Search Results (71)

Limited research has been conducted on the potential and mechanisms of irrigating Suaeda salsa with wastewater and microalgae to improve saline–alkali land. This study used three irrigation treatments (freshwater, saline wastewater, and saline wastewater with microalgae) to irrigate S. salsa, and microalgae promoted the growth of S. salsa and increased soil nutrient content, increasing available nitrogen (4.85%), available phosphorus (44.51%), and organic carbon (24.05%) while alleviating salt stress through reduced soil salinity (13.52%) and electrical conductivity (21.62%). These changes promoted eutrophic bacteria while inhibiting oligotrophic bacteria. Bacterial community composition exhibited significant variations, primarily driven by soil pH, total nitrogen, and organic carbon content. Notably, rhizosphere bacteria showed enhanced functional capabilities, with increased abundance of salt stress resistance and nitrogen metabolism-related genes compared to original soil, particularly under saline irrigation conditions. Furthermore, microalgae addition enriched nitrogen metabolism-related gene abundance. These findings revealed the potential role of key bacteria in enhancing plant growth and the soil environment and highlighted the potential of applying S. salsa, wastewater, and microalgae for the synergistic improvement of saline–alkali land. Full article

The unarmored dinoflagellate Akashiwo sanguinea is a cosmopolitan harmful algal species known for forming intense blooms leading to mass mortality of fish, shellfish, and seabirds. Globally distributed populations of A. sanguinea have been classified into four ribotypes based on their characteristic sequences in LSU rRNA gene and primary geographic distributions. In this study, we compared the bacterial communities co-existing with the six strains of A. sanguinea from China and the USA (belonging to two ribotypes) using high-throughput sequencing of 16S rRNA gene amplicons. Generally, a bacterial microbiome with high diversity was found to be associated with laboratory-cultured A. sanguinea strains from different geographic origins. Based on ribotype classification, the six samples were divided into two groups (ribotype A: AsCHINA; ribotype C: AsUSA) for subsequent comparative analyses of their bacterial communities. Beta diversity analysis revealed a clear separation between the two groups, reflecting significant differences in bacterial community composition between the two ribotypes. Significantly higher abundance of nitrogen-fixing bacteria was found in the AsUSA group, suggesting that ribotype C may benefit from external nitrogen sources provided by their bacterial associates. If this also holds true in natural environments, this nitrogen-fixing partnership likely confers a competitive advantage to ribotype C in oligotrophic offshore waters, and potentially extends bloom duration when environmental nitrogen is depleted. Our study raised the possibility that different ribotypes of A. sanguinea may harbor distinct prokaryotic microbiomes in their phycospheres under stable cultivation conditions. Further comprehensive comparison among more isolates across all four ribotypes is highly necessary to validate this hypothesis. Full article

Despite the global imperative to enhance carbon sequestration in agricultural landscapes, saline–alkali soils present distinctive soil–microbe constraints that limit our understanding of optimal management strategies. This study addresses critical knowledge gaps regarding the mechanistic relationships between bacterial community structure and carbon stabilization processes in saline–alkali soil. A three-year field experiment was conducted in the Yellow River Delta, China, with two N levels (N1, 270 kg N ha⁻¹; N2, 210 kg N ha⁻¹) and three C treatments (S0, 0 kg C ha⁻¹; S1, 5000 kg C ha⁻¹; S2, 10,000 kg C ha⁻¹). SOC sequestration by straw incorporation increased by 16.34–22.86% and 8.18–11.91%, with no significant difference between the S1 and S2 treatments, because the specific C mineralization rate (SCMR) of the S2 treatment was 13.80–41.61% higher than the S1 treatment. The reduced nitrogen application (N2) enhanced SOC sequestration efficiency by 3.40–12.97% compared with conventional rates, particularly when combined with half straw incorporation. Furthermore, compared with the N1S1 treatment, the N2S1 treatment induced qualitative transformations in carbon chemistry, increasing aromatic carbon compounds (28.79%) while reducing carboxylic fractions (10.06%), resulting in enhanced structural stability of sequestered carbon. Bacterial community analysis revealed distinctive shifts in bacterial composition under different treatments. Half straw incorporation (S1) increased the abundance of oligotrophic strategists (Verrucomicrobiae and Acidimicrobiia) while decreasing copiotrophic bacteria (Bacteroidia), indicating a transition from r-strategy to k-strategy microbial communities that fundamentally altered carbon cycling. Half straw incorporation and reduced N application were beneficial to stabilize SOC composition, reduce mineralization rates, optimize bacterial survival strategy, and thus achieve SOC sequestration. Full article

The phytoplankton communities in lakes change seasonally within competitive areas, referred to as seasonal succession, which results in high compositional diversity if conditions remain stable. However, glacial lakes are generally far from human and terrestrial influences due to their location so very few species can be identified and large changes in phytoplankton composition cannot be anticipated. Nonetheless, molecular techniques, as well as classical methods, help us to determine the existence of different species. Additionally, these techniques allow us to evaluate the ecology of glacial lakes from different perspectives with developing technology. Horseshoe Island is located in the area known as Marguerite Bay on the Peninsula region in western Antarctica. This study was carried out to determine phytoplankton genome biodiversity by using the metagenomic analysis method used in 18S rRNA, 16S rRNA, and 23S rRNA gene analyses. 16S rRNA and 23S rRNA gene analyses revealed that bacteria belong to broadly distributed Cyanobacteria taxa, whereas 18S rRNA gene analysis revealed other eukaryotic phytoplankton groups. This method was used for the first time for Horseshoe Island lakes (Col 1, Col 2, Skua, and Zano), and species belonging to Cyanobacteria, Chlorophyta, Ochrophyta, and Bacillariophyta were identified. As a result, the phytoplankton genomic diversity of shallow and oligotrophic glacial lakes was determined, and benthic algal species were also identified in the water samples. These results indicate that benthic algae associated with the sediment can also contribute to aquatic phytoplankton communities in addition to oligotrophic lake phytoplankton biodiversity. Cyanobacterial biodiversity can also be recognized as a sentinel by which to monitor adaptation responses to climate change in this rapidly warming region. Full article

Coral reefs thrive in nutrients-poor waters, and their survival strategy in such oligotrophic marine environments remains largely unexplored. Current coral research has focused on the interplay between the animal hosts, symbiotic Symbiodiniaceae, and associated bacteria, with little attention given to their individual interactions. Here, we integrated biochemical, transcriptomic, and metabonomic analyses of the clade D Symbiodiniaceae strain AG11 to investigate the growth-assisting mechanisms of symbiotic bacteria. Our findings indicate that metabolic trophallaxis between Symbiodiniaceae and symbiotic bacteria plays a crucial role in enhancing survival and population growth under nitrogen-depleted conditions, commonly found in typical coral habitats. Notably, the exchange of organic compounds between Symbiodiniaceae and bacteria significantly boosts nitrogen uptake in their free-living state. Furthermore, we demonstrated how beneficial bacteria influence the survival of Symbiodiniaceae in response to environmental changes, which are vital for coping with nitrogen-depleted conditions where coral reefs are particularly vulnerable. Full article

The initial variations in soil bacteria at the very beginning of reclamation still remains unclear. This study investigates the impact on bacterial communities of eight different treatments, including uncultivated land, unfertilized cultivation, chemical fertilizer, chemical fertilizer + bacterial fertilizer, manure, manure + bacterial fertilizer, manure + chemical fertilizer, and manure + chemical fertilizer + bacterial fertilizer, during the short-term reclamation of coal-mining soils. The results showed that total nitrogen, available phosphorus, soil organic carbon, microbial biomass carbon, and alkaline phosphatase activity were significantly increased in all fertilization treatments compared to uncultivated land (p < 0.05). All fertilization treatments other than chemical fertilizer harbored significantly higher activities of urease, catalase, and invertase than unfertilized cultivation (p < 0.05). The bacterial communities structures in manure-amended treatments significantly differed in uncultivated land and unfertilized cultivation and were phylotypically shifted from oligotrophic to Actinobacteria-dominant copiotrophic traits, accompanied with phenotypic succession of the enriching characteristics of Gram-positive, biofilms formation, and stress tolerance. The co-occurrence network in manure-amended treatments harbored a simple co-occurrence network, indicating more productive soils than in no-manure treatments. Manure amendment, total nitrogen, microbial biomass carbon, invertase, catalase, and soil moisture were the key driving factors. Our study underscores the bacterial initialization characteristics promoted by manure at the very beginning of coal-mining reclamation. Full article

Nitrogen (N) enrichment significantly impacts temperate forest ecosystems, but we lack a comprehensive understanding of the responses of root morphological characteristics, soil microbial communities, and soil multifunctionality concurrently to varying degrees of N enrichment, particularly when exceeding a threefold localized N input in temperate forests. Therefore, we selected four forest communities in China’s temperate forests and experimented with localized N addition to the dominant tree species in each forest community through the root bag method (three N addition treatments were set up: N1, fourfold soil total N; N2, sixfold soil total N; and CK, control). The results showed that (1) N enrichment treatments significantly improved soil multifunctionality and modified root morphological characteristics, leading to increases in RD (root diameter) and RTD (root tissue density) but decreases in SRL (specific root length) and SRA (specific root area). (2) N enrichment treatments also substantially changed microbial community composition and functional taxa. The relative abundance of eutrophic bacteria increased, while that of oligotrophic bacteria and saprotrophic fungi decreased. (3) The microbial α-diversity index decreased, and the microbial co-occurrence networks became less complex and more vulnerable under N enrichment treatments. (4) Soil multifunctionality and the microbial alpha diversity index had a substantial negative correlation. (5) NH₄⁺-N and NO₃⁻-N contents were the key factors affecting microbial dominance phyla, as well as the bacterial Shannon index and the fungal Chao1 index. (6) In addition, soil properties (except NH₄⁺-N and NO₃⁻-N), soil enzyme activities, root morphological characteristics, and the microbial Chao1 index were significantly different among tree species. In summary, N enrichment significantly alters root morphological characteristics and improves soil multifunctionality. Concurrently, it reduced microbial α-diversity, increased the abundance of eutrophic bacteria, and decreased saprophytic fungi, leading to a less complex and more vulnerable microbial community. This study provided important data and insights for a comprehensive study of the repertoire of responses to nitrogen enrichment in temperate forest ecosystems. Full article

This study investigated the effects of various titanium nanoparticles (TiO₂NPs) on the structure, function, and trophic levels of the wheat rhizobiome. In contrast to the typically toxic effects of small nanoparticles (~10 nm), this research focused on molecular TiO₂ and larger nanoparticles, as follows: medium-sized (68 nm, NPs1) and large (>100 nm, NPs2). The results demonstrated significant yet diverse impacts of different TiO₂ forms on the rhizosphere microbiota. Large TiO₂NPs2 and molecular TiO₂ adversely affected the bacteriobiome and mycobiome, leading to an increase in autotrophic microbial groups. In contrast, medium-sized TiO₂NPs1 shifted the microbiome toward chemoheterotrophy, promoting plant growth-associated bacteria, fungal saprotrophs, and potential phytopathogens, suggesting a beneficial r-strategy within the rhizosphere. Other treatments induced oligotrophic conditions, resulting in a less flexible rhizobiome with diminished root associations but an increased abundance of Trichoderma spp. Structural modelling revealed that even minor changes in operational taxonomic units (OTUs) could significantly alter the microbiota’s metabolic potential. These findings highlight the importance of further research to optimize nanoparticle applications for sustainable agriculture. Full article

Extremophiles, microorganisms blooming in extreme environmental conditions, hold particular significance in the domain of microbial research. This review paper focuses on extremophilic microorganisms, emphasizing their adaptations and the diverse products they generate, with a particular emphasis on exopolysaccharides (EPSs). EPSs, high molecular weight carbohydrate biopolymers, stand out as valuable products with applications across various industries. The review explores EPS production by bacteria in extreme conditions, including thermophilic, halophilic, and psychrophilic environments. Noteworthy examples, such as B. thermantarcticus and H. smyrnensis AAD6T, highlight the vast potential of extremophiles in EPS production. Additionally, the paper explores the major synthesis pathways of EPSs, shedding light on the factors influencing biosynthesis. The commercial significance of EPSs, especially for extremophiles, is underlined by their applications in medicine, food, environmental protection, agriculture, cosmetics, and more. Furthermore, the review sheds light on the role of extremophiles in various ecosystems, such as acidophiles, alkaliphiles, halophiles, hyperthermophiles, oligotrophs, osmophiles, piezophiles, and radioresistant organisms. This comprehensive analysis highlights the broad impact of extremophilic microorganisms and their EPS products in scientific exploration and commercial innovation. Full article

Nitrification plays a crucial role in aquatic ecosystems and in the biofilters used in fish farms. Despite their importance, the role of canonical nitrifiers, comammox bacteria, and archaea has not yet been sufficiently investigated. The aim of this study was to characterize the microbiome of the external canister biofilter in a freshwater fish aquarium, with particular focus on the role of comammox Nitrospira and their competition with other nitrifiers. To achieve this, a comprehensive approach combining metagenome sequencing and co-occurrence network analysis was used to study the interactions between microorganisms in portable biofilter. The fish were subjected to a changing feeding regime that affected the ecological relationships and abundance of different microbial taxa. The results showed the presence of two types of nitrifiers in the biofilter: comammox Nitrospira and ammonia-oxidizing archaea (AOA). Five comammox Nitrospira genomes were reconstructed, with comammox clade B being the most abundant with an average abundance of 7.8 ± 0.4%. In addition, two families of archaea were identified: Nitrosopumilaceae and Nitrososphaeraceae, with an average abundance of 4.3 ± 0.4%. Heterotrophs were also abundant in the bacterial community, particularly in the genera Actinomycetota, Planctomycetota, and Pseudomonadota. Network analysis indicated competitive interactions between comammox and heterotrophs, whereas no competition was observed between comammox and AOA. The predominance of comammox Nitrospira, and AOA over canonical nitrifiers emphasizes their better adaptation to oligotrophic environments. This study highlights the importance of competition within the biofilter microbiome and the role of ecological interaction networks, which can contribute to the optimization of water purification systems in RASs. Full article

(1) Background: The rapid growth in the number of nanoparticles today raises questions about studying their impact on the environment, including the soil, as the main absorber of nanoparticles. The purpose of our research was to study the effect of MoO₃ nanoparticles (NPs; 50, 100, 250, 500, and 1000 mg/kg of soil) on the physiological and biochemical parameters of Eisenia fetida, the number of certain ecologo-trophic groups of soil microorganisms, and enzymatic soil activity. (2) Methods: We used 92 ± 0.3 nm nanoparticles of MoO₃ at concentrations of 50, 100, 250, 500, and 1000 mg/kg dry soil. Texture-carbonate chernozem was used in the study. Eisenia fetida worms were used as test objects. (3) Results: The introduction of MoO₃ nanoparticles showed a weak toxic effect towards the animal and microbiological components of the soil at a concentration of 50–250 mg/kg, a medium toxic effect at 500 mg/kg, and a strong or unacceptable toxic effect at 1000 mg/kg. The oxidative stress response of E. fetida depended on the concentration of the NPs. MoO₃ NPs at a concentration of up to 100 mg/kg reduced the number of amylolytic bacteria, oligotrophs, and Azotobacter. In soil, urease and catalase showed mild activity, whereas the activity of invertase decreased by 34%. (4) Conclusions: The entry into the environment and the further deposition of nanoparticles of Mo and its oxides in the soil will lead to the suppression of the vital activity of beneficiary soil animals and the activity of soil enzymes. This phenomenon presents special kinds of ecological risks for the ecosystem. Full article

This study explores the diversity and functions of microbiomes in ancient agroecosystems of the Mixteca Alta Geopark (MAG). Microbiome analysis could provide insights into soil bacterial communities and their role in enhancing soil fertility, nutrient cycling, and plant growth. We used 16S rRNA gene amplicon sequencing to identify key features in the composition of the microbiota of the Lama-bordo, Valley, and Terrace agroecosystems in MAG. Analysis of agroecosystem soils revealed 21 bacterial phyla, with Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi dominating. These microbial communities contribute to soil health, carbon cycling, and disease suppression. The study identified specific phylogroups and metabolic pathways associated with nutrient-rich environments like Lama-bordo and Valley, and nutrient-poor, sandy soils like Terrace. Soils from Lama-bordo and Valley were grouped due to microbiome similarity despite geographic separation, whereas Terrace soils differed. Nutrient-rich Lama-bordo and Valley soils host copiotrophic bacteria, while nutrient-poor Terrace soils favor oligotrophic species like Acidobacteria. Functional analysis of microbiomes reveals distinct metabolic pathways, including antibiotic biosynthesis (streptomycin, vancomycin) suggesting a role in plant disease resistance, amino acid pathways indicating active nitrogen cycling, and vitamin B5 and lipoic acid pathways contributing to energy metabolism and antioxidant functions. Full article

Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats. Full article

This research explores how the availability of substrates affects the regulation of soil microbial communities and the taxonomical composition of bacteria. The goal is to understand the impact of organic matter and substrate availability and quality on the diversity of soil bacteria. The study observed gradual changes in bacterial diversity in response to the addition of different substrate-induced respiration (SIR) substrates. Understanding the structure, dynamics, and functions of soil microbial communities is essential for assessing soil quality in sustainable agriculture. The preference for carbon sources among bacterial phyla is largely influenced by their life history and trophic strategies. Bacterial phyla like Proteobacteria, Bacteroidetes, and Actinobacteria, which thrive in nutrient-rich environments, preferentially utilize glucose. On the other hand, oligotrophic bacterial phyla such as Acidobacteria or Chloroflexi, which are found in lower numbers, have a lower ability to utilize labile C. The main difference between the two lies in their substrate utilization strategies. Understanding these distinct strategies is crucial for uncovering the bacterial functional traits involved in soil organic carbon turnover. Additionally, adding organic matter can promote the growth of copiotrophic bacteria, thus enhancing soil fertility. Full article

Globally, coral reef ecosystems are undergoing significant change related to climate change and anthropogenic activities. Yet, the Cuban archipelago of Jardines de la Reina (JR) has experienced fewer stressors due to its geographical remoteness and high level of conservation. This study examines the surface and benthic reef water microbial communities associated with 32 reef sites along the JR archipelago and explores the relationship between the community composition of reef microorganisms examined using bacterial and archaeal small subunit ribosomal RNA gene (16S rRNA gene) sequencing compared to geographic, conservation/protection level, environmental, physicochemical, and reef benthic and pelagic community features. Reef nutrient concentrations were low and microbial communities dominated by picocyanobacteria and SAR11 and SAR86 clade bacteria, characteristic of an oligotrophic system. Reef water microbial community alpha and beta diversity both varied throughout the archipelago and were strongly related to geography. Three sites in the western archipelago showed unique microbial communities, which may be related to the hydrogeography and influences of the channels linking the Ana Maria gulf with the Caribbean Sea. Overall, this work provides the first extensive description of the reef microbial ecology of the Caribbean’s ‘Crown Jewel’ reef system and a framework to evaluate the influence of ongoing stressors on the reef microorganisms. Full article