Search Results (128)

Seamounts are distributed globally across the oceans and are generally considered oases of biomass abundance as well as hotspots of species richness. Diverse microbial communities are essential for biogeochemical cycling, yet their functional partitioning among seamounts with geographic features remains poorly investigated. Through metagenomic sequencing and genome-resolved analysis, we revealed that Proteobacteria (33.18–40.35%) dominated the bacterial communities, while Thaumarchaeota (5.98–10.86%) were the predominant archaea. Metagenome-assembled genomes uncovered 117 medium-quality genomes, 81.91% of which lacked species-level annotation, highlighting uncultured diversity. In the Nazuna seamount, which is located in the Marcus-Wake seamount region, microbiomes exhibited heightened autotrophic potential via the 3-hydroxypropionate cycle and dissimilatory nitrate reduction, whereas in the Magellan seamounts regions, nitrification and organic nitrogen metabolism were prioritized. Sulfur oxidation genes dominated Nazuna seamount microbes, with 33 MAGs coupling denitrification to sulfur redox pathways. Metal resistance genes for tellurium, mercury, and copper were prevalent, alongside habitat-specific iron transport systems. Cross-feeding interactions mediated by manganese, reduced ferredoxin, and sulfur–metal integration suggested adaptive detoxification strategies. This study elucidates how deep-sea microbes partition metabolic roles and evolve metal resilience mechanisms across geographical niches. It also supports the view that microbial community structure and metabolic function across seamount regions are likely influenced by the geomorphological features of the seamounts. Full article

The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, cas gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material—reflected in the higher complexity and diversity of CRISPR loci in Archaea—and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures. Full article

Type IV pili (T4Ps) are multifunctional surface fibers essential for bacterial motility, adhesion, and virulence, found across Gram-negative and Gram-positive bacteria and archaea. Detailed descriptions of T4P structural biology are allowing progress in understanding T4P biogenesis. Secretins, large outer membrane channels, are crucial for T4P extrusion in Gram-negative bacteria. Using cryo-EM and AlphaFold, we modeled the structure of BfpB, the secretin of the Bundle-Forming Pilus (BFP) of enteropathogenic Escherichia coli. BfpB exhibits a unique 17-fold symmetry, correlating with the thicker BFP filaments, and diverging from the 12–15 subunits typical of T4P, type 2 secretion (T2S), and type 3 secretion (T3S) systems. Additionally, we identified an extended β-hairpin loop in the N3 domain, resembling features of distantly related T3SS secretins, and an N-terminal helix where a C-terminal S-domain is seen in some T2S and T3S secretins. These findings reveal evolutionary parallels and structural adaptations in secretins, highlighting the link between oligomerization and pilus structure. This work advances our understanding of T4P biogenesis, secretin evolution, and bacterial secretion systems, offering insights into pathogenic diversity and future research directions. Full article

This study evaluates the effectiveness of agroecological practices—organic fertilization and biofertilization—in enhancing ecosystem services in agroforestry and pasture systems. A field experiment was conducted over three years, comparing these practices to a control treatment and a natural ecosystem as a reference. Soil chemical, physical, and biological parameters were assessed, including soil organic carbon (SOC), microbial respiration, root density, and gene abundances of key microbial groups (Archaea, Bacteria, and Fungi). Organic fertilization resulted in a significant increase in SOC, phosphorus, microbial biomass, and root density, indicating improved soil structure and fertility. Biofertilization showed selective effects, promoting archaeal abundance but reducing bacterial and fungal diversity. Seasonal variation influenced nutrient cycling, with organic fertilization buffering against dry-season declines in microbial activity and nutrient availability. Aboveground dry biomass and litter deposition were highest in the natural ecosystem, followed by organic fertilization treatments in agroforestry and pasture systems. Despite improvements under agroecological management, the natural ecosystem consistently maintained superior soil quality and biological resilience. The findings highlight that organic inputs and diversified cropping systems enhance soil health but do not fully replicate the ecological benefits of undisturbed forests. In conclusion, agroecological practices provide viable alternatives to mitigate soil degradation and sustain ecosystem services in tropical Oxisols. Organic fertilization emerges as the most effective strategy, fostering long-term improvements in soil fertility and microbial dynamics. However, continued research is needed to optimize these practices for greater resilience and sustainability in Amazonian agroecosystems. Full article

The soil microbial community plays a crucial role in the elemental cycling and energy flow within wetland ecosystems. The temporal dynamics and spatial distribution of soil microbial communities are central topics in ecology. While numerous studies have focused on wetland microbial community structures at low altitudes, microbial diversity across seasons and depths and their environmental determinants remain poorly understudied. To test the seasonal variation in microbial communities with contrasting seasonal fluxes of greenhouse gases, a total of 36 soil samples were collected from different depths in the Namco wetland on the Tibetan Plateau across four seasons. We found significant seasonal variation in bacterial community composition, most pronounced in the Winter, but not in archaea. In particular, Proteobacteria decreased by 11.5% in Winter compared with other seasons (p < 0.05). The bacterial alpha diversity showed hump-shaped seasonal patterns with lower diversity in Winter, whereas archaea showed no significant patterns across depths. A PERMANOVA further revealed significant differences in the bacterial community structure between Winter and the other three seasons (p < 0.05). In addition, bacterial and archaeal community structures differed between surface (0–5 cm) and deeper (5–30 cm) soils (p < 0.01). Redundancy analysis showed that soil total nitrogen, soil total phosphorus, and total soil organic carbon significantly influenced bacteria and archaea (p < 0.05). Furthermore, soil moisture content and temperature strongly affected the bacterial community structure (p < 0.001). Our findings highlighted the seasonal variation in the microbial community and the profound influence of soil moisture and temperature on microbial structure in alpine wetlands on the Tibetan Plateau. Full article

The Okinawa Trough (OT) has been a focus of scientific research for many years due to the presence of vibrant hydrothermal and cold seep activity within its narrow basin. However, the spatial distribution and environmental drivers of microbial communities in OT sediments remain poorly understood. The present study aims to address this knowledge gap by investigating microbial diversity and abundance at ten different sampling sites in a transitional zone between hydrothermal vents and cold seeps in the OT. The microbial community at two sampling sites (G08 and G09) in close proximity to hydrothermal vents showed a high degree of similarity. However, lower bacterial and archaeal abundances were found in these sites. The archaeal groups, classified as Hydrothermarchaeota and Thermoplasmata, showed a comparatively higher relative abundance at these sites. In addition, ammonia-oxidizing archaea (AOA), from the family Nitrosopumilaceae, were found to have a higher relative abundance in the OT surface sediments at sampling sites G03, G04, G05, G06, and G07. This result suggests that ammonia oxidation may be actively occurring in these areas. Furthermore, Methylomirabilaceae, which are responsible for methane oxidation coupled with nitrite reduction, dominated three sampling sites (G07, G08, and G09), implying that N-DAMO may play an important role in mitigating methane emissions. Using the FAPROTAX database, we found that predicted prokaryotic microbial functional groups involved in methyl-reducing methanogenesis and hydrogenotrophic methanogenesis were most abundant at sites G08 and G09. At sampling sites G01 and G02, functional groups such as hydrocarbon degradation, methanotrophy, methanol oxidation, denitrification, sulfate respiration, and sulfur oxidation were more abundant. Nitrogen content is the most important environmental factor determining the bacterial and archaeal communities in the OT surface sediments. These results expand our knowledge of the spatial distribution of microbial communities in the transitional zone between hydrothermal vents and cold seeps in the OT. Full article

Soda lakes are extreme saline–alkaline environments that harbor metabolically versatile microbial communities with significant biotechnological potential. This study employed shotgun metagenomics (NovaSeq PE150) to investigate the functional diversity and metabolic potential of microbial communities in Ethiopia’s Chitu and Shala Lakes. An analysis of gene content revealed 554,609 and 525,097 unique genes in Chitu and Shala, respectively, in addition to a substantial fraction (1,253,334 genes) shared between the two, underscoring significant functional overlap. Taxonomic analysis revealed a diverse phylogenetic composition, with bacteria (89% in Chitu Lake, 92% in Shala Lake) and archaea (4% in Chitu Lake, 0.8% in Shala Lake) as the dominant domains, alongside eukaryotes and viruses. Predominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were prominent among archaea. Key genera identified in both lakes were Nitriliruptor, Halomonas, Wenzhouxiangella, Thioalkalivibrio, Aliidiomarina, Aquisalimonas, and Alkalicoccus. Functional annotation using the KEGG, eggNOG, and CAZy databases revealed that the identified unigenes were associated with various functions. Notably, genes related to amino acid, carbohydrate, and energy metabolism (KEGG levels 1–2) were predominant, indicating that conserved core metabolic functions are essential for microbial survival in extreme conditions. Higher-level pathways included quorum sensing, two-component signal transduction, and ABC transporters (KEGG level 3), facilitating environmental adaptation, stress response, and nutrient acquisition. The eggNOG annotation revealed that 13% of identified genes remain uncharacterized, representing a vast untapped reservoir of novel enzymes and biochemical pathways with potential applications in biofuels, bioremediation, and synthetic biology. This study identified 375 unique metabolic pathways, including those involved in pyruvate metabolism, xenobiotic degradation, lipid metabolism, and oxidative stress resistance, underscoring the microbial communities’ ability to thrive under fluctuating salinity and alkalinity. The presence of carbohydrate-active enzymes (CAZymes), such as glycoside hydrolases, polysaccharide lyases, and oxidoreductases, highlights their role in biomass degradation and carbon cycling. Enzymes such as alkaline proteases (Apr), lipases (Lip), and cellulases further support the lakes’ potential as sources of extremophilic biocatalysts. These findings position soda lakes as reservoirs of microbial innovation for extremophile biotechnology. Future research on unannotated genes and enzyme optimization promises sustainable solutions in bioenergy, agriculture, and environmental management. Full article

The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the ‘Global Archaea Diversity’ (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life. Full article

Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia—including bacteria, fungi, and protozoa—can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity. Full article

Dairy cows rely on their complex rumen microbial community to convert host-indigestible feed into nutrients usable for host growth, maintenance, and milk production. Previous work by our group found that the rumen bacterial community is dynamic over the course of two lactations and that cows with high and low milk production efficiency (MPE) have different taxa associated with either phenotype. Here, we characterized the ruminal fungal and archaeal communities to determine if these microbial populations exhibit properties similar to that of the rumen bacteria with respect to MPE over time. Our results show a decrease in fungal diversity over the course of both lactation cycles with an increase during the transition period. The fungal community had only a few taxa associated with efficiency. For the ruminal archaea, we found no change in diversity across both lactation cycles and only taxa in the genus Methanospera were found to be more abundant in high-MPE cows. Given that our previous study used 454 pyrosequencing, we also sought to determine if a resequencing of these communities using Illumina-based technology would alter our previous findings. We found that resequencing showed no significant deviation from our original broad conclusions, with the exception of some minor taxonomic associations. Full article

While the recession of glaciers in the Antarctic is of global concern under climate change, the impact of deglaciation on soil microbiomes is still limited. Here, soil samples were collected from permafrost (P), moraine (M) and Deschampsia antarctica rhizosphere (R) soils near Ecology Glacier (Antarctic), and their soil physicochemical properties and microbial communities (bacteria, archaea and fungi) were characterized. Our analyses showed that there were significant differences in the soil properties and microbial communities between the R samples and the P and M samples. Specifically, amplicon sequencing of 16S rDNA revealed high bacterial richness and diversity in the studied soils, which were dominated mainly by the phyla Proteobacteria, Actinobacteriota and Bacteroidota. In contrast, lower richness and diversity were observed in the archaeal communities, which were dominated by the phyla Chenarchaeota (M and R) and Thermoplasmadota (M). In addition, fungal community analysis revealed a lower richness and diversity (M and R), dominated by the phylum Ascomycota. Our observations are consistent with previous reports describing the relevant changes in soil microbial communities during glacial recession, including fewer microbial groups studied in soils (archaea and fungi). However, further studies are still needed to elucidate the contributions of microbial communities to soil formation and plant colonization in ice-free soils in Antarctica under global climate change. Full article

The soil microbiome plays an important role in wetland ecosystem services and functions. However, the impact of soil hydrological conditions on wetland microorganisms is not well understood. This study investigated the effects of wetted state (WS); wetting–drying state (WDS); and dried state (DS) on the diversity of soil bacteria, fungi, and archaea. The Shannon index of bacterial diversity was not significantly different in various flooding conditions (p > 0.05), however, fungal diversity and archaeal communities were significantly different in different flooding conditions (p < 0.05). Significant differences were found in the beta diversity of bacterial, fungal, and archaeal communities (p < 0.05). Additionally, the composition of bacteria, fungi, and archaea varied. Bacteria were predominantly composed of Proteobacteria and Actinobacteria, fungi mainly consisted of Ascomycota and Mucoromycota, and archaea were primarily represented by Crenarchaeota and Euryarchaeota. Bacteria exhibited correlations with vegetation coverage, fungi with plant diversity, and archaea with aboveground vegetation biomass. The pH influenced bacterial and archaeal communities, while soil bulk density, moisture, soil carbon, soil nitrogen, and plant community diversity impacted fungal communities. This study provides a scientific basis for understanding the effects of different hydrological conditions on microbial communities in the Huihe Nature Reserve; highlighting their relationship with vegetation and soil properties, and offers insights for the ecological protection of the Huihe wetland. Full article

Anaerobic digestion (AD) is a well-established technology for the sustainable conversion of agricultural organic by-products and waste into bioenergy. Temperature is crucial for optimizing methane production through inocula preservation and reactor start-up in AD. The preservation of inocula induced by temperature has rarely been assessed from an engineering perspective. There has also been limited exploration of the influence of high-to-moderate temperature transition on the initiation of AD. This study employed continuous mesophilic AD reactors with potential engineering applications to conduct revival tests. These tests evaluated the methane production activity of sludge stored at different temperatures and investigated the impact of high-temperature initiation on mesophilic AD. Additionally, we elucidated the correlation between these assessments and microbial diversity as well as composition. The results indicated that bacterial diversity was higher in the inoculum stored at 35 °C compared to 15 °C, ensuring a stable start-up operation of the mesophilic AD. The richness of the bacteria and diversity of the archaea remained stable during the transition from high to mesophilic temperatures. This was conducive to enhancing methanogenic activity of mesophilic AD initiated at 55 °C. The continuously operated AD system showed significant differences in microbial composition compared to its inoculum. Increased abundance of Coriobacteriaceae and Prevotellaceae led to propionate and butyrate accumulation, respectively, reducing AD operational capacity. Methanogenic archaea were less diverse in AD initiated with low-temperature preserved inoculum compared to that with a medium temperature. Streptococcaceae induced by high temperarure could promote AD stability. Hydrogenotrophic methanogens had a competitive advantage in mesophilic AD due to their prior exposure to high-temperature initiation, possibly influenced by Thermotogaceae. Full article

During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31–52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes’ microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes. Full article

To mitigate the issues of soil quality degradation and environmental pollution caused by excessive fertilizer use in apple orchards, the present study investigated the effects of organic fertilizer substitution combined with chemical nitrogen (N) fertilizer reduction on soil nutrient status, enzyme activity, and microbial communities (bacteria, fungi and archaea) over one year in an apple orchard. Five fertilization treatments were implemented, including 100% chemical fertilizer (CK), 80% chemical fertilizer + 20% liquid humic fertilizer (S1), 60% chemical fertilizer + 40% liquid humic fertilizer (S2), 60% chemical fertilizer + 20% liquid humic fertilizer (S3), and 40% chemical fertilizer + 40% liquid humic fertilizer (S4). Substituting chemical fertilizers with liquid humic fertilizers effectively enhanced the soil organic matter (SOM) content in the topsoil (0–20 cm) for all treatments. Compared to CK, the amounts of available N (NO₃⁻-N and NH₄⁺-N) were decreased in the topsoil and the amounts of total N, total phosphorous and available phosphorous were increased in the subsoil (20–40 cm) for all treatments. The β-diversity of bacterial communities exhibited the highest sensitivity to soil environmental changes, followed by that of archaea, whereas fungi demonstrated the least susceptibility. The higher soil carbon/nitrogen ratio and SOM content in S2 altered the abundance of microorganisms (Proteobacteria, Ascomycota, and Crenarchaeota) that were closely related to the decomposition and mineralization of SOM and N, enhancing the efficiency of SOM decomposition. The activities of sucrase (SUC), urease (UE), and phosphatase were increased, also promoting the conversion efficiency of SOM and improving N fixation and soil fertility. In the organic fertilizer substitution treatments (S1 and S2), the abundance of dominant Actinobacteriota, Ascomycota and Crenarchaeota phyla were increased, as well as the activities of SUC and UE, accelerating the decomposition and mineralization of SOM and improving soil fertility. In the top, organic fertilizer substitution combined with reduced chemical N fertilizer (S3 and S4) treatments increased the abundance of bacteria and fungi. In addition, RDA showed that total potassium content could significantly affect changes in the bacterial and fungal community structure in subsoil. Overall, organic fertilizer substitution enhanced the content of soil available nutrients and improved soil nutrient retention. It is recommended to promote organic fertilizer substitution + chemical N fertilizer reduction (S4) with the supplementation of potassium fertilizer in the subsoil. The findings provide a theoretical basis and practical guidance for improving orchard soil management and achieving sustainable development in the apple industry. Full article