site of photon-induced energy transfer and therefore, the core basis of the process. It has two parts: the reaction center and light harvesting complex(es). The variability in composition and overall usage of the apparatus is also reflected in the genome, specifically the photosynthetic gene cluster. In this review, what is known about the differences in structure, light wavelength absorption range, activity, and related genomic content and the insights into potential AAP evolution from anaerobic anoxygenic phototrophs will be discussed. The work provides an elegant summation of knowledge accumulated about the photosynthetic apparatus and prospects that can fill yet remaining gaps. Full article

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19 pages, 5905 KB

Open AccessArticle

Soybean-Bupleurum Rotation System Can Optimize Rhizosphere Soil Microbial Community via Impacting Soil Properties and Enzyme Activities During Bupleurum Seedling Stage

by Qingshan Yang, Peng Dong, Mengni Chen, Hui Wang, Lu Wang, Jiawei Yuan, Chengyu Hu, Zhen Liu, Yongshan Li and Qiaolan Fan

Microorganisms 2025, 13(10), 2346; https://doi.org/10.3390/microorganisms13102346 - 13 Oct 2025

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Abstract

To avoid continuous cropping problems with Bupleurum, we screened suitable preceding crops for rotation with Bupleurum through different crop rotations. Therefore, the objective of this study was to find out the relationships between microbial community characteristics, soil properties, and enzyme activities under [...] Read more.

To avoid continuous cropping problems with Bupleurum, we screened suitable preceding crops for rotation with Bupleurum through different crop rotations. Therefore, the objective of this study was to find out the relationships between microbial community characteristics, soil properties, and enzyme activities under four different rotation patterns, including fallow-Bupleurum (CK), maize-Bupleurum (M), soybean-Bupleurum (So), and sunflower-Bupleurum (Su). Results indicated that under all four rotation patterns, So treatment significantly enhanced soil nutrients and enzyme activities compared to CK. So not only optimized the composition of soil bacterial and fungal communities but markedly enhanced microbial α diversity. Additionally, So exhibited high similarity in bacterial and fungal community composition with M, and featured complex symbiotic relationships within the soil microbial network. While no clear discrepancies were detected in the abundance of the top twenty metabolic pathways in the predictive functions of bacterial and fungal communities across four rotation patterns, the metabolic pathway function MET-SAM-PWY (methionine synthesis pathway) in bacterial communities and the metabolic pathway function VALSYN-PWY (valine synthesis pathway) in fungal communities were particularly prominent under the So rotation pattern. RDA suggested that soil properties (available phosphorus and pH) and enzyme activities (sucrase and alkaline phosphatase activities) were the driving forces for bacterial community composition, while soil properties (soil organic matter and available potassium) and enzyme activities (sucrase and catalase activities) regulated fungal community composition. Hence, the soybean-Bupleurum rotation pattern represents a cultivation practice more beneficial for the sustainable development of the bupleurum industry, which can significantly improve soil fertility and the micro-ecological environment. Full article

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30 pages, 3426 KB

Open AccessArticle

Unraveling the Effect of Soil Moisture on Microbial Diversity and Enzymatic Activity in Agricultural Soils

by Kalisa Amarsingh Bogati, Piotr Sewerniak and Maciej Walczak

Microorganisms 2025, 13(6), 1245; https://doi.org/10.3390/microorganisms13061245 - 28 May 2025

Cited by 12 | Viewed by 3117

Abstract

This study investigates the impact of two months of drought stress on the microbial diversity, enzyme activities and functional diversity in four agricultural soils (Gniewkowo (G); Lulkowo (L); Nieszawa (N); Suchatówka (S)) from Poland during summer season. The physicochemical parameters (pH, organic carbon, [...] Read more.

This study investigates the impact of two months of drought stress on the microbial diversity, enzyme activities and functional diversity in four agricultural soils (Gniewkowo (G); Lulkowo (L); Nieszawa (N); Suchatówka (S)) from Poland during summer season. The physicochemical parameters (pH, organic carbon, calcium carbonate, total nitrogen, nitrate, ammonium, total phosphorus and available phosphate), microbial abundance, community-level physiological profiling, and soil enzymes (acid and alkaline phosphatases, dehydrogenase and urease) were investigated at two time intervals: zero-week (T0) and the eighth week (T8). Generally, microbial enumeration showed higher bacterial populations (496.63 × 10⁴ CFU g⁻¹ dry soil) compared to actinomycetes (13.43 × 10⁴ CFU g⁻¹ dry soil), and the fungal population was the lowest (67.68 × 10² CFU g⁻¹ dry soil) at T8. Functional diversity showed a strong, statistically significant positive effect in the G, N and S sites at T8. Acidobacteriota and Actinobacteriota declined in most places, while Firmicutes, Crenarchaeota and drought-tolerant bacteria such as Gemmatimonadota exhibited resistance. The fungal communities showed site-specific responses, with an increase in drought-tolerant Mortierellomycota and Chytridiomycota and a decrease in Ascomycota and Basidiomycota, suggesting possible adaptability. Overall, the microbial populations, enzyme activity, and functional diversity were positively correlated with soil moisture content across all four investigated sites. The significance of organic matter, soil structure, and moisture retention in determining microbial resilience to drought is underscored by these changes in microbial diversity and function, which in turn affect nutrient cycling and soil ecosystem stability. The findings of our study indicate that soil biological activities in agricultural regions can be modified by a mere two months of drought. Full article

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17 pages, 1809 KB

Open AccessArticle

The Impact of Wheat Growth Stages on Soil Microbial Communities in a Rain-Fed Agroecosystem

by Yosef Steinberger, May Levi, Itaii Applebaum, Chen Sherman, Tirza Doniger and Adrian Unc

Microorganisms 2025, 13(4), 838; https://doi.org/10.3390/microorganisms13040838 - 7 Apr 2025

Viewed by 1150

Abstract

Wheat is the largest terrestrial agricultural crop globally. This study was conducted to determine the soil microbial biomass, soil CO₂ evolution, and physiological profile in the rhizosphere of the winter wheat rain-fed Triticum aestivum along the development stages in a rain-fed semi-arid [...] Read more.

Wheat is the largest terrestrial agricultural crop globally. This study was conducted to determine the soil microbial biomass, soil CO₂ evolution, and physiological profile in the rhizosphere of the winter wheat rain-fed Triticum aestivum along the development stages in a rain-fed semi-arid agro-ecosystem. The data show that a significant, over 100-fold increase in the utilization of four substrate groups (benzoic acid, amino acid, carbohydrates, and carboxylic acid) occurred in the wheat soil rhizosphere along the wheat growth phenology. After the stubble field stage, there was a notable decrease in the utilization of all four substrates. The occurrence of each substrate in the soil aligns with the below-ground rhythm of wheat plant biomass growth. The abundance of fine roots, categorizing wheat plant roots, in the soil at maturity and the stubble field stage may explain the heightened activity and diversity of copiotroph bacteria. This association suggests a potential link between the richness of fine roots and the increased activity and diversity of copiotroph bacteria in the soil. The findings clarify the impact of constraining abiotic factors, coupled with the phenological influences of wheat plants, and their combined effects on substrate utilization by microbial communities in a rain-fed Triticum aestivum wheat field. Full article

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14 pages, 3861 KB

Open AccessArticle

The Reliable Detection of Homocysteine Using a Biosensor Based on Recombinant Cystathionine β-Synthase and Nanoporous Gold

by Zihan Huang, Yan Gao, Lei Zhang, Ting Cai, Ruijun Liu and Xia Wang

Microorganisms 2025, 13(3), 559; https://doi.org/10.3390/microorganisms13030559 - 1 Mar 2025

Cited by 1 | Viewed by 1772

Abstract

Given the essential roles of homocysteine (Hcy) and the interference of cysteine in effectively monitoring human health, this study proposed a synergistic effect strategy that combines the unique structural and functional properties of nanoporous gold (NPG) with the selective recognition capability of a [...] Read more.

Given the essential roles of homocysteine (Hcy) and the interference of cysteine in effectively monitoring human health, this study proposed a synergistic effect strategy that combines the unique structural and functional properties of nanoporous gold (NPG) with the selective recognition capability of a recombinant cystathionine β-synthase (CBS) for the sensitive and specific detection of Hcy. The CBS protein with specific catalytic activity for Hcy was successfully produced in recombinant Escherichia coli BL21 (pET-30a-cbs) using the cbs gene from Pseudomonas aeruginosa PAO1. The electrochemical mechanism demonstrated that the electrooxidation of H₂S, a catalytic product of the CBS, was an irreversibly surface-controlled process on the CBS/NPG/GCE electrode surface. The electrochemical detection of Hcy exhibited excellent linearity, with a high sensitivity reaching 10.43 µA mM⁻¹ cm⁻² and a low detection limit of 1.31 µM. Furthermore, the CBS/NPG/GCE biosensor was successfully used to detect Hcy in urine samples with strong anti-interference capability and high selectivity (relative standard deviation less than 2.81%), while effectively reducing the interference from cysteine. These results confirmed that the proposed CBS/NPG/GCE electrochemical sensor achieved specific, sensitive, and reliable rapid detection of homocysteine, making it highly promising for practical applications in clinical treatment and health assessment. Full article

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18 pages, 4222 KB

Open AccessArticle

Vertical Stratification Reduces Microbial Network Complexity and Disrupts Nitrogen Balance in Seasonally Frozen Ground at Qinghai Lake in Tibet

by Ni Zhang, Zhiyun Zhou, Yijun Wang, Shijia Zhou, Jing Ma, Jianqing Sun and Kelong Chen

Microorganisms 2025, 13(2), 459; https://doi.org/10.3390/microorganisms13020459 - 19 Feb 2025

Cited by 2 | Viewed by 1374

Abstract

Global climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we [...] Read more.

Global climate change has accelerated the reduction of permafrost regions across different altitude gradients, shortening the duration of the freezing period to varying extents. However, the response of the soil microorganisms of frozen soils along altitude gradients remains unclear. In this study, we employed 16S rRNA sequencing and LC-MS metabolomics to investigate the response of soil microbial communities and soil metabolites to vertical stratification in the permafrost soils of the Qinghai Lake region. The results indicated that Proteobacteria, Firmicutes, and Actinobacteria were key soil bacterial phyla in the permafrost soils of Qinghai Lake during the freezing period, with Proteobacteria and Firmicutes showing significant sensitivity to vertical stratification (p < 0.05). The majority of the physicochemical factors exhibited a trend of initially increasing and then decreasing with increasing altitude, whereas pH showed the opposite trend. pH and moisture content were identified as the most important environmental factors influencing soil bacterial community structure. Deterministic processes dominated the assembly of bacterial communities of frozen soils in the Qinghai Lake basin. Co-occurrence network analysis showed that increasing altitude gradients led to a higher average degree of the bacterial network, while reducing network complexity and inter-species connectivity. Soil metabolomics analysis revealed that vertical stratification altered the metabolic profiles of 27 metabolites, with the significantly changed metabolites primarily associated with carbohydrate and amino acid metabolism. In conclusion, the characteristics of the Qinghai Lake permafrost were regulated by regional vertical stratification, which further influenced microbial community structure and soil metabolic characteristics, thereby altering carbon and nitrogen stocks. Specifically, higher altitudes were more favorable for the retention of the carbon and nitrogen stocks of frozen soils in the Qinghai Lake basin. Full article

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