Microorganisms

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25 pages, 3194 KB

Open AccessArticle

Biodiversity and Biotechnological Potential of Dunaliella sp. Isolates from Kalloni Solar Saltworks (Lesvos, Greece)

by Athina Petridi, Aikaterini Koletti, Sofia Marka, Maria-Eleftheria Zografaki, Ioanna Fouskari, Ioannis Karavidas, Alexandros Ntzouvaras, Ioannis Tzovenis, Rodica C. Efrose, Emmanouil Flemetakis, George Tsirtsis and Chrysanthi Kalloniati

Microorganisms 2026, 14(2), 502; https://doi.org/10.3390/microorganisms14020502 - 20 Feb 2026

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Abstract

Hypersaline solar saltworks represent unique ecological niches that harbor extremophilic microalgae with considerable biotechnological potential. Within these environments, members of the genus Dunaliella are particularly noteworthy due to their remarkable metabolic plasticity and ability to accumulate high-value biomolecules. In the present study, we [...] Read more.

Hypersaline solar saltworks represent unique ecological niches that harbor extremophilic microalgae with considerable biotechnological potential. Within these environments, members of the genus Dunaliella are particularly noteworthy due to their remarkable metabolic plasticity and ability to accumulate high-value biomolecules. In the present study, we investigated the biodiversity of Dunaliella in hypersaline saltworks by isolating and identifying autochthonous strains and assessing their growth kinetics and biomass biochemical composition in the context of potential biotechnological applications. Specifically, sixteen strains of Dunaliella were isolated from evaporation and crystallizer ponds of the Kalloni saltworks in Lesvos, Greece, and subjected to an integrative characterization combining morphological observations, molecular phylogenetics, growth kinetics, and biochemical profiling. Phylogenetic analyses based on four genetic markers (18S, ITS, rbcL, tufA) consistently resolved the isolates into three distinct clades: one corresponding to Dunaliella salina/D. minutissima, one to D. parva, and a third representing a clearly divergent lineage. Growth assays revealed marked variability in cell density, biomass productivity and specific growth rate, with certain strains exhibiting enhanced proliferation under controlled conditions. Biochemical analyses demonstrated distinct allocation patterns, with evaporation pond isolates comparatively enriched in proteins (up to 60.8% DW), whereas crystallizer pond isolates accumulated higher levels of carbohydrates (up to 19.0% DW), carotenoids (up to 7.34% mg g⁻¹ DW) and phenolic compounds (up to 8.68% mg GAE g⁻¹ DW). Antioxidant assays (FRAP, TEAC) further indicated significantly elevated reducing and radical scavenging activities among crystallizer isolates. These findings expand current knowledge on the biodiversity of autochthonous Dunaliella strains and support their potential as sustainable sources of bioactive compounds for applications in the agri-food, nutraceutical, pharmaceutical, and cosmeutical sectors. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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13 pages, 3417 KB

Open AccessArticle

Taxonomic and Functional Diversity of Leaves and Stem Endophytes of Eight Agave Species

by Natalia Ysabel Labrín-Sotomayor, Patricia Alejandra Becerra-Lucio, Hugo Ruiz-González and Yuri Jorge Peña-Ramírez

Microorganisms 2026, 14(2), 476; https://doi.org/10.3390/microorganisms14020476 - 15 Feb 2026

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Abstract

More than 63% of Mexico’s territory is classified as arid or semiarid, where plants belonging to the genus Agave have evolved. Adaptation to drylands resulted from biochemical, physiological, and anatomical properties shared with other crassulacean plants; however, microbial symbionts also play critical roles [...] Read more.

More than 63% of Mexico’s territory is classified as arid or semiarid, where plants belonging to the genus Agave have evolved. Adaptation to drylands resulted from biochemical, physiological, and anatomical properties shared with other crassulacean plants; however, microbial symbionts also play critical roles in plants’ growth, health, and drought tolerance. To explore endophytic communities in Agave plants, we used a shotgun metagenomic approach. The taxonomic and functional diversity of endophytes were studied in the leaves and stem organs of Agave americana, A.angustifolia, A. fourcroydes, A. karwinskii, A. potatorum, A. tequilana, A. cupreata, and A. rodacantha. The microbial community structure did not differ significantly among species, regardless of geographic origin or local environmental conditions, whereas significant differences were observed between organs. We found 4058 genera shared among organs, of which 957 genera are exclusive to the stem and 492 to the leaves. The community analysis of stems and leaves identified bacterial genera, including Acinetobacter, Klebsiella, Escherichia, Corynebacterium, and Streptomyces. Significant differences were also observed between organs in the functional annotations. The dominant functional categories were associated with cell signaling and protein metabolism in both organs. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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19 pages, 4006 KB

Open AccessArticle

Prokaryotic Microbial Diversity and Community Assembly in Reclaimed Coastal Agricultural Soils

by Yifan Yin, Weidong Xu, Min Xu, Yuwei Wang, Hao Liu, Hui Cao and Feng Wang

Microorganisms 2026, 14(1), 120; https://doi.org/10.3390/microorganisms14010120 - 6 Jan 2026

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Abstract

Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow [...] Read more.

Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0–1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210–230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance–decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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15 pages, 3134 KB

Open AccessArticle

Characterization of Bacterial Communities in Air and Bedding Materials of Intensive Donkey Farms During Summer

by Wenxuan Si, Jianpeng Zhang, Yu Zhang, Yanfei Ji, Muhammad Zahoor Khan, Yinze Chen, Zhouzhou Cheng, Jinguang Zhuang, Xia Zhao and Wenqiang Liu

Microorganisms 2026, 14(1), 53; https://doi.org/10.3390/microorganisms14010053 - 26 Dec 2025

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Abstract

This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding [...] Read more.

This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding samples were obtained from eight farms housing Dezhou donkeys. Sequencing analysis revealed 894 operational taxonomic units (OTUs) in air samples and 3127 OTUs in bedding samples. Alpha diversity indices indicated that the mare barn exhibited the highest microbial diversity in air, while the foal barn showed the lowest. Actinobacteriota, Proteobacteria, and Firmicutes were the dominant phyla across different functional areas. Rhodococcus was identified as the predominant airborne genus, representing a potential pneumonia risk in foals. In bedding materials, Firmicutes, Actinobacteriota, and Proteobacteria predominated, with Corynebacterium, Salinicoccus, and Solibacillus as dominant genera. Several potentially pathogenic bacteria were detected, including Rhodococcus, Corynebacterium, Clostridium, Streptococcus, and Escherichia-Shigella. These findings provide critical insights into the microbial ecology of intensive donkey farming environments and offer scientific evidence for developing targeted biosecurity strategies to safeguard animal health and promote sustainable livestock production. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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21 pages, 2545 KB

Open AccessArticle

Multi-Regional Study on the Microbial Community Structure, Core Microbiome and Functional Characteristics in Deep Fracture Waters

by Xiaoxuan Li, Tianming Huang, Yiman Li, Zhonghe Pang and Yuran Zhang

Microorganisms 2026, 14(1), 45; https://doi.org/10.3390/microorganisms14010045 - 25 Dec 2025

Cited by 1 | Viewed by 586

Abstract

The deep terrestrial subsurface is the largest reservoir of Earth’s freshwater resources as well as the largest habitat for prokaryotic life. However, the deep-subsurface microbiome, especially its spatial distribution across countries/continents, is still poorly understood. In this study, we compiled and compared 30 [...] Read more.

The deep terrestrial subsurface is the largest reservoir of Earth’s freshwater resources as well as the largest habitat for prokaryotic life. However, the deep-subsurface microbiome, especially its spatial distribution across countries/continents, is still poorly understood. In this study, we compiled and compared 30 16S rRNA gene amplicon libraries from three deep fractured aquifers in different parts of the world (depth range of tens of meters to 2.4 km below surface) to understand the spatial distribution and functions of deep-subsurface microbial community, and to test for the presence of core taxa. The results revealed spatially heterogenous microbial community composition at both the local and the global scales, even at the phylum level. Environmental filtering was identified as an important driver of the microbial community structure of deep groundwaters. Despite the spatial heterogeneity, the three aquifers share a core microbiome at the genus level. Only one family, Comamonadaceae, was present in all the 30 samples analyzed. Several other families were also prevalent, including Hydrogenophilaceae, Omnitrophaceae, BSV26 (Candidatus Kryptonia), and an unclassified Thermodesulfovibrionia. FAPROTAX functional prediction indicated that chemoheterotrophic functions predominate, and the core microbial genera, together with the dominant genera, collectively govern the functional characteristics. Taken together, our findings provide new insights into the spatial heterogeneity and functional potential of deep-subsurface ecosystems across the globe. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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16 pages, 3167 KB

Open AccessArticle

Deciphering the Structure and Genetic Basis of Adaptive Mechanism of Soil Microbial Communities in a Manganese Electrolysis Plant

by Yong Wang, Song Liu, Ziyi Zheng, Jun Ma, Yuan Xiang, Lanyan Wu, Chunlian Ding and Yan Shi

Microorganisms 2026, 14(1), 15; https://doi.org/10.3390/microorganisms14010015 - 20 Dec 2025

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Abstract

The development of China’s manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms [...] Read more.

The development of China’s manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China’s “Manganese Triangle” were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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23 pages, 3903 KB

Open AccessArticle

Integrative Multi-Omics Identify Key Secondary Metabolites Linked to Acid Tolerance in Leptospirillum ferriphilum

by Yiran Li, Jiejie Yang, Xian Zhang, Luhua Jiang, Shiqi Chen, Manjun Miao, Yili Liang and Xueduan Liu

Microorganisms 2025, 13(11), 2493; https://doi.org/10.3390/microorganisms13112493 - 30 Oct 2025

Cited by 1 | Viewed by 899

Abstract

Acid mine drainage (AMD) environments feature extreme acidity (pH ≤ 2) and high heavy metal concentrations. Acidophiles survive these conditions through unique genetic adaptations and secondary metabolite (SM) pathways. Leptospirillum ferriphilum, known for its acid and heavy metal resistance, serves as a [...] Read more.

Acid mine drainage (AMD) environments feature extreme acidity (pH ≤ 2) and high heavy metal concentrations. Acidophiles survive these conditions through unique genetic adaptations and secondary metabolite (SM) pathways. Leptospirillum ferriphilum, known for its acid and heavy metal resistance, serves as a model for AMD bioremediation, though systematic multi-omics studies on its key SMs and biosynthesis pathways remain underexplored. In this study, L. ferriphilum YR01 was isolated and identified from the AMD of the Zijinshan copper mine, China. Pangenomic analysis revealed that YR01 possesses the largest number of genes (2623) among the eight sequenced L. ferriphilum strains. Comparative genomics, antiSMASH, BiG-SCAPE, and metabolomic analyses (LC-MS and HPLC-MS) were integrated to comprehensively explore its biosynthetic capacity. A total of 39 biosynthetic gene clusters (BGCs) were identified, of which 60% shared <50% similarity with known clusters, indicating substantial novel biosynthetic potential. The sequence alignment of SM biosynthetic gene clusters (BGCs) demonstrated the potential of L. ferriphilum to synthesize conserved clusters for ectoine, choline, carotenoids, terpenoids, and terpene precursors. YR01 harbors complete BGCs for all five SM types. Notably, key nonribosomal peptide synthetase (NRPS) modules implicated in N-acyl homoserine lactone (AHL) synthesis were identified. Untargeted metabolomics (LC-MS) revealed the production of diverse SMs (18 types) putatively involved in environmental adaptation, including phosphocholine, carotenoids (e.g., anteraxanthin), cholera autoinducer-1 (CAI-1), and multiple AHLs. Targeted detection (HPLC-MS) further confirmed that YR01 could produce ectoine (0.10 ng/mL) and specific AHLs (C₁₄-HSL, C₁₂-HSL, C₁₂-OH-HSL), which were beneficial for the survival of the strain in extremely acidic environments and interspecies communication through SMs. This study represents the first comprehensive multi-omics characterization of BGCs in L. ferriphilum and experimentally validates the production of key SMs. Collectively, this study provides a comprehensive elucidation of the SM biosynthetic repertoire and environmental adaptation strategies in L. ferriphilum, advancing our understanding of microbial adaptation and interspecies communication in AMD systems, and offering potential implications for biomining applications. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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18 pages, 5085 KB

Open AccessArticle

Developments in Microbial Communities and Interaction Networks in Sludge Treatment Ecosystems During the Transition from Anaerobic to Aerobic Conditions

by Xiaoli Pan, Lijun Luo, Hui Wang, Xinyu Chen, Yongjiang Zhang, Yan Dai and Feng Luo

Microorganisms 2025, 13(9), 2178; https://doi.org/10.3390/microorganisms13092178 - 18 Sep 2025

Cited by 1 | Viewed by 1149

Abstract

The transition between anaerobic and aerobic conditions represents a fundamental ecological process occurring ubiquitously in both natural ecosystems and engineered wastewater treatment systems. This study investigated the microbial community succession and co-occurrence network dynamics during the transition from anaerobic sludge to aerobic cultivation. [...] Read more.

The transition between anaerobic and aerobic conditions represents a fundamental ecological process occurring ubiquitously in both natural ecosystems and engineered wastewater treatment systems. This study investigated the microbial community succession and co-occurrence network dynamics during the transition from anaerobic sludge to aerobic cultivation. High-throughput 16S and 18S rDNA sequencing revealed two distinct succession phases: an initial “aerobic adaptation period” (Day 1) and a subsequent “aerobic stable period” (Day 15). Eukaryotic communities shifted from Cryptomycota to the unassigned eukaryotes dominance, while prokaryotic communities maintained Firmicutes and Proteobacteria as core phyla, with persistent low-abundance archaea indicating functional adaptation. Network analysis highlighted predominant co-occurrence patterns between eukaryotic and prokaryotic communities, suggesting synergistic interactions. These findings provide insights into microbial ecological dynamics during anaerobic-to-aerobic transitions, offering potential applications for optimizing wastewater treatment processes. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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26 pages, 5130 KB

Open AccessArticle

Prescribed Burning Enhances the Stability of Soil Bacterial Co-Occurrence Networks in Pinus yunnanensis Forests in Central Yunnan Province, China

by Yunxian Mo, Xiangwei Bu, Wen Chen, Jinmei Xing, Qiuhua Wang and Yali Song

Microorganisms 2025, 13(9), 2070; https://doi.org/10.3390/microorganisms13092070 - 5 Sep 2025

Viewed by 846

Abstract

Prescribed burning significantly influences the microbial communities and physicochemical characteristics of forest soils. However, studies on the impacts of prescribed burning on the stability of soil microbial co-occurrence networks, as well as on the combined effects of post-fire soil depth gradients and their [...] Read more.

Prescribed burning significantly influences the microbial communities and physicochemical characteristics of forest soils. However, studies on the impacts of prescribed burning on the stability of soil microbial co-occurrence networks, as well as on the combined effects of post-fire soil depth gradients and their interactions on soil physicochemical properties and microbial communities, remain poorly understood. This study was conducted in a subtropical Pinus yunnanensis plantation that has undergone annual prescribed burns since 2007. Using 16S and ITS rRNA gene sequencing techniques alongside analyses of soil physicochemical properties, we collected and examined soil samples from different depths (0–5 cm, 5–10 cm, and 10–20 cm) in June 2024. The study found that prescribed burning enhanced the complexity and stability of bacterial co-occurrence networks, boosting both the diversity (prescribed burning/unburned control: 3/1) and the abundance (prescribed burning/unburned control: 8/2) of key taxa, which were essential for maintaining bacterial community network stability. However, it also intensified competitive interactions (prescribed burning/unburned control: 0.3162/0.0262) within the community. Moreover, prescribed burning had a significant effect on the diversity, structure, and composition of microbial communities and the physicochemical properties in the 0–5 cm soil layer, while also showing notable effects in the 5–20 cm layer. Prescribed burning also enhanced the coupling between the soil environment and bacterial community composition. The bacterial community showed negative correlations with most physicochemical properties. Soil organic matter (SOM) (p = 0.002) and available potassium (AK) (p = 0.042) were identified as key determinants shaping the post-fire bacterial community structure. The relationship between physicochemical parameters and fungal community composition was weaker. Urease (UE) (p = 0.036) and total potassium (TK) (p = 0.001) emerged as two key factors influencing the composition of post-fire fungal communities. These results elucidate the distinct functional roles of bacteria and fungi in post-fire ecosystem recovery, emphasizing their contributions to maintaining the stability and functionality of microbial communities. The study provides valuable insights for refining prescribed burning management strategies to promote sustainable forest ecosystem recovery. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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21 pages, 6575 KB

Open AccessArticle

Isolation of Ultra-Small Opitutaceae-Affiliated Verrucomicrobia from a Methane-Fed Bioreactor

by Olga V. Danilova, Varvara D. Salova, Igor Y. Oshkin, Daniil G. Naumoff, Anastasia A. Ivanova, Natalia E. Suzina and Svetlana N. Dedysh

Microorganisms 2025, 13(8), 1922; https://doi.org/10.3390/microorganisms13081922 - 17 Aug 2025

Cited by 1 | Viewed by 1166

Abstract

The bacterial phylum Verrucomicrobiota accommodates free-living and symbiotic microorganisms, which inhabit a wide range of environments and specialize in polysaccharide degradation. Due to difficulties in cultivation, much of the currently available knowledge about these bacteria originated from cultivation-independent studies. A phylogenetic clade defined [...] Read more.

The bacterial phylum Verrucomicrobiota accommodates free-living and symbiotic microorganisms, which inhabit a wide range of environments and specialize in polysaccharide degradation. Due to difficulties in cultivation, much of the currently available knowledge about these bacteria originated from cultivation-independent studies. A phylogenetic clade defined by the free-living bacterium from oilsands tailings pond, Oleiharenicola alkalitolerans, and the symbiont of the tunicate Lissoclinum sp., Candidatus Didemniditutus mandelae, is a poorly studied verrucomicrobial group. This clade includes two dozen methagenome-assembled genomes (MAGs) retrieved from aquatic and soil habitats all over the world. A new member of this clade, strain Vm1, was isolated from a methane-fed laboratory bioreactor with a Methylococcus-dominated methane-oxidizing consortium and characterized in this study. Strain Vm1 was represented by ultra-small, motile cocci with a mean diameter of 0.4 µm that grew in oxic and micro-oxic conditions at temperatures between 20 and 42 °C. Stable development of strain Vm1 in a co-culture with Methylococcus was due to the ability to utilize organic acids excreted by the methanotroph and its exopolysaccharides. The finished genome of strain Vm1 was 4.8 Mb in size and contained about 4200 predicted protein-coding sequences, including a wide repertoire of CAZyme-encoding genes. Among these CAZymes, two proteins presumably responsible for xylan and arabinan degradation, were encoded in several MAGs of Vm1-related free-living verrucomicrobia, thus offering an insight into the reasons behind wide distribution of these bacteria in the environment. Apparently, many representatives of the Oleiharenicola–Candidatus Didemniditutus clade may occur in nature in trophic associations with methanotrophic bacteria, thus participating in the cycling of methane-derived carbon. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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16 pages, 7371 KB

Open AccessArticle

Effects of Salinity Fluctuation on Antimicrobial Resistance and Virulence Factor Genes of Low and High Nucleic Acid-Content Bacteria in a Marine Environment

by Wei Hu, Xinzhu Zhou, Yu Liu, Yadi Zhang and Yingying Wang

Microorganisms 2025, 13(7), 1710; https://doi.org/10.3390/microorganisms13071710 - 21 Jul 2025

Cited by 2 | Viewed by 1249

Abstract

Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this [...] Read more.

Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this study, metagenomic sequencing analysis was used to reveal the response of ARGs and VFGs, hosted by low and high nucleic acid-content bacteria (HNA and LNA bacteria), to salinity, as it decreased from 26‰ to 16‰. The results showed that a total of 27 ARG types and 13 VFG types in HNA and LNA bacteria were found. Salinity changes had significant effects on the ARGs’ and VFGs’ composition and their hosts’ composition. In the network topology relationship, the complexity of the network between the ARGs and their host as well as the VFGs and their host differed with the decrease in salinity. The abundance of most genera of HNA and LNA bacteria was significantly corrected with the abundance of ARGs and VFGs, respectively. Overall, this study demonstrates the effects of salinity on ARGs and VFGs hosted by HNA and LNA bacteria in the marine environment and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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13 pages, 968 KB

Open AccessArticle

Identification of Parasitic Infections by Analyzing Honeybees, Honey, and Pollen Using Droplet Digital RT-PCR

by Luigi Jacopo D’Auria, Andrea Mancusi, Yolande Thérèse Rose Proroga, Irene Dini, Tiziana Cardellicchio, Orlandina Di Maro, Sabato De Vita, Marica Egidio, Raffaele Marrone and Giuseppe Rofrano

Microorganisms 2025, 13(7), 1487; https://doi.org/10.3390/microorganisms13071487 - 26 Jun 2025

Cited by 1 | Viewed by 1216

Abstract

Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium spp. are common pathogens that contaminate water and food. They can pose serious health risks, especially to vulnerable groups like immunocompromised individuals, pregnant women, young children, and aging people. An all-encompassing approach to minimizing transmission [...] Read more.

Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium spp. are common pathogens that contaminate water and food. They can pose serious health risks, especially to vulnerable groups like immunocompromised individuals, pregnant women, young children, and aging people. An all-encompassing approach to minimizing transmission involves identifying effective techniques for detecting, treating, and preventing protozoan parasites. This study confirmed the effectiveness of a Droplet Digital Reverse Transcription Polymerase Chain Reaction (dd RT-PCR) method for quickly and accurately identifying Toxoplasma gondii, Giardia intestinalis, and Cryptosporidium species in honeybees, honey, and pollen by using ISO 17468 and ISO 16140 standard guidelines. The study evaluated honeybee (n = 16), honey (n = 12), and pollen (n = 8) samples collected from various apiaries in Southern Italy between June and September 2023. The results showed that honeybees, honey, and pollen can be considered bioindicators of infections by T. gondii, G. intestinalis, and Cryptosporidium spp. Furthermore, pollen, along with honey to a lesser degree, can serve as significant indicators for evaluating food safety. Therefore, it is essential to monitor their quality and purity due to environmental influences. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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16 pages, 9902 KB

Open AccessArticle

Genome Sequences of the First Phages Infecting Limnohabitans Reveal Their Global Distribution and Metabolic Potential

by Boxuan Deng, Raoqiong Che, Pinxin Zhu, Yongxia Wang, Zhiying Li, Shiying Zhang and Wei Xiao

Microorganisms 2025, 13(6), 1324; https://doi.org/10.3390/microorganisms13061324 - 6 Jun 2025

Viewed by 1239

Abstract

Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety [...] Read more.

Bacteriophages (phages) are one of the critical biotic drivers of prokaryotic community dynamics, functions, and evolution. Despite their importance in aquatic ecosystems, very few phages have been isolated from freshwater lakes, hampering our understanding of their ecological importance and usage in a variety of biotechnological applications. Limnohabitans, with a ubiquitous distribution, is a metabolically versatile, fast-growing, morphologically diverse freshwater lake bacterial genera. It is especially abundant in pH-neutral and alkaline aquatic habitats, where it represents an average of 12% of freshwater bacterioplankton and plays an important role in funneling carbon from primary producers to higher trophic levels. However, no phages infecting Limnohabitans have been reported to date. Here, we describe, for the first time, three phages infecting Limnohabitans, DC31, DC33, and YIMV22061, isolated from two freshwater lakes in China and characterized using genome content analysis and comparative genomics. DC31 and DC33, recovered from the eutrophic Dianchi Lake, with auxiliary metabolic genes (AMGs), associated with nucleotide metabolism, whereas YIMV22061, isolated from the oligotrophic Fuxian Lake, carried AMGs involved in antibiotic resistance. The AMGs they carried highlight their impacts on Limnohabitans in different environments. Comparative genomic analyses indicate that DC31, DC33, and YIMV22061 represent three novel species in the Caudoviricetes class. IMG/VR database alignment further reveal that these phages are widely distributed across diverse aquatic and terrestrial ecosystems globally, suggesting their ecological significance. This study provides a basis for better understanding Limnohabitans–phage interactions. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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19 pages, 2685 KB

Open AccessArticle

Thresholds and Trade-Offs: Fire Severity Modulates Soil Microbial Biomass-Function Coupling in Taiga Forests, Northeast of China

by Huijiao Qu, Siyu Jiang, Zhichao Cheng, Dan Wei, Libin Yang and Jia Zhou

Microorganisms 2025, 13(6), 1318; https://doi.org/10.3390/microorganisms13061318 - 5 Jun 2025

Viewed by 1243

Abstract

Forest fires critically disrupt soil ecosystems by altering physicochemical properties and microbial structure-function dynamics. This study assessed short-term impacts of fire intensities (light/moderate/heavy) on microbial communities in Larix gmelinii forests one year post-fire. Using phospholipid fatty acid (PLFA) and Biolog EcoPlate analyses, we [...] Read more.

Forest fires critically disrupt soil ecosystems by altering physicochemical properties and microbial structure-function dynamics. This study assessed short-term impacts of fire intensities (light/moderate/heavy) on microbial communities in Larix gmelinii forests one year post-fire. Using phospholipid fatty acid (PLFA) and Biolog EcoPlate analyses, we found the following: (1) fire reduced soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and available nitrogen/potassium (AN/AK) via pyrolytic carbon release, while heavy-intensity fires enriched available phosphorus (AP), AN, and AK through ash deposition. (2) Thermal mortality and nutrient-pH-moisture stress persistently suppressed microbial biomass and metabolic activity. Moderate fires increased taxonomic richness but reduced functional diversity, confirming “functional redundancy.” (3) Neither soil microbial biomass nor metabolic activity at the fire site reached pre-fire levels after one year of recovery. Our findings advance post-fire soil restoration frameworks and advocate multi-omics integration to decode fire-adapted functional gene networks, guiding climate-resilient forest management. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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20 pages, 2829 KB

Open AccessArticle

Actinobacteria Emerge as Novel Dominant Soil Bacterial Taxa in Long-Term Post-Fire Recovery of Taiga Forests

by Siyu Jiang, Huijiao Qu, Zhichao Cheng, Xiaoyu Fu, Libin Yang and Jia Zhou

Microorganisms 2025, 13(6), 1262; https://doi.org/10.3390/microorganisms13061262 - 29 May 2025

Cited by 3 | Viewed by 1389

Abstract

The long-term post-fire recovery phase is a critical stage for forest ecosystems to progress toward regeneration and mature succession. During this process, soil bacteria exhibit greater environmental adaptability, rapidly driving nutrient cycling and facilitating vegetation restoration. This study investigated the community structure and [...] Read more.

The long-term post-fire recovery phase is a critical stage for forest ecosystems to progress toward regeneration and mature succession. During this process, soil bacteria exhibit greater environmental adaptability, rapidly driving nutrient cycling and facilitating vegetation restoration. This study investigated the community structure and diversity of soil bacteria during long-term recovery after forest fires in the cold temperate zone, focusing on soils from the 2000 fires in Daxing’anling. Soil samples were classified into Low (L), Moderate (M), and High (H) fire damage intensity, with bacterial community composition and diversity analyzed using Illumina sequencing technology. After long-term fire recovery, the contents of soil organic carbon, black carbon, total nitrogen, alkaline nitrogen, available phosphorus, and available potassium were significantly higher elevated (p < 0.05), and water content was significantly lower, compared with that in the control check (CK) group. Soil urease, fluorescein diacetate, soil acid phosphatase, and soil dehydrogenase activities were significantly higher, and soil sucrase activity was significantly lower in H. There was a significant difference in the Alpha diversity index among the groups. Compared with CK, the Shannon index was significantly increased (p < 0.05) in L, while both Chao1 and Shannon indices were significantly decreased (p < 0.05) in M and significantly higher in H than CK. The results of the PCoA showed that there was a significant difference in the Beta diversity of the bacterial community among the groups (R² = 0.60 p = 0.001). The dominant bacteria groups were Proteobacteria and Acidobacteriota, while Actinobacteria became the new dominant group during the long-term post-fire recovery. AP, WC, DOC, MBC, S-DHA, and S-SC were significantly and positively correlated with soil bacterial diversity (p < 0.05). The results of the co-occurrence network analysis showed that all groups were dominated by symbiotic relationships, with M having the highest network complexity and strongest competitive effects. This study found that the physicochemical properties of soils recovered over a long period of time after fire returned to or exceeded the unfired forest condition. The Actinobacteria phylum became a new dominant bacterial group, with stronger network complexity and competition, in the process of forest recovery after moderate fire. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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